diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..65c6d20 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "drawsbml"] + path = drawsbml + url = git@github.com:dilawar/drawsbml diff --git a/.travis.yml b/.travis.yml index 7848843..08a99d2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,22 +2,16 @@ notifications: email: recipients: - dilawar.s.rajput@gmail.com - - upi.bhalla@gmail.com - - hrani@ncbs.res.in install: - - wget http://download.opensuse.org/repositories/home:moose/xUbuntu_14.04/Release.key - - sudo apt-key add - < Release.key - - sudo sh -c "echo 'deb http://download.opensuse.org/repositories/home:/moose/xUbuntu_14.04/ /' >> /etc/apt/sources.list.d/moose.list" - sudo apt-get -y update - sudo apt-get -y --force-yes install python3 python-pip - - sudo apt-get -y --force-yes install moose - - sudo -H pip install python-libsbml + - sudo pip install python-libsbml script: - # Making sure no python incompatible file is added. - - python -m compileall -q . - - python -c 'import moose' - - #python -c 'import moogli' - - # More tests here for gui. + - python3 -m pip install pymoose --user --pre + - python3 -m compileall -q . + - python3 -c 'import moose' + - python3 setup.py install --user diff --git a/AUTHOR b/AUTHOR new file mode 100644 index 0000000..58cd432 --- /dev/null +++ b/AUTHOR @@ -0,0 +1,4 @@ +Harsha Rani +Subhasis Ray +Aviral Goel +Dilawar Singh diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..255b2e2 --- /dev/null +++ b/Makefile @@ -0,0 +1,24 @@ +PY := $(shell which python3) + +all : check build + +check : + $(PY) -m compileall -q . + +build : + $(PY) setup.py sdist bdist + +install : uninstall + git clean -fxd . + $(PY) -m pip install . --upgrade --user + +test: install + ( cd /tmp && moosegui ) + +uninstall : + $(PY) -m pip uninstall moosegui -y + +lint: + find . -type f -name *.py -print0 | xargs -0 -I file pyflakes file + +.PHONY : lint uninstall test install build check diff --git a/PlotWidgetContainer.py b/PlotWidgetContainer.py deleted file mode 100644 index d51ab81..0000000 --- a/PlotWidgetContainer.py +++ /dev/null @@ -1,189 +0,0 @@ - -# -*- coding: utf-8 -*- -from __future__ import print_function - -""" -""" -__credits__ = ["Upi Lab"] -__author__ = "Aviral Goel" -__license__ = "GPL3" -__version__ = "1.0.0" -__maintainer__ = "Aviral Goel", "HarshaRani" -__email__ = "goel.aviral@gmail.com" -__status__ = "Development" -__updated__ = "Jul 26 2017" - - -import sys -import os -import PyQt4 -from PyQt4 import QtGui, Qt -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QSizeGrip -from PyQt4.QtGui import QDockWidget -from PyQt4.QtGui import QLayout -from PyQt4.QtGui import QVBoxLayout -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QScrollArea -from PyQt4.QtGui import QToolBar -from PyQt4.QtGui import QSizeGrip -from PyQt4.QtGui import QSplitter - -import moose -import default -import sidebar -# from default import PlotWidget - -ELECTRICAL = 0 -CHEMICAL = 1 -class PlotWidgetContainer(QWidget): - - def __init__(self, modelRoot, *args, **kwargs): - - super(PlotWidgetContainer, self).__init__(*args) - self.modelRoot = modelRoot - if len(moose.wildcardFind(modelRoot + "/##[ISA=ChemCompt]")) == 0: - self.modelType = ELECTRICAL - else: - self.modelType = CHEMICAL - - self.model = moose.element(self.modelRoot) - if self.modelRoot != "/": - self.modelRoot = self.findModelPath(self.modelRoot) - if moose.exists(modelRoot + "/data"): - self.data = moose.element(self.modelRoot + "/data") - else: - self.data = moose.Neutral(self.modelRoot + "/data") - - else: - self.data = moose.element("/data") - - self._layout = QVBoxLayout() - self.graphs = QSplitter() - self.graphs.setOrientation(PyQt4.QtCore.Qt.Vertical) - self.graphsArea = QScrollArea() - # self.graphsLayout = QGridLayout() - # self.menubar = self.createMenuBar() - self.rowIndex = 0 - # self.setSizePolicy( QtGui.QSizePolicy.Expanding - # , QtGui.QSizePolicy.Expanding - # ) - - self.graphs.setSizePolicy( QtGui.QSizePolicy.Expanding - , QtGui.QSizePolicy.Expanding - ) - self.setAcceptDrops(True) - # self._layout.setSizeConstraint( QLayout.SetNoConstraint ) - # self.graphs.setLayout(self.graphsLayout) - self.graphsArea.setWidget(self.graphs) - self.graphsArea.setWidgetResizable(True) - self.graphWidgets = [] - # self._layout.addWidget(self.menubar) - self._layout.addWidget(self.graphsArea) - self.setLayout(self._layout) - - for graph in self.data.children: - self.addPlotWidget(graph = graph) - - if len(self.data.children) == 0: - self.addPlotWidget() - - def mooseIsInstance(self,element, classNames): - return moose.element(element).__class__.__name__ in classNames - - - def findModelPath(self,element): - child = element - while not self.mooseIsInstance(element, "Shell"): - child = moose.element(element).path - element = moose.element(element).parent - return child - - def deleteWidget(self, graphWidget): - # print("Deleted => ", graphWidget) - self.graphWidgets.remove(graphWidget) - graphWidget.setParent(None) - graphWidget.close() - - def createMenuBar(self): - bar = sidebar.sidebar() - bar.addAction(sidebar.add_graph_action(bar, lambda event: self.addPlotWidget() )) - # bar.addAction(sidebar.delete_graph_action(bar, lambda event: self.addPlotWidget() )) - # bar.addAction(sidebar.list_action(bar, self.showPlotView)) - return bar - - def addPlotWidget(self, row = None, col = 0, graph = None): - if graph == None: - graph = moose.Neutral(self.data.path + "/graph_" + str(self.rowIndex)) - widget = default.PlotWidget(self.model, graph, self.rowIndex, self) - - if self.modelType == ELECTRICAL: - for axes in widget.canvas.axes.values(): - # axes.autoscale(False, axis='x', tight=True) - axes.set_ylim(bottom = -0.07, top= 0.03) - - if row == None: - row = self.rowIndex - self.graphs.addWidget(widget) - self.rowIndex += 1 - self.graphWidgets.append(widget) - widget.widgetClosedSignal.connect(self.deleteWidget) - widget.addGraph.connect(lambda event : self.addPlotWidget()) - # widget.resize(1, 1); - return widget - - def showPlotView(self): - pass - - def setModelRoot(self, *args): - pass - - def getMenus(self, *args): - return [] - - def setDataRoot(self, *args): - pass - - def updatePlots(self): - for graphWidget in self.graphWidgets: - graphWidget.updatePlots() - - def rescalePlots(self): - for graphWidget in self.graphWidgets: - graphWidget.rescalePlots() - - def extendXAxes(self, xlim): - for graphWidget in self.graphWidgets: - graphWidget.extendXAxes(xlim) - - def plotAllData(self): - for graphWidget in self.graphWidgets: - graphWidget.plotAllData() - - #print(graphWidget) - # def plotAll(self): - # self.apply(lambda obj: obj.plotAll()) - - # def plotAllData(self): - # selt.plotWidgetContainer.plotAllData() - - # def genColorMap(self,tableObject): - # pass - - # def onclick(self,event1): - # pass - - # def addTimeSeries(self, table, *args, **kwargs): - # pass - - # def addRasterPlot(self, eventtable, yoffset=0, *args, **kwargs): - # pass - - # def extendXAxes(self, xlim): - # pass - - # def saveCsv(self, line,directory): - # pass - - # def saveAllCsv(self): - # pass diff --git a/__init__.py b/__init__.py deleted file mode 100644 index 7ff5c6b..0000000 --- a/__init__.py +++ /dev/null @@ -1 +0,0 @@ -all = [ "plugins", 'suds' ] diff --git a/about.html b/about.html deleted file mode 100644 index 5345c9c..0000000 --- a/about.html +++ /dev/null @@ -1,36 +0,0 @@ - -
-MOOSE is the Multiscale Object-Oriented Simulation Environment (MOOSE) -

Version 3.0.2pre "Ghevar" - -

-

Copyright (C) 2003-2016 Upinder S. Bhalla and NCBS.

- -

MOOSE is released under the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or (at -your option) any later version.

- -

MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed -to simulate neural systems ranging from subcellular components and biochemical -reactions to complex models of single neurons, circuits, and large networks. -MOOSE can operate at many levels of detail, from stochastic chemical -computations, to multicompartment single-neuron models, to spiking neuron -network models. - -MOOSE is multiscale: It can do all these calculations together. For example it -handles interactions seamlessly between electrical and chemical signaling. -MOOSE is object-oriented. Biological concepts are mapped into classes, and a -model is built by creating instances of these classes and connecting them by -messages. MOOSE also has classes whose job is to take over difficult -computations in a certain domain, and do them fast. There are such solver -classes for stochastic and deterministic chemistry, for diffusion, and for -multicompartment neuronal models. MOOSE is a simulation environment, not just a -numerical engine: It provides data representations and solvers (of course!), but -also a scripting interface with Python, graphical displays with Matplotlib, -PyQt, and OpenGL, and support for many model formats. These include SBML, -NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.

- -

Home Page: -http://moose.ncbs.res.in

- - diff --git a/build/lib/moosegui/MooseCanvas.py b/build/lib/moosegui/MooseCanvas.py new file mode 100644 index 0000000..26446c7 --- /dev/null +++ b/build/lib/moosegui/MooseCanvas.py @@ -0,0 +1,104 @@ +"""MooseCanvas.py: + + +Here is my Canvas. + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import sys +import random +import os + +try: + import Tkinter as tk +except ImportError as e: + import tkinter as tk + +import logging + +class MooseCanvas( tk.Frame ): + + def __init__(self, root = None): + + + self.canvas = tk.Canvas( root , width=800, height=800 ) + self.canvas.create_line( 0, 0, 200, 200 ); + + ''' + self.xsb = tk.Scrollbar( self.canvas, + orient="horizontal", command=self.canvas.xview + ) + + self.ysb = tk.Scrollbar( self.canvas, orient="vertical", + command=self.canvas.yview + ) + self.canvas.configure( + yscrollcommand=self.ysb.set, + xscrollcommand=self.xsb.set + ) + + self.xsb.grid(row=1, column=0, sticky="ew") + self.ysb.grid(row=0, column=1, sticky="ns") + # self.grid_rowconfigure(0, weight=1) + # self.grid_columnconfigure(0, weight=1) + ''' + + # This is what enables using the mouse: + self.canvas.bind("", self.move_start) + self.canvas.bind("", self.move_move) + # linux scroll + self.canvas.bind("", self.zoomerP) + self.canvas.bind("", self.zoomerM) + # windows scroll + self.canvas.bind("", self.zoomer) + # self.canvas.bind( "", self.keyboard ) + self.canvas.bind( "Move", self.keyboard ) + self.canvas.bind( "", self.mouseCallback ) + self.canvas.grid( row = 0, column = 0, sticky = 'news' ) + # self.canvas.pack( ) + + # move + def move_start(self, event): + self.canvas.scan_mark(event.x, event.y) + + def move_move(self, event): + self.canvas.scan_dragto(event.x, event.y, gain=1) + + # windows zoom + def zoomer(self, event): + if (event.delta > 0): + self.canvas.scale("all", event.x, event.y, 1.1, 1.1) + elif (event.delta < 0): + self.canvas.scale("all", event.x, event.y, 0.9, 0.9) + self.canvas.configure(scrollregion=self.canvas.bbox("all")) + + # linux zoom + def zoomerP(self, event): + self.canvas.scale("all", event.x, event.y, 1.1, 1.1) + self.canvas.configure(scrollregion=self.canvas.bbox("all")) + + def zoomerM(self, event): + self.canvas.scale("all", event.x, event.y, 0.9, 0.9) + self.canvas.configure(scrollregion=self.canvas.bbox("all")) + + def mouseCallback(self, event ): + logging.info( 'Button pressed %s %s' % ( event.x, event.y ) ) + + def keyboard(self, event ): + logging.info( 'Key pressed %s' % ( event.char ) ) + +if __name__ == "__main__": + root = tk.Tk() + a = MooseCanvas( root ) + # a.plot_random_rects( ) + a.pack(fill="both", expand=True) + root.mainloop() diff --git a/build/lib/moosegui/MooseWindow.py b/build/lib/moosegui/MooseWindow.py new file mode 100644 index 0000000..c2b5cb6 --- /dev/null +++ b/build/lib/moosegui/MooseWindow.py @@ -0,0 +1,44 @@ +"""MooseWindow.py: + +MooseWindow. + +""" + +__author__ = "Me" +__copyright__ = "Copyright 2016, Me" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Me" +__email__ = "" +__status__ = "Development" + +import sys +import os + +try: + import Tkinter as tk +except ImportError as e: + import tkinter as tk + +class MooseWindow( tk.Tk ): + """docstring for MooseWindow""" + + def __init__( self, title = 'MOOSE' ): + tk.Tk.__init__( self ) + self.title( title ) + self.state = None + self.attributes( '-zoomed', True ) + self.bind( "", self.toggle_fullscreen ) + self.bind( "", self.end_fullscreen ) + + + def toggle_fullscreen(self, event=None): + self.state = not self.state # Just toggling the boolean + self.attributes("-fullscreen", self.state) + return "break" + + def end_fullscreen(self, event=None): + self.state = False + self.attributes("-fullscreen", False) + return "break" diff --git a/build/lib/moosegui/PyShell.py b/build/lib/moosegui/PyShell.py new file mode 100644 index 0000000..5b1ccff --- /dev/null +++ b/build/lib/moosegui/PyShell.py @@ -0,0 +1,1628 @@ +#! /usr/bin/env python +from __future__ import print_function + +import os +import os.path +import sys +import string +import getopt +import re +import socket +import time +import threading +import io + +import linecache +from code import InteractiveInterpreter +from platform import python_version, system + +try: + from Tkinter import * +except ImportError: + print("** IDLE can't import Tkinter.\n" + "Your Python may not be configured for Tk. **", file=sys.__stderr__) + sys.exit(1) +import tkMessageBox + +from idlelib.EditorWindow import EditorWindow, fixwordbreaks +from idlelib.FileList import FileList +from idlelib.ColorDelegator import ColorDelegator +from idlelib.UndoDelegator import UndoDelegator +from idlelib.OutputWindow import OutputWindow +from idlelib.configHandler import idleConf +from idlelib import rpc +from idlelib import Debugger +from idlelib import RemoteDebugger +from idlelib import macosxSupport +from idlelib import IOBinding + +IDENTCHARS = string.ascii_letters + string.digits + "_" +HOST = '127.0.0.1' # python execution server on localhost loopback +PORT = 0 # someday pass in host, port for remote debug capability + +try: + from signal import SIGTERM +except ImportError: + SIGTERM = 15 + +# Override warnings module to write to warning_stream. Initialize to send IDLE +# internal warnings to the console. ScriptBinding.check_syntax() will +# temporarily redirect the stream to the shell window to display warnings when +# checking user's code. +warning_stream = sys.__stderr__ # None, at least on Windows, if no console. +import warnings + +def idle_formatwarning(message, category, filename, lineno, line=None): + """Format warnings the IDLE way.""" + + s = "\nWarning (from warnings module):\n" + s += ' File \"%s\", line %s\n' % (filename, lineno) + if line is None: + line = linecache.getline(filename, lineno) + line = line.strip() + if line: + s += " %s\n" % line + s += "%s: %s\n" % (category.__name__, message) + return s + +def idle_showwarning( + message, category, filename, lineno, file=None, line=None): + """Show Idle-format warning (after replacing warnings.showwarning). + + The differences are the formatter called, the file=None replacement, + which can be None, the capture of the consequence AttributeError, + and the output of a hard-coded prompt. + """ + if file is None: + file = warning_stream + try: + file.write(idle_formatwarning( + message, category, filename, lineno, line=line)) + file.write(">>> ") + except (AttributeError, IOError): + pass # if file (probably __stderr__) is invalid, skip warning. + +_warnings_showwarning = None + +def capture_warnings(capture): + "Replace warning.showwarning with idle_showwarning, or reverse." + + global _warnings_showwarning + if capture: + if _warnings_showwarning is None: + _warnings_showwarning = warnings.showwarning + warnings.showwarning = idle_showwarning + else: + if _warnings_showwarning is not None: + warnings.showwarning = _warnings_showwarning + _warnings_showwarning = None + +capture_warnings(True) + +def extended_linecache_checkcache(filename=None, + orig_checkcache=linecache.checkcache): + """Extend linecache.checkcache to preserve the entries + + Rather than repeating the linecache code, patch it to save the + entries, call the original linecache.checkcache() + (skipping them), and then restore the saved entries. + + orig_checkcache is bound at definition time to the original + method, allowing it to be patched. + """ + cache = linecache.cache + save = {} + for key in list(cache): + if key[:1] + key[-1:] == '<>': + save[key] = cache.pop(key) + orig_checkcache(filename) + cache.update(save) + +# Patch linecache.checkcache(): +linecache.checkcache = extended_linecache_checkcache + + +class PyShellEditorWindow(EditorWindow): + "Regular text edit window in IDLE, supports breakpoints" + + def __init__(self, *args): + self.breakpoints = [] + EditorWindow.__init__(self, *args) + self.text.bind("<>", self.set_breakpoint_here) + self.text.bind("<>", self.clear_breakpoint_here) + self.text.bind("<>", self.flist.open_shell) + + self.breakpointPath = os.path.join(idleConf.GetUserCfgDir(), + 'breakpoints.lst') + # whenever a file is changed, restore breakpoints + def filename_changed_hook(old_hook=self.io.filename_change_hook, + self=self): + self.restore_file_breaks() + old_hook() + self.io.set_filename_change_hook(filename_changed_hook) + if self.io.filename: + self.restore_file_breaks() + self.color_breakpoint_text() + + rmenu_specs = [ + ("Cut", "<>", "rmenu_check_cut"), + ("Copy", "<>", "rmenu_check_copy"), + ("Paste", "<>", "rmenu_check_paste"), + ("Set Breakpoint", "<>", None), + ("Clear Breakpoint", "<>", None) + ] + + def color_breakpoint_text(self, color=True): + "Turn colorizing of breakpoint text on or off" + if self.io is None: + # possible due to update in restore_file_breaks + return + if color: + theme = idleConf.CurrentTheme() + cfg = idleConf.GetHighlight(theme, "break") + else: + cfg = {'foreground': '', 'background': ''} + self.text.tag_config('BREAK', cfg) + + def set_breakpoint(self, lineno): + text = self.text + filename = self.io.filename + text.tag_add("BREAK", "%d.0" % lineno, "%d.0" % (lineno+1)) + try: + self.breakpoints.index(lineno) + except ValueError: # only add if missing, i.e. do once + self.breakpoints.append(lineno) + try: # update the subprocess debugger + debug = self.flist.pyshell.interp.debugger + debug.set_breakpoint_here(filename, lineno) + except: # but debugger may not be active right now.... + pass + + def set_breakpoint_here(self, event=None): + text = self.text + filename = self.io.filename + if not filename: + text.bell() + return + lineno = int(float(text.index("insert"))) + self.set_breakpoint(lineno) + + def clear_breakpoint_here(self, event=None): + text = self.text + filename = self.io.filename + if not filename: + text.bell() + return + lineno = int(float(text.index("insert"))) + try: + self.breakpoints.remove(lineno) + except: + pass + text.tag_remove("BREAK", "insert linestart",\ + "insert lineend +1char") + try: + debug = self.flist.pyshell.interp.debugger + debug.clear_breakpoint_here(filename, lineno) + except: + pass + + def clear_file_breaks(self): + if self.breakpoints: + text = self.text + filename = self.io.filename + if not filename: + text.bell() + return + self.breakpoints = [] + text.tag_remove("BREAK", "1.0", END) + try: + debug = self.flist.pyshell.interp.debugger + debug.clear_file_breaks(filename) + except: + pass + + def store_file_breaks(self): + "Save breakpoints when file is saved" + # XXX 13 Dec 2002 KBK Currently the file must be saved before it can + # be run. The breaks are saved at that time. If we introduce + # a temporary file save feature the save breaks functionality + # needs to be re-verified, since the breaks at the time the + # temp file is created may differ from the breaks at the last + # permanent save of the file. Currently, a break introduced + # after a save will be effective, but not persistent. + # This is necessary to keep the saved breaks synched with the + # saved file. + # + # Breakpoints are set as tagged ranges in the text. + # Since a modified file has to be saved before it is + # run, and since self.breakpoints (from which the subprocess + # debugger is loaded) is updated during the save, the visible + # breaks stay synched with the subprocess even if one of these + # unexpected breakpoint deletions occurs. + breaks = self.breakpoints + filename = self.io.filename + try: + with open(self.breakpointPath,"r") as old_file: + lines = old_file.readlines() + except IOError: + lines = [] + try: + with open(self.breakpointPath,"w") as new_file: + for line in lines: + if not line.startswith(filename + '='): + new_file.write(line) + self.update_breakpoints() + breaks = self.breakpoints + if breaks: + new_file.write(filename + '=' + str(breaks) + '\n') + except IOError as err: + if not getattr(self.root, "breakpoint_error_displayed", False): + self.root.breakpoint_error_displayed = True + tkMessageBox.showerror(title='IDLE Error', + message='Unable to update breakpoint list:\n%s' + % str(err), + parent=self.text) + + def restore_file_breaks(self): + self.text.update() # this enables setting "BREAK" tags to be visible + if self.io is None: + # can happen if IDLE closes due to the .update() call + return + filename = self.io.filename + if filename is None: + return + if os.path.isfile(self.breakpointPath): + lines = open(self.breakpointPath,"r").readlines() + for line in lines: + if line.startswith(filename + '='): + breakpoint_linenumbers = eval(line[len(filename)+1:]) + for breakpoint_linenumber in breakpoint_linenumbers: + self.set_breakpoint(breakpoint_linenumber) + + def update_breakpoints(self): + "Retrieves all the breakpoints in the current window" + text = self.text + ranges = text.tag_ranges("BREAK") + linenumber_list = self.ranges_to_linenumbers(ranges) + self.breakpoints = linenumber_list + + def ranges_to_linenumbers(self, ranges): + lines = [] + for index in range(0, len(ranges), 2): + lineno = int(float(ranges[index].string)) + end = int(float(ranges[index+1].string)) + while lineno < end: + lines.append(lineno) + lineno += 1 + return lines + +# XXX 13 Dec 2002 KBK Not used currently +# def saved_change_hook(self): +# "Extend base method - clear breaks if module is modified" +# if not self.get_saved(): +# self.clear_file_breaks() +# EditorWindow.saved_change_hook(self) + + def _close(self): + "Extend base method - clear breaks when module is closed" + self.clear_file_breaks() + EditorWindow._close(self) + + +class PyShellFileList(FileList): + "Extend base class: IDLE supports a shell and breakpoints" + + # override FileList's class variable, instances return PyShellEditorWindow + # instead of EditorWindow when new edit windows are created. + EditorWindow = PyShellEditorWindow + + pyshell = None + + def open_shell(self, event=None): + if self.pyshell: + self.pyshell.top.wakeup() + else: + self.pyshell = PyShell(self) + if self.pyshell: + if not self.pyshell.begin(): + return None + return self.pyshell + + +class ModifiedColorDelegator(ColorDelegator): + "Extend base class: colorizer for the shell window itself" + + def __init__(self): + ColorDelegator.__init__(self) + self.LoadTagDefs() + + def recolorize_main(self): + self.tag_remove("TODO", "1.0", "iomark") + self.tag_add("SYNC", "1.0", "iomark") + ColorDelegator.recolorize_main(self) + + def LoadTagDefs(self): + ColorDelegator.LoadTagDefs(self) + theme = idleConf.CurrentTheme() + self.tagdefs.update({ + "stdin": {'background':None,'foreground':None}, + "stdout": idleConf.GetHighlight(theme, "stdout"), + "stderr": idleConf.GetHighlight(theme, "stderr"), + "console": idleConf.GetHighlight(theme, "console"), + }) + + def removecolors(self): + # Don't remove shell color tags before "iomark" + for tag in self.tagdefs: + self.tag_remove(tag, "iomark", "end") + +class ModifiedUndoDelegator(UndoDelegator): + "Extend base class: forbid insert/delete before the I/O mark" + + def insert(self, index, chars, tags=None): + try: + if self.delegate.compare(index, "<", "iomark"): + self.delegate.bell() + return + except TclError: + pass + UndoDelegator.insert(self, index, chars, tags) + + def delete(self, index1, index2=None): + try: + if self.delegate.compare(index1, "<", "iomark"): + self.delegate.bell() + return + except TclError: + pass + UndoDelegator.delete(self, index1, index2) + + +class MyRPCClient(rpc.RPCClient): + + def handle_EOF(self): + "Override the base class - just re-raise EOFError" + raise EOFError + + +class ModifiedInterpreter(InteractiveInterpreter): + + def __init__(self, tkconsole): + self.tkconsole = tkconsole + locals = sys.modules['__main__'].__dict__ + InteractiveInterpreter.__init__(self, locals=locals) + self.save_warnings_filters = None + self.restarting = False + self.subprocess_arglist = None + self.port = PORT + self.original_compiler_flags = self.compile.compiler.flags + + _afterid = None + rpcclt = None + rpcpid = None + + def spawn_subprocess(self): + if self.subprocess_arglist is None: + self.subprocess_arglist = self.build_subprocess_arglist() + args = self.subprocess_arglist + self.rpcpid = os.spawnv(os.P_NOWAIT, sys.executable, args) + + def build_subprocess_arglist(self): + assert (self.port!=0), ( + "Socket should have been assigned a port number.") + w = ['-W' + s for s in sys.warnoptions] + if 1/2 > 0: # account for new division + w.append('-Qnew') + # Maybe IDLE is installed and is being accessed via sys.path, + # or maybe it's not installed and the idle.py script is being + # run from the IDLE source directory. + del_exitf = idleConf.GetOption('main', 'General', 'delete-exitfunc', + default=False, type='bool') + if __name__ == 'idlelib.PyShell': + command = "__import__('idlelib.run').run.main(%r)" % (del_exitf,) + else: + command = "__import__('run').main(%r)" % (del_exitf,) + if sys.platform[:3] == 'win' and ' ' in sys.executable: + # handle embedded space in path by quoting the argument + decorated_exec = '"%s"' % sys.executable + else: + decorated_exec = sys.executable + return [decorated_exec] + w + ["-c", command, str(self.port)] + + def start_subprocess(self): + addr = (HOST, self.port) + # GUI makes several attempts to acquire socket, listens for connection + for i in range(3): + time.sleep(i) + try: + self.rpcclt = MyRPCClient(addr) + break + except socket.error: + pass + else: + self.display_port_binding_error() + return None + # if PORT was 0, system will assign an 'ephemeral' port. Find it out: + self.port = self.rpcclt.listening_sock.getsockname()[1] + # if PORT was not 0, probably working with a remote execution server + if PORT != 0: + # To allow reconnection within the 2MSL wait (cf. Stevens TCP + # V1, 18.6), set SO_REUSEADDR. Note that this can be problematic + # on Windows since the implementation allows two active sockets on + # the same address! + self.rpcclt.listening_sock.setsockopt(socket.SOL_SOCKET, + socket.SO_REUSEADDR, 1) + self.spawn_subprocess() + #time.sleep(20) # test to simulate GUI not accepting connection + # Accept the connection from the Python execution server + self.rpcclt.listening_sock.settimeout(10) + try: + self.rpcclt.accept() + except socket.timeout: + self.display_no_subprocess_error() + return None + self.rpcclt.register("console", self.tkconsole) + self.rpcclt.register("stdin", self.tkconsole.stdin) + self.rpcclt.register("stdout", self.tkconsole.stdout) + self.rpcclt.register("stderr", self.tkconsole.stderr) + self.rpcclt.register("flist", self.tkconsole.flist) + self.rpcclt.register("linecache", linecache) + self.rpcclt.register("interp", self) + self.transfer_path(with_cwd=True) + self.poll_subprocess() + return self.rpcclt + + def restart_subprocess(self, with_cwd=False, filename=''): + if self.restarting: + return self.rpcclt + self.restarting = True + # close only the subprocess debugger + debug = self.getdebugger() + if debug: + try: + # Only close subprocess debugger, don't unregister gui_adap! + RemoteDebugger.close_subprocess_debugger(self.rpcclt) + except: + pass + # Kill subprocess, spawn a new one, accept connection. + self.rpcclt.close() + self.unix_terminate() + console = self.tkconsole + was_executing = console.executing + console.executing = False + self.spawn_subprocess() + try: + self.rpcclt.accept() + except socket.timeout: + self.display_no_subprocess_error() + return None + self.transfer_path(with_cwd=with_cwd) + console.stop_readline() + # annotate restart in shell window and mark it + console.text.delete("iomark", "end-1c") + tag = 'RESTART: ' + (filename if filename else 'Shell') + halfbar = ((int(console.width) -len(tag) - 4) // 2) * '=' + console.write("\n{0} {1} {0}".format(halfbar, tag)) + console.text.mark_set("restart", "end-1c") + console.text.mark_gravity("restart", "left") + if not filename: + console.showprompt() + # restart subprocess debugger + if debug: + # Restarted debugger connects to current instance of debug GUI + RemoteDebugger.restart_subprocess_debugger(self.rpcclt) + # reload remote debugger breakpoints for all PyShellEditWindows + debug.load_breakpoints() + self.compile.compiler.flags = self.original_compiler_flags + self.restarting = False + return self.rpcclt + + def __request_interrupt(self): + self.rpcclt.remotecall("exec", "interrupt_the_server", (), {}) + + def interrupt_subprocess(self): + threading.Thread(target=self.__request_interrupt).start() + + def kill_subprocess(self): + if self._afterid is not None: + self.tkconsole.text.after_cancel(self._afterid) + try: + self.rpcclt.close() + except AttributeError: # no socket + pass + self.unix_terminate() + self.tkconsole.executing = False + self.rpcclt = None + + def unix_terminate(self): + "UNIX: make sure subprocess is terminated and collect status" + if hasattr(os, 'kill'): + try: + os.kill(self.rpcpid, SIGTERM) + except OSError: + # process already terminated: + return + else: + try: + os.waitpid(self.rpcpid, 0) + except OSError: + return + + def transfer_path(self, with_cwd=False): + if with_cwd: # Issue 13506 + path = [''] # include Current Working Directory + path.extend(sys.path) + else: + path = sys.path + + self.runcommand("""if 1: + import sys as _sys + _sys.path = %r + del _sys + \n""" % (path,)) + + active_seq = None + + def poll_subprocess(self): + clt = self.rpcclt + if clt is None: + return + try: + response = clt.pollresponse(self.active_seq, wait=0.05) + except (EOFError, IOError, KeyboardInterrupt): + # lost connection or subprocess terminated itself, restart + # [the KBI is from rpc.SocketIO.handle_EOF()] + if self.tkconsole.closing: + return + response = None + self.restart_subprocess() + if response: + self.tkconsole.resetoutput() + self.active_seq = None + how, what = response + console = self.tkconsole.console + if how == "OK": + if what is not None: + print(repr(what), file=console) + elif how == "EXCEPTION": + if self.tkconsole.getvar("<>"): + self.remote_stack_viewer() + elif how == "ERROR": + errmsg = "PyShell.ModifiedInterpreter: Subprocess ERROR:\n" + print(errmsg, what, file=sys.__stderr__) + print(errmsg, what, file=console) + # we received a response to the currently active seq number: + try: + self.tkconsole.endexecuting() + except AttributeError: # shell may have closed + pass + # Reschedule myself + if not self.tkconsole.closing: + self._afterid = self.tkconsole.text.after( + self.tkconsole.pollinterval, self.poll_subprocess) + + debugger = None + + def setdebugger(self, debugger): + self.debugger = debugger + + def getdebugger(self): + return self.debugger + + def open_remote_stack_viewer(self): + """Initiate the remote stack viewer from a separate thread. + + This method is called from the subprocess, and by returning from this + method we allow the subprocess to unblock. After a bit the shell + requests the subprocess to open the remote stack viewer which returns a + static object looking at the last exception. It is queried through + the RPC mechanism. + + """ + self.tkconsole.text.after(300, self.remote_stack_viewer) + return + + def remote_stack_viewer(self): + from idlelib import RemoteObjectBrowser + oid = self.rpcclt.remotequeue("exec", "stackviewer", ("flist",), {}) + if oid is None: + self.tkconsole.root.bell() + return + item = RemoteObjectBrowser.StubObjectTreeItem(self.rpcclt, oid) + from idlelib.TreeWidget import ScrolledCanvas, TreeNode + top = Toplevel(self.tkconsole.root) + theme = idleConf.CurrentTheme() + background = idleConf.GetHighlight(theme, 'normal')['background'] + sc = ScrolledCanvas(top, bg=background, highlightthickness=0) + sc.frame.pack(expand=1, fill="both") + node = TreeNode(sc.canvas, None, item) + node.expand() + # XXX Should GC the remote tree when closing the window + + gid = 0 + + def execsource(self, source): + "Like runsource() but assumes complete exec source" + filename = self.stuffsource(source) + self.execfile(filename, source) + + def execfile(self, filename, source=None): + "Execute an existing file" + if source is None: + source = open(filename, "r").read() + try: + code = compile(source, filename, "exec", dont_inherit=True) + except (OverflowError, SyntaxError): + self.tkconsole.resetoutput() + print('*** Error in script or command!\n' + 'Traceback (most recent call last):', + file=self.tkconsole.stderr) + InteractiveInterpreter.showsyntaxerror(self, filename) + self.tkconsole.showprompt() + else: + self.runcode(code) + + def runsource(self, source): + "Extend base class method: Stuff the source in the line cache first" + filename = self.stuffsource(source) + self.more = 0 + self.save_warnings_filters = warnings.filters[:] + warnings.filterwarnings(action="error", category=SyntaxWarning) + if isinstance(source, unicode) and IOBinding.encoding != 'utf-8': + try: + source = '# -*- coding: %s -*-\n%s' % ( + IOBinding.encoding, + source.encode(IOBinding.encoding)) + except UnicodeError: + self.tkconsole.resetoutput() + self.write("Unsupported characters in input\n") + return + try: + # InteractiveInterpreter.runsource() calls its runcode() method, + # which is overridden (see below) + return InteractiveInterpreter.runsource(self, source, filename) + finally: + if self.save_warnings_filters is not None: + warnings.filters[:] = self.save_warnings_filters + self.save_warnings_filters = None + + def stuffsource(self, source): + "Stuff source in the filename cache" + filename = "" % self.gid + self.gid = self.gid + 1 + lines = source.split("\n") + linecache.cache[filename] = len(source)+1, 0, lines, filename + return filename + + def prepend_syspath(self, filename): + "Prepend sys.path with file's directory if not already included" + self.runcommand("""if 1: + _filename = %r + import sys as _sys + from os.path import dirname as _dirname + _dir = _dirname(_filename) + if not _dir in _sys.path: + _sys.path.insert(0, _dir) + del _filename, _sys, _dirname, _dir + \n""" % (filename,)) + + def showsyntaxerror(self, filename=None): + """Extend base class method: Add Colorizing + + Color the offending position instead of printing it and pointing at it + with a caret. + + """ + text = self.tkconsole.text + stuff = self.unpackerror() + if stuff: + msg, lineno, offset, line = stuff + if lineno == 1: + pos = "iomark + %d chars" % (offset-1) + else: + pos = "iomark linestart + %d lines + %d chars" % \ + (lineno-1, offset-1) + text.tag_add("ERROR", pos) + text.see(pos) + char = text.get(pos) + if char and char in IDENTCHARS: + text.tag_add("ERROR", pos + " wordstart", pos) + self.tkconsole.resetoutput() + self.write("SyntaxError: %s\n" % str(msg)) + else: + self.tkconsole.resetoutput() + InteractiveInterpreter.showsyntaxerror(self, filename) + self.tkconsole.showprompt() + + def unpackerror(self): + type, value, tb = sys.exc_info() + ok = type is SyntaxError + if ok: + try: + msg, (dummy_filename, lineno, offset, line) = value + if not offset: + offset = 0 + except: + ok = 0 + if ok: + return msg, lineno, offset, line + else: + return None + + def showtraceback(self): + "Extend base class method to reset output properly" + self.tkconsole.resetoutput() + self.checklinecache() + InteractiveInterpreter.showtraceback(self) + if self.tkconsole.getvar("<>"): + self.tkconsole.open_stack_viewer() + + def checklinecache(self): + c = linecache.cache + for key in c.keys(): + if key[:1] + key[-1:] != "<>": + del c[key] + + def runcommand(self, code): + "Run the code without invoking the debugger" + # The code better not raise an exception! + if self.tkconsole.executing: + self.display_executing_dialog() + return 0 + if self.rpcclt: + self.rpcclt.remotequeue("exec", "runcode", (code,), {}) + else: + exec code in self.locals + return 1 + + def runcode(self, code): + "Override base class method" + if self.tkconsole.executing: + self.interp.restart_subprocess() + self.checklinecache() + if self.save_warnings_filters is not None: + warnings.filters[:] = self.save_warnings_filters + self.save_warnings_filters = None + debugger = self.debugger + try: + self.tkconsole.beginexecuting() + if not debugger and self.rpcclt is not None: + self.active_seq = self.rpcclt.asyncqueue("exec", "runcode", + (code,), {}) + elif debugger: + debugger.run(code, self.locals) + else: + exec code in self.locals + except SystemExit: + if not self.tkconsole.closing: + if tkMessageBox.askyesno( + "Exit?", + "Do you want to exit altogether?", + default="yes", + parent=self.tkconsole.text): + raise + else: + self.showtraceback() + else: + raise + except: + if use_subprocess: + print("IDLE internal error in runcode()", + file=self.tkconsole.stderr) + self.showtraceback() + self.tkconsole.endexecuting() + else: + if self.tkconsole.canceled: + self.tkconsole.canceled = False + print("KeyboardInterrupt", file=self.tkconsole.stderr) + else: + self.showtraceback() + finally: + if not use_subprocess: + try: + self.tkconsole.endexecuting() + except AttributeError: # shell may have closed + pass + + def write(self, s): + "Override base class method" + self.tkconsole.stderr.write(s) + + def display_port_binding_error(self): + tkMessageBox.showerror( + "Port Binding Error", + "IDLE can't bind to a TCP/IP port, which is necessary to " + "communicate with its Python execution server. This might be " + "because no networking is installed on this computer. " + "Run IDLE with the -n command line switch to start without a " + "subprocess and refer to Help/IDLE Help 'Running without a " + "subprocess' for further details.", + parent=self.tkconsole.text) + + def display_no_subprocess_error(self): + tkMessageBox.showerror( + "Subprocess Startup Error", + "IDLE's subprocess didn't make connection. Either IDLE can't " + "start a subprocess or personal firewall software is blocking " + "the connection.", + parent=self.tkconsole.text) + + def display_executing_dialog(self): + tkMessageBox.showerror( + "Already executing", + "The Python Shell window is already executing a command; " + "please wait until it is finished.", + parent=self.tkconsole.text) + + +class PyShell(OutputWindow): + + shell_title = "Python " + python_version() + " Shell" + + # Override classes + ColorDelegator = ModifiedColorDelegator + UndoDelegator = ModifiedUndoDelegator + + # Override menus + menu_specs = [ + ("file", "_File"), + ("edit", "_Edit"), + ("debug", "_Debug"), + ("options", "_Options"), + ("windows", "_Window"), + ("help", "_Help"), + ] + + + # New classes + from idlelib.IdleHistory import History + + def __init__(self, flist=None): + if use_subprocess: + ms = self.menu_specs + if ms[2][0] != "shell": + ms.insert(2, ("shell", "She_ll")) + self.interp = ModifiedInterpreter(self) + if flist is None: + root = Tk() + fixwordbreaks(root) + root.withdraw() + flist = PyShellFileList(root) + # + OutputWindow.__init__(self, flist, None, None) + # +## self.config(usetabs=1, indentwidth=8, context_use_ps1=1) + self.usetabs = True + # indentwidth must be 8 when using tabs. See note in EditorWindow: + self.indentwidth = 8 + self.context_use_ps1 = True + # + text = self.text + text.configure(wrap="char") + text.bind("<>", self.enter_callback) + text.bind("<>", self.linefeed_callback) + text.bind("<>", self.cancel_callback) + text.bind("<>", self.eof_callback) + text.bind("<>", self.open_stack_viewer) + text.bind("<>", self.toggle_debugger) + text.bind("<>", self.toggle_jit_stack_viewer) + if use_subprocess: + text.bind("<>", self.view_restart_mark) + text.bind("<>", self.restart_shell) + # + self.save_stdout = sys.stdout + self.save_stderr = sys.stderr + self.save_stdin = sys.stdin + from idlelib import IOBinding + self.stdin = PseudoInputFile(self, "stdin", IOBinding.encoding) + self.stdout = PseudoOutputFile(self, "stdout", IOBinding.encoding) + self.stderr = PseudoOutputFile(self, "stderr", IOBinding.encoding) + self.console = PseudoOutputFile(self, "console", IOBinding.encoding) + if not use_subprocess: + sys.stdout = self.stdout + sys.stderr = self.stderr + sys.stdin = self.stdin + # + self.history = self.History(self.text) + # + self.pollinterval = 50 # millisec + + def get_standard_extension_names(self): + return idleConf.GetExtensions(shell_only=True) + + reading = False + executing = False + canceled = False + endoffile = False + closing = False + _stop_readline_flag = False + + def set_warning_stream(self, stream): + global warning_stream + warning_stream = stream + + def get_warning_stream(self): + return warning_stream + + def toggle_debugger(self, event=None): + if self.executing: + tkMessageBox.showerror("Don't debug now", + "You can only toggle the debugger when idle", + parent=self.text) + self.set_debugger_indicator() + return "break" + else: + db = self.interp.getdebugger() + if db: + self.close_debugger() + else: + self.open_debugger() + + def set_debugger_indicator(self): + db = self.interp.getdebugger() + self.setvar("<>", not not db) + + def toggle_jit_stack_viewer(self, event=None): + pass # All we need is the variable + + def close_debugger(self): + db = self.interp.getdebugger() + if db: + self.interp.setdebugger(None) + db.close() + if self.interp.rpcclt: + RemoteDebugger.close_remote_debugger(self.interp.rpcclt) + self.resetoutput() + self.console.write("[DEBUG OFF]\n") + sys.ps1 = ">>> " + self.showprompt() + self.set_debugger_indicator() + + def open_debugger(self): + if self.interp.rpcclt: + dbg_gui = RemoteDebugger.start_remote_debugger(self.interp.rpcclt, + self) + else: + dbg_gui = Debugger.Debugger(self) + self.interp.setdebugger(dbg_gui) + dbg_gui.load_breakpoints() + sys.ps1 = "[DEBUG ON]\n>>> " + self.showprompt() + self.set_debugger_indicator() + + def beginexecuting(self): + "Helper for ModifiedInterpreter" + self.resetoutput() + self.executing = 1 + + def endexecuting(self): + "Helper for ModifiedInterpreter" + self.executing = 0 + self.canceled = 0 + self.showprompt() + + def close(self): + "Extend EditorWindow.close()" + if self.executing: + response = tkMessageBox.askokcancel( + "Kill?", + "Your program is still running!\n Do you want to kill it?", + default="ok", + parent=self.text) + if response is False: + return "cancel" + self.stop_readline() + self.canceled = True + self.closing = True + return EditorWindow.close(self) + + def _close(self): + "Extend EditorWindow._close(), shut down debugger and execution server" + self.close_debugger() + if use_subprocess: + self.interp.kill_subprocess() + # Restore std streams + sys.stdout = self.save_stdout + sys.stderr = self.save_stderr + sys.stdin = self.save_stdin + # Break cycles + self.interp = None + self.console = None + self.flist.pyshell = None + self.history = None + EditorWindow._close(self) + + def ispythonsource(self, filename): + "Override EditorWindow method: never remove the colorizer" + return True + + def short_title(self): + return self.shell_title + + COPYRIGHT = \ + 'Type "copyright", "credits" or "license()" for more information.' + + def begin(self): + self.resetoutput() + if use_subprocess: + nosub = '' + client = self.interp.start_subprocess() + if not client: + self.close() + return False + else: + nosub = "==== No Subprocess ====" + self.write("Python %s on %s\n%s\n%s" % + (sys.version, sys.platform, self.COPYRIGHT, nosub)) + self.text.focus_force() + self.showprompt() + import Tkinter + Tkinter._default_root = None # 03Jan04 KBK What's this? + return True + + def stop_readline(self): + if not self.reading: # no nested mainloop to exit. + return + self._stop_readline_flag = True + self.top.quit() + + def readline(self): + save = self.reading + try: + self.reading = 1 + self.top.mainloop() # nested mainloop() + finally: + self.reading = save + if self._stop_readline_flag: + self._stop_readline_flag = False + return "" + line = self.text.get("iomark", "end-1c") + if len(line) == 0: # may be EOF if we quit our mainloop with Ctrl-C + line = "\n" + if isinstance(line, unicode): + from idlelib import IOBinding + try: + line = line.encode(IOBinding.encoding) + except UnicodeError: + pass + self.resetoutput() + if self.canceled: + self.canceled = 0 + if not use_subprocess: + raise KeyboardInterrupt + if self.endoffile: + self.endoffile = 0 + line = "" + return line + + def isatty(self): + return True + + def cancel_callback(self, event=None): + try: + if self.text.compare("sel.first", "!=", "sel.last"): + return # Active selection -- always use default binding + except: + pass + if not (self.executing or self.reading): + self.resetoutput() + self.interp.write("KeyboardInterrupt\n") + self.showprompt() + return "break" + self.endoffile = 0 + self.canceled = 1 + if (self.executing and self.interp.rpcclt): + if self.interp.getdebugger(): + self.interp.restart_subprocess() + else: + self.interp.interrupt_subprocess() + if self.reading: + self.top.quit() # exit the nested mainloop() in readline() + return "break" + + def eof_callback(self, event): + if self.executing and not self.reading: + return # Let the default binding (delete next char) take over + if not (self.text.compare("iomark", "==", "insert") and + self.text.compare("insert", "==", "end-1c")): + return # Let the default binding (delete next char) take over + if not self.executing: + self.resetoutput() + self.close() + else: + self.canceled = 0 + self.endoffile = 1 + self.top.quit() + return "break" + + def linefeed_callback(self, event): + # Insert a linefeed without entering anything (still autoindented) + if self.reading: + self.text.insert("insert", "\n") + self.text.see("insert") + else: + self.newline_and_indent_event(event) + return "break" + + def enter_callback(self, event): + if self.executing and not self.reading: + return # Let the default binding (insert '\n') take over + # If some text is selected, recall the selection + # (but only if this before the I/O mark) + try: + sel = self.text.get("sel.first", "sel.last") + if sel: + if self.text.compare("sel.last", "<=", "iomark"): + self.recall(sel, event) + return "break" + except: + pass + # If we're strictly before the line containing iomark, recall + # the current line, less a leading prompt, less leading or + # trailing whitespace + if self.text.compare("insert", "<", "iomark linestart"): + # Check if there's a relevant stdin range -- if so, use it + prev = self.text.tag_prevrange("stdin", "insert") + if prev and self.text.compare("insert", "<", prev[1]): + self.recall(self.text.get(prev[0], prev[1]), event) + return "break" + next = self.text.tag_nextrange("stdin", "insert") + if next and self.text.compare("insert lineend", ">=", next[0]): + self.recall(self.text.get(next[0], next[1]), event) + return "break" + # No stdin mark -- just get the current line, less any prompt + indices = self.text.tag_nextrange("console", "insert linestart") + if indices and \ + self.text.compare(indices[0], "<=", "insert linestart"): + self.recall(self.text.get(indices[1], "insert lineend"), event) + else: + self.recall(self.text.get("insert linestart", "insert lineend"), event) + return "break" + # If we're between the beginning of the line and the iomark, i.e. + # in the prompt area, move to the end of the prompt + if self.text.compare("insert", "<", "iomark"): + self.text.mark_set("insert", "iomark") + # If we're in the current input and there's only whitespace + # beyond the cursor, erase that whitespace first + s = self.text.get("insert", "end-1c") + if s and not s.strip(): + self.text.delete("insert", "end-1c") + # If we're in the current input before its last line, + # insert a newline right at the insert point + if self.text.compare("insert", "<", "end-1c linestart"): + self.newline_and_indent_event(event) + return "break" + # We're in the last line; append a newline and submit it + self.text.mark_set("insert", "end-1c") + if self.reading: + self.text.insert("insert", "\n") + self.text.see("insert") + else: + self.newline_and_indent_event(event) + self.text.tag_add("stdin", "iomark", "end-1c") + self.text.update_idletasks() + if self.reading: + self.top.quit() # Break out of recursive mainloop() in raw_input() + else: + self.runit() + return "break" + + def recall(self, s, event): + # remove leading and trailing empty or whitespace lines + s = re.sub(r'^\s*\n', '' , s) + s = re.sub(r'\n\s*$', '', s) + lines = s.split('\n') + self.text.undo_block_start() + try: + self.text.tag_remove("sel", "1.0", "end") + self.text.mark_set("insert", "end-1c") + prefix = self.text.get("insert linestart", "insert") + if prefix.rstrip().endswith(':'): + self.newline_and_indent_event(event) + prefix = self.text.get("insert linestart", "insert") + self.text.insert("insert", lines[0].strip()) + if len(lines) > 1: + orig_base_indent = re.search(r'^([ \t]*)', lines[0]).group(0) + new_base_indent = re.search(r'^([ \t]*)', prefix).group(0) + for line in lines[1:]: + if line.startswith(orig_base_indent): + # replace orig base indentation with new indentation + line = new_base_indent + line[len(orig_base_indent):] + self.text.insert('insert', '\n'+line.rstrip()) + finally: + self.text.see("insert") + self.text.undo_block_stop() + + def runit(self): + line = self.text.get("iomark", "end-1c") + # Strip off last newline and surrounding whitespace. + # (To allow you to hit return twice to end a statement.) + i = len(line) + while i > 0 and line[i-1] in " \t": + i = i-1 + if i > 0 and line[i-1] == "\n": + i = i-1 + while i > 0 and line[i-1] in " \t": + i = i-1 + line = line[:i] + self.interp.runsource(line) + + def open_stack_viewer(self, event=None): + if self.interp.rpcclt: + return self.interp.remote_stack_viewer() + try: + sys.last_traceback + except: + tkMessageBox.showerror("No stack trace", + "There is no stack trace yet.\n" + "(sys.last_traceback is not defined)", + parent=self.text) + return + from idlelib.StackViewer import StackBrowser + StackBrowser(self.root, self.flist) + + def view_restart_mark(self, event=None): + self.text.see("iomark") + self.text.see("restart") + + def restart_shell(self, event=None): + "Callback for Run/Restart Shell Cntl-F6" + self.interp.restart_subprocess(with_cwd=True) + + def showprompt(self): + self.resetoutput() + try: + s = str(sys.ps1) + except: + s = "" + self.console.write(s) + self.text.mark_set("insert", "end-1c") + self.set_line_and_column() + self.io.reset_undo() + + def resetoutput(self): + source = self.text.get("iomark", "end-1c") + if self.history: + self.history.store(source) + if self.text.get("end-2c") != "\n": + self.text.insert("end-1c", "\n") + self.text.mark_set("iomark", "end-1c") + self.set_line_and_column() + sys.stdout.softspace = 0 + + def write(self, s, tags=()): + try: + self.text.mark_gravity("iomark", "right") + OutputWindow.write(self, s, tags, "iomark") + self.text.mark_gravity("iomark", "left") + except: + pass + if self.canceled: + self.canceled = 0 + if not use_subprocess: + raise KeyboardInterrupt + + def rmenu_check_cut(self): + try: + if self.text.compare('sel.first', '<', 'iomark'): + return 'disabled' + except TclError: # no selection, so the index 'sel.first' doesn't exist + return 'disabled' + return super(PyShell, self).rmenu_check_cut() + + def rmenu_check_paste(self): + if self.text.compare('insert', '<', 'iomark'): + return 'disabled' + return super(PyShell, self).rmenu_check_paste() + +class PseudoFile(io.TextIOBase): + + def __init__(self, shell, tags, encoding=None): + self.shell = shell + self.tags = tags + self.softspace = 0 + self._encoding = encoding + + @property + def encoding(self): + return self._encoding + + @property + def name(self): + return '<%s>' % self.tags + + def isatty(self): + return True + + +class PseudoOutputFile(PseudoFile): + + def writable(self): + return True + + def write(self, s): + if self.closed: + raise ValueError("write to closed file") + if type(s) not in (unicode, str, bytearray): + # See issue #19481 + if isinstance(s, unicode): + s = unicode.__getitem__(s, slice(None)) + elif isinstance(s, str): + s = str.__str__(s) + elif isinstance(s, bytearray): + s = bytearray.__str__(s) + else: + raise TypeError('must be string, not ' + type(s).__name__) + return self.shell.write(s, self.tags) + + +class PseudoInputFile(PseudoFile): + + def __init__(self, shell, tags, encoding=None): + PseudoFile.__init__(self, shell, tags, encoding) + self._line_buffer = '' + + def readable(self): + return True + + def read(self, size=-1): + if self.closed: + raise ValueError("read from closed file") + if size is None: + size = -1 + elif not isinstance(size, int): + raise TypeError('must be int, not ' + type(size).__name__) + result = self._line_buffer + self._line_buffer = '' + if size < 0: + while True: + line = self.shell.readline() + if not line: break + result += line + else: + while len(result) < size: + line = self.shell.readline() + if not line: break + result += line + self._line_buffer = result[size:] + result = result[:size] + return result + + def readline(self, size=-1): + if self.closed: + raise ValueError("read from closed file") + if size is None: + size = -1 + elif not isinstance(size, int): + raise TypeError('must be int, not ' + type(size).__name__) + line = self._line_buffer or self.shell.readline() + if size < 0: + size = len(line) + eol = line.find('\n', 0, size) + if eol >= 0: + size = eol + 1 + self._line_buffer = line[size:] + return line[:size] + + def close(self): + self.shell.close() + + +usage_msg = """\ + +USAGE: idle [-deins] [-t title] [file]* + idle [-dns] [-t title] (-c cmd | -r file) [arg]* + idle [-dns] [-t title] - [arg]* + + -h print this help message and exit + -n run IDLE without a subprocess (see Help/IDLE Help for details) + +The following options will override the IDLE 'settings' configuration: + + -e open an edit window + -i open a shell window + +The following options imply -i and will open a shell: + + -c cmd run the command in a shell, or + -r file run script from file + + -d enable the debugger + -s run $IDLESTARTUP or $PYTHONSTARTUP before anything else + -t title set title of shell window + +A default edit window will be bypassed when -c, -r, or - are used. + +[arg]* are passed to the command (-c) or script (-r) in sys.argv[1:]. + +Examples: + +idle + Open an edit window or shell depending on IDLE's configuration. + +idle foo.py foobar.py + Edit the files, also open a shell if configured to start with shell. + +idle -est "Baz" foo.py + Run $IDLESTARTUP or $PYTHONSTARTUP, edit foo.py, and open a shell + window with the title "Baz". + +idle -c "import sys; print sys.argv" "foo" + Open a shell window and run the command, passing "-c" in sys.argv[0] + and "foo" in sys.argv[1]. + +idle -d -s -r foo.py "Hello World" + Open a shell window, run a startup script, enable the debugger, and + run foo.py, passing "foo.py" in sys.argv[0] and "Hello World" in + sys.argv[1]. + +echo "import sys; print sys.argv" | idle - "foobar" + Open a shell window, run the script piped in, passing '' in sys.argv[0] + and "foobar" in sys.argv[1]. +""" + +def main( tkroot ): + global flist, root, use_subprocess + root = tkroot + + capture_warnings(True) + use_subprocess = True + enable_shell = False + enable_edit = False + debug = False + cmd = None + script = None + startup = False + try: + opts, args = getopt.getopt(sys.argv[1:], "c:deihnr:st:") + except getopt.error as msg: + print("Error: %s\n%s" % (msg, usage_msg), file=sys.stderr) + sys.exit(2) + for o, a in opts: + if o == '-c': + cmd = a + enable_shell = True + if o == '-d': + debug = True + enable_shell = True + if o == '-e': + enable_edit = True + if o == '-h': + sys.stdout.write(usage_msg) + sys.exit() + if o == '-i': + enable_shell = True + if o == '-n': + use_subprocess = False + if o == '-r': + script = a + if os.path.isfile(script): + pass + else: + print("No script file: ", script, file=sys.stderr) + sys.exit() + enable_shell = True + if o == '-s': + startup = True + enable_shell = True + if o == '-t': + PyShell.shell_title = a + enable_shell = True + if args and args[0] == '-': + cmd = sys.stdin.read() + enable_shell = True + # process sys.argv and sys.path: + for i in range(len(sys.path)): + sys.path[i] = os.path.abspath(sys.path[i]) + if args and args[0] == '-': + sys.argv = [''] + args[1:] + elif cmd: + sys.argv = ['-c'] + args + elif script: + sys.argv = [script] + args + elif args: + enable_edit = True + pathx = [] + for filename in args: + pathx.append(os.path.dirname(filename)) + for dir in pathx: + dir = os.path.abspath(dir) + if dir not in sys.path: + sys.path.insert(0, dir) + else: + dir = os.getcwd() + if not dir in sys.path: + sys.path.insert(0, dir) + # check the IDLE settings configuration (but command line overrides) + edit_start = idleConf.GetOption('main', 'General', + 'editor-on-startup', type='bool') + enable_edit = enable_edit or edit_start + enable_shell = enable_shell or not enable_edit + # start editor and/or shell windows: + + # set application icon + icondir = os.path.join(os.path.dirname(__file__), 'Icons') + if system() == 'Windows': + iconfile = os.path.join(icondir, 'idle.ico') + root.wm_iconbitmap(default=iconfile) + elif TkVersion >= 8.5: + ext = '.png' if TkVersion >= 8.6 else '.gif' + iconfiles = [os.path.join(icondir, 'idle_%d%s' % (size, ext)) + for size in (16, 32, 48)] + icons = [PhotoImage(file=iconfile) for iconfile in iconfiles] + root.tk.call('wm', 'iconphoto', str(root), "-default", *icons) + + fixwordbreaks(root) + root.withdraw() + flist = PyShellFileList(root) + macosxSupport.setupApp(root, flist) + + if macosxSupport.isAquaTk(): + # There are some screwed up <2> class bindings for text + # widgets defined in Tk which we need to do away with. + # See issue #24801. + root.unbind_class('Text', '') + root.unbind_class('Text', '') + root.unbind_class('Text', '<>') + + if enable_edit: + if not (cmd or script): + for filename in args[:]: + if flist.open(filename) is None: + # filename is a directory actually, disconsider it + args.remove(filename) + if not args: + flist.new() + + if enable_shell: + shell = flist.open_shell() + if not shell: + return # couldn't open shell + if macosxSupport.isAquaTk() and flist.dict: + # On OSX: when the user has double-clicked on a file that causes + # IDLE to be launched the shell window will open just in front of + # the file she wants to see. Lower the interpreter window when + # there are open files. + shell.top.lower() + else: + shell = flist.pyshell + + # Handle remaining options. If any of these are set, enable_shell + # was set also, so shell must be true to reach here. + if debug: + shell.open_debugger() + if startup: + filename = os.environ.get("IDLESTARTUP") or \ + os.environ.get("PYTHONSTARTUP") + if filename and os.path.isfile(filename): + shell.interp.execfile(filename) + if cmd or script: + shell.interp.runcommand("""if 1: + import sys as _sys + _sys.argv = %r + del _sys + \n""" % (sys.argv,)) + if cmd: + shell.interp.execsource(cmd) + elif script: + shell.interp.prepend_syspath(script) + shell.interp.execfile(script) + elif shell: + # If there is a shell window and no cmd or script in progress, + # check for problematic OS X Tk versions and print a warning + # message in the IDLE shell window; this is less intrusive + # than always opening a separate window. + tkversionwarning = macosxSupport.tkVersionWarning(root) + if tkversionwarning: + shell.interp.runcommand("print('%s')" % tkversionwarning) + + while flist.inversedict: # keep IDLE running while files are open. + root.mainloop() + root.destroy() + capture_warnings(False) + +if __name__ == "__main__": + sys.modules['PyShell'] = sys.modules['__main__'] + main() + +capture_warnings(False) # Make sure turned off; see issue 18081 diff --git a/build/lib/moosegui/__init__.py b/build/lib/moosegui/__init__.py new file mode 100644 index 0000000..8aa84f1 --- /dev/null +++ b/build/lib/moosegui/__init__.py @@ -0,0 +1 @@ +from moosegui.main import main diff --git a/build/lib/moosegui/_globals.py b/build/lib/moosegui/_globals.py new file mode 100644 index 0000000..509c58f --- /dev/null +++ b/build/lib/moosegui/_globals.py @@ -0,0 +1,29 @@ +"""globals.py: + +Keep all GUI global option here. + +""" + +__author__ = "Me" +__copyright__ = "Copyright 2016, Me" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Me" +__email__ = "" +__status__ = "Development" + +import sys +import os + +# root +root_ = None + +# Main canvas. +canvas_ = None + +# Main canvas. +toolbar_ = None + +# Status bar +statusbar_ = None diff --git a/build/lib/moosegui/canvas.py b/build/lib/moosegui/canvas.py new file mode 100644 index 0000000..3bae5b4 --- /dev/null +++ b/build/lib/moosegui/canvas.py @@ -0,0 +1,71 @@ +""" +Add canvas + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import sys +import os +import logging + +import moosegui._globals +from moosegui.MooseCanvas import MooseCanvas + +try: + from Tkinter import * +except ImportError as e: + from tkinter import * + +class StatusBar(Frame): + + def __init__(self, master): + Frame.__init__(self, master) + self.label = Label(self, bd = 1, relief = SUNKEN, anchor = W) + self.label.config( text = 'LABEL' ) + self.label.grid( row = 2, column = 0, sticky = 'ew' ) + + def set(self, format, *args): + self.label.config(text=format % args) + self.label.update_idletasks() + + def clear(self): + self.label.config(text="") + self.label.update_idletasks() + +def update( ): + logging.info( '.' ) + + +def main( parent ): + """ + Added few frames. + + First frame is editor frame. By default take half of horizontal screen and + 80% of vertical screen. + + """ + + w, h = parent.winfo_screenwidth( ), parent.winfo_screenheight( ) + editCanvas = MooseCanvas( parent ) + # editCanvas.canvas.focus_set( ) + + # Add a statusbar + sbar = StatusBar( parent ) + sbar.grid( row = 3, column = 1, sticky = 'ew' ) + + sbar.bind( '', update ) + + _globals.statusbar_ = sbar + _globals.canvas_ = editCanvas + + +if __name__ == '__main__': + main() diff --git a/build/lib/moosegui/main.py b/build/lib/moosegui/main.py new file mode 100644 index 0000000..0a18a07 --- /dev/null +++ b/build/lib/moosegui/main.py @@ -0,0 +1,70 @@ +""" +Entry point. + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import sys + +try: + import Tkinter as tk +except ImportError as e: + import tkinter as tk + +import os +import traceback + +from moosegui.MooseWindow import MooseWindow +import moosegui.menus +import moosegui.canvas +import moosegui.toolbar +import moosegui._globals + +import logging +logging.basicConfig( level = logging.DEBUG ) + + +class Catcher: + def __init__(self, func, subst, widget): + self.func = func + self.subst = subst + self.widget = widget + + def __call__(self, *args): + try: + if self.subst: + args = apply(self.subst, args) + return apply(self.func, args) + except SystemExit as msg: + logging.info( "Existing ... %s" % msg ) + raise SystemExit + except: + traceback.print_exc( file = open('moosegui.log', 'a') ) + +tk.CallWrapper = Catcher + +def main( ): + root = MooseWindow( ) + root.resizable( width = False, height = False ) + _globals.root_ = root + + # Handle all menues. + menus.main( root ) + + # Add toolbar + toolbar.main( root ) + + # All frames + canvas.main( root ) + tk.mainloop( ) + +if __name__ == '__main__': + main() diff --git a/build/lib/moosegui/menus.py b/build/lib/moosegui/menus.py new file mode 100644 index 0000000..b5bf2ba --- /dev/null +++ b/build/lib/moosegui/menus.py @@ -0,0 +1,73 @@ +"""menus.py: + +Menu management. + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import sys +PY_MAJOR = int( sys.version_info.major ) +if PY_MAJOR == 2: + import Tkinter as tk +else: + import tkinter as tk + +import os +import logging + +menus_ = [ 'File', 'Insert' ] +menu_dict_ = { + "File" : [ ("New Model", "Ctrl+N", "Control-n" ) + , ("Load Model", "Ctrl+O", "Control-o") + , ("Exit", "Ctrl+Q", "Control-q") ] + , "Insert" : [ ( "CubeMesh", ) + , ( "CylMesh" , ) + , ( "Pool" , ) + , ( "BufPool", ) + , ( "Reac" , ) ] + } + +def callback( action, parent ): + logging.info( "Got action %s" % action ) + if action.lower() == 'exit': + raise SystemExit( "Exit command" ) + else: + logging.info( "TODO %s" % action ) + +def main( parent ): + """ + This function adds required menues + + """ + menu = tk.Menu( parent ) + for menuName in menus_ : + logging.info( "Adding menu %s" % menuName ) + thismenu = tk.Menu( menu ) + menu.add_cascade( label = menuName, menu = thismenu ) + for action in menu_dict_[ menuName ]: + shortcut, underline = '', 0 + cmd = action[0] + if len( action ) > 1: + shortcut, underline = action[1], 1 + shortKey = "<%s>" % action[2] + logging.debug( "Bidning key %s to action %s" % (shortKey, cmd)) + parent.bind( shortKey, lambda e, x=cmd: callback(x, parent) ) + + thismenu.add_command( label = action[0] + , command = lambda x=cmd: callback(x, parent) + , underline = underline + , accelerator = shortcut + ) + + parent.config( menu = menu ) + +if __name__ == '__main__': + main() diff --git a/build/lib/moosegui/pyshell.py b/build/lib/moosegui/pyshell.py new file mode 100644 index 0000000..e1eade1 --- /dev/null +++ b/build/lib/moosegui/pyshell.py @@ -0,0 +1,1538 @@ +#! /usr/bin/env python3 + +try: + from tkinter import * +except ImportError: + print("** IDLE can't import Tkinter.\n" + "Your Python may not be configured for Tk. **", file=sys.__stderr__) + sys.exit(1) +import tkinter.messagebox as tkMessageBox +if TkVersion < 8.5: + root = Tk() # otherwise create root in main + root.withdraw() + tkMessageBox.showerror("Idle Cannot Start", + "Idle requires tcl/tk 8.5+, not $s." % TkVersion, + parent=root) + sys.exit(1) + +from code import InteractiveInterpreter +import getopt +import io +import linecache +import os +import os.path +from platform import python_version, system +import re +import socket +import subprocess +import sys +import threading +import time +import tokenize +import warnings + +from idlelib import testing # bool value +from idlelib.colorizer import ColorDelegator +from idlelib.config import idleConf +from idlelib import debugger +from idlelib import debugger_r +from idlelib.editor import EditorWindow, fixwordbreaks +from idlelib.filelist import FileList +from idlelib import macosx +from idlelib.outwin import OutputWindow +from idlelib import rpc +from idlelib.run import idle_formatwarning, PseudoInputFile, PseudoOutputFile +from idlelib.undo import UndoDelegator + +HOST = '127.0.0.1' # python execution server on localhost loopback +PORT = 0 # someday pass in host, port for remote debug capability + +# Override warnings module to write to warning_stream. Initialize to send IDLE +# internal warnings to the console. ScriptBinding.check_syntax() will +# temporarily redirect the stream to the shell window to display warnings when +# checking user's code. +warning_stream = sys.__stderr__ # None, at least on Windows, if no console. + +def idle_showwarning( + message, category, filename, lineno, file=None, line=None): + """Show Idle-format warning (after replacing warnings.showwarning). + + The differences are the formatter called, the file=None replacement, + which can be None, the capture of the consequence AttributeError, + and the output of a hard-coded prompt. + """ + if file is None: + file = warning_stream + try: + file.write(idle_formatwarning( + message, category, filename, lineno, line=line)) + file.write(">>> ") + except (AttributeError, OSError): + pass # if file (probably __stderr__) is invalid, skip warning. + +_warnings_showwarning = None + +def capture_warnings(capture): + "Replace warning.showwarning with idle_showwarning, or reverse." + + global _warnings_showwarning + if capture: + if _warnings_showwarning is None: + _warnings_showwarning = warnings.showwarning + warnings.showwarning = idle_showwarning + else: + if _warnings_showwarning is not None: + warnings.showwarning = _warnings_showwarning + _warnings_showwarning = None + +capture_warnings(True) + +def extended_linecache_checkcache(filename=None, + orig_checkcache=linecache.checkcache): + """Extend linecache.checkcache to preserve the entries + + Rather than repeating the linecache code, patch it to save the + entries, call the original linecache.checkcache() + (skipping them), and then restore the saved entries. + + orig_checkcache is bound at definition time to the original + method, allowing it to be patched. + """ + cache = linecache.cache + save = {} + for key in list(cache): + if key[:1] + key[-1:] == '<>': + save[key] = cache.pop(key) + orig_checkcache(filename) + cache.update(save) + +# Patch linecache.checkcache(): +linecache.checkcache = extended_linecache_checkcache + + +class PyShellEditorWindow(EditorWindow): + "Regular text edit window in IDLE, supports breakpoints" + + def __init__(self, *args): + self.breakpoints = [] + EditorWindow.__init__(self, *args) + self.text.bind("<>", self.set_breakpoint_here) + self.text.bind("<>", self.clear_breakpoint_here) + self.text.bind("<>", self.flist.open_shell) + + self.breakpointPath = os.path.join(idleConf.GetUserCfgDir(), + 'breakpoints.lst') + # whenever a file is changed, restore breakpoints + def filename_changed_hook(old_hook=self.io.filename_change_hook, + self=self): + self.restore_file_breaks() + old_hook() + self.io.set_filename_change_hook(filename_changed_hook) + if self.io.filename: + self.restore_file_breaks() + self.color_breakpoint_text() + + rmenu_specs = [ + ("Cut", "<>", "rmenu_check_cut"), + ("Copy", "<>", "rmenu_check_copy"), + ("Paste", "<>", "rmenu_check_paste"), + (None, None, None), + ("Set Breakpoint", "<>", None), + ("Clear Breakpoint", "<>", None) + ] + + def color_breakpoint_text(self, color=True): + "Turn colorizing of breakpoint text on or off" + if self.io is None: + # possible due to update in restore_file_breaks + return + if color: + theme = idleConf.CurrentTheme() + cfg = idleConf.GetHighlight(theme, "break") + else: + cfg = {'foreground': '', 'background': ''} + self.text.tag_config('BREAK', cfg) + + def set_breakpoint(self, lineno): + text = self.text + filename = self.io.filename + text.tag_add("BREAK", "%d.0" % lineno, "%d.0" % (lineno+1)) + try: + self.breakpoints.index(lineno) + except ValueError: # only add if missing, i.e. do once + self.breakpoints.append(lineno) + try: # update the subprocess debugger + debug = self.flist.pyshell.interp.debugger + debug.set_breakpoint_here(filename, lineno) + except: # but debugger may not be active right now.... + pass + + def set_breakpoint_here(self, event=None): + text = self.text + filename = self.io.filename + if not filename: + text.bell() + return + lineno = int(float(text.index("insert"))) + self.set_breakpoint(lineno) + + def clear_breakpoint_here(self, event=None): + text = self.text + filename = self.io.filename + if not filename: + text.bell() + return + lineno = int(float(text.index("insert"))) + try: + self.breakpoints.remove(lineno) + except: + pass + text.tag_remove("BREAK", "insert linestart",\ + "insert lineend +1char") + try: + debug = self.flist.pyshell.interp.debugger + debug.clear_breakpoint_here(filename, lineno) + except: + pass + + def clear_file_breaks(self): + if self.breakpoints: + text = self.text + filename = self.io.filename + if not filename: + text.bell() + return + self.breakpoints = [] + text.tag_remove("BREAK", "1.0", END) + try: + debug = self.flist.pyshell.interp.debugger + debug.clear_file_breaks(filename) + except: + pass + + def store_file_breaks(self): + "Save breakpoints when file is saved" + # XXX 13 Dec 2002 KBK Currently the file must be saved before it can + # be run. The breaks are saved at that time. If we introduce + # a temporary file save feature the save breaks functionality + # needs to be re-verified, since the breaks at the time the + # temp file is created may differ from the breaks at the last + # permanent save of the file. Currently, a break introduced + # after a save will be effective, but not persistent. + # This is necessary to keep the saved breaks synched with the + # saved file. + # + # Breakpoints are set as tagged ranges in the text. + # Since a modified file has to be saved before it is + # run, and since self.breakpoints (from which the subprocess + # debugger is loaded) is updated during the save, the visible + # breaks stay synched with the subprocess even if one of these + # unexpected breakpoint deletions occurs. + breaks = self.breakpoints + filename = self.io.filename + try: + with open(self.breakpointPath, "r") as fp: + lines = fp.readlines() + except OSError: + lines = [] + try: + with open(self.breakpointPath, "w") as new_file: + for line in lines: + if not line.startswith(filename + '='): + new_file.write(line) + self.update_breakpoints() + breaks = self.breakpoints + if breaks: + new_file.write(filename + '=' + str(breaks) + '\n') + except OSError as err: + if not getattr(self.root, "breakpoint_error_displayed", False): + self.root.breakpoint_error_displayed = True + tkMessageBox.showerror(title='IDLE Error', + message='Unable to update breakpoint list:\n%s' + % str(err), + parent=self.text) + + def restore_file_breaks(self): + self.text.update() # this enables setting "BREAK" tags to be visible + if self.io is None: + # can happen if IDLE closes due to the .update() call + return + filename = self.io.filename + if filename is None: + return + if os.path.isfile(self.breakpointPath): + with open(self.breakpointPath, "r") as fp: + lines = fp.readlines() + for line in lines: + if line.startswith(filename + '='): + breakpoint_linenumbers = eval(line[len(filename)+1:]) + for breakpoint_linenumber in breakpoint_linenumbers: + self.set_breakpoint(breakpoint_linenumber) + + def update_breakpoints(self): + "Retrieves all the breakpoints in the current window" + text = self.text + ranges = text.tag_ranges("BREAK") + linenumber_list = self.ranges_to_linenumbers(ranges) + self.breakpoints = linenumber_list + + def ranges_to_linenumbers(self, ranges): + lines = [] + for index in range(0, len(ranges), 2): + lineno = int(float(ranges[index].string)) + end = int(float(ranges[index+1].string)) + while lineno < end: + lines.append(lineno) + lineno += 1 + return lines + +# XXX 13 Dec 2002 KBK Not used currently +# def saved_change_hook(self): +# "Extend base method - clear breaks if module is modified" +# if not self.get_saved(): +# self.clear_file_breaks() +# EditorWindow.saved_change_hook(self) + + def _close(self): + "Extend base method - clear breaks when module is closed" + self.clear_file_breaks() + EditorWindow._close(self) + + +class PyShellFileList(FileList): + "Extend base class: IDLE supports a shell and breakpoints" + + # override FileList's class variable, instances return PyShellEditorWindow + # instead of EditorWindow when new edit windows are created. + EditorWindow = PyShellEditorWindow + + pyshell = None + + def open_shell(self, event=None): + if self.pyshell: + self.pyshell.top.wakeup() + else: + self.pyshell = PyShell(self) + if self.pyshell: + if not self.pyshell.begin(): + return None + return self.pyshell + + +class ModifiedColorDelegator(ColorDelegator): + "Extend base class: colorizer for the shell window itself" + + def __init__(self): + ColorDelegator.__init__(self) + self.LoadTagDefs() + + def recolorize_main(self): + self.tag_remove("TODO", "1.0", "iomark") + self.tag_add("SYNC", "1.0", "iomark") + ColorDelegator.recolorize_main(self) + + def LoadTagDefs(self): + ColorDelegator.LoadTagDefs(self) + theme = idleConf.CurrentTheme() + self.tagdefs.update({ + "stdin": {'background':None,'foreground':None}, + "stdout": idleConf.GetHighlight(theme, "stdout"), + "stderr": idleConf.GetHighlight(theme, "stderr"), + "console": idleConf.GetHighlight(theme, "console"), + }) + + def removecolors(self): + # Don't remove shell color tags before "iomark" + for tag in self.tagdefs: + self.tag_remove(tag, "iomark", "end") + +class ModifiedUndoDelegator(UndoDelegator): + "Extend base class: forbid insert/delete before the I/O mark" + + def insert(self, index, chars, tags=None): + try: + if self.delegate.compare(index, "<", "iomark"): + self.delegate.bell() + return + except TclError: + pass + UndoDelegator.insert(self, index, chars, tags) + + def delete(self, index1, index2=None): + try: + if self.delegate.compare(index1, "<", "iomark"): + self.delegate.bell() + return + except TclError: + pass + UndoDelegator.delete(self, index1, index2) + + +class MyRPCClient(rpc.RPCClient): + + def handle_EOF(self): + "Override the base class - just re-raise EOFError" + raise EOFError + + +class ModifiedInterpreter(InteractiveInterpreter): + + def __init__(self, tkconsole): + self.tkconsole = tkconsole + locals = sys.modules['__main__'].__dict__ + InteractiveInterpreter.__init__(self, locals=locals) + self.save_warnings_filters = None + self.restarting = False + self.subprocess_arglist = None + self.port = PORT + self.original_compiler_flags = self.compile.compiler.flags + + _afterid = None + rpcclt = None + rpcsubproc = None + + def spawn_subprocess(self): + if self.subprocess_arglist is None: + self.subprocess_arglist = self.build_subprocess_arglist() + self.rpcsubproc = subprocess.Popen(self.subprocess_arglist) + + def build_subprocess_arglist(self): + assert (self.port!=0), ( + "Socket should have been assigned a port number.") + w = ['-W' + s for s in sys.warnoptions] + # Maybe IDLE is installed and is being accessed via sys.path, + # or maybe it's not installed and the idle.py script is being + # run from the IDLE source directory. + del_exitf = idleConf.GetOption('main', 'General', 'delete-exitfunc', + default=False, type='bool') + if __name__ == 'idlelib.pyshell': + command = "__import__('idlelib.run').run.main(%r)" % (del_exitf,) + else: + command = "__import__('run').main(%r)" % (del_exitf,) + return [sys.executable] + w + ["-c", command, str(self.port)] + + def start_subprocess(self): + addr = (HOST, self.port) + # GUI makes several attempts to acquire socket, listens for connection + for i in range(3): + time.sleep(i) + try: + self.rpcclt = MyRPCClient(addr) + break + except OSError: + pass + else: + self.display_port_binding_error() + return None + # if PORT was 0, system will assign an 'ephemeral' port. Find it out: + self.port = self.rpcclt.listening_sock.getsockname()[1] + # if PORT was not 0, probably working with a remote execution server + if PORT != 0: + # To allow reconnection within the 2MSL wait (cf. Stevens TCP + # V1, 18.6), set SO_REUSEADDR. Note that this can be problematic + # on Windows since the implementation allows two active sockets on + # the same address! + self.rpcclt.listening_sock.setsockopt(socket.SOL_SOCKET, + socket.SO_REUSEADDR, 1) + self.spawn_subprocess() + #time.sleep(20) # test to simulate GUI not accepting connection + # Accept the connection from the Python execution server + self.rpcclt.listening_sock.settimeout(10) + try: + self.rpcclt.accept() + except socket.timeout: + self.display_no_subprocess_error() + return None + self.rpcclt.register("console", self.tkconsole) + self.rpcclt.register("stdin", self.tkconsole.stdin) + self.rpcclt.register("stdout", self.tkconsole.stdout) + self.rpcclt.register("stderr", self.tkconsole.stderr) + self.rpcclt.register("flist", self.tkconsole.flist) + self.rpcclt.register("linecache", linecache) + self.rpcclt.register("interp", self) + self.transfer_path(with_cwd=True) + self.poll_subprocess() + return self.rpcclt + + def restart_subprocess(self, with_cwd=False, filename=''): + if self.restarting: + return self.rpcclt + self.restarting = True + # close only the subprocess debugger + debug = self.getdebugger() + if debug: + try: + # Only close subprocess debugger, don't unregister gui_adap! + debugger_r.close_subprocess_debugger(self.rpcclt) + except: + pass + # Kill subprocess, spawn a new one, accept connection. + self.rpcclt.close() + self.terminate_subprocess() + console = self.tkconsole + was_executing = console.executing + console.executing = False + self.spawn_subprocess() + try: + self.rpcclt.accept() + except socket.timeout: + self.display_no_subprocess_error() + return None + self.transfer_path(with_cwd=with_cwd) + console.stop_readline() + # annotate restart in shell window and mark it + console.text.delete("iomark", "end-1c") + tag = 'RESTART: ' + (filename if filename else 'Shell') + halfbar = ((int(console.width) -len(tag) - 4) // 2) * '=' + console.write("\n{0} {1} {0}".format(halfbar, tag)) + console.text.mark_set("restart", "end-1c") + console.text.mark_gravity("restart", "left") + if not filename: + console.showprompt() + # restart subprocess debugger + if debug: + # Restarted debugger connects to current instance of debug GUI + debugger_r.restart_subprocess_debugger(self.rpcclt) + # reload remote debugger breakpoints for all PyShellEditWindows + debug.load_breakpoints() + self.compile.compiler.flags = self.original_compiler_flags + self.restarting = False + return self.rpcclt + + def __request_interrupt(self): + self.rpcclt.remotecall("exec", "interrupt_the_server", (), {}) + + def interrupt_subprocess(self): + threading.Thread(target=self.__request_interrupt).start() + + def kill_subprocess(self): + if self._afterid is not None: + self.tkconsole.text.after_cancel(self._afterid) + try: + self.rpcclt.listening_sock.close() + except AttributeError: # no socket + pass + try: + self.rpcclt.close() + except AttributeError: # no socket + pass + self.terminate_subprocess() + self.tkconsole.executing = False + self.rpcclt = None + + def terminate_subprocess(self): + "Make sure subprocess is terminated" + try: + self.rpcsubproc.kill() + except OSError: + # process already terminated + return + else: + try: + self.rpcsubproc.wait() + except OSError: + return + + def transfer_path(self, with_cwd=False): + if with_cwd: # Issue 13506 + path = [''] # include Current Working Directory + path.extend(sys.path) + else: + path = sys.path + + self.runcommand("""if 1: + import sys as _sys + _sys.path = %r + del _sys + \n""" % (path,)) + + active_seq = None + + def poll_subprocess(self): + clt = self.rpcclt + if clt is None: + return + try: + response = clt.pollresponse(self.active_seq, wait=0.05) + except (EOFError, OSError, KeyboardInterrupt): + # lost connection or subprocess terminated itself, restart + # [the KBI is from rpc.SocketIO.handle_EOF()] + if self.tkconsole.closing: + return + response = None + self.restart_subprocess() + if response: + self.tkconsole.resetoutput() + self.active_seq = None + how, what = response + console = self.tkconsole.console + if how == "OK": + if what is not None: + print(repr(what), file=console) + elif how == "EXCEPTION": + if self.tkconsole.getvar("<>"): + self.remote_stack_viewer() + elif how == "ERROR": + errmsg = "pyshell.ModifiedInterpreter: Subprocess ERROR:\n" + print(errmsg, what, file=sys.__stderr__) + print(errmsg, what, file=console) + # we received a response to the currently active seq number: + try: + self.tkconsole.endexecuting() + except AttributeError: # shell may have closed + pass + # Reschedule myself + if not self.tkconsole.closing: + self._afterid = self.tkconsole.text.after( + self.tkconsole.pollinterval, self.poll_subprocess) + + debugger = None + + def setdebugger(self, debugger): + self.debugger = debugger + + def getdebugger(self): + return self.debugger + + def open_remote_stack_viewer(self): + """Initiate the remote stack viewer from a separate thread. + + This method is called from the subprocess, and by returning from this + method we allow the subprocess to unblock. After a bit the shell + requests the subprocess to open the remote stack viewer which returns a + static object looking at the last exception. It is queried through + the RPC mechanism. + + """ + self.tkconsole.text.after(300, self.remote_stack_viewer) + return + + def remote_stack_viewer(self): + from idlelib import debugobj_r + oid = self.rpcclt.remotequeue("exec", "stackviewer", ("flist",), {}) + if oid is None: + self.tkconsole.root.bell() + return + item = debugobj_r.StubObjectTreeItem(self.rpcclt, oid) + from idlelib.tree import ScrolledCanvas, TreeNode + top = Toplevel(self.tkconsole.root) + theme = idleConf.CurrentTheme() + background = idleConf.GetHighlight(theme, 'normal')['background'] + sc = ScrolledCanvas(top, bg=background, highlightthickness=0) + sc.frame.pack(expand=1, fill="both") + node = TreeNode(sc.canvas, None, item) + node.expand() + # XXX Should GC the remote tree when closing the window + + gid = 0 + + def execsource(self, source): + "Like runsource() but assumes complete exec source" + filename = self.stuffsource(source) + self.execfile(filename, source) + + def execfile(self, filename, source=None): + "Execute an existing file" + if source is None: + with tokenize.open(filename) as fp: + source = fp.read() + try: + code = compile(source, filename, "exec") + except (OverflowError, SyntaxError): + self.tkconsole.resetoutput() + print('*** Error in script or command!\n' + 'Traceback (most recent call last):', + file=self.tkconsole.stderr) + InteractiveInterpreter.showsyntaxerror(self, filename) + self.tkconsole.showprompt() + else: + self.runcode(code) + + def runsource(self, source): + "Extend base class method: Stuff the source in the line cache first" + filename = self.stuffsource(source) + self.more = 0 + self.save_warnings_filters = warnings.filters[:] + warnings.filterwarnings(action="error", category=SyntaxWarning) + # at the moment, InteractiveInterpreter expects str + assert isinstance(source, str) + #if isinstance(source, str): + # from idlelib import iomenu + # try: + # source = source.encode(iomenu.encoding) + # except UnicodeError: + # self.tkconsole.resetoutput() + # self.write("Unsupported characters in input\n") + # return + try: + # InteractiveInterpreter.runsource() calls its runcode() method, + # which is overridden (see below) + return InteractiveInterpreter.runsource(self, source, filename) + finally: + if self.save_warnings_filters is not None: + warnings.filters[:] = self.save_warnings_filters + self.save_warnings_filters = None + + def stuffsource(self, source): + "Stuff source in the filename cache" + filename = "" % self.gid + self.gid = self.gid + 1 + lines = source.split("\n") + linecache.cache[filename] = len(source)+1, 0, lines, filename + return filename + + def prepend_syspath(self, filename): + "Prepend sys.path with file's directory if not already included" + self.runcommand("""if 1: + _filename = %r + import sys as _sys + from os.path import dirname as _dirname + _dir = _dirname(_filename) + if not _dir in _sys.path: + _sys.path.insert(0, _dir) + del _filename, _sys, _dirname, _dir + \n""" % (filename,)) + + def showsyntaxerror(self, filename=None): + """Override Interactive Interpreter method: Use Colorizing + + Color the offending position instead of printing it and pointing at it + with a caret. + + """ + tkconsole = self.tkconsole + text = tkconsole.text + text.tag_remove("ERROR", "1.0", "end") + type, value, tb = sys.exc_info() + msg = getattr(value, 'msg', '') or value or "" + lineno = getattr(value, 'lineno', '') or 1 + offset = getattr(value, 'offset', '') or 0 + if offset == 0: + lineno += 1 #mark end of offending line + if lineno == 1: + pos = "iomark + %d chars" % (offset-1) + else: + pos = "iomark linestart + %d lines + %d chars" % \ + (lineno-1, offset-1) + tkconsole.colorize_syntax_error(text, pos) + tkconsole.resetoutput() + self.write("SyntaxError: %s\n" % msg) + tkconsole.showprompt() + + def showtraceback(self): + "Extend base class method to reset output properly" + self.tkconsole.resetoutput() + self.checklinecache() + InteractiveInterpreter.showtraceback(self) + if self.tkconsole.getvar("<>"): + self.tkconsole.open_stack_viewer() + + def checklinecache(self): + c = linecache.cache + for key in list(c.keys()): + if key[:1] + key[-1:] != "<>": + del c[key] + + def runcommand(self, code): + "Run the code without invoking the debugger" + # The code better not raise an exception! + if self.tkconsole.executing: + self.display_executing_dialog() + return 0 + if self.rpcclt: + self.rpcclt.remotequeue("exec", "runcode", (code,), {}) + else: + exec(code, self.locals) + return 1 + + def runcode(self, code): + "Override base class method" + if self.tkconsole.executing: + self.interp.restart_subprocess() + self.checklinecache() + if self.save_warnings_filters is not None: + warnings.filters[:] = self.save_warnings_filters + self.save_warnings_filters = None + debugger = self.debugger + try: + self.tkconsole.beginexecuting() + if not debugger and self.rpcclt is not None: + self.active_seq = self.rpcclt.asyncqueue("exec", "runcode", + (code,), {}) + elif debugger: + debugger.run(code, self.locals) + else: + exec(code, self.locals) + except SystemExit: + if not self.tkconsole.closing: + if tkMessageBox.askyesno( + "Exit?", + "Do you want to exit altogether?", + default="yes", + parent=self.tkconsole.text): + raise + else: + self.showtraceback() + else: + raise + except: + if use_subprocess: + print("IDLE internal error in runcode()", + file=self.tkconsole.stderr) + self.showtraceback() + self.tkconsole.endexecuting() + else: + if self.tkconsole.canceled: + self.tkconsole.canceled = False + print("KeyboardInterrupt", file=self.tkconsole.stderr) + else: + self.showtraceback() + finally: + if not use_subprocess: + try: + self.tkconsole.endexecuting() + except AttributeError: # shell may have closed + pass + + def write(self, s): + "Override base class method" + return self.tkconsole.stderr.write(s) + + def display_port_binding_error(self): + tkMessageBox.showerror( + "Port Binding Error", + "IDLE can't bind to a TCP/IP port, which is necessary to " + "communicate with its Python execution server. This might be " + "because no networking is installed on this computer. " + "Run IDLE with the -n command line switch to start without a " + "subprocess and refer to Help/IDLE Help 'Running without a " + "subprocess' for further details.", + parent=self.tkconsole.text) + + def display_no_subprocess_error(self): + tkMessageBox.showerror( + "Subprocess Startup Error", + "IDLE's subprocess didn't make connection. Either IDLE can't " + "start a subprocess or personal firewall software is blocking " + "the connection.", + parent=self.tkconsole.text) + + def display_executing_dialog(self): + tkMessageBox.showerror( + "Already executing", + "The Python Shell window is already executing a command; " + "please wait until it is finished.", + parent=self.tkconsole.text) + + +class PyShell(OutputWindow): + + shell_title = "Python " + python_version() + " Shell" + + # Override classes + ColorDelegator = ModifiedColorDelegator + UndoDelegator = ModifiedUndoDelegator + + # Override menus + menu_specs = [ + ("file", "_File"), + ("edit", "_Edit"), + ("debug", "_Debug"), + ("options", "_Options"), + ("windows", "_Window"), + ("help", "_Help"), + ] + + + # New classes + from idlelib.history import History + + def __init__(self, flist=None): + if use_subprocess: + ms = self.menu_specs + if ms[2][0] != "shell": + ms.insert(2, ("shell", "She_ll")) + self.interp = ModifiedInterpreter(self) + if flist is None: + root = Tk() + fixwordbreaks(root) + root.withdraw() + flist = PyShellFileList(root) + # + OutputWindow.__init__(self, flist, None, None) + # +## self.config(usetabs=1, indentwidth=8, context_use_ps1=1) + self.usetabs = True + # indentwidth must be 8 when using tabs. See note in EditorWindow: + self.indentwidth = 8 + self.context_use_ps1 = True + # + text = self.text + text.configure(wrap="char") + text.bind("<>", self.enter_callback) + text.bind("<>", self.linefeed_callback) + text.bind("<>", self.cancel_callback) + text.bind("<>", self.eof_callback) + text.bind("<>", self.open_stack_viewer) + text.bind("<>", self.toggle_debugger) + text.bind("<>", self.toggle_jit_stack_viewer) + if use_subprocess: + text.bind("<>", self.view_restart_mark) + text.bind("<>", self.restart_shell) + # + self.save_stdout = sys.stdout + self.save_stderr = sys.stderr + self.save_stdin = sys.stdin + from idlelib import iomenu + self.stdin = PseudoInputFile(self, "stdin", iomenu.encoding) + self.stdout = PseudoOutputFile(self, "stdout", iomenu.encoding) + self.stderr = PseudoOutputFile(self, "stderr", iomenu.encoding) + self.console = PseudoOutputFile(self, "console", iomenu.encoding) + if not use_subprocess: + sys.stdout = self.stdout + sys.stderr = self.stderr + sys.stdin = self.stdin + try: + # page help() text to shell. + import pydoc # import must be done here to capture i/o rebinding. + # XXX KBK 27Dec07 use TextViewer someday, but must work w/o subproc + pydoc.pager = pydoc.plainpager + except: + sys.stderr = sys.__stderr__ + raise + # + self.history = self.History(self.text) + # + self.pollinterval = 50 # millisec + + def get_standard_extension_names(self): + return idleConf.GetExtensions(shell_only=True) + + reading = False + executing = False + canceled = False + endoffile = False + closing = False + _stop_readline_flag = False + + def set_warning_stream(self, stream): + global warning_stream + warning_stream = stream + + def get_warning_stream(self): + return warning_stream + + def toggle_debugger(self, event=None): + if self.executing: + tkMessageBox.showerror("Don't debug now", + "You can only toggle the debugger when idle", + parent=self.text) + self.set_debugger_indicator() + return "break" + else: + db = self.interp.getdebugger() + if db: + self.close_debugger() + else: + self.open_debugger() + + def set_debugger_indicator(self): + db = self.interp.getdebugger() + self.setvar("<>", not not db) + + def toggle_jit_stack_viewer(self, event=None): + pass # All we need is the variable + + def close_debugger(self): + db = self.interp.getdebugger() + if db: + self.interp.setdebugger(None) + db.close() + if self.interp.rpcclt: + debugger_r.close_remote_debugger(self.interp.rpcclt) + self.resetoutput() + self.console.write("[DEBUG OFF]\n") + sys.ps1 = ">>> " + self.showprompt() + self.set_debugger_indicator() + + def open_debugger(self): + if self.interp.rpcclt: + dbg_gui = debugger_r.start_remote_debugger(self.interp.rpcclt, + self) + else: + dbg_gui = debugger.Debugger(self) + self.interp.setdebugger(dbg_gui) + dbg_gui.load_breakpoints() + sys.ps1 = "[DEBUG ON]\n>>> " + self.showprompt() + self.set_debugger_indicator() + + def beginexecuting(self): + "Helper for ModifiedInterpreter" + self.resetoutput() + self.executing = 1 + + def endexecuting(self): + "Helper for ModifiedInterpreter" + self.executing = 0 + self.canceled = 0 + self.showprompt() + + def close(self): + "Extend EditorWindow.close()" + if self.executing: + response = tkMessageBox.askokcancel( + "Kill?", + "Your program is still running!\n Do you want to kill it?", + default="ok", + parent=self.text) + if response is False: + return "cancel" + self.stop_readline() + self.canceled = True + self.closing = True + return EditorWindow.close(self) + + def _close(self): + "Extend EditorWindow._close(), shut down debugger and execution server" + self.close_debugger() + if use_subprocess: + self.interp.kill_subprocess() + # Restore std streams + sys.stdout = self.save_stdout + sys.stderr = self.save_stderr + sys.stdin = self.save_stdin + # Break cycles + self.interp = None + self.console = None + self.flist.pyshell = None + self.history = None + EditorWindow._close(self) + + def ispythonsource(self, filename): + "Override EditorWindow method: never remove the colorizer" + return True + + def short_title(self): + return self.shell_title + + COPYRIGHT = \ + 'Type "copyright", "credits" or "license()" for more information.' + + def begin(self): + self.text.mark_set("iomark", "insert") + self.resetoutput() + if use_subprocess: + nosub = '' + client = self.interp.start_subprocess() + if not client: + self.close() + return False + else: + nosub = ("==== No Subprocess ====\n\n" + + "WARNING: Running IDLE without a Subprocess is deprecated\n" + + "and will be removed in a later version. See Help/IDLE Help\n" + + "for details.\n\n") + sys.displayhook = rpc.displayhook + + self.write("Python %s on %s\n%s\n%s" % + (sys.version, sys.platform, self.COPYRIGHT, nosub)) + self.text.focus_force() + self.showprompt() + import tkinter + tkinter._default_root = None # 03Jan04 KBK What's this? + return True + + def stop_readline(self): + if not self.reading: # no nested mainloop to exit. + return + self._stop_readline_flag = True + self.top.quit() + + def readline(self): + save = self.reading + try: + self.reading = 1 + self.top.mainloop() # nested mainloop() + finally: + self.reading = save + if self._stop_readline_flag: + self._stop_readline_flag = False + return "" + line = self.text.get("iomark", "end-1c") + if len(line) == 0: # may be EOF if we quit our mainloop with Ctrl-C + line = "\n" + self.resetoutput() + if self.canceled: + self.canceled = 0 + if not use_subprocess: + raise KeyboardInterrupt + if self.endoffile: + self.endoffile = 0 + line = "" + return line + + def isatty(self): + return True + + def cancel_callback(self, event=None): + try: + if self.text.compare("sel.first", "!=", "sel.last"): + return # Active selection -- always use default binding + except: + pass + if not (self.executing or self.reading): + self.resetoutput() + self.interp.write("KeyboardInterrupt\n") + self.showprompt() + return "break" + self.endoffile = 0 + self.canceled = 1 + if (self.executing and self.interp.rpcclt): + if self.interp.getdebugger(): + self.interp.restart_subprocess() + else: + self.interp.interrupt_subprocess() + if self.reading: + self.top.quit() # exit the nested mainloop() in readline() + return "break" + + def eof_callback(self, event): + if self.executing and not self.reading: + return # Let the default binding (delete next char) take over + if not (self.text.compare("iomark", "==", "insert") and + self.text.compare("insert", "==", "end-1c")): + return # Let the default binding (delete next char) take over + if not self.executing: + self.resetoutput() + self.close() + else: + self.canceled = 0 + self.endoffile = 1 + self.top.quit() + return "break" + + def linefeed_callback(self, event): + # Insert a linefeed without entering anything (still autoindented) + if self.reading: + self.text.insert("insert", "\n") + self.text.see("insert") + else: + self.newline_and_indent_event(event) + return "break" + + def enter_callback(self, event): + if self.executing and not self.reading: + return # Let the default binding (insert '\n') take over + # If some text is selected, recall the selection + # (but only if this before the I/O mark) + try: + sel = self.text.get("sel.first", "sel.last") + if sel: + if self.text.compare("sel.last", "<=", "iomark"): + self.recall(sel, event) + return "break" + except: + pass + # If we're strictly before the line containing iomark, recall + # the current line, less a leading prompt, less leading or + # trailing whitespace + if self.text.compare("insert", "<", "iomark linestart"): + # Check if there's a relevant stdin range -- if so, use it + prev = self.text.tag_prevrange("stdin", "insert") + if prev and self.text.compare("insert", "<", prev[1]): + self.recall(self.text.get(prev[0], prev[1]), event) + return "break" + next = self.text.tag_nextrange("stdin", "insert") + if next and self.text.compare("insert lineend", ">=", next[0]): + self.recall(self.text.get(next[0], next[1]), event) + return "break" + # No stdin mark -- just get the current line, less any prompt + indices = self.text.tag_nextrange("console", "insert linestart") + if indices and \ + self.text.compare(indices[0], "<=", "insert linestart"): + self.recall(self.text.get(indices[1], "insert lineend"), event) + else: + self.recall(self.text.get("insert linestart", "insert lineend"), event) + return "break" + # If we're between the beginning of the line and the iomark, i.e. + # in the prompt area, move to the end of the prompt + if self.text.compare("insert", "<", "iomark"): + self.text.mark_set("insert", "iomark") + # If we're in the current input and there's only whitespace + # beyond the cursor, erase that whitespace first + s = self.text.get("insert", "end-1c") + if s and not s.strip(): + self.text.delete("insert", "end-1c") + # If we're in the current input before its last line, + # insert a newline right at the insert point + if self.text.compare("insert", "<", "end-1c linestart"): + self.newline_and_indent_event(event) + return "break" + # We're in the last line; append a newline and submit it + self.text.mark_set("insert", "end-1c") + if self.reading: + self.text.insert("insert", "\n") + self.text.see("insert") + else: + self.newline_and_indent_event(event) + self.text.tag_add("stdin", "iomark", "end-1c") + self.text.update_idletasks() + if self.reading: + self.top.quit() # Break out of recursive mainloop() + else: + self.runit() + return "break" + + def recall(self, s, event): + # remove leading and trailing empty or whitespace lines + s = re.sub(r'^\s*\n', '' , s) + s = re.sub(r'\n\s*$', '', s) + lines = s.split('\n') + self.text.undo_block_start() + try: + self.text.tag_remove("sel", "1.0", "end") + self.text.mark_set("insert", "end-1c") + prefix = self.text.get("insert linestart", "insert") + if prefix.rstrip().endswith(':'): + self.newline_and_indent_event(event) + prefix = self.text.get("insert linestart", "insert") + self.text.insert("insert", lines[0].strip()) + if len(lines) > 1: + orig_base_indent = re.search(r'^([ \t]*)', lines[0]).group(0) + new_base_indent = re.search(r'^([ \t]*)', prefix).group(0) + for line in lines[1:]: + if line.startswith(orig_base_indent): + # replace orig base indentation with new indentation + line = new_base_indent + line[len(orig_base_indent):] + self.text.insert('insert', '\n'+line.rstrip()) + finally: + self.text.see("insert") + self.text.undo_block_stop() + + def runit(self): + line = self.text.get("iomark", "end-1c") + # Strip off last newline and surrounding whitespace. + # (To allow you to hit return twice to end a statement.) + i = len(line) + while i > 0 and line[i-1] in " \t": + i = i-1 + if i > 0 and line[i-1] == "\n": + i = i-1 + while i > 0 and line[i-1] in " \t": + i = i-1 + line = line[:i] + self.interp.runsource(line) + + def open_stack_viewer(self, event=None): + if self.interp.rpcclt: + return self.interp.remote_stack_viewer() + try: + sys.last_traceback + except: + tkMessageBox.showerror("No stack trace", + "There is no stack trace yet.\n" + "(sys.last_traceback is not defined)", + parent=self.text) + return + from idlelib.stackviewer import StackBrowser + StackBrowser(self.root, self.flist) + + def view_restart_mark(self, event=None): + self.text.see("iomark") + self.text.see("restart") + + def restart_shell(self, event=None): + "Callback for Run/Restart Shell Cntl-F6" + self.interp.restart_subprocess(with_cwd=True) + + def showprompt(self): + self.resetoutput() + try: + s = str(sys.ps1) + except: + s = "" + self.console.write(s) + self.text.mark_set("insert", "end-1c") + self.set_line_and_column() + self.io.reset_undo() + + def resetoutput(self): + source = self.text.get("iomark", "end-1c") + if self.history: + self.history.store(source) + if self.text.get("end-2c") != "\n": + self.text.insert("end-1c", "\n") + self.text.mark_set("iomark", "end-1c") + self.set_line_and_column() + + def write(self, s, tags=()): + if isinstance(s, str) and len(s) and max(s) > '\uffff': + # Tk doesn't support outputting non-BMP characters + # Let's assume what printed string is not very long, + # find first non-BMP character and construct informative + # UnicodeEncodeError exception. + for start, char in enumerate(s): + if char > '\uffff': + break + raise UnicodeEncodeError("UCS-2", char, start, start+1, + 'Non-BMP character not supported in Tk') + try: + self.text.mark_gravity("iomark", "right") + count = OutputWindow.write(self, s, tags, "iomark") + self.text.mark_gravity("iomark", "left") + except: + raise ###pass # ### 11Aug07 KBK if we are expecting exceptions + # let's find out what they are and be specific. + if self.canceled: + self.canceled = 0 + if not use_subprocess: + raise KeyboardInterrupt + return count + + def rmenu_check_cut(self): + try: + if self.text.compare('sel.first', '<', 'iomark'): + return 'disabled' + except TclError: # no selection, so the index 'sel.first' doesn't exist + return 'disabled' + return super().rmenu_check_cut() + + def rmenu_check_paste(self): + if self.text.compare('insert','<','iomark'): + return 'disabled' + return super().rmenu_check_paste() + + +def fix_x11_paste(root): + "Make paste replace selection on x11. See issue #5124." + if root._windowingsystem == 'x11': + for cls in 'Text', 'Entry', 'Spinbox': + root.bind_class( + cls, + '<>', + 'catch {%W delete sel.first sel.last}\n' + + root.bind_class(cls, '<>')) + + +usage_msg = """\ + +USAGE: idle [-deins] [-t title] [file]* + idle [-dns] [-t title] (-c cmd | -r file) [arg]* + idle [-dns] [-t title] - [arg]* + + -h print this help message and exit + -n run IDLE without a subprocess (DEPRECATED, + see Help/IDLE Help for details) + +The following options will override the IDLE 'settings' configuration: + + -e open an edit window + -i open a shell window + +The following options imply -i and will open a shell: + + -c cmd run the command in a shell, or + -r file run script from file + + -d enable the debugger + -s run $IDLESTARTUP or $PYTHONSTARTUP before anything else + -t title set title of shell window + +A default edit window will be bypassed when -c, -r, or - are used. + +[arg]* are passed to the command (-c) or script (-r) in sys.argv[1:]. + +Examples: + +idle + Open an edit window or shell depending on IDLE's configuration. + +idle foo.py foobar.py + Edit the files, also open a shell if configured to start with shell. + +idle -est "Baz" foo.py + Run $IDLESTARTUP or $PYTHONSTARTUP, edit foo.py, and open a shell + window with the title "Baz". + +idle -c "import sys; print(sys.argv)" "foo" + Open a shell window and run the command, passing "-c" in sys.argv[0] + and "foo" in sys.argv[1]. + +idle -d -s -r foo.py "Hello World" + Open a shell window, run a startup script, enable the debugger, and + run foo.py, passing "foo.py" in sys.argv[0] and "Hello World" in + sys.argv[1]. + +echo "import sys; print(sys.argv)" | idle - "foobar" + Open a shell window, run the script piped in, passing '' in sys.argv[0] + and "foobar" in sys.argv[1]. +""" + +def main(): + global flist, root, use_subprocess + + capture_warnings(True) + use_subprocess = True + enable_shell = False + enable_edit = False + debug = False + cmd = None + script = None + startup = False + try: + opts, args = getopt.getopt(sys.argv[1:], "c:deihnr:st:") + except getopt.error as msg: + print("Error: %s\n%s" % (msg, usage_msg), file=sys.stderr) + sys.exit(2) + for o, a in opts: + if o == '-c': + cmd = a + enable_shell = True + if o == '-d': + debug = True + enable_shell = True + if o == '-e': + enable_edit = True + if o == '-h': + sys.stdout.write(usage_msg) + sys.exit() + if o == '-i': + enable_shell = True + if o == '-n': + print(" Warning: running IDLE without a subprocess is deprecated.", + file=sys.stderr) + use_subprocess = False + if o == '-r': + script = a + if os.path.isfile(script): + pass + else: + print("No script file: ", script) + sys.exit() + enable_shell = True + if o == '-s': + startup = True + enable_shell = True + if o == '-t': + PyShell.shell_title = a + enable_shell = True + if args and args[0] == '-': + cmd = sys.stdin.read() + enable_shell = True + # process sys.argv and sys.path: + for i in range(len(sys.path)): + sys.path[i] = os.path.abspath(sys.path[i]) + if args and args[0] == '-': + sys.argv = [''] + args[1:] + elif cmd: + sys.argv = ['-c'] + args + elif script: + sys.argv = [script] + args + elif args: + enable_edit = True + pathx = [] + for filename in args: + pathx.append(os.path.dirname(filename)) + for dir in pathx: + dir = os.path.abspath(dir) + if not dir in sys.path: + sys.path.insert(0, dir) + else: + dir = os.getcwd() + if dir not in sys.path: + sys.path.insert(0, dir) + # check the IDLE settings configuration (but command line overrides) + edit_start = idleConf.GetOption('main', 'General', + 'editor-on-startup', type='bool') + enable_edit = enable_edit or edit_start + enable_shell = enable_shell or not enable_edit + + # Setup root. Don't break user code run in IDLE process. + # Don't change environment when testing. + if use_subprocess and not testing: + NoDefaultRoot() + root = Tk(className="Idle") + root.withdraw() + + # set application icon + icondir = os.path.join(os.path.dirname(__file__), 'Icons') + if system() == 'Windows': + iconfile = os.path.join(icondir, 'idle.ico') + root.wm_iconbitmap(default=iconfile) + else: + ext = '.png' if TkVersion >= 8.6 else '.gif' + iconfiles = [os.path.join(icondir, 'idle_%d%s' % (size, ext)) + for size in (16, 32, 48)] + icons = [PhotoImage(master=root, file=iconfile) + for iconfile in iconfiles] + root.wm_iconphoto(True, *icons) + + # start editor and/or shell windows: + fixwordbreaks(root) + fix_x11_paste(root) + flist = PyShellFileList(root) + macosx.setupApp(root, flist) + + if enable_edit: + if not (cmd or script): + for filename in args[:]: + if flist.open(filename) is None: + # filename is a directory actually, disconsider it + args.remove(filename) + if not args: + flist.new() + + if enable_shell: + shell = flist.open_shell() + if not shell: + return # couldn't open shell + if macosx.isAquaTk() and flist.dict: + # On OSX: when the user has double-clicked on a file that causes + # IDLE to be launched the shell window will open just in front of + # the file she wants to see. Lower the interpreter window when + # there are open files. + shell.top.lower() + else: + shell = flist.pyshell + + # Handle remaining options. If any of these are set, enable_shell + # was set also, so shell must be true to reach here. + if debug: + shell.open_debugger() + if startup: + filename = os.environ.get("IDLESTARTUP") or \ + os.environ.get("PYTHONSTARTUP") + if filename and os.path.isfile(filename): + shell.interp.execfile(filename) + if cmd or script: + shell.interp.runcommand("""if 1: + import sys as _sys + _sys.argv = %r + del _sys + \n""" % (sys.argv,)) + if cmd: + shell.interp.execsource(cmd) + elif script: + shell.interp.prepend_syspath(script) + shell.interp.execfile(script) + elif shell: + # If there is a shell window and no cmd or script in progress, + # check for problematic OS X Tk versions and print a warning + # message in the IDLE shell window; this is less intrusive + # than always opening a separate window. + tkversionwarning = macosx.tkVersionWarning(root) + if tkversionwarning: + shell.interp.runcommand("print('%s')" % tkversionwarning) + + while flist.inversedict: # keep IDLE running while files are open. + root.mainloop() + root.destroy() + capture_warnings(False) + +if __name__ == "__main__": + sys.modules['pyshell'] = sys.modules['__main__'] + main() + +capture_warnings(False) # Make sure turned off; see issue 18081 diff --git a/build/lib/moosegui/toolbar.py b/build/lib/moosegui/toolbar.py new file mode 100644 index 0000000..735ce7e --- /dev/null +++ b/build/lib/moosegui/toolbar.py @@ -0,0 +1,74 @@ +"""toolbar.py: + +Add toolbar + +""" + +__author__ = "Me" +__copyright__ = "Copyright 2016, Me" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Me" +__email__ = "" +__status__ = "Development" + +import sys +import os +import logging + +try: + import Tkinter as tk + import ttk +except Exception as e: + import tkinter as tk + import tkinter.ttk as ttk + +from PIL import Image, ImageTk + +import moosegui._globals + +# After each section, put a separator. +toolbar = [['Cylinder', 'Cube'], ['Pool', 'BufPool'], ['Move', 'Exit']] + + +def iconRead(name): + imgFilePath = os.path.join('icons', '%s.png' % name) + img = Image.open(imgFilePath) + img = img.resize((20, 20), Image.ANTIALIAS) + # return tk.PhotoImage( file = imgFilePath ) + return ImageTk.PhotoImage(img) + +def btnCallback( btn ): + if btn.lower( ) == 'exit': + raise SystemExit + if btn.lower( ) == 'cube': + logging.debug( "Drawing cube and changing cursor " ) + _globals.root_.config( cursor = 'wait' ) + print( btn ) + +class ToolBar(tk.Frame): + + def __init__(self, root): + logging.info("Creating a toolbar") + tk.Frame.__init__(self, root ) + i = 0 + for tools in toolbar: + for tool in tools: + i += 1 + btnImg = iconRead(tool) + btn = tk.Button( self + , image=btnImg + , command = lambda x = tool : btnCallback( x ) + ) + btn.image = btnImg + btn.grid(row=i, column=0) + i += 1 + sep = ttk.Separator( root , orient = tk.VERTICAL ) + sep.grid(row=i, column=0 ) + + +def main(parent): + toolbar = ToolBar( parent ) + toolbar.grid( row = 1, column = 0, sticky = 'ns' ) + _globals.toolbar_ = toolbar diff --git a/config.py b/config.py deleted file mode 100644 index cf1a9a6..0000000 --- a/config.py +++ /dev/null @@ -1,232 +0,0 @@ -# config.py --- -# -# Filename: config.py -# Description: -# Author: Subhasis Ray -# Maintainer: -# Created: Sat Feb 13 16:07:56 2010 (+0530) -# Version: -# Last-Updated: Wed Nov 12 19:10:08 2014 (+0530) -# By: Subhasis Ray -# Update #: 369 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# Provides keys for accessing per-user settings. -# Provides initialization of several per-user variables for MooseGUI. -# As part of initialization, creates `~/.moose` and `~/moose` -# directories. -# -# - -# Change log: -# -# 2012-09-22 13:49:36 (+0530) Subha: cleaned up the initialization -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: - -import os -import sys -import tempfile -import logging -import errno -from PyQt4.Qt import Qt -from PyQt4 import QtGui, QtCore - -TEMPDIR = tempfile.gettempdir() -KEY_FIRSTTIME = 'firsttime' -# KEY_STATE_FILE = 'statefile' - -KEY_UNDO_LENGTH = 'main/undolength' -KEY_WINDOW_GEOMETRY = 'main/geometry' -KEY_WINDOW_LAYOUT = 'main/layout' -KEY_RUNTIME_AUTOHIDE = 'main/rtautohide' -KEY_DEMOS_DIR = 'main/demosdir' -KEY_DOCS_DIR = 'main/docsdir' -KEY_HOME_DIR = 'main/homedir' -KEY_ICON_DIR = 'main/icondir' -KEY_COLORMAP_DIR = 'main/colormapdir' -KEY_BIOMODEL_DIR = 'main/biomodelsdir' -KEY_LOCAL_DEMOS_DIR = 'main/localdemosdir' -KEY_MOOSE_LOCAL_DIR = 'main/localdir' -KEY_NUMPTHREADS = 'main/numpthreads' -KEY_LOCAL_BUILD = 'main/localbuild' -KEY_LAST_PLUGIN = 'main/lastplugin' - -# These are the keys for mode specific configuration. -# Ideally the default values should be provided by the plugin. -# We use the QSettings to remember the last values -KEY_KINETICS_SIMDT = 'kinetics/simdt' -KEY_KINETICS_PLOTDT = 'kinetics/plotdt' -KEY_ELECTRICAL_SIMDT = 'electrical/simdt' -KEY_ELECTRICAL_PLOTDT = 'electrical/plotdt' -KEY_SIMTIME = 'main/simtime' - -QT_VERSION = str(QtCore.QT_VERSION_STR).split('.') -QT_MAJOR_VERSION = int(QT_VERSION[0]) -QT_MINOR_VERSION = int(QT_VERSION[1]) - -MOOSE_DOC_URL = 'http://moose.ncbs.res.in/builtins_classes/moose_builtins.html' -MOOSE_REPORT_BUG_URL = 'http://sourceforge.net/tracker/?func=add&group_id=165660&atid=836272' -MOOSE_GUI_BUG_URL = 'https://github.com/BhallaLab/moose-gui/issues' -MOOSE_CORE_BUG_URL = 'https://github.com/BhallaLab/moose-core/issues' -MOOSE_DEMOS_DIR = '/usr/share/moose/Demos' -MOOSE_DOCS_DIR = '/usr/share/doc/moose' -MOOSE_GUI_DIR = os.path.dirname(os.path.abspath(__file__)) -MOOSE_PLUGIN_DIR = os.path.join(MOOSE_GUI_DIR, 'plugins') -NEUROKIT_PLUGIN_DIR = os.path.join(MOOSE_GUI_DIR, 'plugins/NeuroKit') -# MOOSE_CFG_DIR = os.path.join(os.environ['HOME'], '.moose') -MOOSE_LOCAL_DIR = os.path.join(os.environ['HOME'], 'moose') -MOOSE_NUMPTHREADS = '1' - -MOOSE_ABOUT_FILE = os.path.join(MOOSE_GUI_DIR, 'about.html') -MOOSE_UNDO_LENGTH = 128 # Arbitrary undo length -LOCAL_BUILD = False - -sys.path.append(os.path.join(MOOSE_PLUGIN_DIR)) - -class MooseSetting(dict): - """ - dict-like access to QSettings. - - This subclass of dict wraps a QSettings object and lets one set - and get values as Python strings rather than QVariant. - - This is supposed to be a singleton in the whole application (all - QSettings are with same parameters). - """ - _instance = None - def __new__(cls, *args, **kwargs): - # This is designed to check if the class has been - # instantiated, if so, returns the single instance, otherwise - # creates it. - if cls._instance is None: - cls._instance = super(MooseSetting, cls).__new__(cls, *args, **kwargs) - firsttime, errs = init_dirs() - for e in errs: - print e - QtCore.QCoreApplication.setOrganizationName('NCBS') - QtCore.QCoreApplication.setOrganizationDomain('ncbs.res.in') - QtCore.QCoreApplication.setApplicationName('MOOSE') - cls._instance.qsettings = QtCore.QSettings() - # If this is the first time, then set some defaults - cls._instance.qsettings.setValue(KEY_COLORMAP_DIR, os.path.join(MOOSE_GUI_DIR, 'colormaps')) - cls._instance.qsettings.setValue(KEY_BIOMODEL_DIR, os.path.join(MOOSE_GUI_DIR, 'bioModels')) - cls._instance.qsettings.setValue(KEY_ICON_DIR, os.path.join(MOOSE_GUI_DIR, 'icons')) - cls._instance.qsettings.setValue(KEY_NUMPTHREADS, '1') - cls._instance.qsettings.setValue(KEY_UNDO_LENGTH, str(MOOSE_UNDO_LENGTH)) - # These are to be checked at every run - cls._instance.qsettings.setValue(KEY_HOME_DIR, os.environ['HOME']) - cls._instance.qsettings.setValue(KEY_DEMOS_DIR, MOOSE_DEMOS_DIR) - cls._instance.qsettings.setValue(KEY_LOCAL_DEMOS_DIR, os.path.join(MOOSE_LOCAL_DIR, 'Demos/')) - cls._instance.qsettings.setValue(KEY_DOCS_DIR, MOOSE_DOCS_DIR) - cls._instance.qsettings.setValue(KEY_MOOSE_LOCAL_DIR, MOOSE_LOCAL_DIR) - cls._instance.qsettings.setValue(KEY_LOCAL_BUILD, LOCAL_BUILD) - os.environ['NUMPTHREADS'] = str(cls._instance.qsettings.value(KEY_NUMPTHREADS).toString()) - return cls._instance - - def __init__(self, *args, **kwargs): - super(MooseSetting, self).__init__(self, *args, **kwargs) - - def __iter__(self): - return (str(key) for key in self.qsettings.allKeys()) - - def __setitem__(self, key, value): - if isinstance(key, str): - self.qsettings.setValue(key, value) - else: - raise TypeError('Expect only strings as keys') - - def __getitem__(self, key): - return str(self.qsettings.value(key).toString()) - - def keys(self): - return [str(key) for key in self.qsettings.allKeys()] - - def values(self): - return [str(self.qsettings.value(key).toString()) for key in self.qsettings.allKeys()] - - def itervalues(self): - return (str(self.qsettings.value(key).toString()) for key in self.qsettings.allKeys()) - -def init_dirs(): - """Check if there is a `.moose` directory in user's home - directory. If not, we assume this to be the first run of MOOSE. - Then we try to create the `~/.moose` directory and `~/moose` - directory. - """ - firsttime = False - global MOOSE_DEMOS_DIR - global MOOSE_LOCAL_DIR - # global MOOSE_CFG_DIR - global MOOSE_DOCS_DIR - global LOCAL_BUILD - # If we have a Makefile above GUI directory, then this must be a - # locally built version - LOCAL_BUILD = os.access(os.path.join(MOOSE_GUI_DIR, '../Makefile'), os.R_OK) - errors = [] - ''' - moose_cfg_dir = os.path.join(os.environ['HOME'], '.moose') - if not os.path.exists(moose_cfg_dir): - firsttime = True - # try: - # # os.mkdir(moose_cfg_dir) - # # # MOOSE_CFG_DIR = moose_cfg_dir - # # print 'Created moose configuration directory:', moose_cfg_dir - # except OSError, e: - # errors.append(e) - # print e - if LOCAL_BUILD: - MOOSE_LOCAL_DIR = os.path.normpath(os.path.join(MOOSE_GUI_DIR, '..')) - MOOSE_DEMOS_DIR = os.path.join(MOOSE_LOCAL_DIR, 'Demos') - MOOSE_DOCS_DIR = os.path.join(MOOSE_LOCAL_DIR, 'Docs/user/py/_build/html/') - else: - MOOSE_LOCAL_DIR = os.path.join(os.environ['HOME'], 'moose') - if not os.path.exists(MOOSE_LOCAL_DIR): - try: - os.mkdir(MOOSE_LOCAL_DIR) - print 'Created local moose directory:', MOOSE_LOCAL_DIR - except OSError, e: - errors.append(e) - print e - if not os.access(MOOSE_DOCS_DIR, os.R_OK + os.X_OK): - print "Could not access Demos directory: %s" % (MOOSE_DOCS_DIR) - errors.append(OSError(errno.EACCES, 'Cannot access %s' % (MOOSE_DOCS_DIR))) - ''' - return firsttime, errors - -settings = MooseSetting() - -# LOG_FILENAME = os.path.join(TEMPDIR, 'moose.log') -LOG_LEVEL = logging.ERROR -# logging.basicConfig(filename=LOG_FILENAME, level=LOG_LEVEL, filemode='w', format='%(asctime)s %(levelname)s %(name)s %(filename)s %(funcName)s: %(lineno)d: %(message)s') -logging.basicConfig(stream=sys.stdout, level=LOG_LEVEL, filemode='w', format='%(asctime)s %(levelname)s %(name)s %(filename)s %(funcName)s: %(lineno)d: %(message)s') -LOGGER = logging.getLogger('moose') -BENCHMARK_LOGGER = logging.getLogger('moose.benchmark') -BENCHMARK_LOGGER.setLevel(logging.INFO) - -# -# config.py ends here diff --git a/data/Kholodenko.g b/data/Kholodenko.g new file mode 100644 index 0000000..f6d4c5a --- /dev/null +++ b/data/Kholodenko.g @@ -0,0 +1,528 @@ +//genesis +// kkit Version 11 flat dumpfile + +// Saved on Sun May 18 16:25:59 2014 + +include kkit {argv 1} + +FASTDT = 5e-05 +SIMDT = 0.005 +CONTROLDT = 10 +PLOTDT = 10 +MAXTIME = 6000 +TRANSIENT_TIME = 2 +VARIABLE_DT_FLAG = 1 +DEFAULT_VOL = 1.6667e-21 +VERSION = 11.0 +setfield /file/modpath value /home2/bhalla/scripts/modules +kparms + +//genesis + +initdump -version 3 -ignoreorphans 1 +simobjdump doqcsinfo filename accessname accesstype transcriber developer \ + citation species tissue cellcompartment methodology sources \ + model_implementation model_validation x y z +simobjdump table input output alloced step_mode stepsize x y z +simobjdump xtree path script namemode sizescale +simobjdump xcoredraw xmin xmax ymin ymax +simobjdump xtext editable +simobjdump xgraph xmin xmax ymin ymax overlay +simobjdump xplot pixflags script fg ysquish do_slope wy +simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ + link savename file version md5sum mod_save_flag x y z +simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \ + z +simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \ + geomname xtree_fg_req xtree_textfg_req x y z +simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z +simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ + keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z +simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ + trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z +simobjdump xtab input output alloced step_mode stepsize notes editfunc \ + xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z +simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ + xtree_textfg_req x y z +simobjdump transport input output alloced step_mode stepsize dt delay clock \ + kf xtree_fg_req xtree_textfg_req x y z +simobjdump proto x y z +simobjdump text str +simundump geometry /kinetics/geometry 0 1.6667e-21 3 sphere "" white black 0 \ + 0 0 +simundump text /kinetics/notes 0 "" +call /kinetics/notes LOAD \ +"" +simundump group /kinetics/MAPK 0 yellow black x 0 0 "" MAPK \ + /home2/bhalla/scripts/modules/MAPK_0.g 0 0 0 1 10 0 +simundump text /kinetics/MAPK/notes 0 \ + "This is the oscillatory MAPK model from Kholodenko 2000\nEur J. Biochem 267:1583-1588\nThe original model is formulated in terms of idealized\nMichaelis-Menten enzymes and the enzyme-substrate complex\nconcentrations are therefore assumed negligible. The\ncurrent implementation of the model uses explicit enzyme\nreactions involving substrates and is therefore an\napproximation to the Kholodenko...." +call /kinetics/MAPK/notes LOAD \ +"This is the oscillatory MAPK model from Kholodenko 2000" \ +"Eur J. Biochem 267:1583-1588" \ +"The original model is formulated in terms of idealized" \ +"Michaelis-Menten enzymes and the enzyme-substrate complex" \ +"concentrations are therefore assumed negligible. The" \ +"current implementation of the model uses explicit enzyme" \ +"reactions involving substrates and is therefore an" \ +"approximation to the Kholodenko model. The approximation is" \ +"greatly improved if the enzyme is flagged as Available" \ +"which is an option in Kinetikit. This flag means that the" \ +"enzyme protein concentration is not reduced even when it" \ +"is involved in a complex. However, the substrate protein" \ +"continues to participate in enzyme-substrate complexes" \ +"and its concentration is therefore affected. Overall," \ +"this model works almost the same as the Kholodenko model" \ +"but the peak MAPK-PP amplitudes are a little reduced and" \ +"the period of oscillations is about 10% longer." \ +"If the enzymes are not flagged as Available then the" \ +"oscillations commence only when the Km for enzyme 1" \ +"is set to 0.1 uM." +simundump kpool /kinetics/MAPK/MAPK 0 0 0.3 0.3 0.3 0.3 0 0 1 0 \ + /kinetics/geometry 35 yellow -8 -7 0 +simundump text /kinetics/MAPK/MAPK/notes 0 \ + "The total concn. of MAPK is 300nM \nfrom\nKholodenko, 2000." +call /kinetics/MAPK/MAPK/notes LOAD \ +"The total concn. of MAPK is 300nM " \ +"from" \ +"Kholodenko, 2000." +simundump kpool /kinetics/MAPK/MKKK 0 0 0.1 0.1 0.1 0.1 0 0 1 0 \ + /kinetics/geometry 16 yellow -8 5 0 +simundump text /kinetics/MAPK/MKKK/notes 0 \ + "The total concn. of MKKK is 100nM \nfrom\nKholodenko, 2000" +call /kinetics/MAPK/MKKK/notes LOAD \ +"The total concn. of MKKK is 100nM " \ +"from" \ +"Kholodenko, 2000" +simundump kpool /kinetics/MAPK/MKK 0 0 0.3 0.3 0.3 0.3 0 0 1 0 \ + /kinetics/geometry 60 yellow -8 -1 0 +simundump text /kinetics/MAPK/MKK/notes 0 \ + "The total concn. of MKK is 300nM \nfrom\nKholodenko,2000" +call /kinetics/MAPK/MKK/notes LOAD \ +"The total concn. of MKK is 300nM " \ +"from" \ +"Kholodenko,2000" +simundump kpool /kinetics/MAPK/int1 0 0 0.001 0.001 0.001 0.001 0 0 1 0 \ + /kinetics/geometry 30 yellow -4 4 0 +simundump text /kinetics/MAPK/int1/notes 0 \ + "This is the intermediate enzyme which catalyses the \ndephosphorylation of MKKK-P to MKKK. The concentration\nis set to 1 nM based on\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/int1/notes LOAD \ +"This is the intermediate enzyme which catalyses the " \ +"dephosphorylation of MKKK-P to MKKK. The concentration" \ +"is set to 1 nM based on" \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/int1/2 0 0 0 0 0 0.001 156.25 1 0.25 0 1 "" red \ + 30 "" -4 5 0 +simundump text /kinetics/MAPK/int1/2/notes 0 \ + "Km is 8nM and Vmax is 0.25nM.s-1 \nfrom\nKholodenko, 2000." +call /kinetics/MAPK/int1/2/notes LOAD \ +"Km is 8nM and Vmax is 0.25nM.s-1 " \ +"from" \ +"Kholodenko, 2000." +simundump kpool /kinetics/MAPK/MKKK-P 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ + 51 yellow 0 5 0 +simundump text /kinetics/MAPK/MKKK-P/notes 0 \ + "This is the phosphorylated form of MKKK which converts MKK\nto MKK-P and then to MKK-PP\nfrom\nKholodenko, 2000." +call /kinetics/MAPK/MKKK-P/notes LOAD \ +"This is the phosphorylated form of MKKK which converts MKK" \ +"to MKK-P and then to MKK-PP" \ +"from" \ +"Kholodenko, 2000." +simundump kenz /kinetics/MAPK/MKKK-P/3 0 0 0 0 0 0.001 8.3333 0.1 0.025 0 1 \ + "" red 51 "" -4 2 0 +simundump text /kinetics/MAPK/MKKK-P/3/notes 0 \ + "Km is 15 nM and Vmax is 0.025s-1\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/MKKK-P/3/notes LOAD \ +"Km is 15 nM and Vmax is 0.025s-1" \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/MKKK-P/4 0 0 0 0 0 0.001 8.3333 0.1 0.025 0 1 \ + "" red 51 "" 4 2 0 +simundump text /kinetics/MAPK/MKKK-P/4/notes 0 \ + "Km is 15nM and Vmax is 0.025s-1\nfrom \nKholodenko, 2000." +call /kinetics/MAPK/MKKK-P/4/notes LOAD \ +"Km is 15nM and Vmax is 0.025s-1" \ +"from " \ +"Kholodenko, 2000." +simundump kpool /kinetics/MAPK/int3 0 0 0.001 0.001 0.001 0.001 0 0 1 0 \ + /kinetics/geometry blue yellow -4 -2 0 +simundump text /kinetics/MAPK/int3/notes 0 \ + "This intermediate enzyme catalyses the dephosphorylation of\nMKK-P to MKK. The concentration is 1nM\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/int3/notes LOAD \ +"This intermediate enzyme catalyses the dephosphorylation of" \ +"MKK-P to MKK. The concentration is 1nM" \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/int3/6 0 0 0 0 0 0.001 250 3 0.75 0 1 "" red \ + blue "" -4 -1 0 +simundump text /kinetics/MAPK/int3/6/notes 0 \ + "The Km is 15nM and the Vmax is 0.75nM.s-1\nfrom\nKholodenko 2000." +call /kinetics/MAPK/int3/6/notes LOAD \ +"The Km is 15nM and the Vmax is 0.75nM.s-1" \ +"from" \ +"Kholodenko 2000." +simundump kpool /kinetics/MAPK/int5 0 0 0.001 0.001 0.001 0.001 0 0 1 0 \ + /kinetics/geometry 1 yellow -4 -8 0 +simundump text /kinetics/MAPK/int5/notes 0 \ + "This catalyses the conversion of MAPK-P to MAPK. The \nconcenration is 1nM.\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/int5/notes LOAD \ +"This catalyses the conversion of MAPK-P to MAPK. The " \ +"concenration is 1nM." \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/int5/10 0 0 0 0 0 0.001 166.67 2 0.5 0 1 "" red \ + 1 "" -4 -7 0 +simundump text /kinetics/MAPK/int5/10/notes 0 \ + "The Km is 15nM and Vmax is 0.5nM.s-1\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/int5/10/notes LOAD \ +"The Km is 15nM and Vmax is 0.5nM.s-1" \ +"from" \ +"Kholodenko, 2000" +simundump kpool /kinetics/MAPK/MKK-P 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 5 \ + yellow 0 -1 0 +simundump text /kinetics/MAPK/MKK-P/notes 0 \ + "This is the single phoshorylated form of MKK.\nfrom\nKholodenko, 2000." +call /kinetics/MAPK/MKK-P/notes LOAD \ +"This is the single phoshorylated form of MKK." \ +"from" \ +"Kholodenko, 2000." +simundump kpool /kinetics/MAPK/MAPK-P 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ + 55 yellow 0 -7 0 +simundump text /kinetics/MAPK/MAPK-P/notes 0 \ + "This is the single phopshorylated form of MAPK\nfrom\nKholodenko, 2000." +call /kinetics/MAPK/MAPK-P/notes LOAD \ +"This is the single phopshorylated form of MAPK" \ +"from" \ +"Kholodenko, 2000." +simundump kpool /kinetics/MAPK/int2 0 0 0.001 0.001 0.001 0.001 0 0 1 0 \ + /kinetics/geometry 2 yellow 4 -2 0 +simundump text /kinetics/MAPK/int2/notes 0 \ + "This intermediate enzyme which catalyses the dephosphorylation of\nMKK-PP to MKK-P. The concentration is 1nM.\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/int2/notes LOAD \ +"This intermediate enzyme which catalyses the dephosphorylation of" \ +"MKK-PP to MKK-P. The concentration is 1nM." \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/int2/5 0 0 0 0 0 0.001 250 3 0.75 0 1 "" red 2 \ + "" 4 -1 0 +simundump text /kinetics/MAPK/int2/5/notes 0 \ + "The Km is 15nM and Vmax is 0.75nM.s-1 \nfrom\nKholodenko, 2000\n" +call /kinetics/MAPK/int2/5/notes LOAD \ +"The Km is 15nM and Vmax is 0.75nM.s-1 " \ +"from" \ +"Kholodenko, 2000" \ +"" +simundump kpool /kinetics/MAPK/int4 0 0 0.001 0.001 0.001 0.001 0 0 1 0 \ + /kinetics/geometry 17 yellow 4 -8 0 +simundump text /kinetics/MAPK/int4/notes 0 \ + "This intermediate enzyme catalyses the dephosphorylation of\nMAPK-PP to MAPK-P. The concentration is 1nM.\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/int4/notes LOAD \ +"This intermediate enzyme catalyses the dephosphorylation of" \ +"MAPK-PP to MAPK-P. The concentration is 1nM." \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/int4/9 0 0 0 0 0 0.001 166.67 2 0.5 0 1 "" red \ + 17 "" 4 -7 0 +simundump text /kinetics/MAPK/int4/9/notes 0 \ + "The Km is 15nM and Vmax is 0.5nM.s-1 \nfrom\nKholodenko, 2000" +call /kinetics/MAPK/int4/9/notes LOAD \ +"The Km is 15nM and Vmax is 0.5nM.s-1 " \ +"from" \ +"Kholodenko, 2000" +simundump kpool /kinetics/MAPK/Ras-MKKKK 0 0 0.001 0.001 0.001 0.001 0 0 1 0 \ + /kinetics/geometry 11 yellow 6 8 0 +simundump text /kinetics/MAPK/Ras-MKKKK/notes 0 \ + "The concn. of Ras-MKKKK* is set to 1 nM implicitly\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/Ras-MKKKK/notes LOAD \ +"The concn. of Ras-MKKKK* is set to 1 nM implicitly" \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/Ras-MKKKK/1 0 0 0 0 0 0.001 1250 10 2.5 0 1 "" \ + red 11 "" -4 8 0 +simundump text /kinetics/MAPK/Ras-MKKKK/1/notes 0 \ + "The Km is 10nM and Vmax is 2.5nM sec^-1. We assume that\nthere is 1 nM of the Ras-MKKKK.\nFrom Kholodenko, 2000.\n\nIf the enzymes are not flagged as Available, then this\nKm should be set to 0.1 to obtain oscillations." +call /kinetics/MAPK/Ras-MKKKK/1/notes LOAD \ +"The Km is 10nM and Vmax is 2.5nM sec^-1. We assume that" \ +"there is 1 nM of the Ras-MKKKK." \ +"From Kholodenko, 2000." \ +"" \ +"If the enzymes are not flagged as Available, then this" \ +"Km should be set to 0.1 to obtain oscillations." +simundump kpool /kinetics/MAPK/inactiveRas-MKKK 0 0 0 0 0 0 0 0 1 0 \ + /kinetics/geometry 30 yellow 11 8 0 +simundump text /kinetics/MAPK/inactiveRas-MKKK/notes 0 \ + "This is the inactive form of Ras-MKKK. Based on the\nreaction scheme from Kholodenko 2000, this is equivalent\nto a binding of the MAPK-PP to the Ras. The amount of\nRas in the model is small enough that negligible amounts\nof MAPK are involved in this reaction. So it is a fair\napproximation to the negative feedback mechanism from\nKholodenko, 2000." +call /kinetics/MAPK/inactiveRas-MKKK/notes LOAD \ +"This is the inactive form of Ras-MKKK. Based on the" \ +"reaction scheme from Kholodenko 2000, this is equivalent" \ +"to a binding of the MAPK-PP to the Ras. The amount of" \ +"Ras in the model is small enough that negligible amounts" \ +"of MAPK are involved in this reaction. So it is a fair" \ +"approximation to the negative feedback mechanism from" \ +"Kholodenko, 2000." +simundump kreac /kinetics/MAPK/Neg_feedback 0 1 0.009 "" white yellow 11 2 0 +simundump text /kinetics/MAPK/Neg_feedback/notes 0 \ + "From Kholodenko, 2000 Eur J Biochem 267\nthe Kd is 9 nM. We use a rather fast Kf of 1/sec/uM\nso that equilibrium is maintained.\n" +call /kinetics/MAPK/Neg_feedback/notes LOAD \ +"From Kholodenko, 2000 Eur J Biochem 267" \ +"the Kd is 9 nM. We use a rather fast Kf of 1/sec/uM" \ +"so that equilibrium is maintained." \ +"" +simundump kpool /kinetics/MAPK/MKK-PP 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ + 0 yellow 8 -1 0 +simundump text /kinetics/MAPK/MKK-PP/notes 0 \ + "This is the double phosphorylated and active form of MKK\nfrom\nKholodenko, 2000" +call /kinetics/MAPK/MKK-PP/notes LOAD \ +"This is the double phosphorylated and active form of MKK" \ +"from" \ +"Kholodenko, 2000" +simundump kenz /kinetics/MAPK/MKK-PP/7 0 0 0 0 0 0.001 8.3333 0.1 0.025 0 1 \ + "" red 0 "" -4 -4 0 +simundump text /kinetics/MAPK/MKK-PP/7/notes 0 \ + "The Km is 15nM which is 0.015uM Vmax is 0.025s-1\nfrom\nKholodenko, 2000.\n" +call /kinetics/MAPK/MKK-PP/7/notes LOAD \ +"The Km is 15nM which is 0.015uM Vmax is 0.025s-1" \ +"from" \ +"Kholodenko, 2000." \ +"" +simundump kenz /kinetics/MAPK/MKK-PP/8 0 0 0 0 0 0.001 8.3333 0.1 0.025 0 1 \ + "" red 0 "" 4 -4 0 +simundump text /kinetics/MAPK/MKK-PP/8/notes 0 \ + "The Km is 15nM which is 0.015uM and Vmax is 0.025s-1\nfrom\nKholodenko, 2000\n" +call /kinetics/MAPK/MKK-PP/8/notes LOAD \ +"The Km is 15nM which is 0.015uM and Vmax is 0.025s-1" \ +"from" \ +"Kholodenko, 2000" \ +"" +simundump kpool /kinetics/MAPK/MAPK-PP 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ + 58 yellow 8 -7 0 +simundump text /kinetics/MAPK/MAPK-PP/notes 0 \ + "This is the double phosphorylated and active form of MAPK.\nfrom\nKholodenko, 2000." +call /kinetics/MAPK/MAPK-PP/notes LOAD \ +"This is the double phosphorylated and active form of MAPK." \ +"from" \ +"Kholodenko, 2000." +simundump text /kinetics/geometry/notes 0 "" +call /kinetics/geometry/notes LOAD \ +"" +simundump xgraph /graphs/conc1 0 0 6000 0 0.3 0 +simundump xgraph /graphs/conc2 0 0 6000 4.5157e-05 0.3 0 +simundump xplot /graphs/conc1/Ras-MKKKK.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 11 0 0 1 +simundump xplot /graphs/conc1/MKKK-P.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 51 0 0 1 +simundump xplot /graphs/conc1/MKK-PP.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 0 0 0 1 +simundump xplot /graphs/conc1/MAPK-PP.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 58 0 0 1 +simundump xgraph /moregraphs/conc3 0 0 6000 0 1 0 +simundump xgraph /moregraphs/conc4 0 0 6000 0 1 0 +simundump xcoredraw /edit/draw 0 -10 13 -10 12 +simundump xtree /edit/draw/tree 0 \ + /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ + "edit_elm.D ; drag_from_edit.w " auto 0.6 +simundump xtext /file/notes 0 1 +xtextload /file/notes \ +"22 Jan 2002" \ +" " \ +" This model is based on Kholodenko, B.N." \ +" Eur. J. Biochem. 267, 1583-1588(2000)" \ +"" +addmsg /kinetics/MAPK/MKK-PP/7 /kinetics/MAPK/MAPK REAC sA B +addmsg /kinetics/MAPK/int5/10 /kinetics/MAPK/MAPK MM_PRD pA +addmsg /kinetics/MAPK/Ras-MKKKK/1 /kinetics/MAPK/MKKK REAC sA B +addmsg /kinetics/MAPK/int1/2 /kinetics/MAPK/MKKK MM_PRD pA +addmsg /kinetics/MAPK/MKKK-P/3 /kinetics/MAPK/MKK REAC sA B +addmsg /kinetics/MAPK/int3/6 /kinetics/MAPK/MKK MM_PRD pA +addmsg /kinetics/MAPK/int1 /kinetics/MAPK/int1/2 ENZYME n +addmsg /kinetics/MAPK/MKKK-P /kinetics/MAPK/int1/2 SUBSTRATE n +addmsg /kinetics/MAPK/Ras-MKKKK/1 /kinetics/MAPK/MKKK-P MM_PRD pA +addmsg /kinetics/MAPK/int1/2 /kinetics/MAPK/MKKK-P REAC sA B +addmsg /kinetics/MAPK/MKKK-P /kinetics/MAPK/MKKK-P/3 ENZYME n +addmsg /kinetics/MAPK/MKK /kinetics/MAPK/MKKK-P/3 SUBSTRATE n +addmsg /kinetics/MAPK/MKKK-P /kinetics/MAPK/MKKK-P/4 ENZYME n +addmsg /kinetics/MAPK/MKK-P /kinetics/MAPK/MKKK-P/4 SUBSTRATE n +addmsg /kinetics/MAPK/int3 /kinetics/MAPK/int3/6 ENZYME n +addmsg /kinetics/MAPK/MKK-P /kinetics/MAPK/int3/6 SUBSTRATE n +addmsg /kinetics/MAPK/int5 /kinetics/MAPK/int5/10 ENZYME n +addmsg /kinetics/MAPK/MAPK-P /kinetics/MAPK/int5/10 SUBSTRATE n +addmsg /kinetics/MAPK/MKKK-P/4 /kinetics/MAPK/MKK-P REAC sA B +addmsg /kinetics/MAPK/MKKK-P/3 /kinetics/MAPK/MKK-P MM_PRD pA +addmsg /kinetics/MAPK/int3/6 /kinetics/MAPK/MKK-P REAC sA B +addmsg /kinetics/MAPK/int2/5 /kinetics/MAPK/MKK-P MM_PRD pA +addmsg /kinetics/MAPK/MKK-PP/8 /kinetics/MAPK/MAPK-P REAC sA B +addmsg /kinetics/MAPK/MKK-PP/7 /kinetics/MAPK/MAPK-P MM_PRD pA +addmsg /kinetics/MAPK/int5/10 /kinetics/MAPK/MAPK-P REAC sA B +addmsg /kinetics/MAPK/int4/9 /kinetics/MAPK/MAPK-P MM_PRD pA +addmsg /kinetics/MAPK/int2 /kinetics/MAPK/int2/5 ENZYME n +addmsg /kinetics/MAPK/MKK-PP /kinetics/MAPK/int2/5 SUBSTRATE n +addmsg /kinetics/MAPK/int4 /kinetics/MAPK/int4/9 ENZYME n +addmsg /kinetics/MAPK/MAPK-PP /kinetics/MAPK/int4/9 SUBSTRATE n +addmsg /kinetics/MAPK/Neg_feedback /kinetics/MAPK/Ras-MKKKK REAC A B +addmsg /kinetics/MAPK/Ras-MKKKK /kinetics/MAPK/Ras-MKKKK/1 ENZYME n +addmsg /kinetics/MAPK/MKKK /kinetics/MAPK/Ras-MKKKK/1 SUBSTRATE n +addmsg /kinetics/MAPK/Neg_feedback /kinetics/MAPK/inactiveRas-MKKK REAC B A +addmsg /kinetics/MAPK/MAPK-PP /kinetics/MAPK/Neg_feedback SUBSTRATE n +addmsg /kinetics/MAPK/Ras-MKKKK /kinetics/MAPK/Neg_feedback SUBSTRATE n +addmsg /kinetics/MAPK/inactiveRas-MKKK /kinetics/MAPK/Neg_feedback PRODUCT n +addmsg /kinetics/MAPK/MKKK-P/4 /kinetics/MAPK/MKK-PP MM_PRD pA +addmsg /kinetics/MAPK/int2/5 /kinetics/MAPK/MKK-PP REAC sA B +addmsg /kinetics/MAPK/MKK-PP /kinetics/MAPK/MKK-PP/7 ENZYME n +addmsg /kinetics/MAPK/MAPK /kinetics/MAPK/MKK-PP/7 SUBSTRATE n +addmsg /kinetics/MAPK/MKK-PP /kinetics/MAPK/MKK-PP/8 ENZYME n +addmsg /kinetics/MAPK/MAPK-P /kinetics/MAPK/MKK-PP/8 SUBSTRATE n +addmsg /kinetics/MAPK/MKK-PP/8 /kinetics/MAPK/MAPK-PP MM_PRD pA +addmsg /kinetics/MAPK/int4/9 /kinetics/MAPK/MAPK-PP REAC sA B +addmsg /kinetics/MAPK/Neg_feedback /kinetics/MAPK/MAPK-PP REAC A B +addmsg /kinetics/MAPK/Ras-MKKKK /graphs/conc1/Ras-MKKKK.Co PLOT Co *Ras-MKKKK.Co *11 +addmsg /kinetics/MAPK/MKKK-P /graphs/conc1/MKKK-P.Co PLOT Co *MKKK-P.Co *51 +addmsg /kinetics/MAPK/MKK-PP /graphs/conc1/MKK-PP.Co PLOT Co *MKK-PP.Co *0 +addmsg /kinetics/MAPK/MAPK-PP /graphs/conc1/MAPK-PP.Co PLOT Co *MAPK-PP.Co *58 +enddump +// End of dump + +call /kinetics/MAPK/notes LOAD \ +"This is the oscillatory MAPK model from Kholodenko 2000" \ +"Eur J. Biochem 267:1583-1588" \ +"The original model is formulated in terms of idealized" \ +"Michaelis-Menten enzymes and the enzyme-substrate complex" \ +"concentrations are therefore assumed negligible. The" \ +"current implementation of the model uses explicit enzyme" \ +"reactions involving substrates and is therefore an" \ +"approximation to the Kholodenko model. The approximation is" \ +"greatly improved if the enzyme is flagged as Available" \ +"which is an option in Kinetikit. This flag means that the" \ +"enzyme protein concentration is not reduced even when it" \ +"is involved in a complex. However, the substrate protein" \ +"continues to participate in enzyme-substrate complexes" \ +"and its concentration is therefore affected. Overall," \ +"this model works almost the same as the Kholodenko model" \ +"but the peak MAPK-PP amplitudes are a little reduced and" \ +"the period of oscillations is about 10% longer." \ +"If the enzymes are not flagged as Available then the" \ +"oscillations commence only when the Km for enzyme 1" \ +"is set to 0.1 uM." +call /kinetics/MAPK/MAPK/notes LOAD \ +"The total concn. of MAPK is 300nM " \ +"from" \ +"Kholodenko, 2000." +call /kinetics/MAPK/MKKK/notes LOAD \ +"The total concn. of MKKK is 100nM " \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/MKK/notes LOAD \ +"The total concn. of MKK is 300nM " \ +"from" \ +"Kholodenko,2000" +call /kinetics/MAPK/int1/notes LOAD \ +"This is the intermediate enzyme which catalyses the " \ +"dephosphorylation of MKKK-P to MKKK. The concentration" \ +"is set to 1 nM based on" \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/int1/2/notes LOAD \ +"Km is 8nM and Vmax is 0.25nM.s-1 " \ +"from" \ +"Kholodenko, 2000." +call /kinetics/MAPK/MKKK-P/notes LOAD \ +"This is the phosphorylated form of MKKK which converts MKK" \ +"to MKK-P and then to MKK-PP" \ +"from" \ +"Kholodenko, 2000." +call /kinetics/MAPK/MKKK-P/3/notes LOAD \ +"Km is 15 nM and Vmax is 0.025s-1" \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/MKKK-P/4/notes LOAD \ +"Km is 15nM and Vmax is 0.025s-1" \ +"from " \ +"Kholodenko, 2000." +call /kinetics/MAPK/int3/notes LOAD \ +"This intermediate enzyme catalyses the dephosphorylation of" \ +"MKK-P to MKK. The concentration is 1nM" \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/int3/6/notes LOAD \ +"The Km is 15nM and the Vmax is 0.75nM.s-1" \ +"from" \ +"Kholodenko 2000." +call /kinetics/MAPK/int5/notes LOAD \ +"This catalyses the conversion of MAPK-P to MAPK. The " \ +"concenration is 1nM." \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/int5/10/notes LOAD \ +"The Km is 15nM and Vmax is 0.5nM.s-1" \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/MKK-P/notes LOAD \ +"This is the single phoshorylated form of MKK." \ +"from" \ +"Kholodenko, 2000." +call /kinetics/MAPK/MAPK-P/notes LOAD \ +"This is the single phopshorylated form of MAPK" \ +"from" \ +"Kholodenko, 2000." +call /kinetics/MAPK/int2/notes LOAD \ +"This intermediate enzyme which catalyses the dephosphorylation of" \ +"MKK-PP to MKK-P. The concentration is 1nM." \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/int2/5/notes LOAD \ +"The Km is 15nM and Vmax is 0.75nM.s-1 " \ +"from" \ +"Kholodenko, 2000" \ +"" +call /kinetics/MAPK/int4/notes LOAD \ +"This intermediate enzyme catalyses the dephosphorylation of" \ +"MAPK-PP to MAPK-P. The concentration is 1nM." \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/int4/9/notes LOAD \ +"The Km is 15nM and Vmax is 0.5nM.s-1 " \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/Ras-MKKKK/notes LOAD \ +"The concn. of Ras-MKKKK* is set to 1 nM implicitly" \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/Ras-MKKKK/1/notes LOAD \ +"The Km is 10nM and Vmax is 2.5nM sec^-1. We assume that" \ +"there is 1 nM of the Ras-MKKKK." \ +"From Kholodenko, 2000." \ +"" \ +"If the enzymes are not flagged as Available, then this" \ +"Km should be set to 0.1 to obtain oscillations." +call /kinetics/MAPK/inactiveRas-MKKK/notes LOAD \ +"This is the inactive form of Ras-MKKK. Based on the" \ +"reaction scheme from Kholodenko 2000, this is equivalent" \ +"to a binding of the MAPK-PP to the Ras. The amount of" \ +"Ras in the model is small enough that negligible amounts" \ +"of MAPK are involved in this reaction. So it is a fair" \ +"approximation to the negative feedback mechanism from" \ +"Kholodenko, 2000." +call /kinetics/MAPK/Neg_feedback/notes LOAD \ +"From Kholodenko, 2000 Eur J Biochem 267" \ +"the Kd is 9 nM. We use a rather fast Kf of 1/sec/uM" \ +"so that equilibrium is maintained." \ +"" +call /kinetics/MAPK/MKK-PP/notes LOAD \ +"This is the double phosphorylated and active form of MKK" \ +"from" \ +"Kholodenko, 2000" +call /kinetics/MAPK/MKK-PP/7/notes LOAD \ +"The Km is 15nM which is 0.015uM Vmax is 0.025s-1" \ +"from" \ +"Kholodenko, 2000." \ +"" +call /kinetics/MAPK/MKK-PP/8/notes LOAD \ +"The Km is 15nM which is 0.015uM and Vmax is 0.025s-1" \ +"from" \ +"Kholodenko, 2000" \ +"" +call /kinetics/MAPK/MAPK-PP/notes LOAD \ +"This is the double phosphorylated and active form of MAPK." \ +"from" \ +"Kholodenko, 2000." +complete_loading diff --git a/demos/Fig2_elecModels/Fig2A.py b/demos/Fig2_elecModels/Fig2A.py new file mode 100644 index 0000000..9f00a41 --- /dev/null +++ b/demos/Fig2_elecModels/Fig2A.py @@ -0,0 +1,527 @@ +#!/usr/bin/env python +#/********************************************************************** +#** This program is part of 'MOOSE', the +#** Messaging Object Oriented Simulation Environment. +#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS +#** It is made available under the terms of the +#** GNU Lesser General Public License version 2.1 +#** See the file COPYING.LIB for the full notice. +#**********************************************************************/ + +''' +This LIF network with Ca plasticity is based on: +David Higgins, Michael Graupner, Nicolas Brunel + Memory Maintenance in Synapses with Calcium-Based + Plasticity in the Presence of Background Activity + PLOS Computational Biology, 2014. + +Author: Aditya Gilra, NCBS, Bangalore, October, 2014. +''' + +## import modules and functions to be used +import numpy as np +import matplotlib.pyplot as plt +import random +import time +import moose + +np.random.seed(100) # set seed for reproducibility of simulations +random.seed(100) # set seed for reproducibility of simulations +moose.seed(100) # set seed for reproducibility of simulations + +############################################# +# All parameters as per: +# David Higgins, Michael Graupner, Nicolas Brunel +# Memory Maintenance in Synapses with Calcium-Based +# Plasticity in the Presence of Background Activity +# PLOS Computational Biology, 2014. +############################################# + +############################################# +# Neuron model +############################################# + +# equation: dv/dt = (1/taum)*(-(v-el)) + inp +# with spike when v>vt, reset to vr + +el = -70e-3 #V # Resting potential +vt = -50e-3 #V # Spiking threshold +Rm = 20e6 #Ohm # Only taum is needed, but LIF neuron accepts +Cm = 1e-9 #F # Rm and Cm and constructs taum=Rm*Cm +taum = Rm*Cm #s # Membrane time constant is 20 ms +vr = -60e-3 #V # Reset potential +Iinject = 11.5e-3/Rm # constant current injection into LIF neuron + # same as setting el=-70+15=-55 mV and inp=0 +noiseInj = True # inject noisy current into each cell: boolean +noiseInjSD = 5e-3/Rm #A # SD of noise added to 'current' + # SD*sqrt(taum) is used as noise current SD + +############################################# +# Network parameters: numbers +############################################# + +red_fact = 10 # reduction factor for N,C,J +N = 10000/red_fact # Total number of neurons +fexc = 0.8 # Fraction of exc neurons +NE = int(fexc*N) # Number of excitatory cells +NI = N-NE # Number of inhibitory cells + +############################################# +# Simulation parameters +############################################# + +simtime = 1200.0 #s # Simulation time +dt = 1e-3 #s # time step +plotDt = 1.0 #s # Time step for storing output. + +############################################# +# Network parameters: synapses (not for ExcInhNetBase) +############################################# + +## With each presynaptic spike in exc / inh neuron, +## J / -g*J is added to post-synaptic Vm -- delta-fn synapse +## Since LIF neuron used below is derived from Compartment class, +## conductance-based synapses (SynChan class) can also be used. + +C = 500/red_fact # Number of incoming connections on each neuron (exc or inh) + # 5% conn prob between any two neurons + # Since we reduced N from 10000 to 1000, C = 50 instead of 500 + # but we need to increase J by 10 to maintain total input per neuron +fC = fexc # fraction fC incoming connections are exc, rest inhibitory +J = 0.2e-3 #V # exc strength is J (in V as we add to voltage) + # Critical J is ~ 0.45e-3 V in paper for N = 10000, C = 1000 + # See what happens for J = 0.2e-3 V versus J = 0.8e-3 V +J *= red_fact # Multiply J by red_fact to compensate C/red_fact. +g = 4.0 # -gJ is the inh strength. For exc-inh balance g >~ f(1-f)=4 +syndelay = dt # synaptic delay: +refrT = 0.0 # s # absolute refractory time + +############################################# +# Ca Plasticity parameters: synapses (not for ExcInhNetBase) +############################################# + +CaPlasticity = True # set it True or False to turn on/off plasticity +tauCa = 22.6936e-3 # s # Ca decay time scale +tauSyn = 346.3615 # s # synaptic plasticity time scale +## in vitro values in Higgins et al 2014, faster plasticity +CaPre = 0.56175 # mM +CaPost = 1.2964 # mM +## in vivo values in Higgins et al 2014, slower plasticity +#CaPre = 0.33705 # mM +#CaPost = 0.74378 # mM +delayD = 4.6098e-3 # s # CaPre is added to Ca after this delay + # proxy for rise-time of NMDA +thetaD = 1.0 # mM # depression threshold for Ca +thetaP = 1.3 # mM # potentiation threshold for Ca +gammaD = 331.909 # factor for depression term +gammaP = 725.085 # factor for potentiation term + +eqWeight = 0.16 # initial synaptic weight + # gammaP/(gammaP+gammaD) = eq weight w/o noise + # but see eqn (22), noiseSD also appears + +bistable = True # if bistable is True, use bistable potential for weights +noisy = True # use noisy weight updates given by noiseSD +noiseSD = 3.3501 # if noisy, use noiseSD (3.3501 from Higgins et al 2014) +#noiseSD = 0.1 # if bistable==False, use a smaller noise than in Higgins et al 2014 + +############################################# +# Exc-Inh network base class without connections +############################################# + +class ExcInhNetBase: + """Simulates and plots LIF neurons (exc and inh separate). + Author: Aditya Gilra, NCBS, Bangalore, India, October 2014 + """ + + def __init__(self,N=N,fexc=fexc,el=el,vt=vt,Rm=Rm,Cm=Cm,vr=vr,\ + refrT=refrT,Iinject=Iinject): + """ Constructor of the class """ + + self.N = N # Total number of neurons + self.fexc = fexc # Fraction of exc neurons + self.NmaxExc = int(fexc*N) # max idx of exc neurons, rest inh + + self.el = el # Resting potential + self.vt = vt # Spiking threshold + self.taum = taum # Membrane time constant + self.vr = vr # Reset potential + self.refrT = refrT # Absolute refractory period + self.Rm = Rm # Membrane resistance + self.Cm = Cm # Membrane capacitance + self.Iinject = Iinject # constant input current + self.noiseInjSD = noiseInjSD # SD of injected noise + + self.simif = False # whether the simulation is complete + + self._setup_network() + + def __str__(self): + return "LIF network of %d neurons "\ + "having %d exc." % (self.N,self.NmaxExc) + + def _setup_network(self): + """Sets up the network (_init_network is enough)""" + self.network = moose.LIF( 'network', self.N ); + moose.le( '/network' ) + self.network.vec.Em = self.el + self.network.vec.thresh = self.vt + self.network.vec.refractoryPeriod = self.refrT + self.network.vec.Rm = self.Rm + self.network.vec.vReset = self.vr + self.network.vec.Cm = self.Cm + if not noiseInj: + self.network.vec.inject = self.Iinject + else: + ## inject a constant + noisy current + ## values are set in self.simulate() + self.noiseTables = moose.StimulusTable('noiseTables',self.N) + moose.connect( self.noiseTables, 'output', \ + self.network, 'setInject', 'OneToOne') + + def _init_network(self,v0=el): + """Initialises the network variables before simulation""" + self.network.vec.initVm = v0 + + def simulate(self,simtime=simtime,dt=dt,plotif=False,**kwargs): + + self.dt = dt + self.simtime = simtime + self.T = np.ceil(simtime/dt) + self.trange = np.arange(0,self.simtime,dt) + + for i in range(self.N): + if noiseInj: + ## Gaussian white noise SD added every dt interval should be + ## divided by sqrt(dt), as the later numerical integration + ## will multiply it by dt. + ## See the Euler-Maruyama method, numerical integration in + ## http://www.scholarpedia.org/article/Stochastic_dynamical_systems + self.noiseTables.vec[i].vector = self.Iinject + \ + np.random.normal( \ + scale=self.noiseInjSD*np.sqrt(self.Rm*self.Cm/self.dt), \ + size=int(self.T) + ) # scale = SD + self.noiseTables.vec[i].stepSize = 0 # use current time + # as x value for interpolation + self.noiseTables.vec[i].stopTime = self.simtime + + self._init_network(**kwargs) + if plotif: + self._init_plots() + + # moose simulation + #moose.useClock( 1, '/network', 'process' ) + #moose.setClock( 0, dt ) + #moose.setClock( 1, dt ) + #moose.setClock( 2, dt ) + #moose.setClock( 3, dt ) + #moose.setClock( 9, dt ) + ## Do need to set the dt for MOOSE clocks + for i in range(10): + moose.setClock( i, dt ) + moose.setClock( 18, plotDt ) + t1 = time.time() + print('reinit MOOSE -- takes a while ~20s.') + moose.reinit() + print(('reinit time t = ', time.time() - t1)) + t1 = time.time() + print('starting') + simadvance = self.simtime / 50.0 + for i in range( 50 ): + moose.start( simadvance ) + print(('at t = ', i * simadvance, 'realtime = ', time.time() - t1)) + #moose.start(self.simtime) + print(('runtime for ', self.simtime, 'sec, is t = ', time.time() - t1)) + + if plotif: + self._plot() + + def _init_plots(self): + ## make a few tables to store a few Vm-s + numVms = 10 + self.plots = moose.Table2( '/plotVms', numVms ) + ## draw numVms out of N neurons + nrnIdxs = random.sample(list(range(self.N)),numVms) + for i in range( numVms ): + moose.connect( self.network.vec[nrnIdxs[i]], 'VmOut', \ + self.plots.vec[i], 'input') + + ## make self.N tables to store spikes of all neurons + self.spikes = moose.Table2( '/plotSpikes', self.N ) + moose.connect( self.network, 'spikeOut', \ + self.spikes, 'input', 'OneToOne' ) + + ## make 2 tables to store spikes of all exc and all inh neurons + self.spikesExc = moose.Table2( '/plotSpikesAllExc' ) + for i in range(self.NmaxExc): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesExc, 'input' ) + self.spikesInh = moose.Table2( '/plotSpikesAllInh' ) + for i in range(self.NmaxExc,self.N): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesInh, 'input' ) + + def _plot(self): + """ plots the spike raster for the simulated net""" + +############################################# +# Exc-Inh network class with Ca plasticity based connections +# (inherits from ExcInhNetBase) +############################################# + +class ExcInhNet(ExcInhNetBase): + """ Recurrent network simulation """ + + def __init__(self,J=J,incC=C,fC=fC,scaleI=g,syndelay=syndelay,**kwargs): + """Overloads base (parent) class""" + self.J = J # exc connection weight + self.incC = incC # number of incoming connections per neuron + self.fC = fC # fraction of exc incoming connections + self.excC = int(fC*incC)# number of exc incoming connections + self.scaleI = scaleI # inh weight is scaleI*J + self.syndelay = syndelay# synaptic delay + + # call the parent class constructor + ExcInhNetBase.__init__(self,**kwargs) + + def __str__(self): + return "LIF network of %d neurons "\ + "of which %d are exc." % (self.N,self.NmaxExc) + + def _init_network(self,**args): + ExcInhNetBase._init_network(self,**args) + + def _init_plots(self): + ExcInhNetBase._init_plots(self) + self.recN = 50 # number of neurons for which to record weights and Ca + if CaPlasticity: + ## make tables to store weights of recN exc synapses + ## for each post-synaptic exc neuron + self.weights = moose.Table2( '/plotWeights', self.excC*self.recN ) + for i in range(self.recN): # range(self.N) is too large + for j in range(self.excC): + moose.connect( self.weights.vec[self.excC*i+j], 'requestOut', + self.synsEE.vec[i*self.excC+j].synapse[0], 'getWeight') + self.CaTables = moose.Table2( '/plotCa', self.recN ) + for i in range(self.recN): # range(self.N) is too large + moose.connect( self.CaTables.vec[i], 'requestOut', + self.synsEE.vec[i*self.excC+j], 'getCa') + + def _setup_network(self): + ## Set up the neurons without connections + ExcInhNetBase._setup_network(self) + + ## Now, add in the connections... + ## Each pre-synaptic spike cause Vm of post-neuron to rise by + ## synaptic weight in one time step i.e. delta-fn synapse. + ## Since LIF neuron is derived from Compartment class, + ## conductance-based synapses (SynChan class) can also be used. + + ## E to E synapses can be plastic + ## Two ways to do this: + ## 1) Each LIF neuron has one incoming postsynaptic SynHandler, + ## which collects the activation from all presynaptic neurons, + ## but then a common Ca pool is used. + ## 2) Each LIF neuron has multiple postsyanptic SynHandlers, + ## one for each pre-synaptic neuron, i.e. one per synapse, + ## then each synapse has a different Ca pool. + ## Here we go with option 2) as per Higgins et al 2014 (Brunel private email) + ## separate SynHandler per EE synapse, thus NmaxExc*excC + if CaPlasticity: + self.synsEE = moose.GraupnerBrunel2012CaPlasticitySynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + else: + self.synsEE = moose.SimpleSynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + moose.useClock( 0, '/network/synsEE', 'process' ) + + ## I to E synapses are not plastic + self.synsIE = moose.SimpleSynHandler( '/network/synsIE', self.NmaxExc ) + ## all synapses to I neurons are not plastic + self.synsI = moose.SimpleSynHandler( '/network/synsI', self.N-self.NmaxExc ) + ## connect all SynHandlers to their respective neurons + for i in range(self.NmaxExc): + moose.connect( self.synsIE.vec[i], 'activationOut', \ + self.network.vec[i], 'activation' ) + for i in range(self.NmaxExc,self.N): + moose.connect( self.synsI.vec[i-self.NmaxExc], 'activationOut', \ + self.network.vec[i], 'activation' ) + + ## Connections from some Exc/Inh neurons to each Exc neuron + for i in range(0,self.NmaxExc): + self.synsIE.vec[i].numSynapses = self.incC-self.excC + + ## Connections from some Exc neurons to each Exc neuron + ## draw excC number of neuron indices out of NmaxExc neurons + preIdxs = random.sample(list(range(self.NmaxExc)),self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synidx = i*self.excC+synnum + synHand = self.synsEE.vec[synidx] + + ## connect each synhandler to the post-synaptic neuron + moose.connect( synHand, 'activationOut', \ + self.network.vec[i], 'activation' ) + ## important to set numSynapses = 1 for each synHandler, + ## doesn't create synapses if you set the full array of SynHandlers + synHand.numSynapses = 1 + + synij = synHand.synapse[0] + connectExcId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + if CaPlasticity: + ## set parameters for the Ca Plasticity SynHandler + ## have to be set for each SynHandler + ## doesn't set for full array at a time + synHand.CaInit = 0.0 + synHand.tauCa = tauCa + synHand.tauSyn = tauSyn + synHand.CaPre = CaPre + synHand.CaPost = CaPost + synHand.delayD = delayD + synHand.thetaD = thetaD + synHand.thetaP = thetaP + synHand.gammaD = gammaD + synHand.gammaP = gammaP + synHand.weightMax = 1.0 # bounds on the weight + synHand.weightMin = 0.0 + synHand.weightScale = \ + self.J*2.0 # 0.2 mV, weight*weightScale is activation + # typically weight <~ 0.5, so activation <~ J + synHand.noisy = noisy + synHand.noiseSD = noiseSD + synHand.bistable = bistable + + moose.connect( self.network.vec[i], \ + 'spikeOut', synHand, 'addPostSpike') + synij.weight = eqWeight # activation = weight*weightScale + # weightScale = 2*J + # weight <~ 0.5 + ## Randomly set 5% of them to be 1.0 + if np.random.uniform()<0.05: + synij.weight = 1.0 + else: + synij.weight = self.J # no weightScale here, activation = weight + + ## Connections from some Inh neurons to each Exc neuron + ## draw inhC=incC-excC number of neuron indices out of inhibitory neurons + preIdxs = random.sample(list(range(self.NmaxExc,self.N)),self.incC-self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsIE.vec[i].synapse[synnum] + connectInhId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = -self.scaleI*self.J # activation = weight + + ## Connections from some Exc/Inh neurons to each Inh neuron + for i in range(self.N-self.NmaxExc): + ## each neuron has incC number of synapses + self.synsI.vec[i].numSynapses = self.incC + + ## draw excC number of neuron indices out of NmaxExc neurons + preIdxs = random.sample(list(range(self.NmaxExc)),self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsI.vec[i].synapse[synnum] + connectExcId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = self.J # activation = weight + + ## draw inhC=incC-excC number of neuron indices out of inhibitory neurons + preIdxs = random.sample(list(range(self.NmaxExc,self.N)),self.incC-self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsI.vec[i].synapse[ self.excC + synnum ] + connectInhId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = -self.scaleI*self.J # activation = weight + + moose.useClock( 0, '/network/synsIE', 'process' ) + moose.useClock( 0, '/network/synsI', 'process' ) + +############################################# +# Analysis functions +############################################# + +def rate_from_spiketrain(spiketimes,fulltime,dt,tau=50e-3): + """ + Returns a rate series of spiketimes convolved with a Gaussian kernel; + all times must be in SI units. + """ + sigma = tau/2. + ## normalized Gaussian kernel, integral with dt is normed to 1 + ## to count as 1 spike smeared over a finite interval + norm_factor = 1./(np.sqrt(2.*np.pi)*sigma) + gauss_kernel = np.array([norm_factor*np.exp(-x**2/(2.*sigma**2))\ + for x in np.arange(-5.*sigma,5.*sigma+dt,dt)]) + kernel_len = len(gauss_kernel) + ## need to accommodate half kernel_len on either side of fulltime + rate_full = np.zeros(int(fulltime/dt)+kernel_len) + for spiketime in spiketimes: + idx = int(spiketime/dt) + rate_full[idx:idx+kernel_len] += gauss_kernel + ## only the middle fulltime part of the rate series + ## This is already in Hz, + ## since should have multiplied by dt for above convolution + ## and divided by dt to get a rate, so effectively not doing either. + return rate_full[kernel_len/2:kernel_len/2+int(fulltime/dt)] + +############################################# +# Make plots +############################################# + +def extra_plots(net): + ## extra plots apart from the spike rasters + ## individual neuron Vm-s + + timeseries = net.trange + ## individual neuron firing rates + + ## population firing rates + + ## Ca plasticity: weight vs time plots + if CaPlasticity: + ## Ca versus time in post-synaptic neurons + for i in range(net.recN): # range(net.N) is too large + net.CaTables.vec[i].xplot( 'ca.xplot', 'Ca_' + str(i) ) + + for i in range(net.recN): # range(net.N) is too large + for j in range(net.excC): + k = net.excC*i+j + net.weights.vec[k].xplot( 'wt.xplot', 'w_' + str(k) ) + + ## all EE weights are used for a histogram + weights = [ net.synsEE.vec[i*net.excC+j].synapse[0].weight \ + for i in range(net.NmaxExc) for j in range(net.excC) ] + histo, edges = np.histogram( weights, bins=100 ) + print() + print(histo) + print() + print(edges) + print() + + plt.figure() + plt.hist(weights, bins=100) + plt.title("Histogram of efficacies") + plt.xlabel("Efficacy (arb)") + plt.ylabel("# per bin") + +if __name__=='__main__': + ## ExcInhNetBase has unconnected neurons, + ## ExcInhNet connects them + ## Instantiate either ExcInhNetBase or ExcInhNet below + #net = ExcInhNetBase(N=N) + net = ExcInhNet(N=N) + print(net) + ## Important to distribute the initial Vm-s + ## else weak coupling gives periodic synchronous firing + net.simulate(simtime,plotif=True, v0=np.random.uniform(el-20e-3,vt,size=N)) + plt.figure() + extra_plots(net) + plt.show() + diff --git a/demos/Fig2_elecModels/Fig2A_analysis.py b/demos/Fig2_elecModels/Fig2A_analysis.py new file mode 100644 index 0000000..fadc704 --- /dev/null +++ b/demos/Fig2_elecModels/Fig2A_analysis.py @@ -0,0 +1,62 @@ +import os +import numpy as np +from pylab import * +from itertools import islice + +if not os.path.isfile('wx.xplot'): + print("Please run ./Fig2A.py to generate the data") + quit() + +fh = open('wt.xplot',mode='r') + +fulltime = 1200 #s +plotdt = 1 #s +numpts = int(fulltime/plotdt)+1 + +print('reading') +wts = [] +while True: + next_line = '' + while 'plotname' not in next_line: + next_line = fh.readline() + if next_line == '': break + if next_line == '': break + next_wt = [float(fh.readline()) for i in range(numpts)] + wts.append(next_wt) + print('weight',len(wts)) + + +hiAve = np.zeros( len( wts[0] ) ) +loAve = np.zeros( len( wts[0] ) ) +numHi = 0 +for i in wts: + if i[0] > 0.5: + hiAve += np.array( i ) + numHi += 1 + else: + loAve += np.array( i ) + + +hiAve /= numHi +loAve /= ( len( wts ) - numHi ) + +def dumpVec( f, name, vec ): + f.write( '/newplot\n' ) + f.write( '/plotname ' + name + '\n' ) + for i in vec: + f.write( str( i ) + '\n' ) + +f = open( 'averageOfxplots', 'w' ) +dumpVec( f, 'highAverage', hiAve ) +dumpVec( f, 'lowAverage', loAve ) +dumpVec( f, 'highExample', wts[4] ) +dumpVec( f, 'lowExample', wts[5] ) +f.close() + + +print('numHi = ', numHi, ' plotting...') +figure() +plot(transpose(wts)) +plot( hiAve, linewidth=4 ) +plot( loAve, linewidth=4 ) +show() diff --git a/demos/Fig2_elecModels/Fig2C.py b/demos/Fig2_elecModels/Fig2C.py new file mode 100644 index 0000000..90cb21a --- /dev/null +++ b/demos/Fig2_elecModels/Fig2C.py @@ -0,0 +1,356 @@ +######################################################################## +# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015. +# It is licenced under the GPL 2.1 or higher. +# There is no warranty of any kind. You are welcome to make copies under +# the provisions of the GPL. +# This programme illustrates building a panel of multiscale models to +# test neuronal plasticity in different contexts. +######################################################################## +import numpy +import time +import pylab +import moose +from moose import neuroml +from PyQt5 import Qt, QtCore, QtGui +import matplotlib.pyplot as plt +import sys +import os +from moose.neuroml.ChannelML import ChannelML +sys.path.append('../../../Demos/util') +import rdesigneur as rd +import moogli + +PI = 3.14159265359 +useGssa = True +combineSegments = True +# Pick your favourite cell here. +#elecFileName = "ca1_minimal.p" +## Cell morphology from Bannister and Larkman J Neurophys 2015/NeuroMorpho +elecFileName = "h10.CNG.swc" +#elecFileName = "CA1.morph.xml" +#elecFileName = "VHC-neuron.CNG.swc" +synSpineList = [] +synDendList = [] +probeInterval = 0.1 +probeAmplitude = 1.0 +tetanusFrequency = 100.0 +tetanusAmplitude = 1000 +tetanusAmplitudeForSpines = 1000 +frameRunTime = 1e-3 # 1 ms +baselineTime = 0.05 +tetTime = 0.01 +postTetTime = 0.01 +runtime = baselineTime + tetTime + postTetTime + +def buildRdesigneur(): + ''' + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + ''' + cellProto = [ [ "./cells/" + elecFileName, "elec" ] ] + chanProto = [ + ['./chans/hd.xml'], \ + ['./chans/kap.xml'], \ + ['./chans/kad.xml'], \ + ['./chans/kdr.xml'], \ + ['./chans/na3.xml'], \ + ['./chans/nax.xml'], \ + ['./chans/CaConc.xml'], \ + ['./chans/Ca.xml'], \ + ['./chans/NMDA.xml'], \ + ['./chans/Glu.xml'] \ + ] + spineProto = [ \ + ['makeSpineProto()', 'spine' ] + ] + chemProto = [] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are: + # p, g, L, len, dia, maxP, maxG, maxL. + # where + # p = path distance from soma, threaded along dendrite + # g = geometrical distance from soma (shortest distance) + # L = electrotonic distance from soma: number of length constants + # len = length of dendritic compartment + # dia = diameter of dendritic compartment + # maxP = maximal value of 'p' for the cell + # maxG = maximal value of 'g' for the cell + # maxL = maximal value of 'L' for the cell + # + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + passiveDistrib = [ + [ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \ + "Em", "-58e-3", "initVm", "-65e-3" ], \ + [ ".", "#axon#", "RA", "0.5" ] \ + ] + chanDistrib = [ \ + ["hd", "#dend#,#apical#", "Gbar", "5e-2*(1+(p*3e4))" ], \ + ["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \ + ["na3", "#soma#,#dend#,#apical#", "Gbar", "250" ], \ + ["nax", "#soma#,#axon#", "Gbar", "1250" ], \ + ["kap", "#axon#,#soma#", "Gbar", "300" ], \ + ["kap", "#dend#,#apical#", "Gbar", \ + "300*(H(100-p*1e6)) * (1+(p*1e4))" ], \ + ["Ca_conc", "#soma#,#dend#,#apical#", "tau", "0.0133" ], \ + ["kad", "#soma#,#dend#,#apical#", "Gbar", \ + "300*H(p - 100e-6)*(1+p*1e4)" ], \ + ["Ca", "#dend#,#apical#", "Gbar", "p<160e-6? 10+ p*0.25e-6 : 50" ], \ + ["Ca", "#soma#", "Gbar", "10" ], \ + ["glu", "#dend#,#apical#", "Gbar", "200*H(p-200e-6)" ], \ + ["NMDA", "#dend#,#apical#", "Gbar", "2*H(p-200e-6)" ] \ + ] + spineDistrib = [ \ + ["spine", '#apical#', "spineSpacing", "20e-6", \ + "spineSpacingDistrib", "2e-6", \ + "angle", "0", \ + "angleDistrib", str( 2*PI ), \ + "size", "1", \ + "sizeDistrib", "0.5" ] \ + ] + chemDistrib = [] + + ###################################################################### + # Here we define the mappings across scales. Format: + # sourceObj sourceField destObj destField offset scale + # where the coupling expression is anything a muParser can evaluate, + # using the input variable x. For example: 8e-5 + 300*x + # For now, let's use existing adaptors which take an offset and scale. + ###################################################################### + adaptorList = [] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + rd.addSpineProto() # This adds a version with an LCa channel by default. + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + passiveDistrib = passiveDistrib, \ + spineDistrib = spineDistrib, \ + chanDistrib = chanDistrib, \ + chemDistrib = chemDistrib, \ + cellProto = cellProto, \ + chanProto = chanProto, \ + chemProto = chemProto, \ + adaptorList = adaptorList + ) + #spineProto = spineProto, \ + + return rdes + +def buildPlots( rdes ): + graphs = moose.Neutral( '/graphs' ) + vtab = moose.Table( '/graphs/VmTab' ) + moose.connect( vtab, 'requestOut', rdes.soma, 'getVm' ) + +def displayPlots(): + pylab.figure(1, figsize = (8,10 ) ) + pylab.subplot( 1,1,1) + for i in moose.wildcardFind( "/graphs/#VmTab" ): + t = numpy.arange( 0, i.vector.size, 1 ) * i.dt + pylab.plot( t, i.vector, label = i.name ) + pylab.xlabel( "Time (s)" ) + pylab.legend() + pylab.title( 'Vm' ) + + pylab.figure(2, figsize= (8,10)) + ax = pylab.subplot( 1,1,1 ) + neuron = moose.element( '/model/elec' ) + comptDistance = dict( list(zip( neuron.compartments, neuron.pathDistanceFromSoma )) ) + for i in moose.wildcardFind( '/library/#[ISA=ChanBase]' ): + chans = moose.wildcardFind( '/model/elec/#/' + i.name ) + print(i.name, len( chans )) + p = [ 1e6*comptDistance.get( j.parent, 0) for j in chans ] + Gbar = [ j.Gbar/(j.parent.length * j.parent.diameter * PI) for j in chans ] + if len( p ) > 2: + pylab.plot( p, Gbar, linestyle = 'None', marker = ".", label = i.name ) + sortedGbar = sorted(zip(p, Gbar), key=lambda x: x[0]) + ax.set_yscale( 'log' ) + pylab.xlabel( "Distance from soma (microns)" ) + pylab.ylabel( "Channel density (Seimens/sq mtr)" ) + pylab.legend() + pylab.title( 'Channel distribution' ) + pylab.show() + +def create_vm_viewer(rdes): + network = moogli.extensions.moose.read(rdes.elecid.path) + normalizer = moogli.utilities.normalizer(-0.08, + 0.02, + clipleft=True, + clipright=True) + colormap = moogli.colors.UniformColorMap([moogli.colors.Color(0.0, + 0.0, + 1.0, + 1.0), + moogli.colors.Color(1.0, + 1.0, + 0.0, + 0.1)]) + mapper = moogli.utilities.mapper(colormap, normalizer) + vms = [moose.element(x).Vm for x in list(network.shapes.keys())] + network.set("color", vms, mapper) + + def prelude(view): + view.pitch(PI/2) + view.zoom(0.4) + + def interlude(view): + moose.start(frameRunTime) + vms = [moose.element(x).Vm for x in list(network.shapes.keys())] + network.set("color", vms, mapper) + view.yaw(0.01) + currTime = moose.element('/clock').currentTime + if currTime < runtime: + deliverStim(currTime) + else: + view.stop() + + def postlude(view): + displayPlots() + + viewer = moogli.Viewer("vm-viewer") + viewer.attach_shapes(list(network.shapes.values())) + view = moogli.View("vm-view", + prelude=prelude, + interlude=interlude, + postlude=postlude) + viewer.attach_view(view) + return viewer + + +def create_ca_viewer(rdes): + network = moogli.extensions.moose.read(rdes.elecid.path) + ca_elements = [] + for compartment_path in list(network.shapes.keys()): + if moose.exists(compartment_path + '/Ca_conc'): + ca_elements.append(moose.element(compartment_path + '/Ca_conc')) + else: + ca_elements.append(moose.element('/library/Ca_conc')) + + normalizer = moogli.utilities.normalizer(0.0, + 0.002, + clipleft=True, + clipright=True) + colormap = moogli.colors.UniformColorMap([moogli.colors.Color(1.0, + 0.0, + 0.0, + 1.0), + moogli.colors.Color(0.0, + 1.0, + 1.0, + 0.1)]) + mapper = moogli.utilities.mapper(colormap, normalizer) + + cas = [element.Ca for element in ca_elements] + network.set("color", cas, mapper) + + def prelude(view): + view.pitch(PI/2) + view.zoom(0.4) + + def interlude(view): + moose.start(frameRunTime) + cas = [element.Ca for element in ca_elements] + network.set("color", cas, mapper) + view.yaw(0.01) + currTime = moose.element('/clock').currentTime + if currTime < runtime: + deliverStim(currTime) + else: + view.stop() + + viewer = moogli.Viewer("ca-viewer") + viewer.attach_shapes(list(network.shapes.values())) + view = moogli.View("ca-view", + prelude=prelude, + interlude=interlude) + viewer.attach_view(view) + return viewer + +def build3dDisplay(rdes): + print("building 3d Display") + app = QtGui.QApplication(sys.argv) + + vm_viewer = create_vm_viewer(rdes) + vm_viewer.resize(700, 900) + vm_viewer.show() + vm_viewer.start() + + ca_viewer = create_ca_viewer(rdes) + ca_viewer.resize(700, 900) + ca_viewer.show() + ca_viewer.start() + + return app.exec_() + + +def deliverStim( currTime ): + if currTime > baselineTime and currTime < baselineTime + tetTime: + # deliver tet stim + step = int ( (currTime - baselineTime) / frameRunTime ) + tetStep = int( 1.0 / (tetanusFrequency * frameRunTime ) ) + if step % tetStep == 0: + for i in synDendList: + i.activation( tetanusAmplitude ) + for i in synSpineList: + i.activation( tetanusAmplitudeForSpines ) + else: + # deliver probe stim + step = int (currTime / frameRunTime ) + probeStep = int( probeInterval / frameRunTime ) + if step % probeStep == 0: + print("Doing probe Stim at ", currTime) + for i in synSpineList: + i.activation( probeAmplitude ) + + +def main(): + global synSpineList + global synDendList + numpy.random.seed( 1234 ) + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + assert( moose.exists( '/model' ) ) + synSpineList = moose.wildcardFind( "/model/elec/#head#/glu,/model/elec/#head#/NMDA" ) + temp = set( moose.wildcardFind( "/model/elec/#/glu,/model/elec/#/NMDA" ) ) + + synDendList = list( temp - set( synSpineList ) ) + print("num spine, dend syns = ", len( synSpineList ), len( synDendList )) + moose.reinit() + #for i in moose.wildcardFind( '/model/elec/#apical#/#[ISA=CaConcBase]' ): + #print i.path, i.length, i.diameter, i.parent.length, i.parent.diameter + + buildPlots(rdes) + # Run for baseline, tetanus, and post-tetanic settling time + t1 = time.time() + build3dDisplay(rdes) + print('real time = ', time.time() - t1) + +if __name__ == '__main__': + main() diff --git a/demos/Fig2_elecModels/Fig2D.py b/demos/Fig2_elecModels/Fig2D.py new file mode 100644 index 0000000..5d7db8f --- /dev/null +++ b/demos/Fig2_elecModels/Fig2D.py @@ -0,0 +1,104 @@ +######################################################################### +## This program is part of 'MOOSE', the +## Messaging Object Oriented Simulation Environment. +## Copyright (C) 2015 Upinder S. Bhalla. and NCBS +## It is made available under the terms of the +## GNU Lesser General Public License version 2.1 +## See the file COPYING.LIB for the full notice. +######################################################################### +# This example illustrates loading a model from an SWC file, inserting +# spines, and viewing it. + +import moogli +import moose +from PyQt5 import Qt, QtCore, QtGui +import sys +import os +import rdesigneur as rd + +PI = 3.14159265358979 +frameRunTime = 0.0001 +runtime = 0.1 +inject = 15e-10 +simdt = 5e-5 +RM = 1.0 +RA = 1.0 +CM = 0.01 +# This is the expression used to set spine spacing: +spineSpacing = "dia * 2" +minSpacing = 0.1e-6 +spineSize = 1.0 +spineSizeDistrib = 0.5 +spineAngle = 0 +spineAngleDistrib = 2*PI + + +def create_vm_viewer(rdes): + network = moogli.extensions.moose.read(rdes.elecid.path, + vertices=10) + normalizer = moogli.utilities.normalizer(-0.08, + 0.02, + clipleft=True, + clipright=True) + colormap = moogli.colors.UniformColorMap([moogli.colors.Color(0.0, + 0.5, + 1.0, + 1.0), + moogli.colors.Color(1.0, + 0.0, + 0.0, + 0.9)]) + mapper = moogli.utilities.mapper(colormap, normalizer) + vms = [moose.element(x).Vm for x in list(network.shapes.keys())] + network.set("color", vms, mapper) + + def interlude(view): + moose.start(frameRunTime) + #vms = [moose.element(x).Vm for x in network.shapes.keys()] + #network.set("color", vms, mapper) + view.pitch(0.01) + currTime = moose.element('/clock').currentTime + if currTime >= runtime: + view.stop() + + viewer = moogli.Viewer("vm-viewer") + viewer.attach_shapes(list(network.shapes.values())) + view = moogli.View("vm-view", + interlude=interlude) + viewer.attach_view(view) + return viewer + + +def main(): + ######## Put your favourite cell model here ###### + ##This one is from PMID 19146814: Peng et al Neuron 2009 + filename = 'cells/K-18.CNG.swc' + moose.Neutral( '/library' ) + rdes = rd.rdesigneur( \ + cellProto = [[ filename, 'elec' ] ],\ + spineProto = [['makeSpineProto()', 'spine' ]] ,\ + spineDistrib = [ \ + ['spine', '#', \ + 'spacing', spineSpacing, \ + 'spacingDistrib', str( minSpacing ), \ + 'angle', str( spineAngle ), \ + 'angleDistrib', str( spineAngleDistrib ), \ + 'size', str( spineSize ), \ + 'sizeDistrib', str( spineSizeDistrib ) ] \ + ] \ + ) + rdes.buildModel('/model') + moose.reinit() + compts = moose.wildcardFind( "/model/elec/#[ISA=CompartmentBase]" ) + compts[0].inject = inject + + ################## Now we set up the display ######################## + print("Setting Up 3D Display") + app = QtGui.QApplication(sys.argv) + vm_viewer = create_vm_viewer(rdes) + vm_viewer.showMaximized() + vm_viewer.start() + return app.exec_() + +if __name__ == '__main__': + main() diff --git a/demos/Fig2_elecModels/Fig2E.py b/demos/Fig2_elecModels/Fig2E.py new file mode 100644 index 0000000..6cd3e13 --- /dev/null +++ b/demos/Fig2_elecModels/Fig2E.py @@ -0,0 +1,125 @@ +######################################################################### +## This program is part of 'MOOSE', the +## Messaging Object Oriented Simulation Environment. +## Copyright (C) 2015 Upinder S. Bhalla. and NCBS +## It is made available under the terms of the +## GNU Lesser General Public License version 2.1 +## See the file COPYING.LIB for the full notice. +######################################################################### +# This example illustrates loading a model from an SWC file, inserting +# channels, and running it. + +import moogli +import moose +from PyQt5 import Qt, QtCore, QtGui +import numpy +import pylab +import sys +import os +import rdesigneur as rd + +PI = 3.14159265358979 +frameRunTime = 0.0005 +runtime = 0.1 +inject = 1e-9 +chanProto_ = [ + ['./chans/KChannel_HH.xml'], + ['./chans/NaChannel_HH.xml'], + ['./chans/LeakConductance.xml'], + [ './chans/kdr.xml' ] + ] + +passiveDistrib_ = [ + [ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", + "Em", "-58e-3", "initVm", "-65e-3" ] + , [ ".", "#axon#", "RA", "0.5" ] + ] + +chanDistrib_ = [ + [ "NaConductance", "#", "Gbar", "1200" ] + , [ "KConductance", "#", "Gbar", "360" ] + , [ "LeakConductance", "#", "Gbar", "3" ] + , [ "kdr", "#", "Gbar", "10" ] + ] + + +def create_vm_viewer(rdes, somaVm): + network = moogli.extensions.moose.read(rdes.elecid.path) + normalizer = moogli.utilities.normalizer(-0.08, + 0.02, + clipleft=True, + clipright=True) + colormap = moogli.colors.UniformColorMap([moogli.colors.Color(0.0, + 0.5, + 1.0, + 1.0), + moogli.colors.Color(1.0, + 0.0, + 0.0, + 0.9)]) + mapper = moogli.utilities.mapper(colormap, normalizer) + + vms = [moose.element(x).Vm for x in list(network.shapes.keys())] + network.set("color", vms, mapper) + + def prelude(view): + view.pitch(PI/2.0) + + def interlude(view): + moose.start(frameRunTime) + vms = [moose.element(x).Vm for x in list(network.shapes.keys())] + network.set("color", vms, mapper) + view.yaw(0.01) + currTime = moose.element('/clock').currentTime + if currTime >= runtime: + view.stop() + + def postlude(view): + pylab.plot(numpy.linspace(0, + runtime, + len(somaVm.vector)), + somaVm.vector * 1000) + pylab.xlabel("Time (s)") + pylab.ylabel("Vm (mV)") + pylab.show() + + viewer = moogli.Viewer("vm-viewer") + viewer.attach_shapes(list(network.shapes.values())) + view = moogli.View("vm-view", + prelude=prelude, + interlude=interlude, + postlude=postlude) + viewer.attach_view(view) + return viewer + + +def main(): + ######## Put your favourite cell model here ###### + ##This one is from PMID 22730554: Suo et al J. Mol Cell Biol 2012 + filename = 'cells/ko20x-07.CNG.swc' + moose.Neutral( '/library' ) + rdes = rd.rdesigneur( \ + cellProto = [[ filename, 'elec' ] ],\ + passiveDistrib = passiveDistrib_, + chanProto = chanProto_, + chanDistrib = chanDistrib_ + ) + rdes.buildModel( '/model' ) + moose.reinit() + + ################## Now we store plots ######################## + somaVm = moose.Table( '/somaVm' ) + moose.connect( somaVm, 'requestOut', rdes.soma, 'getVm' ) + ################## Now we set up the display ######################## + compts = moose.wildcardFind( "/model/elec/#[ISA=CompartmentBase]" ) + compts[0].inject = inject + + print("Setting Up 3D Display") + app = QtGui.QApplication(sys.argv) + vm_viewer = create_vm_viewer(rdes, somaVm) + vm_viewer.show() + vm_viewer.start() + return app.exec_() + +if __name__ == '__main__': + main() diff --git a/demos/Fig2_elecModels/cells/CA1.morph.xml b/demos/Fig2_elecModels/cells/CA1.morph.xml new file mode 100644 index 0000000..dcae7ae --- /dev/null +++ b/demos/Fig2_elecModels/cells/CA1.morph.xml @@ -0,0 +1,12535 @@ + + + + + + + Cell exported from NEURON ModelView in NeuroML Level 2 format and imported into neuroConstruct. The densities of hd, kap, kad have been replaced with variable mechanisms recreating the densities as used in the original model from ModelDB. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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See StdSwc1.31.doc for more information. +# +# Neurolucida to SWC conversion from L-Measure. 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-1.02 0.54 2945 +2947 4 -61.87 463.13 -1.44 0.54 2946 +2948 4 -62.44 464.91 -2.35 0.54 2947 +2949 4 -62.81 466.19 -2.88 0.54 2948 +2950 4 -62.67 466.98 -3.04 0.54 2949 +2951 4 -5.99 292.26 22.29 0.865 2088 +2952 4 -5.25 294.24 22.42 0.865 2951 +2953 4 -4.94 296.38 22.6 0.865 2952 +2954 4 -3.89 299.58 22.82 0.865 2953 +2955 4 -1.99 302.56 22.11 0.865 2954 +2956 4 -0.94 304.26 22.18 0.865 2955 +2957 4 -0.79 306.85 22.41 0.865 2956 +2958 4 -1.4 310.18 22.8 0.865 2957 +2959 4 -2.07 313.26 24.29 0.865 2958 +2960 4 -1.92 315.84 24.61 0.865 2959 +2961 4 -2.08 318.11 24.91 0.865 2960 +2962 4 -2.39 321.15 25.24 0.865 2961 +2963 4 -3.31 324.17 25.7 0.865 2962 +2964 4 -4.07 326.74 26.09 0.65 2963 +2965 4 -6.04 328.69 26.61 0.65 2964 +2966 4 -7.57 332.02 27.16 0.65 2965 +2967 4 -8.07 332.51 28.39 0.65 2966 +2968 4 -9.45 333.87 28.64 0.65 2967 +2969 4 -11.59 335.97 29.04 0.65 2968 +2970 4 -12.81 339.01 29.46 0.65 2969 +2971 4 -14.35 342.33 29.92 0.65 2970 +2972 4 -16.34 344.9 30.36 0.65 2971 +2973 4 -18.01 346.25 30.64 0.65 2972 +2974 4 -19.26 348.09 32.3 0.65 2973 +2975 4 -19.83 349.85 33.05 0.65 2974 +2976 4 -20.38 351.0 33.9 0.65 2975 +2977 4 -21.41 352.01 34.62 0.65 2976 +2978 4 -21.71 352.9 34.81 0.65 2977 +2979 4 -21.97 353.78 35.37 0.65 2978 +2980 4 -21.82 356.05 35.65 0.65 2979 +2981 4 -21.83 358.78 35.92 0.65 2980 +2982 4 -21.29 360.38 36.93 0.65 2981 +2983 4 -20.75 362.49 38.54 0.65 2982 +2984 4 -19.8 363.97 39.11 0.65 2983 +2985 4 -19.08 364.47 40.23 0.65 2984 +2986 4 -18.66 364.64 41.56 0.65 2985 +2987 4 -18.04 365.84 41.93 0.65 2986 +2988 4 -17.67 365.79 42.5 0.65 2987 +2989 4 -17.2 365.91 44.37 0.65 2988 +2990 4 -6.61 91.18 9.77 0.435 1189 +2991 4 -7.98 91.62 9.94 0.435 2990 +2992 4 -8.7 91.42 10.44 0.435 2991 +2993 4 -8.69 91.11 10.56 0.65 2992 +2994 4 -8.95 90.75 11.08 0.65 2993 +2995 4 -8.89 90.09 11.62 0.65 2994 +2996 4 -9.16 89.43 11.96 0.65 2995 +2997 4 -9.56 88.31 12.41 0.65 2996 +2998 4 -9.55 87.99 12.53 0.65 2997 +2999 4 -9.83 87.06 12.69 0.65 2998 +3000 4 -9.81 86.44 12.78 0.65 2999 +3001 4 -9.77 86.09 13.2 0.65 3000 +3002 4 -9.87 85.27 13.65 0.65 3001 +3003 4 -9.68 84.79 13.89 0.65 3002 +3004 4 -9.21 84.32 13.95 0.65 3003 +3005 4 -8.85 83.96 14.57 0.65 3004 +3006 4 -8.62 83.72 15.35 0.65 3005 +3007 4 -8.21 83.31 16.42 0.65 3006 +3008 4 -7.9 82.7 16.39 0.65 3007 +3009 4 -7.85 82.04 16.93 0.65 3008 +3010 4 -7.79 81.68 17.42 0.65 3009 +3011 4 -7.91 80.57 17.78 0.435 3010 +3012 4 -7.99 80.05 18.49 0.435 3011 +3013 4 -7.97 79.73 18.53 0.435 3012 +3014 4 -8.26 79.11 18.65 0.435 3013 +3015 4 -8.4 78.63 18.84 0.435 3014 +3016 4 -8.68 78.0 18.96 0.435 3015 diff --git a/demos/Fig2_elecModels/cells/ca1_minimal.p b/demos/Fig2_elecModels/cells/ca1_minimal.p new file mode 100644 index 0000000..4395d62 --- /dev/null +++ b/demos/Fig2_elecModels/cells/ca1_minimal.p @@ -0,0 +1,58 @@ +// genesis +// cell parameter file for the 1991 Traub CA1 hippocampal cell +// "phi" parameter reduced by e-3 +*cartesian +*relative + +*set_global RM 1.0 //ohm*m^2 +*set_global RA 1.0 //ohm*m +*set_global CM 0.03 //F/m^2 +*set_global EREST_ACT -0.06 // volts + +// The format for each compartment parameter line is : +// name parent x y z d ch dens ... +// For channels, "dens" = maximum conductance per unit area of compartment + + +dend_3 none 0 220 0 3.84 +dend_5 . 0 220 0 3.84 +dend_6 . 0 220 0 3.84 +dend_8 . 0 110 0 3.84 + +soma dend_8 0 125 0 8.46 + + +apical_10 soma 0 120 0 4.0 +apical_11 apical_10 0 120 0 3 +apical_12 apical_11 0 120 0 3 +apical_13 apical_12 0 120 0 2.6 +apical_14 apical_13 0 120 0 2.6 +apical_15 apical_14 0 120 0 2.6 +apical_16 apical_15 0 120 0 2.6 +apical_17 apical_16 0 120 0 2.6 +apical_18 apical_17 0 120 0 2.6 +apical_19 apical_18 0 120 0 2.6 + +apical_11_1 apical_10 -60 60 0 2 +apical_11_2 apical_11_1 -60 60 0 1.8 +apical_11_3 apical_11_2 0 80 0 1.5 +apical_11_4 apical_11_3 0 80 0 1.5 + +apical_13_1 apical_12 40 40 0 1.0 +apical_13_2 apical_13_1 40 40 0 1.0 + +apical_14_1 apical_13_2 0 10 0 1.0 +apical_14_2 . 0 10 0 1.0 +apical_14_3 . 0 10 0 1.0 +apical_14_4 . 0 10 0 1.0 +apical_14_5 . 0 10 0 1.0 +apical_14_6 . 0 10 0 1.0 +apical_14_7 . 0 10 0 1.0 +apical_14_8 . 0 10 0 1.0 +apical_14_9 . 0 10 0 1.0 +apical_14_10 . 0 10 0 1.0 +apical_14_11 . 0 10 0 1.0 +apical_14_12 . 0 10 0 1.0 +apical_14_13 . 0 10 0 1.0 +apical_15_1 . 0 30 0 1.0 +apical_15_2 . 0 60 0 1.0 diff --git a/demos/Fig2_elecModels/cells/h10.CNG.swc b/demos/Fig2_elecModels/cells/h10.CNG.swc new file mode 100644 index 0000000..554dbe2 --- /dev/null +++ b/demos/Fig2_elecModels/cells/h10.CNG.swc @@ -0,0 +1,226 @@ +# Original file h10.swc edited by Duncan Donohue using StdSwc version 1.21 on 9/6/05. +# Irregularities and fixes documented in h10.swc.std. See StdSwc1.21.doc for more information. +# +#---------------------------------------------------------------------- +# This file was obtained using ban2swc.pl on file h10.txt +# (Jose Ambros-Ingerson, jose@kiubo.net): Sun Oct 19 18:38:56 2003 +#---------------------------------------------------------------------- +# ORIGINAL_SOURCE +# CREATURE +# REGION +# FIELD/LAYER +# TYPE +# CONTRIBUTOR +# REFERENCE +# RAW +# EXTRAS +# SOMA_AREA +# SHRINKAGE_CORRECTION +# VERSION_NUMBER +# VERSION_DATE +# ********************************************* +# SCALE 1.0 1.0 1.0 + 1 1 0. 23. 0. 3.35 -1 + 2 1 0. 18. 0. 2.5 1 + 3 1 0. 0. 0. 1.058 2 + 4 3 -4.157 -2.778 0. 0.6 3 + 5 3 -5.925 -3.510 -4.62 0.55 4 + 6 3 -15.47 -7.464 -29.560 0.4 5 + 7 3 -23.89 -9.139 -72.72 0.4 6 + 8 3 -24.39 -13.43 -83.51 0.350 6 + 9 3 -9.814 -5.121 -14.780 0.5 5 + 10 3 -15.81 -6.313 -23.93 0.5 9 + 11 3 -65.94 -16.29 -100.4 0.4 10 + 12 3 -54.5 -14.01 -82.960 0.4 10 + 13 3 -17.2 -10.06 -28.09 0.4 9 + 14 3 -78.64 -51.11 -138.70 0.4 13 + 15 3 -41.69 -26.42 -72.15 0.350 13 + 16 3 -10.11 -8.731 -20.330 0.45 4 + 17 3 -14.44 -13.06 -35.11 0.350 16 + 18 3 -26.61 -21.19 -108.7 0.3 17 + 19 3 -24.2 -27.66 -123.4 0.3 17 + 20 3 -32.3 -30.92 -96.08 0.350 16 + 21 3 -45.7 -39.87 -120.2 0.3 20 + 22 3 -56.99 -67.88 -162.60 0.350 20 + 23 3 -8.889 -13.3 0. 0.65 3 + 24 3 -11.39 -15.8 -3.54 0.55 23 + 25 3 -19.39 -23.8 -14.85 0.5 24 + 26 3 -21.7 -25.35 -19.01 0.45 25 + 27 3 -33.25 -33.06 -39.79 0.4 26 + 28 3 -64.36 -45.95 -121.10 0.350 27 + 29 3 -53.54 -53.36 -109.10 0.350 27 + 30 3 -26.32 -28.43 -27.32 0.4 26 + 31 3 -68.78 -46.02 -73.28 0.3 30 + 32 3 -71.820 -73.93 -91.67 0.350 30 + 33 3 -59.82 -84.320 -123.80 0.350 25 + 34 3 -84.52 -121.30 -190.3 0.25 33 + 35 3 -34.39 -38.80 -36.06 0.350 24 + 36 3 -96.61 -80.38 -86.06 0.3 35 + 37 3 -93.98 -128. -107.7 0.3 35 + 38 3 -15.65 -29.64 -17.68 0.5 23 + 39 3 -17.01 -32.9 -21.21 0.5 38 + 40 3 -21.95 -40.29 -34.52 0.4 39 + 41 3 -50.03 -82.33 -110.2 0.3 40 + 42 3 -49.730 -81.87 -109.30 0.350 40 + 43 3 -22.75 -61.78 -65.28 0.3 39 + 44 3 -37.30 -81.9 -74.25 0.3 38 + 45 3 -2.146 -10.790 0. 0.75 3 + 46 3 -24.77 -65.42 -24.490 0.350 45 + 47 3 -54.47 -137.1 -56.64 0.350 46 + 48 3 -55.18 -138.8 -57.4 0.350 46 + 49 3 -2.146 -20.95 -4.21 0.6 45 + 50 3 -2.146 -35.730 -10.33 0.45 49 + 51 3 -22.75 -139.3 -80.89 0.3 50 + 52 3 29. -192.3 -117. 0.350 50 + 53 3 -2.146 -25.57 -6.12 0.55 49 + 54 3 -3.103 -30.38 -7.10 0.5 53 + 55 3 -49.410 -263.2 -54.31 0.350 54 + 56 3 -22.05 -125.60 -26.41 0.3 54 + 57 3 16.990 -121.80 -25.63 0.3 53 + 58 3 2.146 -10.790 0. 0.65 3 + 59 3 2.146 -20.79 0. 0.4 58 + 60 3 2.146 -235.8 0. 0.350 59 + 61 3 2.146 -250.8 0. 0.25 60 + 62 3 4.059 -15.41 0. 0.4 58 + 63 3 8.269 -25.57 0. 0.350 62 + 64 3 35.63 -163.10 -27.90 0.4 63 + 65 3 45.32 -81.02 -13.27 0.3 63 + 66 3 20.13 -54.21 0. 0.350 62 + 67 3 35.25 -130.20 15.41 0.3 66 + 68 3 78.98 -142.3 21.07 0.350 66 + 69 3 8.889 -13.3 0. 0.6 3 + 70 3 16.67 -32.08 8.42 0.5 69 + 71 3 24.45 -50.86 16.84 0.45 70 + 72 3 49.32 -175.9 42.2 0.350 71 + 73 3 84.38 -140.6 38.30 0.350 71 + 74 3 42.45 -141.4 78.51 0.4 70 + 75 3 48.94 -174. 100.7 0.3 74 + 76 3 16.080 -20.490 4.21 0.4 69 + 77 3 99.04 -103.5 52.81 0.3 76 + 78 3 41.550 -45.97 19.13 0.3 76 + 79 3 63.71 -109.60 64.06 0.3 78 + 80 3 75.26 -126.9 77.95 0.2 79 + 81 3 18.29 -12.22 0. 0.6 3 + 82 3 20.79 -14.72 3.54 0.55 81 + 83 3 26.29 -20.22 11.31 0.5 82 + 84 3 101.10 -132.20 101.30 0.350 83 + 85 3 97.5 -67.8 68.54 0.3 83 + 86 3 47.29 -41.22 41.01 0.25 82 + 87 3 21.56 -13.58 3.54 0.5 81 + 88 3 28.09 -16.28 10.61 0.45 87 + 89 3 122.10 -79.11 86.16 0.3 88 + 90 3 85.99 -27.8 50.050 0.3 88 + 91 3 43.12 -22.51 26.87 0.4 87 + 92 3 75.45 -44.11 85.070 0.350 91 + 93 3 97.61 -33.34 110. 0.350 91 + 94 4 0. 41. 0. 2.550 1 + 95 4 0. 127. 0. 0.3 94 + 96 4 5.932 70.820 -6.05 2.25 94 + 97 4 18.37 133.3 -18.73 1.25 96 + 98 4 26.63 153.3 -23.02 0.6 97 + 99 4 56.65 225.8 -38.63 0.3 98 + 100 4 29.63 160.5 -24.580 0.6 98 + 101 4 91.850 253.70 -24.580 0.350 100 + 102 4 63.97 333.1 -24.580 0.350 100 + 103 4 18.37 142.20 -20.48 1.25 97 + 104 4 18.37 145.1 -21.07 1.25 103 + 105 4 28.28 195. -42.12 0.45 104 + 106 4 33.69 222.10 -53.6 0.350 105 + 107 4 39.1 249.3 -65.08 0.25 106 + 108 4 17.47 149.6 -22.98 1.25 104 + 109 4 4.851 213.10 -49.77 0.5 108 + 110 4 -10.07 288.1 -100.9 0.350 109 + 111 4 15.85 157.8 -26.43 1.25 108 + 112 4 15.85 182.3 -31.3 0.5 111 + 113 4 15.85 235.3 -41.84 0.350 112 + 114 4 15.85 272.2 -57.15 0.3 113 + 115 4 15.85 195.10 -33.84 0.350 112 + 116 4 30.09 266.7 -33.84 0.3 115 + 117 4 0.2380 273.5 -33.84 0.3 115 + 118 4 11.72 167.8 -28.57 1.25 111 + 119 4 3.46 187.70 -32.87 1.25 118 + 120 4 -0.506 207.60 -41.28 1.25 119 + 121 4 -3.39 222.10 -47.410 1.25 120 + 122 4 -3.39 223.8 -48.52 1.25 121 + 123 4 -3.39 247.10 -64.070 0.45 122 + 124 4 1.439 271.40 -88.820 0.3 123 + 125 4 -16.080 310.90 -129.1 0.350 123 + 126 4 -3.39 248.70 -65.19 1.25 122 + 127 4 -3.209 249.70 -65.570 1.25 126 + 128 4 1.297 272.3 -75.14 0.5 127 + 129 4 12. 326.1 -111.80 0.350 128 + 130 4 -0.506 263.2 -71.31 1.25 127 + 131 4 0.2450 265.1 -71.7 0.6 130 + 132 4 3.623 273.2 -73.45 0.55 131 + 133 4 46.230 337. -105.2 0.3 132 + 134 4 22.55 368.40 -113.60 0.350 132 + 135 4 19.01 310.40 -81.45 0.45 131 + 136 4 42.74 367.6 -81.45 0.350 135 + 137 4 -0.506 280.90 -74.820 1.25 130 + 138 4 -0.506 284.8 -75.60 0.850 137 + 139 4 14.450 360. -107.4 0.4 138 + 140 4 18.06 378.1 -115. 0.3 139 + 141 4 -14.02 352.8 -104.30 0.850 138 + 142 4 -20.330 384.5 -117.7 0.70 141 + 143 4 -20.330 441.8 -141.4 0.70 142 + 144 4 -20.330 494.40 -163.20 0.45 143 + 145 4 -20.330 544.30 -196.60 0.350 144 + 146 4 -20.330 582.6 -222.10 0.3 145 + 147 4 -20.330 622.5 -248.8 0.3 145 + 148 4 -20.330 462.1 -149.8 0.6 143 + 149 4 -7.321 527.5 -163.10 0.45 148 + 150 4 -1.389 557.30 -169.20 0.350 149 + 151 4 21.51 612.6 -181.10 0.3 150 + 152 4 -1.389 630.90 -183.8 0.25 150 + 153 4 -36.6 543.9 -166.4 0.6 148 + 154 4 -46.36 592.9 -176.4 0.350 153 + 155 4 -46.36 669.6 -208.10 0.25 154 + 156 4 -74.99 662.1 -207.4 0.25 154 + 157 4 -44.44 583.30 -174.4 0.5 153 + 158 4 -44.44 665.30 -174.4 0.350 157 + 159 4 -44.44 705.30 -174.4 0.25 158 + 160 4 -87.3 686.80 -174.4 0.350 157 + 161 4 -121.7 769.90 -174.4 0.25 160 + 162 4 -32.71 414.40 -131.1 0.45 142 + 163 4 -85.74 542.4 -188.5 0.350 162 + 164 4 -120. 625.2 -225.60 0.3 163 + 165 4 -137.4 667. -244.4 0.25 164 + 166 4 -132.4 655.1 -239. 0.2 164 + 167 4 -0.506 290.7 -76.77 0.9 137 + 168 4 6.713 327. -76.77 0.8 167 + 169 4 8.664 336.8 -76.77 0.6 168 + 170 4 12.49 356. -80.67 0.5 169 + 171 4 21.48 401.3 -89.84 0.350 170 + 172 4 13.74 362.3 -76.77 0.5 168 + 173 4 23.12 385. -71.89 0.25 172 + 174 4 13.74 396.6 -69.94 0.350 172 + 175 4 -20.6 391.70 -76.77 0.350 167 + 176 4 -15.83 311.3 -91.59 0.4 126 + 177 4 -28.44 374.70 -118.4 0.3 176 + 178 4 -14.84 249.8 -67.41 0.45 121 + 179 4 -37.12 303.6 -106.30 0.350 178 + 180 4 -55.25 347.3 -138. 0.3 178 + 181 4 -3.209 221.20 -47.02 0.45 120 + 182 4 -3.209 356.6 -73.95 0.350 181 + 183 4 -31.36 289.2 -61.660 0.350 181 + 184 4 -11.94 210.70 -44.35 0.6 119 + 185 4 -36.06 246.9 -62.33 0.5 184 + 186 4 -67.18 322. -96.01 0.3 185 + 187 4 -81.14 291.90 -88.74 0.3 185 + 188 4 1.208 193.10 -34.04 0.4 118 + 189 4 -21.42 306.90 -34.04 0.3 188 + 190 4 -77.13 310.40 -34.04 0.350 188 + 191 4 18.37 165.70 -25.17 0.5 103 + 192 4 25.78 203. -25.17 0.350 191 + 193 4 56.22 356. -25.17 0.3 192 + 194 4 50.36 326.6 -25.17 0.3 192 + 195 4 16.22 176.5 -25.17 0.350 191 + 196 4 -10.31 309.90 -25.17 0.350 195 + 197 4 2.957 243.20 -25.17 0.3 195 + 198 4 -2.105 51.58 -2.15 0.350 94 + 199 4 -20.09 142. -20.48 0.350 198 + 200 4 -3.061 56.39 -3.12 0.3 198 + 201 4 -3.061 76.39 -3.12 0.3 200 + 202 4 -3.061 142.4 -3.12 0.3 201 + 203 4 -3.061 167.4 -3.12 0.3 201 + 204 4 -32.910 128.5 -3.12 0.3 200 diff --git a/demos/Fig2_elecModels/cells/ko20x-07.CNG.swc b/demos/Fig2_elecModels/cells/ko20x-07.CNG.swc new file mode 100644 index 0000000..066eaf4 --- /dev/null +++ b/demos/Fig2_elecModels/cells/ko20x-07.CNG.swc @@ -0,0 +1,165 @@ +# Original file ko20x-07.swc edited using StdSwc version 1.31 on 7/9/13. +# Irregularities and fixes documented in ko20x-07.swc.std. 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ModelViewParmSubset_5 + + + + ModelViewParmSubset_5 + + + + + + soma_group + + + + soma_group + + + + + + ModelViewParmSubset_7 + + + + ModelViewParmSubset_7 + + + + + + axon_group + soma_group + + + + + + all + + + + + + ModelViewParmSubset_2 + + + + ModelViewParmSubset_2 + + + + + + OneSecGrp_SectionRef_5 + + + + + + all + + + all + + + + + + + + dendrite_group + + + + + + + + + + dendrite_group + + + + + + + + + + dendrite_group + + + + + + + + all + + + + + + ModelViewParmSubset_2 + + + + OneSecGrp_SectionRef_5 + + + + + + all + + + + + + all + + + + + + + all + + + + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/CA1.morph.xml.REMOVED.git-id b/demos/Fig2_elecModels/chans/CA1.morph.xml.REMOVED.git-id new file mode 100644 index 0000000..be0ea2f --- /dev/null +++ b/demos/Fig2_elecModels/chans/CA1.morph.xml.REMOVED.git-id @@ -0,0 +1 @@ +2a3815b394f8bcb4b6450081d9ba45d20abdf3cf \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/Ca.xml b/demos/Fig2_elecModels/chans/Ca.xml new file mode 100644 index 0000000..645161c --- /dev/null +++ b/demos/Fig2_elecModels/chans/Ca.xml @@ -0,0 +1,62 @@ + + + + + A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a + Detailed Network Model of the Cerebellar Granule Cell Layer + + + + + + + Voltage-gated Ca2+ channel, based on Traub + + + + Traub, R. + + + Upi Bhalla + NCBS + bhalla - at - ncbs.res.in + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/demos/Fig2_elecModels/chans/CaConc.xml b/demos/Fig2_elecModels/chans/CaConc.xml new file mode 100644 index 0000000..fe10a98 --- /dev/null +++ b/demos/Fig2_elecModels/chans/CaConc.xml @@ -0,0 +1,36 @@ + + + + Ca pool + + + Signifies that the ion is involved in a process which alters its concentration + + + + + + + Upi Bhalla + + + + An expontially decaying pool of calcium + + + + Upi Bhalla + National Centre for Biological Sciences, Bangalore, India. + bhalla - at - ncbs.res.in + + + + + + + + + + + + diff --git a/demos/Fig2_elecModels/chans/DoubExpSyn.xml b/demos/Fig2_elecModels/chans/DoubExpSyn.xml new file mode 100644 index 0000000..58cc74e --- /dev/null +++ b/demos/Fig2_elecModels/chans/DoubExpSyn.xml @@ -0,0 +1,32 @@ + + + + ChannelML file describing a single synaptic mechanism + + + + + + + Simple example of a synaptic mechanism, which consists of a postsynaptic conductance which changes as + double exponential function of time. Mappings exist for NEURON and GENESIS. + + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Receptor properties + http://senselab.med.yale.edu/senselab/NeuronDB/receptors2.asp + + + + + + + + diff --git a/demos/Fig2_elecModels/chans/Generated.net.xml b/demos/Fig2_elecModels/chans/Generated.net.xml new file mode 100644 index 0000000..d2f3f34 --- /dev/null +++ b/demos/Fig2_elecModels/chans/Generated.net.xml @@ -0,0 +1,59 @@ + + + + + +Network structure (NeuroML 1.x) for project: CA1PyramidalCell saved with neuroConstruct v1.7.1 on: 11:29:49, 18-Jul-14 + +Cell Group: CA1_CG contains 1 cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/Glu.xml b/demos/Fig2_elecModels/chans/Glu.xml new file mode 100644 index 0000000..c1a7d7c --- /dev/null +++ b/demos/Fig2_elecModels/chans/Glu.xml @@ -0,0 +1,16 @@ + + + + + Glutamate receptor synchan, 2 ms tau. + + + + Simple double exponential waveform glu synapse + + + diff --git a/demos/Fig2_elecModels/chans/HChannel.xml b/demos/Fig2_elecModels/chans/HChannel.xml new file mode 100644 index 0000000..c1c91b4 --- /dev/null +++ b/demos/Fig2_elecModels/chans/HChannel.xml @@ -0,0 +1,73 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and l traces on single comp with current pulse + + Padraig Gleeson + + + + H current. Comment from original mod: I-h channel from Magee 1998 for distal dendrites + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + diff --git a/demos/Fig2_elecModels/chans/KChannel_HH.xml b/demos/Fig2_elecModels/chans/KChannel_HH.xml new file mode 100644 index 0000000..dfd1d3c --- /dev/null +++ b/demos/Fig2_elecModels/chans/KChannel_HH.xml @@ -0,0 +1,49 @@ + + + + ChannelML file containing a single Channel description + + + + + Equations adapted from HH paper for modern convention of external potential being zero + + Padraig Gleeson + + + + Simple example of K conductance in squid giant axon. Based on channel from Hodgkin and Huxley 1952 + + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + A. L. Hodgkin and A. F. Huxley, A quantitative description of membrane current and its application + to conduction and excitation in nerve, J. Physiol., vol. 117, pp. 500-544, 1952. + http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12991237 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/LeakConductance.xml b/demos/Fig2_elecModels/chans/LeakConductance.xml new file mode 100644 index 0000000..c40270d --- /dev/null +++ b/demos/Fig2_elecModels/chans/LeakConductance.xml @@ -0,0 +1,17 @@ + + + + ChannelML file containing a single Channel description + + + + + + Simple example of a leak/passive conductance. Note: for GENESIS cells with a single leak conductance, + it is better to use the Rm and Em variables for a passive current. + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/NMDA.xml b/demos/Fig2_elecModels/chans/NMDA.xml new file mode 100644 index 0000000..ce7e3dd --- /dev/null +++ b/demos/Fig2_elecModels/chans/NMDA.xml @@ -0,0 +1,16 @@ + + + + + NMDA receptor synchan, 20 ms tau. + + + + Simple double exponential waveform NMDA synapse + + + diff --git a/demos/Fig2_elecModels/chans/NaChannel_HH.xml b/demos/Fig2_elecModels/chans/NaChannel_HH.xml new file mode 100644 index 0000000..5e52c69 --- /dev/null +++ b/demos/Fig2_elecModels/chans/NaChannel_HH.xml @@ -0,0 +1,58 @@ + + + + ChannelML file containing a single Channel description + + + + + Equations adapted from HH paper for modern convention of external potential being zero + + Padraig Gleeson + + + + Simple example of Na conductance in squid giant axon. Based on channel from Hodgkin and Huxley 1952 + + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + A. L. Hodgkin and A. F. Huxley, A quantitative description of membrane current and + its application to conduction and excitation in nerve, J. Physiol., vol. 117, pp. 500-544, 1952. + http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12991237 + + + + Na channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2 + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/hd.xml b/demos/Fig2_elecModels/chans/hd.xml new file mode 100644 index 0000000..a882baa --- /dev/null +++ b/demos/Fig2_elecModels/chans/hd.xml @@ -0,0 +1,73 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and l traces on single comp with current pulse + + Padraig Gleeson + + + + H current. Comment from original mod: I-h channel from Magee 1998 for distal dendrites + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/kad.xml b/demos/Fig2_elecModels/chans/kad.xml new file mode 100644 index 0000000..bb7c5af --- /dev/null +++ b/demos/Fig2_elecModels/chans/kad.xml @@ -0,0 +1,84 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + A type K channel for distal dendrites. Comment from original mod: K-A channel from Klee Ficker and Heinemann, modified to account for Dax A Current, M.Migliore Jun 1997 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/kap.xml b/demos/Fig2_elecModels/chans/kap.xml new file mode 100644 index 0000000..58fdea0 --- /dev/null +++ b/demos/Fig2_elecModels/chans/kap.xml @@ -0,0 +1,86 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + A type K channel. Comment from original mod: K-A channel from Klee Ficker and Heinemann, + modified to account for Dax A Current --- M.Migliore Jun 1997, + modified to be used with cvode M.Migliore 2001 + + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/kdr.xml b/demos/Fig2_elecModels/chans/kdr.xml new file mode 100644 index 0000000..180c563 --- /dev/null +++ b/demos/Fig2_elecModels/chans/kdr.xml @@ -0,0 +1,75 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + Delayed rectifier K channel. Comment from original mod: K-DR channel, from Klee Ficker and Heinemann, + modified to account for Dax et al., M.Migliore 1997 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/na3.xml b/demos/Fig2_elecModels/chans/na3.xml new file mode 100644 index 0000000..94e9713 --- /dev/null +++ b/demos/Fig2_elecModels/chans/na3.xml @@ -0,0 +1,107 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + Note: the inactivation gate s is not included here as it was disabled in original mod file for Migliore et al. Changing the parameter below ar from 1 will not enable s! + + Padraig Gleeson + + + + Na channel. Comment from original mod: Na current, modified from Jeff Magee. M.Migliore may97, + added sh to account for higher threshold M.Migliore, Apr.2002 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + Na channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig2_elecModels/chans/nax.xml b/demos/Fig2_elecModels/chans/nax.xml new file mode 100644 index 0000000..1225d6a --- /dev/null +++ b/demos/Fig2_elecModels/chans/nax.xml @@ -0,0 +1,88 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + Na channel for axon. Comment from original mod: Na current for axon. No slow inact. M.Migliore Jul. 1997, + added sh to account for higher threshold M.Migliore, Apr.2002 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + Na channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + + + diff --git a/demos/Fig2_elecModels/chans/pas.xml b/demos/Fig2_elecModels/chans/pas.xml new file mode 100644 index 0000000..9abffeb --- /dev/null +++ b/demos/Fig2_elecModels/chans/pas.xml @@ -0,0 +1,17 @@ + + + + ChannelML file containing a single Channel description + + + + + + Simple example of a leak/passive conductance. Note: for GENESIS cells with a single leak conductance, + it is better to use the Rm and Em variables for a passive current. + + + + + + \ No newline at end of file diff --git a/demos/Fig3_chemModels/Fig3ABC.g b/demos/Fig3_chemModels/Fig3ABC.g new file mode 100644 index 0000000..d784b24 --- /dev/null +++ b/demos/Fig3_chemModels/Fig3ABC.g @@ -0,0 +1,832 @@ +//genesis +// kkit Version 11 flat dumpfile + +// Saved on Sun May 18 16:56:17 2014 + +include kkit {argv 1} + +FASTDT = 5e-05 +SIMDT = 0.01 +CONTROLDT = 10 +PLOTDT = 10 +MAXTIME = 10000 +TRANSIENT_TIME = 2 +VARIABLE_DT_FLAG = 1 +DEFAULT_VOL = 3e-18 +VERSION = 11.0 +setfield /file/modpath value /home2/bhalla/scripts/modules +kparms + +//genesis + +initdump -version 3 -ignoreorphans 1 +simobjdump doqcsinfo filename accessname accesstype transcriber developer \ + citation species tissue cellcompartment methodology sources \ + model_implementation model_validation x y z +simobjdump table input output alloced step_mode stepsize x y z +simobjdump xtree path script namemode sizescale +simobjdump xcoredraw xmin xmax ymin ymax +simobjdump xtext editable +simobjdump xgraph xmin xmax ymin ymax overlay +simobjdump xplot pixflags script fg ysquish do_slope wy +simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ + link savename file version md5sum mod_save_flag x y z +simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \ + z +simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \ + geomname xtree_fg_req xtree_textfg_req x y z +simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z +simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ + keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z +simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ + trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z +simobjdump xtab input output alloced step_mode stepsize notes editfunc \ + xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z +simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ + xtree_textfg_req x y z +simobjdump transport input output alloced step_mode stepsize dt delay clock \ + kf xtree_fg_req xtree_textfg_req x y z +simobjdump proto x y z +simobjdump text str +simundump geometry /kinetics/geometry 0 3e-18 3 sphere "" white black 0 0 0 +simundump text /kinetics/notes 0 "" +call /kinetics/notes LOAD \ +"" +simundump group /kinetics/lac_gene 0 yellow black x 0 0 "" lac_gene \ + /home2/bhalla/scripts/modules/lac_gene_0.g 0 0 0 27 0 0 +simundump text /kinetics/lac_gene/notes 0 \ + "This is a group of reactions resulting in the production\nof Lac" +call /kinetics/lac_gene/notes LOAD \ +"This is a group of reactions resulting in the production" \ +"of Lac" +simundump kpool /kinetics/lac_gene/l_op_2nd_bound[1] 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 52 yellow 26 -12 0 +simundump text /kinetics/lac_gene/l_op_2nd_bound[1]/notes 0 \ + "it represents the promotor with both of its sites\n bound by the inhibitor" +call /kinetics/lac_gene/l_op_2nd_bound[1]/notes LOAD \ +"it represents the promotor with both of its sites" \ +" bound by the inhibitor" +simundump kenz /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 0 0 0 \ + 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 26 -11 0 +simundump text /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1/notes 0 \ + "Rates from\nBox 1 Elowitz et al Nature (2000)\n403: 335-338" +call /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al Nature (2000)" \ +"403: 335-338" +simundump kreac /kinetics/lac_gene/inhib_reac[1] 0 0.0055556 0.09 "" white \ + yellow 30 -13 0 +simundump text /kinetics/lac_gene/inhib_reac[1]/notes 0 \ + "It signifies the first binding of the repressor\n with the operator\n\nKf=1 /nM/sec\nKb=9 /sec\n\nBox 1 Elowitz et al Nature 2000 vol 403:335-338" +call /kinetics/lac_gene/inhib_reac[1]/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=9 /sec" \ +"" \ +"Box 1 Elowitz et al Nature 2000 vol 403:335-338" +simundump kpool /kinetics/lac_gene/l_op_1rst_bound 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 2 yellow 33 -12 0 +simundump text /kinetics/lac_gene/l_op_1rst_bound/notes 0 \ + "it represents the promotor with one of its sites\n bound by the inhibitor" +call /kinetics/lac_gene/l_op_1rst_bound/notes LOAD \ +"it represents the promotor with one of its sites" \ +" bound by the inhibitor" +simundump kenz /kinetics/lac_gene/l_op_1rst_bound/lac_transcription 0 0 0 0 0 \ + 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 33 -10 0 +simundump text /kinetics/lac_gene/l_op_1rst_bound/lac_transcription/notes 0 \ + "Rates from\nBox 1 Elowitz et al Nature 2000\n403: 335-338" +call /kinetics/lac_gene/l_op_1rst_bound/lac_transcription/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al Nature 2000" \ +"403: 335-338" +simundump kreac /kinetics/lac_gene/inhib_reac 0 0.0055556 2.24 "" white \ + yellow 36 -13 0 +simundump text /kinetics/lac_gene/inhib_reac/notes 0 \ + "It signifies the first binding of the repressor\n with the operator\n\nKf = 1 /nM/sec\nKb = 224 /sec\n\nBox 1 Elowitz et al Nature 2000 vol 403:335-338" +call /kinetics/lac_gene/inhib_reac/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf = 1 /nM/sec" \ +"Kb = 224 /sec" \ +"" \ +"Box 1 Elowitz et al Nature 2000 vol 403:335-338" +simundump kpool /kinetics/lac_gene/lac_operator 0 0 0.022222 0.022222 40 40 0 \ + 0 1800 0 /kinetics/geometry 36 yellow 40 -12 0 +simundump text /kinetics/lac_gene/lac_operator/notes 0 \ + "The lac operator under normal conditions\n drives transcription of lac\n\nElowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/lac_gene/lac_operator/notes LOAD \ +"The lac operator under normal conditions" \ +" drives transcription of lac" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +simundump kenz /kinetics/lac_gene/lac_operator/lac_transcription2 0 0 0 0 0 \ + 1800 2.4998 2 0.5 0 1 "" red 36 "" 40 -11 0 +simundump text /kinetics/lac_gene/lac_operator/lac_transcription2/notes 0 \ + "Rates from\nBox 1 Elowitz et al (2000)\n403:335-338" +call /kinetics/lac_gene/lac_operator/lac_transcription2/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"403:335-338" +simundump kpool /kinetics/lac_gene/lac_mRNA 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 12 yellow 26 -8 0 +simundump text /kinetics/lac_gene/lac_mRNA/notes 0 \ + "The m-RNA transcribed by the lac operator\n\nElowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/lac_gene/lac_mRNA/notes LOAD \ +"The m-RNA transcribed by the lac operator" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +simundump kenz /kinetics/lac_gene/lac_mRNA/lac_translation 0 0 0 0 0 1800 \ + 0.83494 0.668 0.167 0 1 "" red 12 "" 20 -10 0 +simundump text /kinetics/lac_gene/lac_mRNA/lac_translation/notes 0 \ + "Rates from \nBox 1 Elowitz et al Nature (2000)\n403: 335-338" +call /kinetics/lac_gene/lac_mRNA/lac_translation/notes LOAD \ +"Rates from " \ +"Box 1 Elowitz et al Nature (2000)" \ +"403: 335-338" +simundump kpool /kinetics/lac_gene/lac 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 62 yellow 20 -15 0 +simundump text /kinetics/lac_gene/lac/notes 0 \ + "Lac translated from lac m-RNA\nDerived from Figure 1(c) stochastic version\n\nElowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/lac_gene/lac/notes LOAD \ +"Lac translated from lac m-RNA" \ +"Derived from Figure 1(c) stochastic version" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +simundump kpool /kinetics/lac_gene/degraded_lac 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 2 yellow 20 -19 0 +simundump text /kinetics/lac_gene/degraded_lac/notes 0 \ + "Degradation product of lac protein" +call /kinetics/lac_gene/degraded_lac/notes LOAD \ +"Degradation product of lac protein" +simundump kpool /kinetics/lac_gene/degraded_lac_mRNA 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 1 yellow 33 -8 0 +simundump text /kinetics/lac_gene/degraded_lac_mRNA/notes 0 \ + "Degradation product of lac m-RNA" +call /kinetics/lac_gene/degraded_lac_mRNA/notes LOAD \ +"Degradation product of lac m-RNA" +simundump kreac /kinetics/lac_gene/lac_mRNA_degradation 0 0.005775 0 "" white \ + yellow 29 -7 0 +simundump text /kinetics/lac_gene/lac_mRNA_degradation/notes 0 \ + "This reaction denotes the degradation of the Lac m-RNA,\n the half life of which is two minutes.\nt1/2=.693/k where k denotes kf" +call /kinetics/lac_gene/lac_mRNA_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac m-RNA," \ +" the half life of which is two minutes." \ +"t1/2=.693/k where k denotes kf" +simundump kreac /kinetics/lac_gene/lac_degradation 0 0.016666 0 "" white \ + yellow 20 -17 0 +simundump text /kinetics/lac_gene/lac_degradation/notes 0 \ + "This reaction denotes the degradation of the Lac\n the half life of which is ten minutes.\nt1/2=.693/k where k denotes kf\n\nNote: Rates had to scaled by approx 1.4 to get desired levels\n\nElowitz et al Nature 2000. Vol403 335-338" +call /kinetics/lac_gene/lac_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac" \ +" the half life of which is ten minutes." \ +"t1/2=.693/k where k denotes kf" \ +"" \ +"Note: Rates had to scaled by approx 1.4 to get desired levels" \ +"" \ +"Elowitz et al Nature 2000. Vol403 335-338" +simundump kpool /kinetics/lac_gene/AminoAcids 0 0 0.00055555 0.00055555 \ + 0.99999 0.99999 0 0 1800 4 /kinetics/geometry 52 yellow 20 -8 0 +simundump text /kinetics/lac_gene/AminoAcids/notes 0 "" +call /kinetics/lac_gene/AminoAcids/notes LOAD \ +"" +simundump kpool /kinetics/lac_gene/Nucleotides 0 0 0.00055555 0.00055555 \ + 0.99999 0.99999 0 0 1800 4 /kinetics/geometry 6 yellow 40 -8 0 +simundump text /kinetics/lac_gene/Nucleotides/notes 0 "" +call /kinetics/lac_gene/Nucleotides/notes LOAD \ +"" +simundump group /kinetics/TetR_gene 0 61 black x 0 0 "" TetR_gene \ + /home2/bhalla/scripts/modules/TetR_gene_0.g 0 0 0 -2 0 0 +simundump text /kinetics/TetR_gene/notes 0 \ + "This is a group of reactions resulting in the production\nof Tet R" +call /kinetics/TetR_gene/notes LOAD \ +"This is a group of reactions resulting in the production" \ +"of Tet R" +simundump kpool /kinetics/TetR_gene/l_op_2nd_bound[1] 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 46 61 -3 -12 0 +simundump text /kinetics/TetR_gene/l_op_2nd_bound[1]/notes 0 \ + "it represents the promotor with both of its sites\n bound by the inhibitor" +call /kinetics/TetR_gene/l_op_2nd_bound[1]/notes LOAD \ +"it represents the promotor with both of its sites" \ +" bound by the inhibitor" +simundump kenz /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 0 0 \ + 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 46 "" -3 -11 0 +simundump text /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1/notes 0 \ + "Rates from \nBox 1 Elowitz et al (2000)\nNature 403:335-338" +call /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1/notes LOAD \ +"Rates from " \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +simundump kreac /kinetics/TetR_gene/inhib_reac[1] 0 0.0055556 0.09 "" white \ + 61 1 -13 0 +simundump text /kinetics/TetR_gene/inhib_reac[1]/notes 0 \ + "It signifies the first binding of the repressor\n with the operator\n\nKf = 1 /nM/sec\nKb = 9 /sec\n\nBox 1 Elowitz et al Nature 2000 vol 403:335-338" +call /kinetics/TetR_gene/inhib_reac[1]/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf = 1 /nM/sec" \ +"Kb = 9 /sec" \ +"" \ +"Box 1 Elowitz et al Nature 2000 vol 403:335-338" +simundump kpool /kinetics/TetR_gene/l_op_1rst_bound 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 2 61 4 -12 0 +simundump text /kinetics/TetR_gene/l_op_1rst_bound/notes 0 \ + "it represents the promotor with one of its sites\n bound by the inhibitor" +call /kinetics/TetR_gene/l_op_1rst_bound/notes LOAD \ +"it represents the promotor with one of its sites" \ +" bound by the inhibitor" +simundump kenz /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription 0 0 0 0 \ + 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 4 -10 0 +simundump text /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription/notes 0 \ + "Rates from \nBox 1 Elowitz et al (2000)\nNature 403:335-338" +call /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription/notes LOAD \ +"Rates from " \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +simundump kreac /kinetics/TetR_gene/inhib_reac 0 0.0055556 2.24 "" white 61 7 \ + -13 0 +simundump text /kinetics/TetR_gene/inhib_reac/notes 0 \ + "It signifies the first binding of the repressor\n with the operator\n\nKf=1 /nM/sec\nKb=224 /sec\n\nBox1 Elowitz etal Nature 2000 vol 403:335-338" +call /kinetics/TetR_gene/inhib_reac/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=224 /sec" \ +"" \ +"Box1 Elowitz etal Nature 2000 vol 403:335-338" +simundump kpool /kinetics/TetR_gene/TetR 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 11 61 -9 -15 0 +simundump text /kinetics/TetR_gene/TetR/notes 0 \ + "Lac translated from lac m-RNA\nDerived from Figure 1(c) stochastic version\n\nElowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/TetR_gene/TetR/notes LOAD \ +"Lac translated from lac m-RNA" \ +"Derived from Figure 1(c) stochastic version" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +simundump kpool /kinetics/TetR_gene/degraded_TetR 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 2 61 -9 -19 0 +simundump text /kinetics/TetR_gene/degraded_TetR/notes 0 \ + "Degradation product of lac protein" +call /kinetics/TetR_gene/degraded_TetR/notes LOAD \ +"Degradation product of lac protein" +simundump kreac /kinetics/TetR_gene/TetR_degradation 0 0.01666 0 "" white 61 \ + -9 -17 0 +simundump text /kinetics/TetR_gene/TetR_degradation/notes 0 \ + "This reaction denotes the degradation of the Lac\n the half life of which is ten minutes.\nt1/2=.693/k where k denotes kf\n\nNote: Rates had to be scaled by 1.4 to get appropriate levels\n\nElowitz etal Nature 2000. Vol403 335-338" +call /kinetics/TetR_gene/TetR_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac" \ +" the half life of which is ten minutes." \ +"t1/2=.693/k where k denotes kf" \ +"" \ +"Note: Rates had to be scaled by 1.4 to get appropriate levels" \ +"" \ +"Elowitz etal Nature 2000. Vol403 335-338" +simundump kpool /kinetics/TetR_gene/TetR_mRNA 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 12 61 -3 -8 0 +simundump text /kinetics/TetR_gene/TetR_mRNA/notes 0 \ + "The m-RNA transcribed by the lac operator\n\nElowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/TetR_gene/TetR_mRNA/notes LOAD \ +"The m-RNA transcribed by the lac operator" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +simundump kenz /kinetics/TetR_gene/TetR_mRNA/TetR_translation 0 0 0 0 0 1800 \ + 0.83494 0.668 0.167 0 1 "" red 12 "" -9 -10 0 +simundump text /kinetics/TetR_gene/TetR_mRNA/TetR_translation/notes 0 \ + "Rates from\nBox 1 Elowitz et al (2000)\nNature 403:335-338" +call /kinetics/TetR_gene/TetR_mRNA/TetR_translation/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +simundump kreac /kinetics/TetR_gene/TetR_mRNA_degradation 0 0.005775 0 "" \ + white 61 1 -7 0 +simundump text /kinetics/TetR_gene/TetR_mRNA_degradation/notes 0 \ + "This reaction denotes the degradation of the Lac m-RNA,\n the half life of which is two minutes.\nt1/2=.693/k where k denotes kf" +call /kinetics/TetR_gene/TetR_mRNA_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac m-RNA," \ +" the half life of which is two minutes." \ +"t1/2=.693/k where k denotes kf" +simundump kpool /kinetics/TetR_gene/degraded_TetR_mRNA 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 1 61 4 -8 0 +simundump text /kinetics/TetR_gene/degraded_TetR_mRNA/notes 0 \ + "Degradation product of lac m-RNA" +call /kinetics/TetR_gene/degraded_TetR_mRNA/notes LOAD \ +"Degradation product of lac m-RNA" +simundump kpool /kinetics/TetR_gene/TetR_operator 0 0 0.022222 0.022222 40 40 \ + 0 0 1800 0 /kinetics/geometry 36 61 11 -12 0 +simundump text /kinetics/TetR_gene/TetR_operator/notes 0 \ + "The lac operator under normal conditions\n drives transcription of lac\n\nElowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/TetR_gene/TetR_operator/notes LOAD \ +"The lac operator under normal conditions" \ +" drives transcription of lac" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +simundump kenz /kinetics/TetR_gene/TetR_operator/TetR_transcription2 0 0 0 0 \ + 0 1800 2.4998 2 0.5 0 1 "" red 36 "" 11 -11 0 +simundump text /kinetics/TetR_gene/TetR_operator/TetR_transcription2/notes 0 \ + "Rates from\nBox 1 Elowitz et al (2000)\nNature 403:335-338" +call /kinetics/TetR_gene/TetR_operator/TetR_transcription2/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +simundump kpool /kinetics/TetR_gene/Nucleotides 0 0 0.00055555 0.00055555 \ + 0.99999 0.99999 0 0 1800 4 /kinetics/geometry blue 61 11 -8 0 +simundump text /kinetics/TetR_gene/Nucleotides/notes 0 "" +call /kinetics/TetR_gene/Nucleotides/notes LOAD \ +"" +simundump kpool /kinetics/TetR_gene/AminoAcids 0 0 0.00055555 0.00055555 \ + 0.99999 0.99999 0 0 1800 4 /kinetics/geometry blue 61 -9 -8 0 +simundump text /kinetics/TetR_gene/AminoAcids/notes 0 "" +call /kinetics/TetR_gene/AminoAcids/notes LOAD \ +"" +simundump group /kinetics/Lcl 0 15 black x 0 0 "" yellow \ + /home2/bhalla/scripts/modules/yellow_0.g 0 0 0 56 0 0 +simundump text /kinetics/Lcl/notes 0 \ + "This is a group of reactions resulting in the production\nof Lambda cl" +call /kinetics/Lcl/notes LOAD \ +"This is a group of reactions resulting in the production" \ +"of Lambda cl" +simundump kpool /kinetics/Lcl/l_op_2nd_bound[1] 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 52 15 55 -12 0 +simundump text /kinetics/Lcl/l_op_2nd_bound[1]/notes 0 \ + "it represents the promotor with both of its sites\n bound by the inhibitor" +call /kinetics/Lcl/l_op_2nd_bound[1]/notes LOAD \ +"it represents the promotor with both of its sites" \ +" bound by the inhibitor" +simundump kenz /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 0 0 0 0 0 \ + 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 55 -11 0 +simundump text /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1/notes 0 "" +call /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1/notes LOAD \ +"" +simundump kreac /kinetics/Lcl/inhib_reac[1] 0 0.0055556 0.09 "" white 15 59 \ + -13 0 +simundump text /kinetics/Lcl/inhib_reac[1]/notes 0 \ + "It signifies the first binding of the repressor\n with the operator\n\nKf=1 /nM/sec\nKb=9 /sec\n\nBox1 Elowitz etal Nature 2000 vol 403:335-338" +call /kinetics/Lcl/inhib_reac[1]/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=9 /sec" \ +"" \ +"Box1 Elowitz etal Nature 2000 vol 403:335-338" +simundump kpool /kinetics/Lcl/l_op_1rst_bound 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 2 15 62 -12 0 +simundump text /kinetics/Lcl/l_op_1rst_bound/notes 0 \ + "it represents the promotor with one of its sites\n bound by the inhibitor" +call /kinetics/Lcl/l_op_1rst_bound/notes LOAD \ +"it represents the promotor with one of its sites" \ +" bound by the inhibitor" +simundump kenz /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription 0 0 0 0 0 1800 \ + 0.0024998 0.002 0.0005 0 1 "" red 2 "" 62 -10 0 +simundump text /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription/notes 0 \ + "Rates from\nBox 1 Elowitz et al (2000)\nNature 403:335-338" +call /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +simundump kreac /kinetics/Lcl/inhib_reac 0 0.0055556 2.24 "" white 15 65 -13 \ + 0 +simundump text /kinetics/Lcl/inhib_reac/notes 0 \ + "It signifies the first binding of the repressor\n with the operator\n\nKf=1 /nM/sec\nKb=224 /sec\n\nBox1 Elowitz etal Nature 2000 vol 403:335-338" +call /kinetics/Lcl/inhib_reac/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=224 /sec" \ +"" \ +"Box1 Elowitz etal Nature 2000 vol 403:335-338" +simundump kpool /kinetics/Lcl/AminoAcids 0 0 0.00055555 0.00055555 0.99999 \ + 0.99999 0 0 1800 4 /kinetics/geometry 52 15 48 -8 0 +simundump text /kinetics/Lcl/AminoAcids/notes 0 "" +call /kinetics/Lcl/AminoAcids/notes LOAD \ +"" +simundump kpool /kinetics/Lcl/Nucleotides 0 0 0.00055555 0.00055555 0.99999 \ + 0.99999 0 0 1800 4 /kinetics/geometry 6 15 69 -8 0 +simundump text /kinetics/Lcl/Nucleotides/notes 0 "" +call /kinetics/Lcl/Nucleotides/notes LOAD \ +"" +simundump kreac /kinetics/Lcl/Lcl_mRNA_degradation 0 0.005775 0 "" white 15 \ + 58 -7 0 +simundump text /kinetics/Lcl/Lcl_mRNA_degradation/notes 0 \ + "This reaction denotes the degradation of the Lac m-RNA,\n the half life of which is two minutes.\nt1/2=.693/k where k denotes kf" +call /kinetics/Lcl/Lcl_mRNA_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac m-RNA," \ +" the half life of which is two minutes." \ +"t1/2=.693/k where k denotes kf" +simundump kpool /kinetics/Lcl/Lcl_mRNA 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 5 15 55 -8 0 +simundump text /kinetics/Lcl/Lcl_mRNA/notes 0 \ + "The m-RNA transcribed by the lac operator\n\nElowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/Lcl/Lcl_mRNA/notes LOAD \ +"The m-RNA transcribed by the lac operator" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +simundump kenz /kinetics/Lcl/Lcl_mRNA/Lcl_translation 0 0 0 0 0 1800 0.83494 \ + 0.668 0.167 0 1 "" red 5 "" 48 -10 0 +simundump text /kinetics/Lcl/Lcl_mRNA/Lcl_translation/notes 0 \ + "Rates from\nBox 1 Elowitz et al (2003)\nNature 403:335-338" +call /kinetics/Lcl/Lcl_mRNA/Lcl_translation/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2003)" \ +"Nature 403:335-338" +simundump kpool /kinetics/Lcl/Lcl 0 0 0.055555 0.055555 99.999 99.999 0 0 \ + 1800 0 /kinetics/geometry 24 15 48 -15 0 +simundump text /kinetics/Lcl/Lcl/notes 0 \ + "Lac translated from lac m-RNA\nDerived from Figure 1(c) stochastic version\n\nElowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/Lcl/Lcl/notes LOAD \ +"Lac translated from lac m-RNA" \ +"Derived from Figure 1(c) stochastic version" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +simundump kreac /kinetics/Lcl/Lcl_degradation 0 0.016666 0 "" white 15 48 -17 \ + 0 +simundump text /kinetics/Lcl/Lcl_degradation/notes 0 \ + "This reaction denotes the degradation of the Lac\n the half life of which is ten minutes.\nt1/2=.693/k where k denotes kf\n\nNote: Rates had to be scaled by 1.4 to get the desired levels\n\nElowitz etal Nature 2000. Vol403 335-338" +call /kinetics/Lcl/Lcl_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac" \ +" the half life of which is ten minutes." \ +"t1/2=.693/k where k denotes kf" \ +"" \ +"Note: Rates had to be scaled by 1.4 to get the desired levels" \ +"" \ +"Elowitz etal Nature 2000. Vol403 335-338" +simundump kpool /kinetics/Lcl/degraded_Lcl 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 2 15 48 -19 0 +simundump text /kinetics/Lcl/degraded_Lcl/notes 0 \ + "Degradation product of lac protein" +call /kinetics/Lcl/degraded_Lcl/notes LOAD \ +"Degradation product of lac protein" +simundump kpool /kinetics/Lcl/degraded_Lcl_mRNA 0 0 0 0 0 0 0 0 1800 0 \ + /kinetics/geometry 1 15 62 -8 0 +simundump text /kinetics/Lcl/degraded_Lcl_mRNA/notes 0 \ + "Degradation product of lac m-RNA" +call /kinetics/Lcl/degraded_Lcl_mRNA/notes LOAD \ +"Degradation product of lac m-RNA" +simundump kpool /kinetics/Lcl/Lcl_operator 0 0 0.022222 0.022222 40 40 0 0 \ + 1800 0 /kinetics/geometry 36 15 69 -12 0 +simundump text /kinetics/Lcl/Lcl_operator/notes 0 \ + "The lac operator under normal conditions\n drives transcription of lac\n\nElowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/Lcl/Lcl_operator/notes LOAD \ +"The lac operator under normal conditions" \ +" drives transcription of lac" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +simundump kenz /kinetics/Lcl/Lcl_operator/Lcl_transcription2 0 0 0 0 0 1800 \ + 2.4998 2 0.5 0 1 "" red 36 "" 69 -11 0 +simundump text /kinetics/Lcl/Lcl_operator/Lcl_transcription2/notes 0 \ + "Rates from\nBox 1 Elowitz et al (2003)\nNature 403:335-338" +call /kinetics/Lcl/Lcl_operator/Lcl_transcription2/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2003)" \ +"Nature 403:335-338" +simundump text /kinetics/geometry/notes 0 "" +call /kinetics/geometry/notes LOAD \ +"" +simundump xgraph /graphs/conc1 0 0 10000 0 2.0691 0 +simundump xgraph /graphs/conc2 0 0 10000 0 3.33 0 +simundump xplot /graphs/conc1/TetR.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 11 0 0 1 +simundump xplot /graphs/conc1/lac.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 62 0 0 1 +simundump xplot /graphs/conc1/Lcl.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 24 0 0 1 +simundump xgraph /moregraphs/conc3 0 0 10000 0 95.756 0 +simundump xgraph /moregraphs/conc4 0 0 10000 0 1 0 +simundump xcoredraw /edit/draw 0 -11 71 -21 2 +simundump xtree /edit/draw/tree 0 \ + /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ + "edit_elm.D ; drag_from_edit.w " auto 0.6 +simundump xtext /file/notes 0 1 +xtextload /file/notes \ +"Repressilator model: A synthetic oscillatory network" \ +"of transcriptional regulators designed by Michael B. Elowitz and" \ +"Stanislas Leibler 2000 Nature 403(6767):335-338" +addmsg /kinetics/lac_gene/inhib_reac[1] /kinetics/lac_gene/l_op_2nd_bound[1] REAC B A +addmsg /kinetics/lac_gene/l_op_2nd_bound[1] /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 ENZYME n +addmsg /kinetics/lac_gene/Nucleotides /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 SUBSTRATE n +addmsg /kinetics/lac_gene/l_op_1rst_bound /kinetics/lac_gene/inhib_reac[1] SUBSTRATE n +addmsg /kinetics/lac_gene/l_op_2nd_bound[1] /kinetics/lac_gene/inhib_reac[1] PRODUCT n +addmsg /kinetics/Lcl/Lcl /kinetics/lac_gene/inhib_reac[1] SUBSTRATE n +addmsg /kinetics/lac_gene/inhib_reac /kinetics/lac_gene/l_op_1rst_bound REAC B A +addmsg /kinetics/lac_gene/inhib_reac[1] /kinetics/lac_gene/l_op_1rst_bound REAC A B +addmsg /kinetics/lac_gene/l_op_1rst_bound /kinetics/lac_gene/l_op_1rst_bound/lac_transcription ENZYME n +addmsg /kinetics/lac_gene/Nucleotides /kinetics/lac_gene/l_op_1rst_bound/lac_transcription SUBSTRATE n +addmsg /kinetics/lac_gene/lac_operator /kinetics/lac_gene/inhib_reac SUBSTRATE n +addmsg /kinetics/lac_gene/l_op_1rst_bound /kinetics/lac_gene/inhib_reac PRODUCT n +addmsg /kinetics/Lcl/Lcl /kinetics/lac_gene/inhib_reac SUBSTRATE n +addmsg /kinetics/lac_gene/inhib_reac /kinetics/lac_gene/lac_operator REAC A B +addmsg /kinetics/lac_gene/lac_operator /kinetics/lac_gene/lac_operator/lac_transcription2 ENZYME n +addmsg /kinetics/lac_gene/Nucleotides /kinetics/lac_gene/lac_operator/lac_transcription2 SUBSTRATE n +addmsg /kinetics/lac_gene/lac_mRNA_degradation /kinetics/lac_gene/lac_mRNA REAC A B +addmsg /kinetics/lac_gene/lac_operator/lac_transcription2 /kinetics/lac_gene/lac_mRNA MM_PRD pA +addmsg /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 /kinetics/lac_gene/lac_mRNA MM_PRD pA +addmsg /kinetics/lac_gene/l_op_1rst_bound/lac_transcription /kinetics/lac_gene/lac_mRNA MM_PRD pA +addmsg /kinetics/lac_gene/lac_mRNA /kinetics/lac_gene/lac_mRNA/lac_translation ENZYME n +addmsg /kinetics/lac_gene/AminoAcids /kinetics/lac_gene/lac_mRNA/lac_translation SUBSTRATE n +addmsg /kinetics/lac_gene/lac_degradation /kinetics/lac_gene/lac REAC A B +addmsg /kinetics/lac_gene/lac_mRNA/lac_translation /kinetics/lac_gene/lac MM_PRD pA +addmsg /kinetics/TetR_gene/inhib_reac /kinetics/lac_gene/lac REAC A B +addmsg /kinetics/TetR_gene/inhib_reac[1] /kinetics/lac_gene/lac REAC A B +addmsg /kinetics/lac_gene/lac_degradation /kinetics/lac_gene/degraded_lac REAC B A +addmsg /kinetics/lac_gene/lac_mRNA_degradation /kinetics/lac_gene/degraded_lac_mRNA REAC B A +addmsg /kinetics/lac_gene/lac_mRNA /kinetics/lac_gene/lac_mRNA_degradation SUBSTRATE n +addmsg /kinetics/lac_gene/degraded_lac_mRNA /kinetics/lac_gene/lac_mRNA_degradation PRODUCT n +addmsg /kinetics/lac_gene/degraded_lac /kinetics/lac_gene/lac_degradation PRODUCT n +addmsg /kinetics/lac_gene/lac /kinetics/lac_gene/lac_degradation SUBSTRATE n +addmsg /kinetics/lac_gene/lac_mRNA/lac_translation /kinetics/lac_gene/AminoAcids REAC sA B +addmsg /kinetics/lac_gene/lac_operator/lac_transcription2 /kinetics/lac_gene/Nucleotides REAC sA B +addmsg /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 /kinetics/lac_gene/Nucleotides REAC sA B +addmsg /kinetics/lac_gene/l_op_1rst_bound/lac_transcription /kinetics/lac_gene/Nucleotides REAC sA B +addmsg /kinetics/TetR_gene/inhib_reac[1] /kinetics/TetR_gene/l_op_2nd_bound[1] REAC B A +addmsg /kinetics/TetR_gene/l_op_2nd_bound[1] /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 ENZYME n +addmsg /kinetics/TetR_gene/Nucleotides /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 SUBSTRATE n +addmsg /kinetics/TetR_gene/l_op_2nd_bound[1] /kinetics/TetR_gene/inhib_reac[1] PRODUCT n +addmsg /kinetics/TetR_gene/l_op_1rst_bound /kinetics/TetR_gene/inhib_reac[1] SUBSTRATE n +addmsg /kinetics/lac_gene/lac /kinetics/TetR_gene/inhib_reac[1] SUBSTRATE n +addmsg /kinetics/TetR_gene/inhib_reac[1] /kinetics/TetR_gene/l_op_1rst_bound REAC A B +addmsg /kinetics/TetR_gene/inhib_reac /kinetics/TetR_gene/l_op_1rst_bound REAC B A +addmsg /kinetics/TetR_gene/l_op_1rst_bound /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription ENZYME n +addmsg /kinetics/TetR_gene/Nucleotides /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription SUBSTRATE n +addmsg /kinetics/TetR_gene/l_op_1rst_bound /kinetics/TetR_gene/inhib_reac PRODUCT n +addmsg /kinetics/TetR_gene/TetR_operator /kinetics/TetR_gene/inhib_reac SUBSTRATE n +addmsg /kinetics/lac_gene/lac /kinetics/TetR_gene/inhib_reac SUBSTRATE n +addmsg /kinetics/TetR_gene/TetR_mRNA/TetR_translation /kinetics/TetR_gene/TetR MM_PRD pA +addmsg /kinetics/TetR_gene/TetR_degradation /kinetics/TetR_gene/TetR REAC A B +addmsg /kinetics/Lcl/inhib_reac[1] /kinetics/TetR_gene/TetR REAC A B +addmsg /kinetics/Lcl/inhib_reac /kinetics/TetR_gene/TetR REAC A B +addmsg /kinetics/TetR_gene/TetR_degradation /kinetics/TetR_gene/degraded_TetR REAC B A +addmsg /kinetics/TetR_gene/TetR /kinetics/TetR_gene/TetR_degradation SUBSTRATE n +addmsg /kinetics/TetR_gene/degraded_TetR /kinetics/TetR_gene/TetR_degradation PRODUCT n +addmsg /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 /kinetics/TetR_gene/TetR_mRNA MM_PRD pA +addmsg /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription /kinetics/TetR_gene/TetR_mRNA MM_PRD pA +addmsg /kinetics/TetR_gene/TetR_operator/TetR_transcription2 /kinetics/TetR_gene/TetR_mRNA MM_PRD pA +addmsg /kinetics/TetR_gene/TetR_mRNA_degradation /kinetics/TetR_gene/TetR_mRNA REAC A B +addmsg /kinetics/TetR_gene/TetR_mRNA /kinetics/TetR_gene/TetR_mRNA/TetR_translation ENZYME n +addmsg /kinetics/TetR_gene/AminoAcids /kinetics/TetR_gene/TetR_mRNA/TetR_translation SUBSTRATE n +addmsg /kinetics/TetR_gene/TetR_mRNA /kinetics/TetR_gene/TetR_mRNA_degradation SUBSTRATE n +addmsg /kinetics/TetR_gene/degraded_TetR_mRNA /kinetics/TetR_gene/TetR_mRNA_degradation PRODUCT n +addmsg /kinetics/TetR_gene/TetR_mRNA_degradation /kinetics/TetR_gene/degraded_TetR_mRNA REAC B A +addmsg /kinetics/TetR_gene/inhib_reac /kinetics/TetR_gene/TetR_operator REAC A B +addmsg /kinetics/TetR_gene/TetR_operator /kinetics/TetR_gene/TetR_operator/TetR_transcription2 ENZYME n +addmsg /kinetics/TetR_gene/Nucleotides /kinetics/TetR_gene/TetR_operator/TetR_transcription2 SUBSTRATE n +addmsg /kinetics/TetR_gene/TetR_operator/TetR_transcription2 /kinetics/TetR_gene/Nucleotides REAC sA B +addmsg /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription /kinetics/TetR_gene/Nucleotides REAC sA B +addmsg /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 /kinetics/TetR_gene/Nucleotides REAC sA B +addmsg /kinetics/TetR_gene/TetR_mRNA/TetR_translation /kinetics/TetR_gene/AminoAcids REAC sA B +addmsg /kinetics/Lcl/inhib_reac[1] /kinetics/Lcl/l_op_2nd_bound[1] REAC B A +addmsg /kinetics/Lcl/l_op_2nd_bound[1] /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 ENZYME n +addmsg /kinetics/Lcl/Nucleotides /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 SUBSTRATE n +addmsg /kinetics/Lcl/l_op_2nd_bound[1] /kinetics/Lcl/inhib_reac[1] PRODUCT n +addmsg /kinetics/Lcl/l_op_1rst_bound /kinetics/Lcl/inhib_reac[1] SUBSTRATE n +addmsg /kinetics/TetR_gene/TetR /kinetics/Lcl/inhib_reac[1] SUBSTRATE n +addmsg /kinetics/Lcl/inhib_reac[1] /kinetics/Lcl/l_op_1rst_bound REAC A B +addmsg /kinetics/Lcl/inhib_reac /kinetics/Lcl/l_op_1rst_bound REAC B A +addmsg /kinetics/Lcl/l_op_1rst_bound /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription ENZYME n +addmsg /kinetics/Lcl/Nucleotides /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription SUBSTRATE n +addmsg /kinetics/Lcl/l_op_1rst_bound /kinetics/Lcl/inhib_reac PRODUCT n +addmsg /kinetics/Lcl/Lcl_operator /kinetics/Lcl/inhib_reac SUBSTRATE n +addmsg /kinetics/TetR_gene/TetR /kinetics/Lcl/inhib_reac SUBSTRATE n +addmsg /kinetics/Lcl/Lcl_mRNA/Lcl_translation /kinetics/Lcl/AminoAcids REAC sA B +addmsg /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 /kinetics/Lcl/Nucleotides REAC sA B +addmsg /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription /kinetics/Lcl/Nucleotides REAC sA B +addmsg /kinetics/Lcl/Lcl_operator/Lcl_transcription2 /kinetics/Lcl/Nucleotides REAC sA B +addmsg /kinetics/Lcl/Lcl_mRNA /kinetics/Lcl/Lcl_mRNA_degradation SUBSTRATE n +addmsg /kinetics/Lcl/degraded_Lcl_mRNA /kinetics/Lcl/Lcl_mRNA_degradation PRODUCT n +addmsg /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 /kinetics/Lcl/Lcl_mRNA MM_PRD pA +addmsg /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription /kinetics/Lcl/Lcl_mRNA MM_PRD pA +addmsg /kinetics/Lcl/Lcl_operator/Lcl_transcription2 /kinetics/Lcl/Lcl_mRNA MM_PRD pA +addmsg /kinetics/Lcl/Lcl_mRNA_degradation /kinetics/Lcl/Lcl_mRNA REAC A B +addmsg /kinetics/Lcl/Lcl_mRNA /kinetics/Lcl/Lcl_mRNA/Lcl_translation ENZYME n +addmsg /kinetics/Lcl/AminoAcids /kinetics/Lcl/Lcl_mRNA/Lcl_translation SUBSTRATE n +addmsg /kinetics/Lcl/Lcl_mRNA/Lcl_translation /kinetics/Lcl/Lcl MM_PRD pA +addmsg /kinetics/Lcl/Lcl_degradation /kinetics/Lcl/Lcl REAC A B +addmsg /kinetics/lac_gene/inhib_reac /kinetics/Lcl/Lcl REAC A B +addmsg /kinetics/lac_gene/inhib_reac[1] /kinetics/Lcl/Lcl REAC A B +addmsg /kinetics/Lcl/Lcl /kinetics/Lcl/Lcl_degradation SUBSTRATE n +addmsg /kinetics/Lcl/degraded_Lcl /kinetics/Lcl/Lcl_degradation PRODUCT n +addmsg /kinetics/Lcl/Lcl_degradation /kinetics/Lcl/degraded_Lcl REAC B A +addmsg /kinetics/Lcl/Lcl_mRNA_degradation /kinetics/Lcl/degraded_Lcl_mRNA REAC B A +addmsg /kinetics/Lcl/inhib_reac /kinetics/Lcl/Lcl_operator REAC A B +addmsg /kinetics/Lcl/Lcl_operator /kinetics/Lcl/Lcl_operator/Lcl_transcription2 ENZYME n +addmsg /kinetics/Lcl/Nucleotides /kinetics/Lcl/Lcl_operator/Lcl_transcription2 SUBSTRATE n +addmsg /kinetics/TetR_gene/TetR /graphs/conc1/TetR.Co PLOT Co *TetR.Co *11 +addmsg /kinetics/lac_gene/lac /graphs/conc1/lac.Co PLOT Co *lac.Co *62 +addmsg /kinetics/Lcl/Lcl /graphs/conc1/Lcl.Co PLOT Co *Lcl.Co *24 +enddump +// End of dump + +call /kinetics/lac_gene/notes LOAD \ +"This is a group of reactions resulting in the production" \ +"of Lac" +call /kinetics/lac_gene/l_op_2nd_bound[1]/notes LOAD \ +"it represents the promotor with both of its sites" \ +" bound by the inhibitor" +call /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al Nature (2000)" \ +"403: 335-338" +call /kinetics/lac_gene/inhib_reac[1]/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=9 /sec" \ +"" \ +"Box 1 Elowitz et al Nature 2000 vol 403:335-338" +call /kinetics/lac_gene/l_op_1rst_bound/notes LOAD \ +"it represents the promotor with one of its sites" \ +" bound by the inhibitor" +call /kinetics/lac_gene/l_op_1rst_bound/lac_transcription/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al Nature 2000" \ +"403: 335-338" +call /kinetics/lac_gene/inhib_reac/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf = 1 /nM/sec" \ +"Kb = 224 /sec" \ +"" \ +"Box 1 Elowitz et al Nature 2000 vol 403:335-338" +call /kinetics/lac_gene/lac_operator/notes LOAD \ +"The lac operator under normal conditions" \ +" drives transcription of lac" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/lac_gene/lac_operator/lac_transcription2/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"403:335-338" +call /kinetics/lac_gene/lac_mRNA/notes LOAD \ +"The m-RNA transcribed by the lac operator" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/lac_gene/lac_mRNA/lac_translation/notes LOAD \ +"Rates from " \ +"Box 1 Elowitz et al Nature (2000)" \ +"403: 335-338" +call /kinetics/lac_gene/lac/notes LOAD \ +"Lac translated from lac m-RNA" \ +"Derived from Figure 1(c) stochastic version" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/lac_gene/degraded_lac/notes LOAD \ +"Degradation product of lac protein" +call /kinetics/lac_gene/degraded_lac_mRNA/notes LOAD \ +"Degradation product of lac m-RNA" +call /kinetics/lac_gene/lac_mRNA_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac m-RNA," \ +" the half life of which is two minutes." \ +"t1/2=.693/k where k denotes kf" +call /kinetics/lac_gene/lac_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac" \ +" the half life of which is ten minutes." \ +"t1/2=.693/k where k denotes kf" \ +"" \ +"Note: Rates had to scaled by approx 1.4 to get desired levels" \ +"" \ +"Elowitz et al Nature 2000. Vol403 335-338" +call /kinetics/TetR_gene/notes LOAD \ +"This is a group of reactions resulting in the production" \ +"of Tet R" +call /kinetics/TetR_gene/l_op_2nd_bound[1]/notes LOAD \ +"it represents the promotor with both of its sites" \ +" bound by the inhibitor" +call /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1/notes LOAD \ +"Rates from " \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +call /kinetics/TetR_gene/inhib_reac[1]/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf = 1 /nM/sec" \ +"Kb = 9 /sec" \ +"" \ +"Box 1 Elowitz et al Nature 2000 vol 403:335-338" +call /kinetics/TetR_gene/l_op_1rst_bound/notes LOAD \ +"it represents the promotor with one of its sites" \ +" bound by the inhibitor" +call /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription/notes LOAD \ +"Rates from " \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +call /kinetics/TetR_gene/inhib_reac/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=224 /sec" \ +"" \ +"Box1 Elowitz etal Nature 2000 vol 403:335-338" +call /kinetics/TetR_gene/TetR/notes LOAD \ +"Lac translated from lac m-RNA" \ +"Derived from Figure 1(c) stochastic version" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/TetR_gene/degraded_TetR/notes LOAD \ +"Degradation product of lac protein" +call /kinetics/TetR_gene/TetR_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac" \ +" the half life of which is ten minutes." \ +"t1/2=.693/k where k denotes kf" \ +"" \ +"Note: Rates had to be scaled by 1.4 to get appropriate levels" \ +"" \ +"Elowitz etal Nature 2000. Vol403 335-338" +call /kinetics/TetR_gene/TetR_mRNA/notes LOAD \ +"The m-RNA transcribed by the lac operator" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/TetR_gene/TetR_mRNA/TetR_translation/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +call /kinetics/TetR_gene/TetR_mRNA_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac m-RNA," \ +" the half life of which is two minutes." \ +"t1/2=.693/k where k denotes kf" +call /kinetics/TetR_gene/degraded_TetR_mRNA/notes LOAD \ +"Degradation product of lac m-RNA" +call /kinetics/TetR_gene/TetR_operator/notes LOAD \ +"The lac operator under normal conditions" \ +" drives transcription of lac" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/TetR_gene/TetR_operator/TetR_transcription2/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +call /kinetics/Lcl/notes LOAD \ +"This is a group of reactions resulting in the production" \ +"of Lambda cl" +call /kinetics/Lcl/l_op_2nd_bound[1]/notes LOAD \ +"it represents the promotor with both of its sites" \ +" bound by the inhibitor" +call /kinetics/Lcl/inhib_reac[1]/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=9 /sec" \ +"" \ +"Box1 Elowitz etal Nature 2000 vol 403:335-338" +call /kinetics/Lcl/l_op_1rst_bound/notes LOAD \ +"it represents the promotor with one of its sites" \ +" bound by the inhibitor" +call /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2000)" \ +"Nature 403:335-338" +call /kinetics/Lcl/inhib_reac/notes LOAD \ +"It signifies the first binding of the repressor" \ +" with the operator" \ +"" \ +"Kf=1 /nM/sec" \ +"Kb=224 /sec" \ +"" \ +"Box1 Elowitz etal Nature 2000 vol 403:335-338" +call /kinetics/Lcl/Lcl_mRNA_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac m-RNA," \ +" the half life of which is two minutes." \ +"t1/2=.693/k where k denotes kf" +call /kinetics/Lcl/Lcl_mRNA/notes LOAD \ +"The m-RNA transcribed by the lac operator" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/Lcl/Lcl_mRNA/Lcl_translation/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2003)" \ +"Nature 403:335-338" +call /kinetics/Lcl/Lcl/notes LOAD \ +"Lac translated from lac m-RNA" \ +"Derived from Figure 1(c) stochastic version" \ +"" \ +"Elowitz et al Nature 2000 Vol 403:335-338" +call /kinetics/Lcl/Lcl_degradation/notes LOAD \ +"This reaction denotes the degradation of the Lac" \ +" the half life of which is ten minutes." \ +"t1/2=.693/k where k denotes kf" \ +"" \ +"Note: Rates had to be scaled by 1.4 to get the desired levels" \ +"" \ +"Elowitz etal Nature 2000. Vol403 335-338" +call /kinetics/Lcl/degraded_Lcl/notes LOAD \ +"Degradation product of lac protein" +call /kinetics/Lcl/degraded_Lcl_mRNA/notes LOAD \ +"Degradation product of lac m-RNA" +call /kinetics/Lcl/Lcl_operator/notes LOAD \ +"The lac operator under normal conditions" \ +" drives transcription of lac" \ +"" \ +"Elowitz etal Nature 2000 Vol 403:335-338" +call /kinetics/Lcl/Lcl_operator/Lcl_transcription2/notes LOAD \ +"Rates from" \ +"Box 1 Elowitz et al (2003)" \ +"Nature 403:335-338" +complete_loading diff --git a/demos/Fig3_chemModels/Fig3D.py b/demos/Fig3_chemModels/Fig3D.py new file mode 100644 index 0000000..531758b --- /dev/null +++ b/demos/Fig3_chemModels/Fig3D.py @@ -0,0 +1,67 @@ +import numpy +import pylab +import moose +import time + +''' +This example implements a reaction-diffusion like system which is +bistable and propagates losslessly. It is based on the NEURON example +rxdrun.py, but incorporates more compartments and runs for a longer time. +The system is implemented in a function rather than as a proper system +of chemical reactions. Please see rxdReacDiffusion.py for a variant that +uses a reaction plus a function object to control its rates. +''' + +dt = 0.1 + +# define the geometry +compt = moose.CylMesh( '/cylinder' ) +compt.r0 = compt.r1 = 1 +compt.x1 = 100 +compt.diffLength = 0.2 +assert( compt.numDiffCompts == compt.x1/compt.diffLength ) + +#define the molecule. Its geometry is defined by its parent volume, cylinder +c = moose.Pool( '/cylinder/pool' ) +c.diffConst = 1 # define diffusion constant + +# Here we set up a function calculation +func = moose.Function( '/cylinder/pool/func' ) +func.expr = "-x0 * (0.3 - x0) * (1 - x0)" +func.x.num = 1 #specify number of input variables. + +#Connect the molecules to the func +moose.connect( c, 'nOut', func.x[0], 'input' ) +#Connect the function to the pool +moose.connect( func, 'valueOut', c, 'increment' ) + +#Set up solvers +ksolve = moose.Ksolve( '/cylinder/ksolve' ) +dsolve = moose.Dsolve( '/cylinder/dsolve' ) +stoich = moose.Stoich( '/cylinder/stoich' ) +stoich.compartment = compt +stoich.ksolve = ksolve +stoich.dsolve = dsolve +stoich.path = '/cylinder/##' +for i in range( 10, 18 ): + moose.setClock( i, dt ) + +#initialize +x = numpy.arange( 0, compt.x1, compt.diffLength ) +c.vec.nInit = [ (q < 0.2 * compt.x1) for q in x ] + +# Run and plot it. +moose.reinit() +updateDt = 50 +runtime = updateDt * 4 +plt = pylab.plot( x, c.vec.n, label='t = 0 ') +t1 = time.time() +for t in range( 0, runtime-1, updateDt ): + moose.start( updateDt ) + plt = pylab.plot( x, c.vec.n, label='t = '+str(t + updateDt) ) +print("Time = ", time.time() - t1) + +pylab.ylim( 0, 1.05 ) +pylab.legend() +pylab.show() + diff --git a/demos/Fig3_chemModels/Fig3_NEURON.py b/demos/Fig3_chemModels/Fig3_NEURON.py new file mode 100644 index 0000000..6032b2c --- /dev/null +++ b/demos/Fig3_chemModels/Fig3_NEURON.py @@ -0,0 +1,44 @@ +from neuron import h, rxd +import numpy +from matplotlib import pyplot +import time + +# needed for standard run system +h.load_file('stdrun.hoc') + +dend = h.Section() +dend.nseg = 501 + +# WHERE the dynamics will take place +where = rxd.Region(h.allsec()) + +# WHO the actors are +u = rxd.Species(where, d=1, initial=0) + +# HOW they act +bistable_reaction = rxd.Rate(u, -u * (1 - u) * (0.3 - u)) + +# initial conditions +h.finitialize() +for node in u.nodes: + if node.x < .2: node.concentration = 1 + +def plot_it(color='k'): + y = u.nodes.concentration + x = u.nodes.x + + # convert x from normalized position to microns + x = dend.L * numpy.array(x) + + pyplot.plot(x, y, color) + +plot_it('r') +interval = 50 + +t1 = time.time() +for i in range(1, 5): + h.continuerun(i * interval) + plot_it() +print("Time = ", time.time() - t1) + +pyplot.show() diff --git a/demos/Fig4_ReacDiff/CaMKII_merged77.g b/demos/Fig4_ReacDiff/CaMKII_merged77.g new file mode 100644 index 0000000..41b8311 --- /dev/null +++ b/demos/Fig4_ReacDiff/CaMKII_merged77.g @@ -0,0 +1,2076 @@ +//genesis +// kkit Version 11 flat dumpfile + +// Saved on Sun Nov 15 09:10:36 2015 + +include kkit {argv 1} + +FASTDT = 0.0001 +SIMDT = 0.001 +CONTROLDT = 10 +PLOTDT = 10 +MAXTIME = 2000 +TRANSIENT_TIME = 10 +VARIABLE_DT_FLAG = 1 +DEFAULT_VOL = 1e-20 +VERSION = 11.0 +setfield /file/modpath value /home2/bhalla/scripts/modules +kparms + +//genesis + +initdump -version 3 -ignoreorphans 1 +simobjdump doqcsinfo filename accessname accesstype transcriber developer \ + citation species tissue cellcompartment methodology sources \ + model_implementation model_validation x y z +simobjdump table input output alloced step_mode stepsize x y z +simobjdump xtree path script namemode sizescale +simobjdump xcoredraw xmin xmax ymin ymax +simobjdump xtext editable +simobjdump xgraph xmin xmax ymin ymax overlay +simobjdump xplot pixflags script fg ysquish do_slope wy +simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ + link savename file version md5sum mod_save_flag x y z +simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \ + z +simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \ + geomname xtree_fg_req xtree_textfg_req x y z +simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z +simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ + keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z +simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ + trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z +simobjdump xtab input output alloced step_mode stepsize notes editfunc \ + xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z +simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ + xtree_textfg_req x y z +simobjdump transport input output alloced step_mode stepsize dt delay clock \ + kf xtree_fg_req xtree_textfg_req x y z +simobjdump proto x y z +simobjdump text str +simundump geometry /kinetics/geometry 0 1e-20 3 sphere "" white black -4 -26 \ + 0 +simundump geometry /kinetics/geometry[1] 0 1e-18 3 sphere "" white black 1 \ + -24 0 +simundump geometry /kinetics/geometry[2] 0 9e-20 3 sphere "" white black 4 \ + -20 0 +simundump geometry /kinetics/geometry[3] 0 1e-20 3 sphere "" white black 3 -6 \ + 0 +simundump geometry /kinetics/geometry[4] 0 1e-18 3 sphere "" white black -2 \ + -12 0 +simundump geometry /kinetics/geometry[5] 0 1e-18 3 sphere "" white black 9 \ + -11 0 +simundump geometry /kinetics/geometry[6] 0 9e-20 3 sphere "" white black 10 \ + -15 0 +simundump geometry /kinetics/geometry[7] 0 1e-20 3 sphere "" white black 0 0 \ + 0 +simundump text /kinetics/notes 0 "" +call /kinetics/notes LOAD \ +"" +simundump text /kinetics/geometry/notes 0 "" +call /kinetics/geometry/notes LOAD \ +"" +simundump text /kinetics/geometry[1]/notes 0 "" +call /kinetics/geometry[1]/notes LOAD \ +"" +simundump text /kinetics/geometry[2]/notes 0 "" +call /kinetics/geometry[2]/notes LOAD \ +"" +simundump text /kinetics/geometry[3]/notes 0 "" +call /kinetics/geometry[3]/notes LOAD \ +"" +simundump text /kinetics/geometry[4]/notes 0 "" +call /kinetics/geometry[4]/notes LOAD \ +"" +simundump text /kinetics/geometry[5]/notes 0 "" +call /kinetics/geometry[5]/notes LOAD \ +"" +simundump text /kinetics/geometry[6]/notes 0 "" +call /kinetics/geometry[6]/notes LOAD \ +"" +simundump text /kinetics/geometry[7]/notes 0 "" +call /kinetics/geometry[7]/notes LOAD \ +"" +simundump group /kinetics/PSD 0 20 black x 0 0 "" PSD defaultfile.g 0 0 0 27 \ + 12 0 +simundump text /kinetics/PSD/notes 0 "" +call /kinetics/PSD/notes LOAD \ +"" +simundump kpool /kinetics/PSD/tot_PSD_R 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry blue 0 -4 7 0 +simundump text /kinetics/PSD/tot_PSD_R/notes 0 "" +call /kinetics/PSD/tot_PSD_R/notes LOAD \ +"" +simundump kpool /kinetics/PSD/actCaMKII 0 0 2 2 12 12 0 0 6 0 \ + /kinetics/geometry 12 20 70 33 0 +simundump text /kinetics/PSD/actCaMKII/notes 0 "" +call /kinetics/PSD/actCaMKII/notes LOAD \ +"" +simundump kenz /kinetics/PSD/actCaMKII/CaMKII_1 0 0 0 0 0 6 0.083325 8 2 0 0 \ + "" red 35 "" -6 3 0 +simundump text /kinetics/PSD/actCaMKII/CaMKII_1/notes 0 "" +call /kinetics/PSD/actCaMKII/CaMKII_1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/actCaMKII/CaMKII_2 0 0 0 0 0 6 0.083325 8 2 0 0 \ + "" red 35 "" -2 3 0 +simundump text /kinetics/PSD/actCaMKII/CaMKII_2/notes 0 "" +call /kinetics/PSD/actCaMKII/CaMKII_2/notes LOAD \ +"" +simundump group /kinetics/PSD/PP1_PSD 1 yellow 20 x 0 0 "" PP1_PSD \ + /home2/bhalla/scripts/modules/PP1_PSD_0.g 0 \ + 62a600ae10e53f567e47decb4f2b6488 0 12 27 0 +simundump text /kinetics/PSD/PP1_PSD/notes 0 "" +call /kinetics/PSD/PP1_PSD/notes LOAD \ +"" +simundump kpool /kinetics/PSD/PP1_PSD/PP1-active 1 0 4 4 24 24 0 0 6 0 \ + /kinetics/geometry cyan yellow 44 25 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-active/notes 0 \ + "Cohen et al Meth Enz 159 390-408 is main source of info\nconc = 1.8 uM" +call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \ +"Cohen et al Meth Enz 159 390-408 is main source of info" \ +"conc = 1.8 uM" +simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 0 0 0 0 0 54.001 \ + 0.083333 2 0.5 0 0 "" red cyan "" 61 25 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes 0 "" +call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286/notes LOAD \ +"" +simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b 0 0 0 0 0 54.001 \ + 0.083333 2 0.5 0 0 "" red cyan "" 71 25 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes 0 "" +call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b/notes LOAD \ +"" +simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 0 0 0 0 0 54.001 \ + 0.083333 2 0.5 0 0 "" red cyan "" 78 25 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes 0 "" +call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305/notes LOAD \ +"" +simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c 0 0 0 0 0 54.001 \ + 0.020833 0.5 0.125 0 0 "" red cyan "" 88 25 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes 0 "" +call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c/notes LOAD \ +"" +simundump kenz /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a 0 0 0 0 0 54.001 \ + 0.083333 2 0.5 0 0 "" red cyan "" 83 25 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes 0 "" +call /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a/notes LOAD \ +"" +simundump kpool /kinetics/PSD/PP1_PSD/I1 1 0 4 4 24 24 0 0 6 0 \ + /kinetics/geometry orange yellow 35.35 21.88 0 +simundump text /kinetics/PSD/PP1_PSD/I1/notes 0 \ + "I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet\ninhibitor (Foulkes et al Eur J Biochem 132 309-313 9183).\nWe treat it as non-compet, so it just turns the enz off\nwithout interacting with the binding site.\nCohen et al ann rev bioch refer to results where conc is \n1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM,\nwe need >= 1.8 uM.\n\n" +call /kinetics/PSD/PP1_PSD/I1/notes LOAD \ +"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \ +"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \ +"We treat it as non-compet, so it just turns the enz off" \ +"without interacting with the binding site." \ +"Cohen et al ann rev bioch refer to results where conc is " \ +"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \ +"we need >= 1.8 uM." \ +"" \ +"" +simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1 1 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry brown yellow 36 29 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-I1/notes 0 "" +call /kinetics/PSD/PP1_PSD/PP1-I1/notes LOAD \ +"" +simundump kreac /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 1 1 0 "" white yellow 33 \ + 26 0 +simundump text /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes 0 \ + "Let us assume that the equil in this case is very far over to the\nright. This is probably safe.\n" +call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \ +"Let us assume that the equil in this case is very far over to the" \ +"right. This is probably safe." \ +"" +simundump kreac /kinetics/PSD/PP1_PSD/Inact-PP1 1 83.33 0.1 "" white yellow \ + 17 26 0 +simundump text /kinetics/PSD/PP1_PSD/Inact-PP1/notes 0 \ + "K inhib = 1nM from Cohen Ann Rev Bioch 1989, \n4 nM from Foukes et al \nAssume 2 nM. kf /kb = 8.333e-4" +call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \ +"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \ +"4 nM from Foukes et al " \ +"Assume 2 nM. kf /kb = 8.333e-4" +simundump kpool /kinetics/PSD/PP1_PSD/PP1-I1_p 1 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry brown yellow 22 29 0 +simundump text /kinetics/PSD/PP1_PSD/PP1-I1_p/notes 0 "" +call /kinetics/PSD/PP1_PSD/PP1-I1_p/notes LOAD \ +"" +simundump kpool /kinetics/PSD/PP1_PSD/I1_p 1 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry orange yellow 21 22 0 +simundump text /kinetics/PSD/PP1_PSD/I1_p/notes 0 \ + "Dephosph is mainly by PP2B" +call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \ +"Dephosph is mainly by PP2B" +simundump kpool /kinetics/PSD/PP1_PSD/CaN 0 0 1 1 6 6 0 0 6 0 \ + /kinetics/geometry 1 yellow -1 33 0 +simundump text /kinetics/PSD/PP1_PSD/CaN/notes 0 "" +call /kinetics/PSD/PP1_PSD/CaN/notes LOAD \ +"" +simundump kreac /kinetics/PSD/PP1_PSD/CaM-Bind-CaN 0 7.6667 0.5 "" white \ + yellow 21 40 0 +simundump text /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes 0 "" +call /kinetics/PSD/PP1_PSD/CaM-Bind-CaN/notes LOAD \ +"" +simundump kpool /kinetics/PSD/PP1_PSD/Ca2_CaN 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry blue yellow 12 33 0 +simundump text /kinetics/PSD/PP1_PSD/Ca2_CaN/notes 0 "" +call /kinetics/PSD/PP1_PSD/Ca2_CaN/notes LOAD \ +"" +simundump kreac /kinetics/PSD/PP1_PSD/Ca_bind_CaN 0 0.69444 1 "" white yellow \ + 7 40 0 +simundump text /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes 0 "" +call /kinetics/PSD/PP1_PSD/Ca_bind_CaN/notes LOAD \ +"" +simundump kreac /kinetics/PSD/move_to_PSD 0 0.1 3 "" white 0 -8 -5 0 +simundump text /kinetics/PSD/move_to_PSD/notes 0 "" +call /kinetics/PSD/move_to_PSD/notes LOAD \ +"" +simundump kpool /kinetics/PSD/R_S2 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry 4 0 \ + -8 1 0 +simundump text /kinetics/PSD/R_S2/notes 0 "" +call /kinetics/PSD/R_S2/notes LOAD \ +"" +simundump kpool /kinetics/PSD/R_SpS 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry \ + blue 0 -4 1 0 +simundump text /kinetics/PSD/R_SpS/notes 0 "" +call /kinetics/PSD/R_SpS/notes LOAD \ +"" +simundump kpool /kinetics/PSD/R_SpSp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry \ + 28 0 0 1 0 +simundump text /kinetics/PSD/R_SpSp/notes 0 "" +call /kinetics/PSD/R_SpSp/notes LOAD \ +"" +simundump kpool /kinetics/PSD/basal_phosphatase 0 0 1 1 6 6 0 0 6 0 \ + /kinetics/geometry 61 0 -4 -2 0 +simundump text /kinetics/PSD/basal_phosphatase/notes 0 \ + "There isn't any clear info for this. I had originally called \nit PP2A, but that causes odd interactions with other pathways.\n" +call /kinetics/PSD/basal_phosphatase/notes LOAD \ +"There isn't any clear info for this. I had originally called " \ +"it PP2A, but that causes odd interactions with other pathways." \ +"" +simundump kenz /kinetics/PSD/basal_phosphatase/P1 0 0 0 0 0 60 0.62499 \ + 0.59998 0.15 0 0 "" red 61 "" -6 -1 0 +simundump text /kinetics/PSD/basal_phosphatase/P1/notes 0 "" +call /kinetics/PSD/basal_phosphatase/P1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/basal_phosphatase/P2 0 0 0 0 0 60 0.62499 \ + 0.59998 0.15 0 0 "" red 61 "" -2 -1 0 +simundump text /kinetics/PSD/basal_phosphatase/P2/notes 0 "" +call /kinetics/PSD/basal_phosphatase/P2/notes LOAD \ +"" +simundump kpool /kinetics/PSD/PKA-active 1 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry yellow 20 14 17 0 +simundump text /kinetics/PSD/PKA-active/notes 0 "" +call /kinetics/PSD/PKA-active/notes LOAD \ +"" +simundump kenz /kinetics/PSD/PKA-active/PKA-phosph-I1 0 0 0 0 0 54.001 \ + 0.012345 4 1 0 0 "" red 27 "" 27 19 0 +simundump text /kinetics/PSD/PKA-active/PKA-phosph-I1/notes 0 "" +call /kinetics/PSD/PKA-active/PKA-phosph-I1/notes LOAD \ +"" +simundump group /kinetics/PSD/CaMKII_PSD 0 33 20 x 0 0 "" CaMKII_PSD \ + defaultfile.g 0 0 0 39 32 0 +simundump text /kinetics/PSD/CaMKII_PSD/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/tot-auto 0 0 2 0.5 3 12 0 0 6 0 \ + /kinetics/geometry 29 33 74 36 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot-auto/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph 0 0 0 0 0 7.732 \ + 0.066667 8 2 0 0 "" red 29 "" 72 23 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 0 0 0 0 0 7.732 \ + 0.016667 2 0.5 0 0 "" red 29 "" 59 23 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305 0 0 0 0 0 54.001 \ + 0.2 24 6 0 0 "" red 29 "" 78 23 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/tot_CaMKII 0 0 2 2 12 12 0 0 6 0 \ + /kinetics/geometry 23 33 84 36 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot_CaMKII/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/286P 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry 59 33 52 33 0 +simundump text /kinetics/PSD/CaMKII_PSD/286P/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/286P/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry 47 33 61 33 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph 0 0 0 0 \ + 0 7.732 0.10417 8 2 0 0 "" red 47 "" 72 20 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes 0 \ + "" +call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305 0 0 0 0 0 \ + 54.001 0.3125 24 6 0 0 "" red 47 "" 78 20 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 0 0 0 0 0 \ + 7.732 0.026042 2 0.5 0 0 "" red 47 "" 60 20 0 +simundump text /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/basal_CaMKII 0 0 0.5 0.5 3 3 0 0 6 0 \ + /kinetics/geometry blue 33 81 33 0 +simundump text /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/basal_CaMKII/notes LOAD \ +"" +simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM 0 10.945 \ + 0.0022 "" white 33 54 28 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes 0 \ + "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?" +call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \ +"Same values as for the main compartment" \ +"Can the main compartment pool of Ca/CaM be used?" +simundump kreac /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM 0 10.945 2.2 "" \ + white 33 65 28 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/NMDAR 0 0 40 40 240 240 0 0 6 0 \ + /kinetics/geometry blue 33 67 8 0 +simundump text /kinetics/PSD/CaMKII_PSD/NMDAR/notes 0 \ + "The stochiometry is a bit off here. Each NMDAR actually\nbinds to a holoenzyme, about 12 CaMKII subunits. But\nour CaMKII calculations are in terms of individual\nsubunits. So as a hack, we put in much more NMDAR than\nis actually there.\n\nDec 2011: Reconsidered this, now only 120 NMDARs.\n\nJune 02 2012. Consider these as anchor points for a dodecamer.\nThere are far more effected CaMKII bindin...." +call /kinetics/PSD/CaMKII_PSD/NMDAR/notes LOAD \ +"The stochiometry is a bit off here. Each NMDAR actually" \ +"binds to a holoenzyme, about 12 CaMKII subunits. But" \ +"our CaMKII calculations are in terms of individual" \ +"subunits. So as a hack, we put in much more NMDAR than" \ +"is actually there." \ +"" \ +"Dec 2011: Reconsidered this, now only 120 NMDARs." \ +"" \ +"June 02 2012. Consider these as anchor points for a dodecamer." \ +"There are far more effected CaMKII binding sites then, than" \ +"individual molecules of NMDAR. Raised limit to 40." +simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_2 0 0.002 0 "" white 33 56 \ + 12 0 +simundump text /kinetics/PSD/CaMKII_PSD/transloc_2/notes 0 \ + "Same as for transloc_1\n\n\n" +call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \ +"Same as for transloc_1" \ +"" \ +"" \ +"" +simundump kreac /kinetics/PSD/CaMKII_PSD/transloc_1 0 0.002 0 "" white 33 63 \ + 12 0 +simundump text /kinetics/PSD/CaMKII_PSD/transloc_1/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/transloc_1/notes LOAD \ +"" +simundump kreac /kinetics/PSD/CaMKII_PSD/back_1 0 0.04 6.6667e-06 "" white 33 \ + 75 12 0 +simundump text /kinetics/PSD/CaMKII_PSD/back_1/notes 0 \ + "Rates set by the translocation experiments of \nShen and Meyer, Science 1999." +call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \ +"Rates set by the translocation experiments of " \ +"Shen and Meyer, Science 1999." +simundump kreac /kinetics/PSD/CaMKII_PSD/back_2 0 0.04 6.6667e-06 "" white 33 \ + 89 13 0 +simundump text /kinetics/PSD/CaMKII_PSD/back_2/notes 0 "Same as for back_1\n" +call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \ +"Same as for back_1" \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM 0 0 0 0 0 0 0 0 6 \ + 0 /kinetics/geometry 47 33 56 22 0 +simundump text /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry 50 33 63 22 0 +simundump text /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/sCaMKII 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry 62 33 75 22 0 +simundump text /kinetics/PSD/CaMKII_PSD/sCaMKII/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/sCaMKII/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/sCaMKII_p_p_p 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry 0 33 81 22 0 +simundump text /kinetics/PSD/CaMKII_PSD/sCaMKII_p_p_p/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/sCaMKII_p_p_p/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/sCaMKII-thr305 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry 30 33 88 22 0 +simundump text /kinetics/PSD/CaMKII_PSD/sCaMKII-thr305/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/sCaMKII-thr305/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-CaM 0 1e-12 0 0 0 0 0 0 6 0 \ + /kinetics/geometry[7] 50 black 66 17 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/CaMKII-CaM/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p 0 1e-12 0 0 0 0 0 0 6 0 \ + /kinetics/geometry[7] 2 black 84 17 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/CaMKII_p_p_p/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM 0 1e-12 0 0 0 0 0 \ + 0 6 0 /kinetics/geometry[7] 46 black 58 17 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII 0 5e-13 0 0 0 0 0 0 6 0 \ + /kinetics/geometry[7] 61 black 78 17 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/CaMKII/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr305 0 1e-12 0 0 0 0 0 0 6 \ + 0 /kinetics/geometry[7] 36 black 91 17 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/CaMKII-thr305/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry 57 33 69 22 0 +simundump text /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaMKII_PSD/CaMKII-thr286 0 1e-12 0 0 0 0 0 0 6 \ + 0 /kinetics/geometry[7] 54 black 73 17 0 +simundump text /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes 0 "" +call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286/notes LOAD \ +"" +simundump kpool /kinetics/PSD/PP2A 1 0 1 1 6 6 0 0 6 0 /kinetics/geometry red \ + 20 45 17 0 +simundump text /kinetics/PSD/PP2A/notes 0 "" +call /kinetics/PSD/PP2A/notes LOAD \ +"" +simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p 1 0 0 0 0 54.001 \ + 0.0013289 0.92593 0.22222 0 0 "" red red "" 29 27 0 +simundump text /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes 0 \ + "k1 changed from 3.3e-6 to 6.6e-6\n" +call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \ +"k1 changed from 3.3e-6 to 6.6e-6" \ +"" +simundump kenz /kinetics/PSD/PP2A/PP2A-dephosph-I1 1 0 0 0 0 54.001 0.0013289 \ + 0.92593 0.22222 0 0 "" red red "" 27 20 0 +simundump text /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes 0 \ + "PP2A does most of the dephosph of I1 at basal Ca levels. See\nthe review by Cohen in Ann Rev Biochem 1989.\nFor now, lets halve Km. k1 was 3.3e-6, now 6.6e-6\n" +call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \ +"PP2A does most of the dephosph of I1 at basal Ca levels. See" \ +"the review by Cohen in Ann Rev Biochem 1989." \ +"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \ +"" +simundump group /kinetics/PSD/CaM 1 blue 20 x 0 0 "" defaultfile \ + defaultfile.g 0 fbb0ff81553508bc01f3dd51428742fb 0 31 37 0 +simundump text /kinetics/PSD/CaM/notes 0 "" +call /kinetics/PSD/CaM/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaM/CaM 1 5e-13 20 20 120 120 0 0 6 0 \ + /kinetics/geometry pink blue 35 39 0 +simundump text /kinetics/PSD/CaM/CaM/notes 0 \ + "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n" +call /kinetics/PSD/CaM/CaM/notes LOAD \ +"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \ +"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \ +"it is comparable to CaMK levels. " \ +"" +simundump kreac /kinetics/PSD/CaM/CaM-Ca3-bind-Ca 1 0.6 10 "" white blue 49 \ + 36 0 +simundump text /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes 0 \ + "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10\n24 Sep 2015\nThis is a bit too low affinity. Changing to match K2 at \nKd = 2.8." +call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \ +"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \ +"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" \ +"24 Sep 2015" \ +"This is a bit too low affinity. Changing to match K2 at " \ +"Kd = 2.8." +simundump kpool /kinetics/PSD/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 6 0 \ + /kinetics/geometry hotpink blue 47 39 0 +simundump text /kinetics/PSD/CaM/CaM-Ca3/notes 0 "" +call /kinetics/PSD/CaM/CaM-Ca3/notes LOAD \ +"" +simundump kreac /kinetics/PSD/CaM/CaM-bind-Ca 1 1.4141 8.4853 "" white blue \ + 37 36 0 +simundump text /kinetics/PSD/CaM/CaM-bind-Ca/notes 0 \ + "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...." +call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +simundump kpool /kinetics/PSD/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 6 0 \ + /kinetics/geometry pink blue 43 39 0 +simundump text /kinetics/PSD/CaM/CaM-Ca2/notes 0 \ + "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not." +call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +simundump kreac /kinetics/PSD/CaM/CaM-Ca2-bind-Ca 1 0.60001 10 "" white blue \ + 45 36 0 +simundump text /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes 0 \ + "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n" +call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \ +"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \ +"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \ +"" +simundump kreac /kinetics/PSD/CaM/CaM-Ca-bind-Ca 1 1.4141 8.4853 "" white \ + blue 41 36 0 +simundump text /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes 0 \ + "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...." +call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +simundump kpool /kinetics/PSD/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 6 0 \ + /kinetics/geometry pink blue 39 39 0 +simundump text /kinetics/PSD/CaM/CaM-Ca/notes 0 \ + "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not." +call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +simundump kpool /kinetics/PSD/CaM/Ca 1 1e-11 0.08 0.08 0.48 0.48 0 0 6 0 \ + /kinetics/geometry red blue 43 33 0 +simundump text /kinetics/PSD/CaM/Ca/notes 0 "" +call /kinetics/PSD/CaM/Ca/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaM/CaM-Ca4 1 1e-12 0 0 0 0 0 0 6 0 \ + /kinetics/geometry blue blue 52 39 0 +simundump text /kinetics/PSD/CaM/CaM-Ca4/notes 0 "" +call /kinetics/PSD/CaM/CaM-Ca4/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaM/Ca_input 0 0 0.08 0.08 0.48 0.48 0 0 6 4 \ + /kinetics/geometry[3] blue black 49 33 0 +simundump text /kinetics/PSD/CaM/Ca_input/notes 0 "" +call /kinetics/PSD/CaM/Ca_input/notes LOAD \ +"" +simundump kreac /kinetics/PSD/CaM/Ca_stim 0 50 50 "" white black 46 31 0 +simundump text /kinetics/PSD/CaM/Ca_stim/notes 0 "" +call /kinetics/PSD/CaM/Ca_stim/notes LOAD \ +"" +simundump kpool /kinetics/PSD/CaM_CaN 1 0 0 0 0 0 0 0 6 0 /kinetics/geometry \ + 1 20 30 33 0 +simundump text /kinetics/PSD/CaM_CaN/notes 0 "" +call /kinetics/PSD/CaM_CaN/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p 1 0 0 0 0 54.001 \ + 0.0063334 1.36 0.34 0 0 "" white 1 "" 29 30 0 +simundump text /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p/notes 0 "" +call /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaM_CaN/dephosph_inhib1 1 0 0 0 0 54.001 \ + 0.0063334 1.36 0.34 0 0 "" red 1 "" 29 24 0 +simundump text /kinetics/PSD/CaM_CaN/dephosph_inhib1/notes 0 "" +call /kinetics/PSD/CaM_CaN/dephosph_inhib1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaM_CaN/CaN_1 0 0 0 0 0 6 0.033333 8 2 0 0 "" \ + red pink "" -6 -4 0 +simundump text /kinetics/PSD/CaM_CaN/CaN_1/notes 0 "" +call /kinetics/PSD/CaM_CaN/CaN_1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/CaM_CaN/CaN_2 0 0 0 0 0 6 0.033333 8 2 0 0 "" \ + red pink "" -2 -4 0 +simundump text /kinetics/PSD/CaM_CaN/CaN_2/notes 0 "" +call /kinetics/PSD/CaM_CaN/CaN_2/notes LOAD \ +"" +simundump group /kinetics/DEND 0 13 black x 0 0 "" DEND defaultfile.g 0 0 0 \ + 11 -30 0 +simundump text /kinetics/DEND/notes 0 "" +call /kinetics/DEND/notes LOAD \ +"" +simundump group /kinetics/DEND/CaM 1 blue 13 x 0 0 "" defaultfile \ + defaultfile.g 0 fbb0ff81553508bc01f3dd51428742fb 0 34 -32 0 +simundump text /kinetics/DEND/CaM/notes 0 "" +call /kinetics/DEND/CaM/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaM/CaM 1 5e-13 1 1 600 600 0 0 600 0 \ + /kinetics/geometry pink blue 38 -30 0 +simundump text /kinetics/DEND/CaM/CaM/notes 0 \ + "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n" +call /kinetics/DEND/CaM/CaM/notes LOAD \ +"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \ +"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \ +"it is comparable to CaMK levels. " \ +"" +simundump kreac /kinetics/DEND/CaM/CaM-Ca3-bind-Ca 1 0.006 10 "" white blue \ + 52 -33 0 +simundump text /kinetics/DEND/CaM/CaM-Ca3-bind-Ca/notes 0 \ + "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" +call /kinetics/DEND/CaM/CaM-Ca3-bind-Ca/notes LOAD \ +"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \ +"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" +simundump kpool /kinetics/DEND/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 600 0 \ + /kinetics/geometry hotpink blue 50 -30 0 +simundump text /kinetics/DEND/CaM/CaM-Ca3/notes 0 "" +call /kinetics/DEND/CaM/CaM-Ca3/notes LOAD \ +"" +simundump kreac /kinetics/DEND/CaM/CaM-bind-Ca 1 0.014141 8.4853 "" white \ + blue 40 -33 0 +simundump text /kinetics/DEND/CaM/CaM-bind-Ca/notes 0 \ + "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...." +call /kinetics/DEND/CaM/CaM-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +simundump kpool /kinetics/DEND/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 600 0 \ + /kinetics/geometry pink blue 46 -30 0 +simundump text /kinetics/DEND/CaM/CaM-Ca2/notes 0 \ + "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not." +call /kinetics/DEND/CaM/CaM-Ca2/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +simundump kreac /kinetics/DEND/CaM/CaM-Ca2-bind-Ca 1 0.006 10 "" white blue \ + 48 -33 0 +simundump text /kinetics/DEND/CaM/CaM-Ca2-bind-Ca/notes 0 \ + "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n" +call /kinetics/DEND/CaM/CaM-Ca2-bind-Ca/notes LOAD \ +"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \ +"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \ +"" +simundump kreac /kinetics/DEND/CaM/CaM-Ca-bind-Ca 1 0.014141 8.4853 "" white \ + blue 44 -33 0 +simundump text /kinetics/DEND/CaM/CaM-Ca-bind-Ca/notes 0 \ + "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...." +call /kinetics/DEND/CaM/CaM-Ca-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +simundump kpool /kinetics/DEND/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 600 0 \ + /kinetics/geometry pink blue 42 -30 0 +simundump text /kinetics/DEND/CaM/CaM-Ca/notes 0 \ + "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not." +call /kinetics/DEND/CaM/CaM-Ca/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +simundump kpool /kinetics/DEND/CaM/CaM-Ca4 1 1e-12 0 0 0 0 0 0 600 0 \ + /kinetics/geometry blue blue 55 -30 0 +simundump text /kinetics/DEND/CaM/CaM-Ca4/notes 0 "" +call /kinetics/DEND/CaM/CaM-Ca4/notes LOAD \ +"" +simundump kreac /kinetics/DEND/CaM/CaM_x2 0 10 10 "" white black 28 -30 0 +simundump text /kinetics/DEND/CaM/CaM_x2/notes 0 "" +call /kinetics/DEND/CaM/CaM_x2/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaM/CaM_xchange 0 2e-11 0 0 0 0 0 0 600 0 \ + /kinetics/geometry[1] blue blue 19 -32 0 +simundump text /kinetics/DEND/CaM/CaM_xchange/notes 0 "" +call /kinetics/DEND/CaM/CaM_xchange/notes LOAD \ +"" +simundump group /kinetics/DEND/CaMKII_BULK 0 33 13 x 0 0 "" CaMKII_BULK \ + defaultfile.g 0 0 0 42 -37 0 +simundump text /kinetics/DEND/CaMKII_BULK/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/tot-auto 0 0 0.18 0.5 300 108 0 0 \ + 600 0 /kinetics/geometry 29 33 77 -33 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-auto/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/tot-auto/notes LOAD \ +"" +simundump kenz /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph 0 0 0 0 0 \ + 69.588 0.00066667 8 2 0 0 "" red 29 "" 75 -46 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph/notes LOAD \ +"" +simundump kenz /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286 0 0 0 0 0 69.588 \ + 0.00016667 2 0.5 0 0 "" red 29 "" 62 -46 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286/notes LOAD \ +"" +simundump kenz /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305 0 0 0 0 0 486.01 \ + 0.002 24 6 0 0 "" red 29 "" 81 -46 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/tot_CaMKII 0 0 0.18 1.18 708 108 0 \ + 0 600 0 /kinetics/geometry 23 33 87 -33 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot_CaMKII/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/tot_CaMKII/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII 0 0 0 0 0 0 0 0 600 \ + 0 /kinetics/geometry 47 33 64 -36 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/notes LOAD \ +"" +simundump kenz /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph 0 0 0 \ + 0 0 69.588 0.0010417 8 2 0 0 "" red 47 "" 75 -49 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph/notes 0 \ + "" +call /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph/notes LOAD \ +"" +simundump kenz /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 0 0 0 0 \ + 0 486.01 0.003125 24 6 0 0 "" red 47 "" 81 -49 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305/notes 0 \ + "" +call /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305/notes LOAD \ +"" +simundump kenz /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 0 0 0 0 \ + 0 69.588 0.00026042 2 0.5 0 0 "" red 47 "" 63 -49 0 +simundump text /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes 0 \ + "" +call /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/basal_CaMKII 0 0 0.5 0.5 300 300 0 \ + 0 600 0 /kinetics/geometry blue 33 84 -36 0 +simundump text /kinetics/DEND/CaMKII_BULK/basal_CaMKII/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/basal_CaMKII/notes LOAD \ +"" +simundump kreac /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM 0 0.10945 \ + 0.0022 "" white 33 57 -41 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes 0 \ + "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?" +call /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \ +"Same values as for the main compartment" \ +"Can the main compartment pool of Ca/CaM be used?" +simundump kreac /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM 0 0.10945 2.2 "" \ + white 33 68 -41 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM 0 1e-12 0 0 0 0 \ + 0 0 600 0 /kinetics/geometry 47 33 59 -47 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/CaMKII-CaM 0 1e-12 0 0 0 0 0 0 600 \ + 0 /kinetics/geometry 50 33 66 -47 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII-CaM/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII-CaM/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 0 1e-12 0 0 0 0 0 0 \ + 600 0 /kinetics/geometry 57 33 72 -47 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII-thr286/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII-thr286/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/CaMKII 0 5e-13 1 1 600 600 0 0 600 \ + 0 /kinetics/geometry 62 33 78 -47 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/CaMKII-thr305 0 1e-12 0 0 0 0 0 0 \ + 600 0 /kinetics/geometry 30 33 91 -47 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII-thr305/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII-thr305/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p 0 1e-12 0 0 0 0 0 0 \ + 600 0 /kinetics/geometry 0 33 84 -47 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p/notes LOAD \ +"" +simundump kreac /kinetics/DEND/CaMKII_BULK/CaMKII_x2 0 10 10 "" white black \ + 95 -49 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII_x2/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII_x2/notes LOAD \ +"" +simundump kpool /kinetics/DEND/CaMKII_BULK/CaMKII_xchange 0 2e-11 0 0 0 0 0 0 \ + 600 0 /kinetics/geometry[5] blue black 99 -47 0 +simundump text /kinetics/DEND/CaMKII_BULK/CaMKII_xchange/notes 0 "" +call /kinetics/DEND/CaMKII_BULK/CaMKII_xchange/notes LOAD \ +"" +simundump kpool /kinetics/DEND/actCaMKII 0 0 0.18 0.18 108 108 0 0 600 0 \ + /kinetics/geometry 12 5 73 -36 0 +simundump text /kinetics/DEND/actCaMKII/notes 0 "" +call /kinetics/DEND/actCaMKII/notes LOAD \ +"" +simundump kpool /kinetics/DEND/PP2A 1 0 1.2 1.2 720 720 0 0 600 0 \ + /kinetics/geometry 62 5 47 -44 0 +simundump text /kinetics/DEND/PP2A/notes 0 \ + "Strack et al JBC 1997 show that PP2A is the primary\nphosphatase acting on CaMKII in the bulk." +call /kinetics/DEND/PP2A/notes LOAD \ +"Strack et al JBC 1997 show that PP2A is the primary" \ +"phosphatase acting on CaMKII in the bulk." +simundump kenz /kinetics/DEND/PP2A/Deph-thr286 0 0 0 0 0 486.01 0.0033334 8 2 \ + 0 0 "" red 62 "" 64 -44 0 +simundump text /kinetics/DEND/PP2A/Deph-thr286/notes 0 "" +call /kinetics/DEND/PP2A/Deph-thr286/notes LOAD \ +"" +simundump kenz /kinetics/DEND/PP2A/Deph-thr286b 0 0 0 0 0 486.01 0.0033334 8 \ + 2 0 0 "" red 62 "" 74 -44 0 +simundump text /kinetics/DEND/PP2A/Deph-thr286b/notes 0 "" +call /kinetics/DEND/PP2A/Deph-thr286b/notes LOAD \ +"" +simundump kenz /kinetics/DEND/PP2A/Deph-thr305 0 0 0 0 0 486.01 0.0033334 8 2 \ + 0 0 "" red 62 "" 81 -44 0 +simundump text /kinetics/DEND/PP2A/Deph-thr305/notes 0 "" +call /kinetics/DEND/PP2A/Deph-thr305/notes LOAD \ +"" +simundump kenz /kinetics/DEND/PP2A/Deph-thr286c 0 0 0 0 0 486.01 0.00083332 2 \ + 0.5 0 0 "" red 62 "" 91 -44 0 +simundump text /kinetics/DEND/PP2A/Deph-thr286c/notes 0 "" +call /kinetics/DEND/PP2A/Deph-thr286c/notes LOAD \ +"" +simundump kenz /kinetics/DEND/PP2A/Deph-thr305a 0 0 0 0 0 486.01 0.0033334 8 \ + 2 0 0 "" red 62 "" 86 -44 0 +simundump text /kinetics/DEND/PP2A/Deph-thr305a/notes 0 "" +call /kinetics/DEND/PP2A/Deph-thr305a/notes LOAD \ +"" +simundump kpool /kinetics/DEND/Ca_input 0 0 0.08 0.08 48 48 0 0 600 4 \ + /kinetics/geometry[4] blue black 53 -37 0 +simundump text /kinetics/DEND/Ca_input/notes 0 "" +call /kinetics/DEND/Ca_input/notes LOAD \ +"" +simundump kreac /kinetics/DEND/Ca_stim 0 50 50 "" white black 49 -38 0 +simundump text /kinetics/DEND/Ca_stim/notes 0 "" +call /kinetics/DEND/Ca_stim/notes LOAD \ +"" +simundump group /kinetics/SPINE 0 5 black x 0 0 "" SPINE defaultfile.g 0 0 0 \ + 29 -23 0 +simundump text /kinetics/SPINE/notes 0 "" +call /kinetics/SPINE/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/iR 0 0 4.4444 4.4444 240 240 0 0 54 0 \ + /kinetics/geometry 0 yellow -8 -10 0 +simundump text /kinetics/SPINE/iR/notes 0 "Same as Fus3\n" +call /kinetics/SPINE/iR/notes LOAD \ +"Same as Fus3" \ +"" +simundump group /kinetics/SPINE/CaM 1 blue 5 x 0 0 "" defaultfile \ + defaultfile.g 0 fbb0ff81553508bc01f3dd51428742fb 0 33 2 0 +simundump text /kinetics/SPINE/CaM/notes 0 "" +call /kinetics/SPINE/CaM/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaM/CaM 1 5e-13 20 20 1080 1080 0 0 54 0 \ + /kinetics/geometry pink blue 37 4 0 +simundump text /kinetics/SPINE/CaM/CaM/notes 0 \ + "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)\nSay 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying\nit is comparable to CaMK levels. \n" +call /kinetics/SPINE/CaM/CaM/notes LOAD \ +"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \ +"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \ +"it is comparable to CaMK levels. " \ +"" +simundump kreac /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca 1 0.066667 10 "" white \ + blue 51 1 0 +simundump text /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes 0 \ + "Use K3 = 21.5 uM here from Stemmer and Klee table 3.\nkb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" +call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \ +"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \ +"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" +simundump kpool /kinetics/SPINE/CaM/CaM-Ca3 1 1e-12 0 0 0 0 0 0 54 0 \ + /kinetics/geometry hotpink blue 49 4 0 +simundump text /kinetics/SPINE/CaM/CaM-Ca3/notes 0 "" +call /kinetics/SPINE/CaM/CaM-Ca3/notes LOAD \ +"" +simundump kreac /kinetics/SPINE/CaM/CaM-bind-Ca 1 0.15712 8.4853 "" white \ + blue 39 1 0 +simundump text /kinetics/SPINE/CaM/CaM-bind-Ca/notes 0 \ + "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...." +call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +simundump kpool /kinetics/SPINE/CaM/CaM-Ca2 1 1e-12 0 0 0 0 0 0 54 0 \ + /kinetics/geometry pink blue 45 4 0 +simundump text /kinetics/SPINE/CaM/CaM-Ca2/notes 0 \ + "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not." +call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +simundump kreac /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca 1 0.066668 10 "" white \ + blue 47 1 0 +simundump text /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes 0 \ + "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get\nkb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10\n" +call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \ +"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \ +"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \ +"" +simundump kreac /kinetics/SPINE/CaM/CaM-Ca-bind-Ca 1 0.15712 8.4853 "" white \ + blue 43 1 0 +simundump text /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes 0 \ + "Lets use the fast rate consts here. Since the rates are so different, I am not\nsure whether the order is relevant. These correspond to the TR2C fragment.\nWe use the Martin et al rates here, plus the Drabicowski binding consts.\nAll are scaled by 3X to cell temp.\nkf = 2e-10 kb = 72\nStemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11.\nIf kb=72, kf = 2e-10 (Exactly the same !)...." +call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +simundump kpool /kinetics/SPINE/CaM/CaM-Ca 1 1e-12 0 0 0 0 0 0 54 0 \ + /kinetics/geometry pink blue 41 4 0 +simundump text /kinetics/SPINE/CaM/CaM-Ca/notes 0 \ + "This is the intermediate where the TR2 end (the high-affinity end) has\nbound the Ca but the TR1 end has not." +call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +simundump kpool /kinetics/SPINE/CaM/Ca 1 1e-11 0.08 0.08 4.32 4.32 0 0 54 0 \ + /kinetics/geometry red blue 45 -2 0 +simundump text /kinetics/SPINE/CaM/Ca/notes 0 "" +call /kinetics/SPINE/CaM/Ca/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaM/CaM-Ca4 1 1e-12 0 0 0 0 0 0 54 0 \ + /kinetics/geometry blue blue 54 4 0 +simundump text /kinetics/SPINE/CaM/CaM-Ca4/notes 0 "" +call /kinetics/SPINE/CaM/CaM-Ca4/notes LOAD \ +"" +simundump kreac /kinetics/SPINE/CaM/CaM_x2 0 1 100 "" white black 34 10 0 +simundump text /kinetics/SPINE/CaM/CaM_x2/notes 0 "" +call /kinetics/SPINE/CaM/CaM_x2/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaM/CaM_xchange 0 2e-11 0 0 0 0 0 0 54 0 \ + /kinetics/geometry[2] blue black 29 7 0 +simundump text /kinetics/SPINE/CaM/CaM_xchange/notes 0 "" +call /kinetics/SPINE/CaM/CaM_xchange/notes LOAD \ +"" +simundump group /kinetics/SPINE/CaMKII_BULK 0 33 5 x 0 0 "" CaMKII_BULK \ + defaultfile.g 0 0 0 41 -3 0 +simundump text /kinetics/SPINE/CaMKII_BULK/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/tot-auto 0 0 2 0.5 27 108 0 0 54 \ + 0 /kinetics/geometry 29 33 76 1 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-auto/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/tot-auto/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph 0 0 0 0 0 \ + 69.588 0.0074074 8 2 0 0 "" red 29 "" 74 -12 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286 0 0 0 0 0 \ + 69.588 0.0018519 2 0.5 0 0 "" red 29 "" 61 -12 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 0 0 0 0 0 \ + 486.01 0.022222 24 6 0 0 "" red 29 "" 80 -12 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/tot_CaMKII 0 0 2 22 1188 108 0 0 \ + 54 0 /kinetics/geometry 23 33 86 1 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot_CaMKII/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/tot_CaMKII/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/286P 0 0 0 0 0 0 0 0 54 0 \ + /kinetics/geometry 59 33 54 -2 0 +simundump text /kinetics/SPINE/CaMKII_BULK/286P/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/286P/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII 0 0 0 0 0 0 0 0 54 \ + 0 /kinetics/geometry 47 33 63 -2 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph 0 0 \ + 0 0 0 69.588 0.011574 8 2 0 0 "" red 47 "" 74 -15 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph/notes 0 \ + "" +call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 0 0 0 0 \ + 0 486.01 0.034722 24 6 0 0 "" red 47 "" 80 -15 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305/notes 0 \ + "" +call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 0 0 0 0 \ + 0 69.588 0.0028935 2 0.5 0 0 "" red 47 "" 62 -15 0 +simundump text /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes 0 \ + "" +call /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/basal_CaMKII 0 0 0.5 0.5 27 27 0 \ + 0 54 0 /kinetics/geometry blue 33 83 -2 0 +simundump text /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/basal_CaMKII/notes LOAD \ +"" +simundump kreac /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM 0 1.2161 \ + 0.0022 "" white 33 56 -7 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes 0 \ + "Same values as for the main compartment\nCan the main compartment pool of Ca/CaM be used?" +call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \ +"Same values as for the main compartment" \ +"Can the main compartment pool of Ca/CaM be used?" +simundump kreac /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM 0 1.2161 2.2 "" \ + white 33 67 -7 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM 0 1e-12 0 0 0 0 \ + 0 0 54 0 /kinetics/geometry 47 33 58 -13 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM 0 1e-12 0 0 0 0 0 0 54 \ + 0 /kinetics/geometry 50 33 65 -13 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 0 1e-12 0 0 0 0 0 0 \ + 54 0 /kinetics/geometry 57 33 71 -13 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/CaMKII 0 5e-13 20 20 1080 1080 0 \ + 0 54 0 /kinetics/geometry 62 33 77 -13 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 0 1e-12 0 0 0 0 0 0 \ + 54 0 /kinetics/geometry 30 33 90 -13 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p 0 1e-12 0 0 0 0 0 0 \ + 54 0 /kinetics/geometry 0 33 83 -13 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p/notes LOAD \ +"" +simundump kreac /kinetics/SPINE/CaMKII_BULK/CaMKII_x2 0 1 100 "" white black \ + 92 -15 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII_x2/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII_x2/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaMKII_BULK/CaMKII_xchange 0 2e-11 0 0 0 0 0 \ + 0 54 0 /kinetics/geometry[6] blue black 98 -13 0 +simundump text /kinetics/SPINE/CaMKII_BULK/CaMKII_xchange/notes 0 "" +call /kinetics/SPINE/CaMKII_BULK/CaMKII_xchange/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaM_CaN 1 0 0 0 0 0 0 0 54 0 \ + /kinetics/geometry 1 5 32 -2 0 +simundump text /kinetics/SPINE/CaM_CaN/notes 0 "" +call /kinetics/SPINE/CaM_CaN/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/actCaMKII 0 0 2 2 108 108 0 0 54 0 \ + /kinetics/geometry 12 5 72 -2 0 +simundump text /kinetics/SPINE/actCaMKII/notes 0 "" +call /kinetics/SPINE/actCaMKII/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/PP2A 1 0 5 5 270 270 0 0 54 0 \ + /kinetics/geometry 62 5 46 -10 0 +simundump text /kinetics/SPINE/PP2A/notes 0 \ + "Strack et al JBC 1997 show that PP2A is the primary\nphosphatase acting on CaMKII in the bulk." +call /kinetics/SPINE/PP2A/notes LOAD \ +"Strack et al JBC 1997 show that PP2A is the primary" \ +"phosphatase acting on CaMKII in the bulk." +simundump kenz /kinetics/SPINE/PP2A/Deph-thr286 0 0 0 0 0 486.01 0.037038 8 2 \ + 0 0 "" red 62 "" 63 -10 0 +simundump text /kinetics/SPINE/PP2A/Deph-thr286/notes 0 "" +call /kinetics/SPINE/PP2A/Deph-thr286/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/PP2A/Deph-thr286b 0 0 0 0 0 486.01 0.037038 8 \ + 2 0 0 "" red 62 "" 73 -10 0 +simundump text /kinetics/SPINE/PP2A/Deph-thr286b/notes 0 "" +call /kinetics/SPINE/PP2A/Deph-thr286b/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/PP2A/Deph-thr305 0 0 0 0 0 486.01 0.037038 8 2 \ + 0 0 "" red 62 "" 80 -10 0 +simundump text /kinetics/SPINE/PP2A/Deph-thr305/notes 0 "" +call /kinetics/SPINE/PP2A/Deph-thr305/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/PP2A/Deph-thr286c 0 0 0 0 0 486.01 0.0092593 2 \ + 0.5 0 0 "" red 62 "" 90 -10 0 +simundump text /kinetics/SPINE/PP2A/Deph-thr286c/notes 0 "" +call /kinetics/SPINE/PP2A/Deph-thr286c/notes LOAD \ +"" +simundump kenz /kinetics/SPINE/PP2A/Deph-thr305a 0 0 0 0 0 486.01 0.037038 8 \ + 2 0 0 "" red 62 "" 85 -10 0 +simundump text /kinetics/SPINE/PP2A/Deph-thr305a/notes 0 "" +call /kinetics/SPINE/PP2A/Deph-thr305a/notes LOAD \ +"" +simundump group /kinetics/SPINE/CaN_BULK 1 yellow 5 x 0 0 "" CaN_BULK \ + /home2/bhalla/scripts/modules/PP1_PSD_0.g 0 \ + 62a600ae10e53f567e47decb4f2b6488 0 14 -8 0 +simundump text /kinetics/SPINE/CaN_BULK/notes 0 "" +call /kinetics/SPINE/CaN_BULK/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaN_BULK/CaN 0 0 1 1 54 54 0 0 54 0 \ + /kinetics/geometry 1 yellow 4 -2 0 +simundump text /kinetics/SPINE/CaN_BULK/CaN/notes 0 "" +call /kinetics/SPINE/CaN_BULK/CaN/notes LOAD \ +"" +simundump kreac /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN 0 0.85185 0.5 "" white \ + yellow 23 5 0 +simundump text /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes 0 \ + "From Quintana et al 2005" +call /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes LOAD \ +"From Quintana et al 2005" +simundump kreac /kinetics/SPINE/CaN_BULK/Ca_bind_CaN 0 0.0085734 1 "" white \ + yellow 8 5 0 +simundump text /kinetics/SPINE/CaN_BULK/Ca_bind_CaN/notes 0 "" +call /kinetics/SPINE/CaN_BULK/Ca_bind_CaN/notes LOAD \ +"" +simundump kpool /kinetics/SPINE/CaN_BULK/Ca2_CaN 0 0 0 0 0 0 0 0 54 0 \ + /kinetics/geometry[1] blue yellow 15 -2 0 +simundump text /kinetics/SPINE/CaN_BULK/Ca2_CaN/notes 0 "" +call /kinetics/SPINE/CaN_BULK/Ca2_CaN/notes LOAD \ +"" +simundump kpool /kinetics/Ca 1 1e-11 0.08 0.08 48 48 0 0 600 0 \ + /kinetics/geometry red 13 46 -36 0 +simundump text /kinetics/Ca/notes 0 "" +call /kinetics/Ca/notes LOAD \ +"" +simundump xgraph /graphs/conc1 0 0 2000 0 4 0 +simundump xgraph /graphs/conc2 0 0 2000 0 16.804 0 +simundump xplot /graphs/conc1/Ca.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " red 0 0 1 +simundump xplot /graphs/conc1/actCaMKII.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 12 0 0 1 +simundump xplot /graphs/conc1/tot_PSD_R.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xplot /graphs/conc1/CaM-Ca4.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xplot /graphs/conc2/Ca.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " red 0 0 1 +simundump xplot /graphs/conc2/actCaMKII.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 12 0 0 1 +simundump xplot /graphs/conc2/CaM-Ca4.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xgraph /moregraphs/conc3 0 0 2000 0 4 0 +simundump xgraph /moregraphs/conc4 0 0 2000 0 4 0 +simundump xplot /moregraphs/conc3/Ca.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " red 0 0 1 +simundump xplot /moregraphs/conc3/actCaMKII.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 12 0 0 1 +simundump xplot /moregraphs/conc3/CaM-Ca4.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xcoredraw /edit/draw 0 -10 101 -51 42 +simundump xtree /edit/draw/tree 0 \ + /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ + "edit_elm.D ; drag_from_edit.w " auto 0.6 +simundump xtext /file/notes 0 1 +xtextload /file/notes \ +"23 Dec 2011" \ +"CaMKII_merged16.g" \ +"Added Ca-binding step to the CaN activation pathway." \ +"Based on CaMKII_merged15.g" \ +"" \ +"CaMKII_merged16a.g" \ +"Halved the Kb for CaN-bind-CaM" \ +"" \ +"CaMKII_merged17.g" \ +" Used more rates from Saucerman and Bers BPJ 2008" \ +"" \ +"CaMKII_merged17a.g" \ +"Fix to init conc of PP1-active in PSD: from 2 to 4." \ +"" \ +"CaMKII_merged17b.g" \ +"Raised PP2A CoInit from 0.1111 uM to 1 uM, to avoid sub-molecular" \ +"levels in PSD. Scaled kcats down to match." \ +"" \ +"CaMKII_merged20.g" \ +"First pass at a version with a reasonable basal PKA and a less" \ +"saturating effect on PP1-active of CaMKII." \ +"" \ +"CaMKII_merged20c.g: This version turns on but does not go off" \ +"afterwards. " \ +"" \ +"CaMKII_merged20d.g: 10x higher Km and kcat for PP1 on CaMKII." \ +"" \ +"CaMKII_merged20e.g: Km = 5 and kcat =0.5" \ +"" \ +"02 June 2012. CaMKII_merged20g.g: NMDAR = 40, effective # of" \ +"sites given that CaMKII is a dodecamer." \ +"" \ +"CaMKII_merged20h.g: Lowered Kb for CaM-Bind-CaN from 0.006 to " \ +"0.002/sec." \ +"" \ +"CaMKII_merged20i.g: Set PKA-active in both compts to be 0.02 uM." \ +"" \ +"CaMKII_merged20j.g: Faster CaN diffusion, by 6x. Now matches" \ +"CaM with 6:54." \ +"" \ +"CaMKII_merged20k.g: Halved CaMKII affinity for NMDAR." \ +"" \ +"CaMKII_merged21.g: Removed bulk PP1. Use PP2A to dephosphorylate" \ +"CaMKII in bulk." \ +"" \ +"19 July 2013. psd_merged30.g: Variant for signeur loading." \ +"" \ +"22 Aug 2015. CaMKII_merged32.g: Duplicated spine head CaMKII and" \ +"ancillary reactions, into Dend. Will need to figure out how to " \ +"keep hihger CaMKII and CaM levels in spine head rather than" \ +"dend." \ +"23 Aug 2015. CaMKII_merged33.g: Added pools and reactions to " \ +"sustain the gradients of CaM and CaMKII between DEND and SPINE." \ +"Needed because we have diffusion of CaM, CaMKII and various " \ +"converted forms of these molecules." \ +"" \ +"23 Aug 2015. CaMKII_merged34.g: Added Ca_input for PSD and DEND." \ +"" \ +"24 Aug 2015. CaMKII_merged35.g" \ +"Increased CaDiffusion rate to 10 microns^2/sec. " \ +"Increased Ca_stim Kf and Kb to 50 from 20." \ +"" \ +"13 Sep 2015. CaMKII_merged36.g" \ +"Set PSD/PKA-active nInit to zero. It was a tiny fractional value" \ +"leading to a possible discrepancy between stochastic and determ" \ +"calculations." \ +"" \ +"14 Sep 2015. CaMKII_merged37.g" \ +"PP2A in the PSD had some tiny nComplexInits in its enz sites." \ +"Zeroed." \ +"" \ +"24 Sep 2015. CaMKII_merged38.g" \ +"Fixed some discrepancies in rates in the Dend compartment. Seems" \ +"that vol scaling had not happened properly." \ +"Also raised affinity of final stage of CaM.Ca3 binding to Ca to" \ +"the same value as for CaM.Ca2 binding." \ +"" \ +"25 Sep 2015. CaMKII_merged39.g" \ +"Fixed CaM_xchange reactions, also similar for CaMKII. These set" \ +"up the higher conc in the spine and PSD, but were not effective." \ +"" \ +"26 Sep 2015. CaMKII_merged42.g" \ +"Moved PP1_1 and PP1_2 enzymes to CaM_CaN" \ +"Some rates changes." \ +"CaMKII_merged42a.g: moved /kinetics/DEND/Ca to /kinetics/Ca so" \ +"that the system isn't confused during diffusions setup." \ +"" \ +"29 Sep 2015. CaMKII_merged43.g" \ +"Added back the CaMKII exchange reaction, and CaMKII diffusion" \ +"between dend and spine. Also moved the CaM_xchange reaction to" \ +"the dend as its substrate is there." \ +"CaMKII_merged44.g: Lower Keq rate of both xchangeReactions from" \ +"10 to 2. kb now 0.5, kf still 1." \ +"" \ +"02 Oct 2015: CaMKII_merged50.g. Moved NMDAR to Spine rather than" \ +"PSD, to keep both substrates in same compt. Also moved reac to" \ +"same compt as substrates." \ +"" \ +"05 Nov 2015: CaMKII_merged57.g. Put all the translocation reactions" \ +"in the PSD itself, now the CaMKII phospho forms just diffuse" \ +"into the PSD if they want to translocate. Then they bind to" \ +"NMDAR and form the scaffolded version." \ +"CaMKII_merged58.g: There was too little CaM and CaMKII in the " \ +"spine. Increased the rate of the reactions pumping them in." \ +"" \ +"09 Nov 2015" \ +"CaMKII_merged59.g: 3 major changes. " \ +"1. Lowered basal activity of CaMKII to 0.5 uM from 1 uM." \ +"2. Fixed Km of intramolecular CaMKII. Divide Km by 20 for" \ +" each of the intramolecular reactions, this brings it into the" \ +" same range as the total amount of CaMKII" \ +"3. CaN is now activated by Ca2.CaM, not by Ca4.CaM." \ +"CaMKII_merged60.g. Fix to Km for PP2A on CaMKII in Dend: it had" \ +" been reduced to 0.45, restored to 5 so that it is the same as" \ +" in PSD. Also doubled kcat for PP2A action on CaMKII phospho-" \ +" forms, across the board." \ +"" \ +"CaMKII_merged61.g: Zero out diffusion constt for all CaN forms." \ +"CaMKII_merged62.g: Double PP2A rates on CaMKII phosph forms in" \ +" dend and spine. Raise back-reac rate for Ca2.CaM binding to" \ +" CaN by factor of 10." \ +"" \ +"10 Nov 2015. CaMKII_merged63.g: Raised PP2A levels in dend and" \ +"spine head by 25%. Doubled kcat for CaMKII on PSDR. Doubled" \ +"back rate for CaM binding to CaN." \ +"" \ +"" \ +"11 Nov 2015. CaMKII_merged65.g: (64 was a dead end). Removed" \ +"xchange reacs between dend and spine, which were there for setting" \ +"up the steady-state conc gradient of CaM and CaMKII. Replaced" \ +"with a diffusion process and local reacs to achieve gradient." \ +"CaMKII_merged66.g: Changed local rates to steepen gradient." \ +"CaMKII_merged67.g: Further sped up diffusion of xchange molecules" \ +"to steepen gradient. Also lowered CaN affinity for CaM." \ +"CaMKII_merged68.g: Lowered CaN affinity for CaM. Lowered CaMKII" \ +"activity on PSDR. Increased 10x rate for NMDAR binding to CaMKII." \ +"CaMKII_merged69.g: further lowered CaN affinity for CaM to ~0.1." \ +"Lowered CaMKII basal activity to 0.2 uM." \ +"Increased 2x further NMDAR binding to CaMKII." \ +"CaMKII_merged70.g: Double CaMKII rate on PSDR." \ +"" \ +"13 Nov 2015. CaMKII_merged71.g. Fine-tuning to restore bistability" \ +"in the PSDR. Lowered CaN kcas on PSDR to 0.8. Raised basal" \ +"CaMKII back to 0.5 uM, from 0.2, in PSD." \ +"" \ +"14 Nov 2015. CaMKII_merged74.g. Did various tests for the" \ +"bistability of the PSDR system. This one has slower CaN kcat on" \ +"PSDR, from 0.8 to 0.2. Based on psdr2.g" \ +"CaMKII_merged75.g. The prev one didn't acheive turnoff. Doubled" \ +"CaN kcat on psdr, now at 0.4." \ +"15 Nov 2015." \ +"CaMKII_merged76.g. Raised kcat and Km both for CaN on PSDR, to" \ +"lessen saturation." \ +"CaMKII_merged77.g. Raised kcat of basal_phosphatase for PSDR from" \ +"0.11 to 0.15, in order to raise threshold and lessen spontaneous" \ +"turnons." \ +"" \ +"" +addmsg /kinetics/PSD/R_S2 /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/R_SpS /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/R_SpSp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/actCaMKII/CaMKII_1 /kinetics/PSD/actCaMKII REAC eA B +addmsg /kinetics/PSD/actCaMKII/CaMKII_2 /kinetics/PSD/actCaMKII REAC eA B +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM /kinetics/PSD/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM /kinetics/PSD/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /kinetics/PSD/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/actCaMKII /kinetics/PSD/actCaMKII/CaMKII_1 ENZYME n +addmsg /kinetics/PSD/R_S2 /kinetics/PSD/actCaMKII/CaMKII_1 SUBSTRATE n +addmsg /kinetics/PSD/actCaMKII /kinetics/PSD/actCaMKII/CaMKII_2 ENZYME n +addmsg /kinetics/PSD/R_SpS /kinetics/PSD/actCaMKII/CaMKII_2 SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 /kinetics/PSD/PP1_PSD/PP1-active REAC eA B +addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b /kinetics/PSD/PP1_PSD/PP1-active REAC eA B +addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 /kinetics/PSD/PP1_PSD/PP1-active REAC eA B +addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a /kinetics/PSD/PP1_PSD/PP1-active REAC eA B +addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c /kinetics/PSD/PP1_PSD/PP1-active REAC eA B +addmsg /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 /kinetics/PSD/PP1_PSD/PP1-active REAC B A +addmsg /kinetics/PSD/PP1_PSD/Inact-PP1 /kinetics/PSD/PP1_PSD/PP1-active REAC A B +addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286b SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII_p_p_p /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII_p_p_p /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286c SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr305 /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305a SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 /kinetics/PSD/PP1_PSD/I1 REAC B A +addmsg /kinetics/PSD/PKA-active/PKA-phosph-I1 /kinetics/PSD/PP1_PSD/I1 REAC sA B +addmsg /kinetics/PSD/CaM_CaN/dephosph_inhib1 /kinetics/PSD/PP1_PSD/I1 MM_PRD pA +addmsg /kinetics/PSD/PP2A/PP2A-dephosph-I1 /kinetics/PSD/PP1_PSD/I1 MM_PRD pA +addmsg /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p /kinetics/PSD/PP1_PSD/PP1-I1 MM_PRD pA +addmsg /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p /kinetics/PSD/PP1_PSD/PP1-I1 MM_PRD pA +addmsg /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 /kinetics/PSD/PP1_PSD/PP1-I1 REAC A B +addmsg /kinetics/PSD/PP1_PSD/I1 /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 PRODUCT n +addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 PRODUCT n +addmsg /kinetics/PSD/PP1_PSD/PP1-I1 /kinetics/PSD/PP1_PSD/dissoc-PP1-I1 SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/I1_p /kinetics/PSD/PP1_PSD/Inact-PP1 SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/PP1-I1_p /kinetics/PSD/PP1_PSD/Inact-PP1 PRODUCT n +addmsg /kinetics/PSD/PP1_PSD/PP1-active /kinetics/PSD/PP1_PSD/Inact-PP1 SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/Inact-PP1 /kinetics/PSD/PP1_PSD/PP1-I1_p REAC B A +addmsg /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p /kinetics/PSD/PP1_PSD/PP1-I1_p REAC sA B +addmsg /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p /kinetics/PSD/PP1_PSD/PP1-I1_p REAC sA B +addmsg /kinetics/PSD/PP1_PSD/Inact-PP1 /kinetics/PSD/PP1_PSD/I1_p REAC A B +addmsg /kinetics/PSD/PKA-active/PKA-phosph-I1 /kinetics/PSD/PP1_PSD/I1_p MM_PRD pA +addmsg /kinetics/PSD/CaM_CaN/dephosph_inhib1 /kinetics/PSD/PP1_PSD/I1_p REAC sA B +addmsg /kinetics/PSD/PP2A/PP2A-dephosph-I1 /kinetics/PSD/PP1_PSD/I1_p REAC sA B +addmsg /kinetics/PSD/PP1_PSD/Ca_bind_CaN /kinetics/PSD/PP1_PSD/CaN REAC A B +addmsg /kinetics/PSD/CaM_CaN /kinetics/PSD/PP1_PSD/CaM-Bind-CaN PRODUCT n +addmsg /kinetics/PSD/PP1_PSD/Ca2_CaN /kinetics/PSD/PP1_PSD/CaM-Bind-CaN SUBSTRATE n +addmsg /kinetics/PSD/CaM/CaM-Ca2 /kinetics/PSD/PP1_PSD/CaM-Bind-CaN SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/Ca_bind_CaN /kinetics/PSD/PP1_PSD/Ca2_CaN REAC B A +addmsg /kinetics/PSD/PP1_PSD/CaM-Bind-CaN /kinetics/PSD/PP1_PSD/Ca2_CaN REAC A B +addmsg /kinetics/PSD/PP1_PSD/CaN /kinetics/PSD/PP1_PSD/Ca_bind_CaN SUBSTRATE n +addmsg /kinetics/PSD/PP1_PSD/Ca2_CaN /kinetics/PSD/PP1_PSD/Ca_bind_CaN PRODUCT n +addmsg /kinetics/PSD/CaM/Ca /kinetics/PSD/PP1_PSD/Ca_bind_CaN SUBSTRATE n +addmsg /kinetics/PSD/CaM/Ca /kinetics/PSD/PP1_PSD/Ca_bind_CaN SUBSTRATE n +addmsg /kinetics/SPINE/iR /kinetics/PSD/move_to_PSD SUBSTRATE n +addmsg /kinetics/PSD/R_S2 /kinetics/PSD/move_to_PSD PRODUCT n +addmsg /kinetics/PSD/basal_phosphatase/P1 /kinetics/PSD/R_S2 MM_PRD pA +addmsg /kinetics/PSD/CaM_CaN/CaN_1 /kinetics/PSD/R_S2 MM_PRD pA +addmsg /kinetics/PSD/move_to_PSD /kinetics/PSD/R_S2 REAC B A +addmsg /kinetics/PSD/actCaMKII/CaMKII_1 /kinetics/PSD/R_S2 REAC sA B +addmsg /kinetics/PSD/basal_phosphatase/P2 /kinetics/PSD/R_SpS MM_PRD pA +addmsg /kinetics/PSD/basal_phosphatase/P1 /kinetics/PSD/R_SpS REAC sA B +addmsg /kinetics/PSD/CaM_CaN/CaN_2 /kinetics/PSD/R_SpS MM_PRD pA +addmsg /kinetics/PSD/CaM_CaN/CaN_1 /kinetics/PSD/R_SpS REAC sA B +addmsg /kinetics/PSD/actCaMKII/CaMKII_1 /kinetics/PSD/R_SpS MM_PRD pA +addmsg /kinetics/PSD/actCaMKII/CaMKII_2 /kinetics/PSD/R_SpS REAC sA B +addmsg /kinetics/PSD/basal_phosphatase/P2 /kinetics/PSD/R_SpSp REAC sA B +addmsg /kinetics/PSD/CaM_CaN/CaN_2 /kinetics/PSD/R_SpSp REAC sA B +addmsg /kinetics/PSD/actCaMKII/CaMKII_2 /kinetics/PSD/R_SpSp MM_PRD pA +addmsg /kinetics/PSD/basal_phosphatase/P1 /kinetics/PSD/basal_phosphatase REAC eA B +addmsg /kinetics/PSD/basal_phosphatase/P2 /kinetics/PSD/basal_phosphatase REAC eA B +addmsg /kinetics/PSD/basal_phosphatase /kinetics/PSD/basal_phosphatase/P1 ENZYME n +addmsg /kinetics/PSD/R_SpS /kinetics/PSD/basal_phosphatase/P1 SUBSTRATE n +addmsg /kinetics/PSD/basal_phosphatase /kinetics/PSD/basal_phosphatase/P2 ENZYME n +addmsg /kinetics/PSD/R_SpSp /kinetics/PSD/basal_phosphatase/P2 SUBSTRATE n +addmsg /kinetics/PSD/PKA-active/PKA-phosph-I1 /kinetics/PSD/PKA-active REAC eA B +addmsg /kinetics/PSD/PKA-active /kinetics/PSD/PKA-active/PKA-phosph-I1 ENZYME n +addmsg /kinetics/PSD/PP1_PSD/I1 /kinetics/PSD/PKA-active/PKA-phosph-I1 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 /kinetics/PSD/CaMKII_PSD/tot-auto SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII_p_p_p /kinetics/PSD/CaMKII_PSD/tot-auto SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305 /kinetics/PSD/CaMKII_PSD/tot-auto REAC eA B +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 /kinetics/PSD/CaMKII_PSD/tot-auto REAC eA B +addmsg /kinetics/PSD/CaMKII_PSD/basal_CaMKII /kinetics/PSD/CaMKII_PSD/tot-auto SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph /kinetics/PSD/CaMKII_PSD/tot-auto REAC eA B +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305 ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 /kinetics/PSD/CaMKII_PSD/tot-auto/auton-305 SUBSTRATE n +addmsg /kinetics/PSD/actCaMKII /kinetics/PSD/CaMKII_PSD/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII /kinetics/PSD/CaMKII_PSD/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr305 /kinetics/PSD/CaMKII_PSD/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM /kinetics/PSD/CaMKII_PSD/286P SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 /kinetics/PSD/CaMKII_PSD/286P SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII SUMTOTAL n nInit +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305 /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305 ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-305 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 ENZYME n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM PRODUCT n +addmsg /kinetics/PSD/CaM/CaM-Ca4 /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM SUBSTRATE n +addmsg /kinetics/PSD/CaM/CaM-Ca4 /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM PRODUCT n +addmsg /kinetics/PSD/CaMKII_PSD/transloc_2 /kinetics/PSD/CaMKII_PSD/NMDAR REAC A B +addmsg /kinetics/PSD/CaMKII_PSD/transloc_1 /kinetics/PSD/CaMKII_PSD/NMDAR REAC A B +addmsg /kinetics/PSD/CaMKII_PSD/back_1 /kinetics/PSD/CaMKII_PSD/NMDAR REAC B A +addmsg /kinetics/PSD/CaMKII_PSD/back_2 /kinetics/PSD/CaMKII_PSD/NMDAR REAC B A +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM /kinetics/PSD/CaMKII_PSD/transloc_2 PRODUCT n +addmsg /kinetics/PSD/CaMKII_PSD/NMDAR /kinetics/PSD/CaMKII_PSD/transloc_2 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-CaM /kinetics/PSD/CaMKII_PSD/transloc_2 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM /kinetics/PSD/CaMKII_PSD/transloc_1 PRODUCT n +addmsg /kinetics/PSD/CaMKII_PSD/NMDAR /kinetics/PSD/CaMKII_PSD/transloc_1 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-CaM /kinetics/PSD/CaMKII_PSD/transloc_1 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII /kinetics/PSD/CaMKII_PSD/back_1 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/NMDAR /kinetics/PSD/CaMKII_PSD/back_1 PRODUCT n +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII /kinetics/PSD/CaMKII_PSD/back_1 PRODUCT n +addmsg /kinetics/PSD/CaMKII_PSD/sCaMKII-thr305 /kinetics/PSD/CaMKII_PSD/back_2 SUBSTRATE n +addmsg /kinetics/PSD/CaMKII_PSD/NMDAR /kinetics/PSD/CaMKII_PSD/back_2 PRODUCT n +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr305 /kinetics/PSD/CaMKII_PSD/back_2 PRODUCT n +addmsg /kinetics/PSD/CaMKII_PSD/transloc_2 /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM REAC B A +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM REAC B A +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM MM_PRD pA +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM MM_PRD pA +addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286-CaM REAC sA B +addmsg /kinetics/PSD/CaMKII_PSD/transloc_1 /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM REAC B A +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM-act-286 /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM REAC sA B +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-286 /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM REAC sA B +addmsg /kinetics/PSD/PP1_PSD/PP1-active/Deph-thr286 /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM MM_PRD pA +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM /kinetics/PSD/CaMKII_PSD/sCaMKII-CaM REAC B A +addmsg /kinetics/PSD/CaMKII_PSD/back_1 /kinetics/PSD/CaMKII_PSD/sCaMKII REAC A B 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/kinetics/PSD/PP1_PSD/PP1-active/Deph-thr305 /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 MM_PRD pA +addmsg /kinetics/PSD/CaMKII_PSD/tot-CaM-CaMKII/CaM_act_autoph /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 MM_PRD pA +addmsg /kinetics/PSD/CaMKII_PSD/tot-auto/auton-autoph /kinetics/PSD/CaMKII_PSD/sCaMKII-thr286 MM_PRD pA +addmsg /kinetics/PSD/PP2A/PP2A-dephosph-I1 /kinetics/PSD/PP2A REAC eA B +addmsg /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p /kinetics/PSD/PP2A REAC eA B +addmsg /kinetics/PSD/PP2A /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p ENZYME n +addmsg /kinetics/PSD/PP1_PSD/PP1-I1_p /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p SUBSTRATE n +addmsg /kinetics/PSD/PP2A /kinetics/PSD/PP2A/PP2A-dephosph-I1 ENZYME n +addmsg /kinetics/PSD/PP1_PSD/I1_p /kinetics/PSD/PP2A/PP2A-dephosph-I1 SUBSTRATE n +addmsg /kinetics/PSD/CaM/CaM-bind-Ca /kinetics/PSD/CaM/CaM REAC A B +addmsg /kinetics/PSD/CaM/CaM-Ca3 /kinetics/PSD/CaM/CaM-Ca3-bind-Ca SUBSTRATE n +addmsg /kinetics/PSD/CaM/Ca /kinetics/PSD/CaM/CaM-Ca3-bind-Ca 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n +addmsg /kinetics/PSD/CaM/Ca /kinetics/PSD/CaM/CaM-Ca-bind-Ca SUBSTRATE n +addmsg /kinetics/PSD/CaM/CaM-Ca2 /kinetics/PSD/CaM/CaM-Ca-bind-Ca PRODUCT n +addmsg /kinetics/PSD/CaM/CaM-bind-Ca /kinetics/PSD/CaM/CaM-Ca REAC B A +addmsg /kinetics/PSD/CaM/CaM-Ca-bind-Ca /kinetics/PSD/CaM/CaM-Ca REAC A B +addmsg /kinetics/PSD/CaM/CaM-bind-Ca /kinetics/PSD/CaM/Ca REAC A B +addmsg /kinetics/PSD/CaM/CaM-Ca2-bind-Ca /kinetics/PSD/CaM/Ca REAC A B +addmsg /kinetics/PSD/CaM/CaM-Ca3-bind-Ca /kinetics/PSD/CaM/Ca REAC A B +addmsg /kinetics/PSD/CaM/CaM-Ca-bind-Ca /kinetics/PSD/CaM/Ca REAC A B +addmsg /kinetics/PSD/PP1_PSD/Ca_bind_CaN /kinetics/PSD/CaM/Ca REAC A B +addmsg /kinetics/PSD/PP1_PSD/Ca_bind_CaN /kinetics/PSD/CaM/Ca REAC A B +addmsg /kinetics/PSD/CaM/Ca_stim /kinetics/PSD/CaM/Ca REAC B A +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM /kinetics/PSD/CaM/CaM-Ca4 REAC A B +addmsg /kinetics/PSD/CaMKII_PSD/CaMKII-bind-CaM /kinetics/PSD/CaM/CaM-Ca4 REAC A B +addmsg /kinetics/PSD/CaM/CaM-Ca3-bind-Ca /kinetics/PSD/CaM/CaM-Ca4 REAC B A +addmsg /kinetics/PSD/CaM/Ca_stim /kinetics/PSD/CaM/Ca_input REAC A B +addmsg /kinetics/PSD/CaM/Ca_input /kinetics/PSD/CaM/Ca_stim SUBSTRATE n +addmsg /kinetics/PSD/CaM/Ca /kinetics/PSD/CaM/Ca_stim PRODUCT n +addmsg /kinetics/PSD/CaM_CaN/dephosph_inhib1 /kinetics/PSD/CaM_CaN REAC eA B +addmsg /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p /kinetics/PSD/CaM_CaN REAC eA B +addmsg /kinetics/PSD/PP1_PSD/CaM-Bind-CaN /kinetics/PSD/CaM_CaN REAC B A +addmsg /kinetics/PSD/CaM_CaN/CaN_1 /kinetics/PSD/CaM_CaN REAC eA B +addmsg /kinetics/PSD/CaM_CaN/CaN_2 /kinetics/PSD/CaM_CaN REAC eA B +addmsg /kinetics/PSD/CaM_CaN /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p ENZYME n +addmsg /kinetics/PSD/PP1_PSD/PP1-I1_p /kinetics/PSD/CaM_CaN/dephosph-PP1-I_p SUBSTRATE n +addmsg /kinetics/PSD/CaM_CaN /kinetics/PSD/CaM_CaN/dephosph_inhib1 ENZYME n +addmsg /kinetics/PSD/PP1_PSD/I1_p /kinetics/PSD/CaM_CaN/dephosph_inhib1 SUBSTRATE n +addmsg /kinetics/PSD/R_SpS /kinetics/PSD/CaM_CaN/CaN_1 SUBSTRATE n +addmsg /kinetics/PSD/CaM_CaN /kinetics/PSD/CaM_CaN/CaN_1 ENZYME n +addmsg /kinetics/PSD/R_SpSp /kinetics/PSD/CaM_CaN/CaN_2 SUBSTRATE n +addmsg /kinetics/PSD/CaM_CaN /kinetics/PSD/CaM_CaN/CaN_2 ENZYME n +addmsg /kinetics/DEND/CaM/CaM-bind-Ca /kinetics/DEND/CaM/CaM REAC A B +addmsg /kinetics/DEND/CaM/CaM_x2 /kinetics/DEND/CaM/CaM REAC A B +addmsg /kinetics/DEND/CaM/CaM-Ca3 /kinetics/DEND/CaM/CaM-Ca3-bind-Ca SUBSTRATE n +addmsg /kinetics/Ca /kinetics/DEND/CaM/CaM-Ca3-bind-Ca SUBSTRATE n +addmsg /kinetics/DEND/CaM/CaM-Ca4 /kinetics/DEND/CaM/CaM-Ca3-bind-Ca PRODUCT n +addmsg /kinetics/DEND/CaM/CaM-Ca2-bind-Ca /kinetics/DEND/CaM/CaM-Ca3 REAC B A +addmsg /kinetics/DEND/CaM/CaM-Ca3-bind-Ca /kinetics/DEND/CaM/CaM-Ca3 REAC A B +addmsg /kinetics/DEND/CaM/CaM /kinetics/DEND/CaM/CaM-bind-Ca SUBSTRATE n +addmsg /kinetics/Ca /kinetics/DEND/CaM/CaM-bind-Ca SUBSTRATE n +addmsg /kinetics/DEND/CaM/CaM-Ca /kinetics/DEND/CaM/CaM-bind-Ca PRODUCT n 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/kinetics/DEND/CaM/CaM-Ca4 REAC B A +addmsg /kinetics/DEND/CaM/CaM /kinetics/DEND/CaM/CaM_x2 SUBSTRATE n +addmsg /kinetics/DEND/CaM/CaM_xchange /kinetics/DEND/CaM/CaM_x2 PRODUCT n +addmsg /kinetics/DEND/CaM/CaM_x2 /kinetics/DEND/CaM/CaM_xchange REAC B A +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 /kinetics/DEND/CaMKII_BULK/tot-auto SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p /kinetics/DEND/CaMKII_BULK/tot-auto SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305 /kinetics/DEND/CaMKII_BULK/tot-auto REAC eA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286 /kinetics/DEND/CaMKII_BULK/tot-auto REAC eA B +addmsg /kinetics/DEND/CaMKII_BULK/basal_CaMKII /kinetics/DEND/CaMKII_BULK/tot-auto SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph /kinetics/DEND/CaMKII_BULK/tot-auto REAC eA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286 ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-CaM /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286 SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305 ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305 SUBSTRATE n +addmsg /kinetics/DEND/actCaMKII /kinetics/DEND/CaMKII_BULK/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII /kinetics/DEND/CaMKII_BULK/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr305 /kinetics/DEND/CaMKII_BULK/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-CaM /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-CaM /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM PRODUCT n +addmsg /kinetics/DEND/CaM/CaM-Ca4 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM SUBSTRATE n +addmsg /kinetics/DEND/CaM/CaM-Ca4 /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-CaM /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM PRODUCT n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM REAC B A +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM MM_PRD pA +addmsg /kinetics/DEND/PP2A/Deph-thr286 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM REAC sA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 /kinetics/DEND/CaMKII_BULK/CaMKII-CaM REAC sA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-286 /kinetics/DEND/CaMKII_BULK/CaMKII-CaM REAC sA B +addmsg /kinetics/DEND/PP2A/Deph-thr286 /kinetics/DEND/CaMKII_BULK/CaMKII-CaM MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM /kinetics/DEND/CaMKII_BULK/CaMKII-CaM REAC B A +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 REAC sA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 REAC sA B +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 REAC A B +addmsg /kinetics/DEND/PP2A/Deph-thr286b /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 REAC sA B +addmsg /kinetics/DEND/PP2A/Deph-thr305 /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-bind-CaM /kinetics/DEND/CaMKII_BULK/CaMKII REAC A B +addmsg /kinetics/DEND/PP2A/Deph-thr305a /kinetics/DEND/CaMKII_BULK/CaMKII MM_PRD pA +addmsg /kinetics/DEND/PP2A/Deph-thr286b /kinetics/DEND/CaMKII_BULK/CaMKII MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/DEND/CaMKII_BULK/CaMKII REAC sA B +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-autoph /kinetics/DEND/CaMKII_BULK/CaMKII REAC sA B +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII_x2 /kinetics/DEND/CaMKII_BULK/CaMKII REAC A B +addmsg /kinetics/DEND/PP2A/Deph-thr305a /kinetics/DEND/CaMKII_BULK/CaMKII-thr305 REAC sA B +addmsg /kinetics/DEND/PP2A/Deph-thr286c /kinetics/DEND/CaMKII_BULK/CaMKII-thr305 MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto/auton-305 /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA +addmsg /kinetics/DEND/PP2A/Deph-thr305 /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p REAC sA B +addmsg /kinetics/DEND/PP2A/Deph-thr286c /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p REAC sA B +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII /kinetics/DEND/CaMKII_BULK/CaMKII_x2 SUBSTRATE n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII_xchange /kinetics/DEND/CaMKII_BULK/CaMKII_x2 PRODUCT n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII_x2 /kinetics/DEND/CaMKII_BULK/CaMKII_xchange REAC B A +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/DEND/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-CaM /kinetics/DEND/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/CaMKII_BULK/tot-auto /kinetics/DEND/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/DEND/PP2A/Deph-thr286 /kinetics/DEND/PP2A REAC eA B +addmsg /kinetics/DEND/PP2A/Deph-thr286b /kinetics/DEND/PP2A REAC eA B +addmsg /kinetics/DEND/PP2A/Deph-thr305 /kinetics/DEND/PP2A REAC eA B +addmsg /kinetics/DEND/PP2A/Deph-thr305a /kinetics/DEND/PP2A REAC eA B +addmsg /kinetics/DEND/PP2A/Deph-thr286c /kinetics/DEND/PP2A REAC eA B +addmsg /kinetics/DEND/PP2A /kinetics/DEND/PP2A/Deph-thr286 ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/DEND/PP2A/Deph-thr286 SUBSTRATE n +addmsg /kinetics/DEND/PP2A /kinetics/DEND/PP2A/Deph-thr286b ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr286 /kinetics/DEND/PP2A/Deph-thr286b SUBSTRATE n +addmsg /kinetics/DEND/PP2A /kinetics/DEND/PP2A/Deph-thr305 ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p /kinetics/DEND/PP2A/Deph-thr305 SUBSTRATE n +addmsg /kinetics/DEND/PP2A /kinetics/DEND/PP2A/Deph-thr286c ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII_p_p_p /kinetics/DEND/PP2A/Deph-thr286c SUBSTRATE n +addmsg /kinetics/DEND/PP2A /kinetics/DEND/PP2A/Deph-thr305a ENZYME n +addmsg /kinetics/DEND/CaMKII_BULK/CaMKII-thr305 /kinetics/DEND/PP2A/Deph-thr305a SUBSTRATE n +addmsg /kinetics/DEND/Ca_stim /kinetics/DEND/Ca_input REAC A B +addmsg /kinetics/DEND/Ca_input /kinetics/DEND/Ca_stim SUBSTRATE n +addmsg /kinetics/Ca /kinetics/DEND/Ca_stim PRODUCT n +addmsg /kinetics/PSD/move_to_PSD /kinetics/SPINE/iR REAC A B +addmsg /kinetics/SPINE/CaM/CaM-bind-Ca /kinetics/SPINE/CaM/CaM REAC A B +addmsg /kinetics/SPINE/CaM/CaM_x2 /kinetics/SPINE/CaM/CaM REAC A B +addmsg /kinetics/SPINE/CaM/CaM-Ca3 /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/CaM-Ca4 /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca PRODUCT n +addmsg /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca /kinetics/SPINE/CaM/CaM-Ca3 REAC B A +addmsg /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca /kinetics/SPINE/CaM/CaM-Ca3 REAC A B +addmsg /kinetics/SPINE/CaM/CaM /kinetics/SPINE/CaM/CaM-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaM/CaM-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/CaM-Ca /kinetics/SPINE/CaM/CaM-bind-Ca PRODUCT n +addmsg /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca /kinetics/SPINE/CaM/CaM-Ca2 REAC A B +addmsg /kinetics/SPINE/CaM/CaM-Ca-bind-Ca /kinetics/SPINE/CaM/CaM-Ca2 REAC B A +addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaM/CaM-Ca2 REAC A B +addmsg /kinetics/SPINE/CaM/CaM-Ca2 /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/CaM-Ca3 /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca PRODUCT n +addmsg /kinetics/SPINE/CaM/CaM-Ca /kinetics/SPINE/CaM/CaM-Ca-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaM/CaM-Ca-bind-Ca SUBSTRATE n +addmsg /kinetics/SPINE/CaM/CaM-Ca2 /kinetics/SPINE/CaM/CaM-Ca-bind-Ca PRODUCT n +addmsg /kinetics/SPINE/CaM/CaM-bind-Ca /kinetics/SPINE/CaM/CaM-Ca REAC B A +addmsg /kinetics/SPINE/CaM/CaM-Ca-bind-Ca /kinetics/SPINE/CaM/CaM-Ca REAC A B +addmsg /kinetics/SPINE/CaM/CaM-bind-Ca /kinetics/SPINE/CaM/Ca REAC A B +addmsg /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca /kinetics/SPINE/CaM/Ca REAC A B +addmsg /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca /kinetics/SPINE/CaM/Ca REAC A B +addmsg /kinetics/SPINE/CaM/CaM-Ca-bind-Ca /kinetics/SPINE/CaM/Ca REAC A B +addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaM/Ca REAC A B +addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaM/Ca REAC A B +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM /kinetics/SPINE/CaM/CaM-Ca4 REAC A B +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM /kinetics/SPINE/CaM/CaM-Ca4 REAC A B +addmsg /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca /kinetics/SPINE/CaM/CaM-Ca4 REAC B A +addmsg /kinetics/SPINE/CaM/CaM /kinetics/SPINE/CaM/CaM_x2 SUBSTRATE n +addmsg /kinetics/SPINE/CaM/CaM_xchange /kinetics/SPINE/CaM/CaM_x2 PRODUCT n +addmsg /kinetics/SPINE/CaM/CaM_x2 /kinetics/SPINE/CaM/CaM_xchange REAC B A +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/CaMKII_BULK/tot-auto SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/CaMKII_BULK/tot-auto SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 /kinetics/SPINE/CaMKII_BULK/tot-auto REAC eA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286 /kinetics/SPINE/CaMKII_BULK/tot-auto REAC eA B +addmsg /kinetics/SPINE/CaMKII_BULK/basal_CaMKII /kinetics/SPINE/CaMKII_BULK/tot-auto SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph /kinetics/SPINE/CaMKII_BULK/tot-auto REAC eA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286 ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286 SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 SUBSTRATE n +addmsg /kinetics/SPINE/actCaMKII /kinetics/SPINE/CaMKII_BULK/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII /kinetics/SPINE/CaMKII_BULK/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 /kinetics/SPINE/CaMKII_BULK/tot_CaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/CaMKII_BULK/286P SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/CaMKII_BULK/286P SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII REAC eA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM PRODUCT n +addmsg /kinetics/SPINE/CaM/CaM-Ca4 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM SUBSTRATE n +addmsg /kinetics/SPINE/CaM/CaM-Ca4 /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM PRODUCT n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM REAC B A +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM MM_PRD pA +addmsg /kinetics/SPINE/PP2A/Deph-thr286 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM REAC sA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-286 /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM REAC sA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-286 /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM REAC sA B +addmsg /kinetics/SPINE/PP2A/Deph-thr286 /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM REAC B A +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 REAC sA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 REAC sA B +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 REAC A B +addmsg /kinetics/SPINE/PP2A/Deph-thr286b /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 REAC sA B +addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-bind-CaM /kinetics/SPINE/CaMKII_BULK/CaMKII REAC A B +addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/CaMKII_BULK/CaMKII MM_PRD pA +addmsg /kinetics/SPINE/PP2A/Deph-thr286b /kinetics/SPINE/CaMKII_BULK/CaMKII MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM_act_autoph /kinetics/SPINE/CaMKII_BULK/CaMKII REAC sA B +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-autoph /kinetics/SPINE/CaMKII_BULK/CaMKII REAC sA B +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_x2 /kinetics/SPINE/CaMKII_BULK/CaMKII REAC A B +addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 REAC sA B +addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/tot-CaM-CaMKII/CaM-act-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto/auton-305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p MM_PRD pA +addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B +addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p REAC sA B +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII /kinetics/SPINE/CaMKII_BULK/CaMKII_x2 SUBSTRATE n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_xchange /kinetics/SPINE/CaMKII_BULK/CaMKII_x2 PRODUCT n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_x2 /kinetics/SPINE/CaMKII_BULK/CaMKII_xchange REAC B A +addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaM_CaN REAC B A +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-CaM /kinetics/SPINE/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/CaMKII_BULK/tot-auto /kinetics/SPINE/actCaMKII SUMTOTAL n nInit +addmsg /kinetics/SPINE/PP2A/Deph-thr286 /kinetics/SPINE/PP2A REAC eA B +addmsg /kinetics/SPINE/PP2A/Deph-thr286b /kinetics/SPINE/PP2A REAC eA B +addmsg /kinetics/SPINE/PP2A/Deph-thr305 /kinetics/SPINE/PP2A REAC eA B +addmsg /kinetics/SPINE/PP2A/Deph-thr305a /kinetics/SPINE/PP2A REAC eA B +addmsg /kinetics/SPINE/PP2A/Deph-thr286c /kinetics/SPINE/PP2A REAC eA B +addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286 ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-CaM /kinetics/SPINE/PP2A/Deph-thr286 SUBSTRATE n +addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286b ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286 /kinetics/SPINE/PP2A/Deph-thr286b SUBSTRATE n +addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305 ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr305 SUBSTRATE n +addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr286c ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII_p_p_p /kinetics/SPINE/PP2A/Deph-thr286c SUBSTRATE n +addmsg /kinetics/SPINE/PP2A /kinetics/SPINE/PP2A/Deph-thr305a ENZYME n +addmsg /kinetics/SPINE/CaMKII_BULK/CaMKII-thr305 /kinetics/SPINE/PP2A/Deph-thr305a SUBSTRATE n +addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/CaN REAC A B +addmsg /kinetics/SPINE/CaM_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN PRODUCT n +addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n +addmsg /kinetics/SPINE/CaM/CaM-Ca2 /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN SUBSTRATE n +addmsg /kinetics/SPINE/CaN_BULK/CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n +addmsg /kinetics/SPINE/CaN_BULK/Ca2_CaN /kinetics/SPINE/CaN_BULK/Ca_bind_CaN PRODUCT n +addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n +addmsg /kinetics/SPINE/CaM/Ca /kinetics/SPINE/CaN_BULK/Ca_bind_CaN SUBSTRATE n +addmsg /kinetics/SPINE/CaN_BULK/Ca_bind_CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC B A +addmsg /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN /kinetics/SPINE/CaN_BULK/Ca2_CaN REAC A B +addmsg /kinetics/DEND/CaM/CaM-bind-Ca /kinetics/Ca REAC A B +addmsg /kinetics/DEND/CaM/CaM-Ca2-bind-Ca /kinetics/Ca REAC A B +addmsg /kinetics/DEND/CaM/CaM-Ca3-bind-Ca /kinetics/Ca REAC A B +addmsg /kinetics/DEND/CaM/CaM-Ca-bind-Ca /kinetics/Ca REAC A B +addmsg /kinetics/DEND/Ca_stim /kinetics/Ca REAC B A +addmsg /kinetics/PSD/CaM/Ca /graphs/conc1/Ca.Co PLOT Co *Ca.Co *red +addmsg /kinetics/PSD/actCaMKII /graphs/conc1/actCaMKII.Co PLOT Co *actCaMKII.Co *12 +addmsg /kinetics/PSD/tot_PSD_R /graphs/conc1/tot_PSD_R.Co PLOT Co *tot_PSD_R.Co *blue +addmsg /kinetics/PSD/CaM/CaM-Ca4 /graphs/conc1/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue +addmsg /kinetics/SPINE/CaM/Ca /graphs/conc2/Ca.Co PLOT Co *Ca.Co *red +addmsg /kinetics/SPINE/actCaMKII /graphs/conc2/actCaMKII.Co PLOT Co *actCaMKII.Co *12 +addmsg /kinetics/SPINE/CaM/CaM-Ca4 /graphs/conc2/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue +addmsg /kinetics/Ca /moregraphs/conc3/Ca.Co PLOT Co *Ca.Co *red +addmsg /kinetics/DEND/actCaMKII /moregraphs/conc3/actCaMKII.Co PLOT Co *actCaMKII.Co *12 +addmsg /kinetics/DEND/CaM/CaM-Ca4 /moregraphs/conc3/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue +enddump +// End of dump + +call /kinetics/PSD/PP1_PSD/PP1-active/notes LOAD \ +"Cohen et al Meth Enz 159 390-408 is main source of info" \ +"conc = 1.8 uM" +call /kinetics/PSD/PP1_PSD/I1/notes LOAD \ +"I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet" \ +"inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183)." \ +"We treat it as non-compet, so it just turns the enz off" \ +"without interacting with the binding site." \ +"Cohen et al ann rev bioch refer to results where conc is " \ +"1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM," \ +"we need >= 1.8 uM." \ +"" \ +"" +call /kinetics/PSD/PP1_PSD/dissoc-PP1-I1/notes LOAD \ +"Let us assume that the equil in this case is very far over to the" \ +"right. This is probably safe." \ +"" +call /kinetics/PSD/PP1_PSD/Inact-PP1/notes LOAD \ +"K inhib = 1nM from Cohen Ann Rev Bioch 1989, " \ +"4 nM from Foukes et al " \ +"Assume 2 nM. kf /kb = 8.333e-4" +call /kinetics/PSD/PP1_PSD/I1_p/notes LOAD \ +"Dephosph is mainly by PP2B" +call /kinetics/PSD/basal_phosphatase/notes LOAD \ +"There isn't any clear info for this. I had originally called " \ +"it PP2A, but that causes odd interactions with other pathways." \ +"" +call /kinetics/PSD/CaMKII_PSD/CaMKII-thr286-bind-CaM/notes LOAD \ +"Same values as for the main compartment" \ +"Can the main compartment pool of Ca/CaM be used?" +call /kinetics/PSD/CaMKII_PSD/NMDAR/notes LOAD \ +"The stochiometry is a bit off here. Each NMDAR actually" \ +"binds to a holoenzyme, about 12 CaMKII subunits. But" \ +"our CaMKII calculations are in terms of individual" \ +"subunits. So as a hack, we put in much more NMDAR than" \ +"is actually there." \ +"" \ +"Dec 2011: Reconsidered this, now only 120 NMDARs." \ +"" \ +"June 02 2012. Consider these as anchor points for a dodecamer." \ +"There are far more effected CaMKII binding sites then, than" \ +"individual molecules of NMDAR. Raised limit to 40." +call /kinetics/PSD/CaMKII_PSD/transloc_2/notes LOAD \ +"Same as for transloc_1" \ +"" \ +"" \ +"" +call /kinetics/PSD/CaMKII_PSD/back_1/notes LOAD \ +"Rates set by the translocation experiments of " \ +"Shen and Meyer, Science 1999." +call /kinetics/PSD/CaMKII_PSD/back_2/notes LOAD \ +"Same as for back_1" \ +"" +call /kinetics/PSD/PP2A/PP2A-dephosph-PP1-I_p/notes LOAD \ +"k1 changed from 3.3e-6 to 6.6e-6" \ +"" +call /kinetics/PSD/PP2A/PP2A-dephosph-I1/notes LOAD \ +"PP2A does most of the dephosph of I1 at basal Ca levels. See" \ +"the review by Cohen in Ann Rev Biochem 1989." \ +"For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6" \ +"" +call /kinetics/PSD/CaM/CaM/notes LOAD \ +"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \ +"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \ +"it is comparable to CaMK levels. " \ +"" +call /kinetics/PSD/CaM/CaM-Ca3-bind-Ca/notes LOAD \ +"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \ +"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" \ +"24 Sep 2015" \ +"This is a bit too low affinity. Changing to match K2 at " \ +"Kd = 2.8." +call /kinetics/PSD/CaM/CaM-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +call /kinetics/PSD/CaM/CaM-Ca2/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +call /kinetics/PSD/CaM/CaM-Ca2-bind-Ca/notes LOAD \ +"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \ +"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \ +"" +call /kinetics/PSD/CaM/CaM-Ca-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +call /kinetics/PSD/CaM/CaM-Ca/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +call /kinetics/DEND/CaM/CaM/notes LOAD \ +"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \ +"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \ +"it is comparable to CaMK levels. " \ +"" +call /kinetics/DEND/CaM/CaM-Ca3-bind-Ca/notes LOAD \ +"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \ +"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" +call /kinetics/DEND/CaM/CaM-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +call /kinetics/DEND/CaM/CaM-Ca2/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +call /kinetics/DEND/CaM/CaM-Ca2-bind-Ca/notes LOAD \ +"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \ +"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \ +"" +call /kinetics/DEND/CaM/CaM-Ca-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +call /kinetics/DEND/CaM/CaM-Ca/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +call /kinetics/DEND/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \ +"Same values as for the main compartment" \ +"Can the main compartment pool of Ca/CaM be used?" +call /kinetics/DEND/PP2A/notes LOAD \ +"Strack et al JBC 1997 show that PP2A is the primary" \ +"phosphatase acting on CaMKII in the bulk." +call /kinetics/SPINE/iR/notes LOAD \ +"Same as Fus3" \ +"" +call /kinetics/SPINE/CaM/CaM/notes LOAD \ +"There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \ +"Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \ +"it is comparable to CaMK levels. " \ +"" +call /kinetics/SPINE/CaM/CaM-Ca3-bind-Ca/notes LOAD \ +"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \ +"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" +call /kinetics/SPINE/CaM/CaM-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +call /kinetics/SPINE/CaM/CaM-Ca2/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +call /kinetics/SPINE/CaM/CaM-Ca2-bind-Ca/notes LOAD \ +"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \ +"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \ +"" +call /kinetics/SPINE/CaM/CaM-Ca-bind-Ca/notes LOAD \ +"Lets use the fast rate consts here. Since the rates are so different, I am not" \ +"sure whether the order is relevant. These correspond to the TR2C fragment." \ +"We use the Martin et al rates here, plus the Drabicowski binding consts." \ +"All are scaled by 3X to cell temp." \ +"kf = 2e-10 kb = 72" \ +"Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ +"If kb=72, kf = 2e-10 (Exactly the same !)" \ +"" \ +"19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ +"two steps, each binding 1 Ca. This improves numerical" \ +"stability and is conceptually better too." \ +"" \ +"Overall rates are the same, so each kf and kb is the " \ +"square root of the earlier ones. So" \ +"kf = 1.125e-4, kb = 8.4853" \ +"" +call /kinetics/SPINE/CaM/CaM-Ca/notes LOAD \ +"This is the intermediate where the TR2 end (the high-affinity end) has" \ +"bound the Ca but the TR1 end has not." +call /kinetics/SPINE/CaMKII_BULK/CaMKII-thr286-bind-CaM/notes LOAD \ +"Same values as for the main compartment" \ +"Can the main compartment pool of Ca/CaM be used?" +call /kinetics/SPINE/PP2A/notes LOAD \ +"Strack et al JBC 1997 show that PP2A is the primary" \ +"phosphatase acting on CaMKII in the bulk." +call /kinetics/SPINE/CaN_BULK/CaM-Bind-CaN/notes LOAD \ +"From Quintana et al 2005" +complete_loading diff --git a/demos/Fig4_ReacDiff/Fig4B.py b/demos/Fig4_ReacDiff/Fig4B.py new file mode 100644 index 0000000..a6ad5da --- /dev/null +++ b/demos/Fig4_ReacDiff/Fig4B.py @@ -0,0 +1,185 @@ +######################################################################## +# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015. +# It is licenced under the GPL 2.1 or higher. +# There is no warranty of any kind. You are welcome to make copies under +# the provisions of the GPL. +# This program builds a multiscale model with a few spines inserted into +# a simplified cellular morphology. Each spine has a signaling model in it +# too. The program doesn't run the model, it just displays it in 3D. +######################################################################## +import moogli +import numpy +import time +import pylab +import moose +from moose import neuroml +from PyQt5 import Qt, QtCore, QtGui +import matplotlib.pyplot as plt +import sys +import os +from moose.neuroml.ChannelML import ChannelML +sys.path.append('/home/bhalla/moose/trunk/Demos/util') +import rdesigneur as rd + +PI = 3.14159265359 +useGssa = True +combineSegments = False +baselineTime = 1 +tetTime = 1 +interTetTime = 0.1 +postTetTime = 0.1 +ltdTime = 0.1 +postLtdTime = 0.1 +do3D = True +dt = 0.01 +plotdt = 0.1 +psdTetCa = 8e-3 +basalCa = 0.08e-3 +ltdCa = 0.25e-3 + +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + cellProto = [ ['ca1_minimal.p', 'elec'] ] + spineProto = [ ['makeSpineProto()', 'spine' ]] + chemProto = [ ['CaMKII_merged77.g', 'chem'] ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + chemRange = "H(1.1e-6 - dia) * H(p - 1300e-6)" + spineDistrib = [ \ + ["spine", '#apical#', \ + "spineSpacing", chemRange + " * 5e-6", \ + "spineSpacingDistrib", "1e-6", \ + "angle", "0", \ + "angleDistrib", "6.28", \ + "size", "6", \ + "sizeDistrib", "0" ] \ + ] + chemDistrib = [ \ + [ "chem", "#apical#", "install", chemRange ] + ] + + ###################################################################### + # Here we define the mappings across scales. Format: + # sourceObj sourceField destObj destField couplingExpr [wildcard][spatialExpn] + # where the coupling expression is anything a muParser can evaluate, + # using the input variable x. For example: 8e-5 + 300*x + # For now, let's use existing adaptors which take an offset and scale. + ###################################################################### + adaptorList = [ + [ 'Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 8e-5, 1 ], + [ 'Ca_conc', 'Ca', 'dend/DEND/Ca_input', 'concInit', 8e-5, 1 ], + [ 'psd/tot_PSD_R', 'n', 'glu', 'Gbar', 0, 0.01 ], + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + spineDistrib = spineDistrib, \ + chemDistrib = chemDistrib, \ + cellProto = cellProto, \ + spineProto = spineProto, \ + chemProto = chemProto + ) + + return rdes + +def createVmViewer(rdes): + network = moogli.extensions.moose.read(rdes.elecid.path) + normalizer = moogli.utilities.normalizer(-0.08, + 0.02, + clipleft=True, + clipright=True) + colormap = moogli.colors.UniformColorMap([moogli.colors.Color(0.0, + 0.5, + 1.0, + 1.0), + moogli.colors.Color(1.0, + 0.0, + 0.0, + 0.9)]) + mapper = moogli.utilities.mapper(colormap, normalizer) + + def prelude(view): + vms = [moose.element(x).Vm for x in list(network.shapes.keys())] + network.set("color", vms, mapper) + view.pitch(PI/2.0) + view.down(450) + view.left(100) + view.h = 2.0 + view.zoom(5.0) + + def interlude(view): + if view.h > 0.10: + view.h /= 1.005 + view.zoom(0.005) + view.yaw(0.01) + + viewer = moogli.Viewer("vm-viewer") + viewer.attach_shapes(list(network.shapes.values())) + view = moogli.View("vm-view", + prelude=prelude, + interlude=interlude) + viewer.attach_view(view) + return viewer + + +def main(): + numpy.random.seed( 1234 ) + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + assert( moose.exists( '/model' ) ) + moose.element( '/model/elec/hsolve' ).tick = -1 + for i in range( 10, 18 ): + moose.setClock( i, dt ) + moose.setClock( 18, plotdt ) + moose.reinit() + + if do3D: + app = QtGui.QApplication(sys.argv) + compts = moose.wildcardFind( "/model/elec/#[ISA=CompartmentBase]" ) + print("LEN = ", len( compts )) + for i in compts: + n = i.name[:4] + if ( n == 'head' or n == 'shaf' ): + i.diameter *= 1.0 + i.Vm = 0.02 + else: + i.diameter *= 4.0 + i.Vm = -0.05 + vm_viewer = createVmViewer(rdes) + vm_viewer.showMaximized() + vm_viewer.start() + app.exec_() + +if __name__ == '__main__': + main() diff --git a/demos/Fig4_ReacDiff/Fig4CDEF.py b/demos/Fig4_ReacDiff/Fig4CDEF.py new file mode 100644 index 0000000..88f5e03 --- /dev/null +++ b/demos/Fig4_ReacDiff/Fig4CDEF.py @@ -0,0 +1,242 @@ +######################################################################## +# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015. +# It is licenced under the GPL 2.1 or higher. +# There is no warranty of any kind. You are welcome to make copies under +# the provisions of the GPL. +# This program builds a multiscale model with a few spines inserted into +# a simplified cellular morphology. Each spine has a signaling model in it +# too. The program runs the model with a strong but brief calcium input +# synapses at 10 seconds, and a long but smaller Ca influx from 290 to +# 650 seconds. This simulation runs using a deterministic method. +# The runtime on a 2.2 GHz Intel core I7 processor is about 550 s. +######################################################################## +import moogli +import numpy +import time +import pylab +import moose +from moose import neuroml +from PyQt5 import Qt, QtCore, QtGui +import matplotlib.pyplot as plt +import sys +import os +from moose.neuroml.ChannelML import ChannelML +sys.path.append('/home/bhalla/moose/trunk/Demos/util') +import rdesigneur as rd + +PI = 3.14159265359 +useGssa = False +combineSegments = False +baselineTime = 10 +tetTime = 1 +interTetTime = 20 +postTetTime = 240 +ltdTime = 360 +postLtdTime = 60 +do3D = False +dt = 0.001 +plotdt = 0.1 +psdTetCa = 8e-3 +dendTetCa = 2e-3 +basalCa = 0.08e-3 +ltdCa = 0.25e-3 + +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + cellProto = [ ['ca1_minimal.p', 'elec'] ] + spineProto = [ ['makeSpineProto()', 'spine' ]] + chemProto = [ ['CaMKII_merged77.g', 'chem'] ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + chemRange = "H(1.1e-6 - dia) * H(p - 1300e-6)" + spineDistrib = [ \ + ["spine", '#apical#', \ + "spineSpacing", chemRange + " * 5e-6", \ + "spineSpacingDistrib", "1e-6", \ + "angle", "0", \ + "angleDistrib", "0", \ + "size", "1", \ + "sizeDistrib", "0" ] \ + ] + chemDistrib = [ \ + [ "chem", "#apical#", "install", chemRange ] + ] + + ###################################################################### + # Here we define the mappings across scales. Format: + # sourceObj sourceField destObj destField couplingExpr [wildcard][spatialExpn] + # where the coupling expression is anything a muParser can evaluate, + # using the input variable x. For example: 8e-5 + 300*x + # For now, let's use existing adaptors which take an offset and scale. + ###################################################################### + adaptorList = [ + [ 'Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 8e-5, 1 ], + [ 'Ca_conc', 'Ca', 'dend/Ca_dend_input', 'concInit', 8e-5, 1 ], + [ 'psd/tot_PSD_R', 'n', 'glu', 'Gbar', 0, 0.01 ], + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + spineDistrib = spineDistrib, \ + chemDistrib = chemDistrib, \ + cellProto = cellProto, \ + spineProto = spineProto, \ + chemProto = chemProto + ) + + return rdes + +def buildOnePlot( path, field = 'getConc' ): + elist = moose.vec( '/model/chem/' + path ) + tabname = path.replace( '/', '_' ) + tab = moose.Table2( '/graphs/' + tabname, len( elist ) ).vec + moose.connect( tab, 'requestOut', elist, field, 'OneToOne' ) + +def buildPlots(): + if not moose.exists( '/graphs' ): + moose.Neutral( '/graphs' ) + buildOnePlot( 'psd/actCaMKII' ) + buildOnePlot( 'spine/actCaMKII' ) + buildOnePlot( 'dend/DEND/actCaMKII' ) + buildOnePlot( 'psd/tot_PSD_R', 'getN' ) + +def displayPlots(): + #plt.style.use( 'ggplot' ) + #fig = plt.figure( figsize=( 6, 10 ), frameon=False, facecolor='white' ) + fig = plt.figure( figsize=( 5, 10 ), facecolor='white' ) + fig.subplots_adjust( left = 0.18 ) + elist = moose.wildcardFind( '/graphs/#[0]' ) + n = len(elist) + j = 1 + timePts = numpy.arange( 0, len( elist[0].vector ) ) * elist[0].dt + labelName = [ "[CaMKII] (uM)", "[CaMKII] (uM)", + "[CaMKII] (uM)", "# AMPAR" ] + showTickLabels = [0,0,0,1] + plotTitle = ['C', 'D', 'E', 'F'] + plotScale = [1000,1000,1000,1] + for i in zip( elist, labelName, showTickLabels, plotTitle, plotScale ): + ax = plt.subplot( 4, 1, j ) + ax.spines['top'].set_visible( False ) + ax.spines['right'].set_visible( False ) + + #This function does the same as below, one axis at a time + #ax.xaxis.set_tick_params( direction = 'out' ) + #ax.yaxis.set_tick_params( direction = 'out' ) + ax.tick_params( direction = 'out' ) + + # These two are equivalent, get rid of the ticks but not the border + #ax.xaxis.set_visible( False ) + #ax.get_xaxis().set_visible( False ) + if not i[2]: + ax.set_xticklabels([]) + for tick in ax.xaxis.get_major_ticks(): + tick.tick2On = False + for tick in ax.yaxis.get_major_ticks(): + tick.tick2On = False + + plt.ylabel( i[1], fontsize = 16 ) + # alternate way of doing this separately. + #plt.yaxis.label.size_size(16) + #plt.title( 'B' ) + ax.text( -0.18, 1.0, i[3], fontsize = 18, weight = 'bold', + transform=ax.transAxes ) + j = j + 1 + for k in i[0].vec: + plt.plot( timePts, k.vector * i[4] ) + #plt.title( i.name ) + print(i[0].name) + + plt.xlabel( 'Time (s)', fontsize = 16 ) + plt.show() + +def main(): + numpy.random.seed( 1234 ) + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + assert( moose.exists( '/model' ) ) + moose.element( '/model/elec/hsolve' ).tick = -1 + for i in range( 0, 10 ): + moose.setClock( i, 100 ) + for i in range( 10, 18 ): + moose.setClock( i, dt ) + moose.setClock( 18, plotdt ) + moose.reinit() + buildPlots() + # Run for baseline, tetanus, and post-tetanic settling time + print('starting...') + t1 = time.time() + moose.start( baselineTime ) + caPsd = moose.vec( '/model/chem/psd/Ca_input' ) + caDend = moose.vec( '/model/chem/dend/DEND/Ca_input' ) + castim = (numpy.random.rand( len( caPsd.concInit ) ) * 0.8 + 0.2) * psdTetCa + caPsd.concInit = castim + caDend.concInit = numpy.random.rand( len( caDend.concInit ) ) * dendTetCa + moose.start( tetTime ) + caPsd.concInit = basalCa + caDend.concInit = basalCa + moose.start( interTetTime ) + caPsd.concInit = castim + caDend.concInit = numpy.random.rand( len( caDend.concInit ) ) * dendTetCa + moose.start( tetTime ) + caPsd.concInit = basalCa + caDend.concInit = basalCa + moose.start( postTetTime ) + caPsd.concInit = ltdCa + caDend.concInit = ltdCa + moose.start( ltdTime ) + caPsd.concInit = basalCa + caDend.concInit = basalCa + moose.start( postLtdTime ) + print('real time = ', time.time() - t1) + + if do3D: + app = QtGui.QApplication(sys.argv) + compts = moose.wildcardFind( "/model/elec/#[ISA=compartmentBase]" ) + ecomptPath = [x.path for x in compts] + morphology = moogli.read_morphology_from_moose(name = "", path = "/model/elec") + morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \ + [0.0, 0.5, 1.0, 1.0], [1.0, 0.0, 0.0, 0.9] ) + viewer = moogli.DynamicMorphologyViewerWidget(morphology) + def callback( morphology, viewer ): + moose.start( 0.1 ) + return True + viewer.set_callback( callback, idletime = 0 ) + viewer.showMaximized() + viewer.show() + app.exec_() + + displayPlots() + +if __name__ == '__main__': + main() diff --git a/demos/Fig4_ReacDiff/Fig4GHIJ.py b/demos/Fig4_ReacDiff/Fig4GHIJ.py new file mode 100644 index 0000000..f305c87 --- /dev/null +++ b/demos/Fig4_ReacDiff/Fig4GHIJ.py @@ -0,0 +1,242 @@ +######################################################################## +# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015. +# It is licenced under the GPL 2.1 or higher. +# There is no warranty of any kind. You are welcome to make copies under +# the provisions of the GPL. +# This program builds a multiscale model with a few spines inserted into +# a simplified cellular morphology. Each spine has a signaling model in it +# too. The program runs the model with a strong but brief calcium input +# synapses at 10 seconds, and a long but smaller Ca influx from 290 to +# 650 seconds. This simulation runs using a stochastic method. +# The runtime on a 2.2 GHz Intel core I7 processor is about 465 s. +######################################################################## +import moogli +import numpy +import time +import pylab +import moose +from moose import neuroml +from PyQt5 import Qt, QtCore, QtGui +import matplotlib.pyplot as plt +import sys +import os +from moose.neuroml.ChannelML import ChannelML +sys.path.append('/home/bhalla/moose/trunk/Demos/util') +import rdesigneur as rd + +PI = 3.14159265359 +useGssa = True +combineSegments = False +baselineTime = 10 +tetTime = 1 +interTetTime = 20 +postTetTime = 240 +ltdTime = 360 +postLtdTime = 60 +do3D = False +dt = 0.001 +plotdt = 0.1 +psdTetCa = 8e-3 +dendTetCa = 2e-3 +basalCa = 0.08e-3 +ltdCa = 0.25e-3 + +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + cellProto = [ ['ca1_minimal.p', 'elec'] ] + spineProto = [ ['makeSpineProto()', 'spine' ]] + chemProto = [ ['CaMKII_merged77.g', 'chem'] ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + chemRange = "H(1.1e-6 - dia) * H(p - 1300e-6)" + spineDistrib = [ \ + ["spine", '#apical#', \ + "spineSpacing", chemRange + " * 5e-6", \ + "spineSpacingDistrib", "1e-6", \ + "angle", "0", \ + "angleDistrib", "0", \ + "size", "1", \ + "sizeDistrib", "0" ] \ + ] + chemDistrib = [ \ + [ "chem", "#apical#", "install", chemRange ] + ] + + ###################################################################### + # Here we define the mappings across scales. Format: + # sourceObj sourceField destObj destField couplingExpr [wildcard][spatialExpn] + # where the coupling expression is anything a muParser can evaluate, + # using the input variable x. For example: 8e-5 + 300*x + # For now, let's use existing adaptors which take an offset and scale. + ###################################################################### + adaptorList = [ + [ 'Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 8e-5, 1 ], + [ 'Ca_conc', 'Ca', 'dend/Ca_dend_input', 'concInit', 8e-5, 1 ], + [ 'psd/tot_PSD_R', 'n', 'glu', 'Gbar', 0, 0.01 ], + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + spineDistrib = spineDistrib, \ + chemDistrib = chemDistrib, \ + cellProto = cellProto, \ + spineProto = spineProto, \ + chemProto = chemProto + ) + + return rdes + +def buildOnePlot( path, field = 'getConc' ): + elist = moose.vec( '/model/chem/' + path ) + tabname = path.replace( '/', '_' ) + tab = moose.Table2( '/graphs/' + tabname, len( elist ) ).vec + moose.connect( tab, 'requestOut', elist, field, 'OneToOne' ) + +def buildPlots(): + if not moose.exists( '/graphs' ): + moose.Neutral( '/graphs' ) + buildOnePlot( 'psd/actCaMKII' ) + buildOnePlot( 'spine/actCaMKII' ) + buildOnePlot( 'dend/DEND/actCaMKII' ) + buildOnePlot( 'psd/tot_PSD_R', 'getN' ) + +def displayPlots(): + #plt.style.use( 'ggplot' ) + #fig = plt.figure( figsize=( 6, 10 ), frameon=False, facecolor='white' ) + fig = plt.figure( figsize=( 5, 10 ), facecolor='white' ) + fig.subplots_adjust( left = 0.18 ) + elist = moose.wildcardFind( '/graphs/#[0]' ) + n = len(elist) + j = 1 + timePts = numpy.arange( 0, len( elist[0].vector ) ) * elist[0].dt + labelName = [ "[CaMKII] (uM)", "[CaMKII] (uM)", + "[CaMKII] (uM)", "# AMPAR" ] + showTickLabels = [0,0,0,1] + plotTitle = ['G', 'H', 'I', 'J'] + plotScale = [1000,1000,1000,1] + for i in zip( elist, labelName, showTickLabels, plotTitle, plotScale ): + ax = plt.subplot( 4, 1, j ) + ax.spines['top'].set_visible( False ) + ax.spines['right'].set_visible( False ) + + #This function does the same as below, one axis at a time + #ax.xaxis.set_tick_params( direction = 'out' ) + #ax.yaxis.set_tick_params( direction = 'out' ) + ax.tick_params( direction = 'out' ) + + # These two are equivalent, get rid of the ticks but not the border + #ax.xaxis.set_visible( False ) + #ax.get_xaxis().set_visible( False ) + if not i[2]: + ax.set_xticklabels([]) + for tick in ax.xaxis.get_major_ticks(): + tick.tick2On = False + for tick in ax.yaxis.get_major_ticks(): + tick.tick2On = False + + plt.ylabel( i[1], fontsize = 16 ) + # alternate way of doing this separately. + #plt.yaxis.label.size_size(16) + #plt.title( 'B' ) + ax.text( -0.18, 1.0, i[3], fontsize = 18, weight = 'bold', + transform=ax.transAxes ) + j = j + 1 + for k in i[0].vec: + plt.plot( timePts, k.vector * i[4] ) + #plt.title( i.name ) + print(i[0].name) + + plt.xlabel( 'Time (s)', fontsize = 16 ) + plt.show() + +def main(): + numpy.random.seed( 1234 ) + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + assert( moose.exists( '/model' ) ) + moose.element( '/model/elec/hsolve' ).tick = -1 + for i in range( 0, 10 ): + moose.setClock( i, 100 ) + for i in range( 10, 18 ): + moose.setClock( i, dt ) + moose.setClock( 18, plotdt ) + moose.reinit() + buildPlots() + # Run for baseline, tetanus, and post-tetanic settling time + print('starting...') + t1 = time.time() + moose.start( baselineTime ) + caPsd = moose.vec( '/model/chem/psd/Ca_input' ) + caDend = moose.vec( '/model/chem/dend/DEND/Ca_input' ) + castim = (numpy.random.rand( len( caPsd.concInit ) ) * 0.8 + 0.2) * psdTetCa + caPsd.concInit = castim + caDend.concInit = numpy.random.rand( len( caDend.concInit ) ) * dendTetCa + moose.start( tetTime ) + caPsd.concInit = basalCa + caDend.concInit = basalCa + moose.start( interTetTime ) + caPsd.concInit = castim + caDend.concInit = numpy.random.rand( len( caDend.concInit ) ) * dendTetCa + moose.start( tetTime ) + caPsd.concInit = basalCa + caDend.concInit = basalCa + moose.start( postTetTime ) + caPsd.concInit = ltdCa + caDend.concInit = ltdCa + moose.start( ltdTime ) + caPsd.concInit = basalCa + caDend.concInit = basalCa + moose.start( postLtdTime ) + print('real time = ', time.time() - t1) + + if do3D: + app = QtGui.QApplication(sys.argv) + compts = moose.wildcardFind( "/model/elec/#[ISA=compartmentBase]" ) + ecomptPath = [x.path for x in compts] + morphology = moogli.read_morphology_from_moose(name = "", path = "/model/elec") + morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \ + [0.0, 0.5, 1.0, 1.0], [1.0, 0.0, 0.0, 0.9] ) + viewer = moogli.DynamicMorphologyViewerWidget(morphology) + def callback( morphology, viewer ): + moose.start( 0.1 ) + return True + viewer.set_callback( callback, idletime = 0 ) + viewer.showMaximized() + viewer.show() + app.exec_() + + displayPlots() + +if __name__ == '__main__': + main() diff --git a/demos/Fig4_ReacDiff/ca1_minimal.p b/demos/Fig4_ReacDiff/ca1_minimal.p new file mode 100644 index 0000000..4395d62 --- /dev/null +++ b/demos/Fig4_ReacDiff/ca1_minimal.p @@ -0,0 +1,58 @@ +// genesis +// cell parameter file for the 1991 Traub CA1 hippocampal cell +// "phi" parameter reduced by e-3 +*cartesian +*relative + +*set_global RM 1.0 //ohm*m^2 +*set_global RA 1.0 //ohm*m +*set_global CM 0.03 //F/m^2 +*set_global EREST_ACT -0.06 // volts + +// The format for each compartment parameter line is : +// name parent x y z d ch dens ... +// For channels, "dens" = maximum conductance per unit area of compartment + + +dend_3 none 0 220 0 3.84 +dend_5 . 0 220 0 3.84 +dend_6 . 0 220 0 3.84 +dend_8 . 0 110 0 3.84 + +soma dend_8 0 125 0 8.46 + + +apical_10 soma 0 120 0 4.0 +apical_11 apical_10 0 120 0 3 +apical_12 apical_11 0 120 0 3 +apical_13 apical_12 0 120 0 2.6 +apical_14 apical_13 0 120 0 2.6 +apical_15 apical_14 0 120 0 2.6 +apical_16 apical_15 0 120 0 2.6 +apical_17 apical_16 0 120 0 2.6 +apical_18 apical_17 0 120 0 2.6 +apical_19 apical_18 0 120 0 2.6 + +apical_11_1 apical_10 -60 60 0 2 +apical_11_2 apical_11_1 -60 60 0 1.8 +apical_11_3 apical_11_2 0 80 0 1.5 +apical_11_4 apical_11_3 0 80 0 1.5 + +apical_13_1 apical_12 40 40 0 1.0 +apical_13_2 apical_13_1 40 40 0 1.0 + +apical_14_1 apical_13_2 0 10 0 1.0 +apical_14_2 . 0 10 0 1.0 +apical_14_3 . 0 10 0 1.0 +apical_14_4 . 0 10 0 1.0 +apical_14_5 . 0 10 0 1.0 +apical_14_6 . 0 10 0 1.0 +apical_14_7 . 0 10 0 1.0 +apical_14_8 . 0 10 0 1.0 +apical_14_9 . 0 10 0 1.0 +apical_14_10 . 0 10 0 1.0 +apical_14_11 . 0 10 0 1.0 +apical_14_12 . 0 10 0 1.0 +apical_14_13 . 0 10 0 1.0 +apical_15_1 . 0 30 0 1.0 +apical_15_2 . 0 60 0 1.0 diff --git a/demos/Fig4_ReacDiff/rxdSpineSize.py b/demos/Fig4_ReacDiff/rxdSpineSize.py new file mode 100644 index 0000000..22782de --- /dev/null +++ b/demos/Fig4_ReacDiff/rxdSpineSize.py @@ -0,0 +1,293 @@ +################################################################## +## This program is part of 'MOOSE', the +## Messaging Object Oriented Simulation Environment. +## Copyright (C) 2015 Upinder S. Bhalla. and NCBS +## It is made available under the terms of the +## GNU Lesser General Public License version 2.1 +## See the file COPYING.LIB for the full notice. +## +## rxdSpineSize.py: Builds a cell with spines and a propagating reaction +## wave. Products diffuse into the spine and cause it to get bigger. +################################################################## +import math +import pylab +import numpy +import matplotlib.pyplot as plt +import moose +import sys +sys.path.append( '../util' ) +import rdesigneur as rd +from PyQt5 import QtGui +import moogli +import moogli.extensions.moose +import matplotlib + +PI = 3.141592653 +ScalingForTesting = 10 +RM = 1.0 / ScalingForTesting +RA = 1.0 * ScalingForTesting +CM = 0.01 * ScalingForTesting +runtime = 100.0 +frameruntime = 1.0 +diffConst = 5e-12 +dendLen = 100e-6 +diffLen = 1.0e-6 +dendDia = 2e-6 +somaDia = 5e-6 +concInit = 0.001 # 1 millimolar +spineSpacing = 10e-6 +spineSpacingDistrib = 1e-6 +spineSize = 1.0 +spineSizeDistrib = 0.5 +spineAngle= numpy.pi / 2.0 +spineAngleDistrib = 0.0 + +def makeCellProto( name ): + elec = moose.Neuron( '/library/' + name ) + ecompt = [] + soma = rd.buildCompt( elec, 'soma', somaDia, somaDia, -somaDia, RM, RA, CM ) + dend = rd.buildCompt( elec, 'dend', dendLen, dendDia, 0, RM, RA, CM ) + moose.connect( soma, 'axial', dend, 'raxial' ) + elec.buildSegmentTree() + +def makeChemProto( name ): + chem = moose.Neutral( '/library/' + name ) + comptVol = diffLen * dendDia * dendDia * PI / 4.0 + for i in ( ['dend', comptVol], ['spine', 1e-19], ['psd', 1e-20] ): + print('making ', i) + compt = moose.CubeMesh( chem.path + '/' + i[0] ) + compt.volume = i[1] + #x = moose.Pool( compt.path + '/x' ) + #y = moose.BufPool( compt.path + '/y' ) + z = moose.Pool( compt.path + '/z' ) + #x.concInit = 0.0 + #x.diffConst = diffConst + #y.concInit = concInit + z.concInit = 0.0 + z.diffConst = diffConst + nInit = comptVol * 6e23 * concInit + nstr = str( 1/nInit) + + x = moose.Pool( chem.path + '/dend/x' ) + x.diffConst = diffConst + func = moose.Function( x.path + '/func' ) + func.expr = "-x0 * (0.3 - " + nstr + " * x0) * ( 1 - " + nstr + " * x0)" + print(func.expr) + func.x.num = 1 + moose.connect( x, 'nOut', func.x[0], 'input' ) + moose.connect( func, 'valueOut', x, 'increment' ) + z = moose.element( '/library/' + name + '/dend/z' ) + reac = moose.Reac( '/library/' + name + '/dend/reac' ) + reac.Kf = 1 + reac.Kb = 10 + moose.connect( reac, 'sub', x, 'reac' ) + moose.connect( reac, 'prd', z, 'reac' ) + +def makeSpineProto2( name ): + spine = moose.Neutral( '/library/' + name ) + shaft = rd.buildCompt( spine, 'shaft', 0.5e-6, 0.4e-6, 0, RM, RA, CM ) + head = rd.buildCompt( spine, 'head', 0.5e-6, 0.5e-6, 0.5e-6, RM, RA, CM ) + moose.connect( shaft, 'axial', head, 'raxial' ) + +def makeModel(): + moose.Neutral( '/library' ) + makeCellProto( 'cellProto' ) + makeChemProto( 'cProto' ) + makeSpineProto2( 'spine' ) + rdes = rd.rdesigneur( useGssa = False, \ + combineSegments = False, \ + stealCellFromLibrary = True, \ + diffusionLength = 1e-6, \ + cellProto = [['cellProto', 'elec' ]] ,\ + spineProto = [['spineProto', 'spine' ]] ,\ + chemProto = [['cProto', 'chem' ]] ,\ + spineDistrib = [ \ + ['spine', '#', \ + 'spacing', str( spineSpacing ), \ + 'spacingDistrib', str( spineSpacingDistrib ), \ + 'angle', str( spineAngle ), \ + 'angleDistrib', str( spineAngleDistrib ), \ + 'size', str( spineSize ), \ + 'sizeDistrib', str( spineSizeDistrib ) ] \ + ], \ + chemDistrib = [ \ + [ "chem", "dend", "install", "1" ] \ + ], + adaptorList = [ \ + [ 'psd/z', 'n', 'spine', 'psdArea', 10.0e-15, 300e-15 ], \ + ] \ + ) + rdes.buildModel( '/model' ) + x = moose.vec( '/model/chem/dend/x' ) + x.concInit = 0.0 + for i in range( 0,20 ): + x[i].concInit = concInit + +def makePlot( name, srcVec, field ): + tab = moose.Table2('/graphs/' + name + 'Tab', len( srcVec ) ).vec + for i in zip(srcVec, tab): + moose.connect(i[1], 'requestOut', i[0], field) + return tab + + +def displayPlots(): + for x in moose.wildcardFind( '/graphs/#[0]' ): + tab = moose.vec( x ) + for i in range( len( tab ) ): + pylab.plot( tab[i].vector, label=x.name[:-3] + " " + str( i ) ) + pylab.legend() + pylab.figure() + +def main(): + """ + This illustrates the use of rdesigneur to build a simple dendrite with + spines, and then to resize them using spine fields. These are the + fields that would be changed dynamically in a simulation with reactions + that affect spine geometry. + In this simulation there is a propagating reaction wave using a + highly abstracted equation, whose product diffuses into the spines and + makes them bigger. + """ + makeModel() + elec = moose.element( '/model/elec' ) + elec.setSpineAndPsdMesh( moose.element('/model/chem/spine'), moose.element('/model/chem/psd') ) + + eHead = moose.wildcardFind( '/model/elec/#head#' ) + oldDia = [ i.diameter for i in eHead ] + graphs = moose.Neutral( '/graphs' ) + #makePlot( 'psd_x', moose.vec( '/model/chem/psd/x' ), 'getN' ) + #makePlot( 'head_x', moose.vec( '/model/chem/spine/x' ), 'getN' ) + makePlot( 'dend_x', moose.vec( '/model/chem/dend/x' ), 'getN' ) + makePlot( 'dend_z', moose.vec( '/model/chem/dend/z' ), 'getN' ) + makePlot( 'head_z', moose.vec( '/model/chem/spine/z' ), 'getN' ) + makePlot( 'psd_z', moose.vec( '/model/chem/psd/z' ), 'getN' ) + makePlot( 'headDia', eHead, 'getDiameter' ) + + ''' + debug = moose.PyRun( '/pyrun' ) + debug.tick = 10 + debug.runString = """print "RUNNING: ", moose.element( '/model/chem/psd/z' ).n, moose.element( '/model/elec/head0' ).diameter""" + ''' + moose.reinit() + moose.start( runtime ) + + displayPlots() + pylab.plot( oldDia, label = 'old Diameter' ) + pylab.plot( [ i.diameter for i in eHead ], label = 'new Diameter' ) + pylab.legend() + pylab.show() + + app = QtGui.QApplication(sys.argv) + #widget = mv.MoogliViewer( '/model' ) + morphology = moogli.read_morphology_from_moose( name="", path = '/model/elec' ) + widget = moogli.MorphologyViewerWidget( morphology ) + widget.show() + return app.exec_() + quit() + +# Run the 'main' if this script is executed standalone. + +def showVisualization(): + makeModel() + elec = moose.element( '/model/elec' ) + elec.setSpineAndPsdMesh( moose.element('/model/chem/spine'), moose.element('/model/chem/psd') ) + + eHead = moose.wildcardFind( '/model/elec/#head#' ) + oldDia = [ i.diameter for i in eHead ] + graphs = moose.Neutral( '/graphs' ) + #makePlot( 'psd_x', moose.vec( '/model/chem/psd/x' ), 'getN' ) + #makePlot( 'head_x', moose.vec( '/model/chem/spine/x' ), 'getN' ) + makePlot( 'dend_x', moose.vec( '/model/chem/dend/x' ), 'getN' ) + dendZ = makePlot( 'dend_z', moose.vec( '/model/chem/dend/z' ), 'getN' ) + makePlot( 'head_z', moose.vec( '/model/chem/spine/z' ), 'getN' ) + psdZ = makePlot( 'psd_z', moose.vec( '/model/chem/psd/z' ), 'getN' ) + diaTab = makePlot( 'headDia', eHead, 'getDiameter' ) + # print diaTab[0].vector[-1] + # return + dendrite = moose.element("/model/elec/dend") + dendrites = [dendrite.path + "/" + str(i) for i in range(len(dendZ))] + # print dendrites + moose.reinit() + + spineHeads = moose.wildcardFind( '/model/elec/#head#') + # print moose.wildcardFind( '/model/elec/##') + + # print "dendZ", readValues(dendZ) + # print dendrite + + app = QtGui.QApplication(sys.argv) + viewer = create_viewer("/model/elec", dendrite, dendZ, diaTab, psdZ) + viewer.showMaximized() + viewer.start() + return app.exec_() + + +def create_viewer(path, moose_dendrite, dendZ, diaTab, psdZ): + network = moogli.extensions.moose.read(path=path, + vertices=15) + + dendrite = network.groups["dendrite"].shapes[moose_dendrite.path] + chem_compt_group = dendrite.subdivide(len(dendZ)) + normalizer = moogli.utilities.normalizer(0.0, + 300.0, + clipleft=True, + clipright=True) + colormap = moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow) + mapper = moogli.utilities.mapper(colormap, normalizer) + + def readValues(tables): + values = [] + for i in range(len(tables)): + values.append(tables[i].vector[-1]) + return values + + def prelude(view): + view.home() + view.pitch(math.pi / 3.0) + view.zoom(0.3) + network.groups["soma"].set("color", moogli.colors.RED) + network.groups["spine"].groups["shaft"].set("color", + moogli.colors.RED) + + def interlude(view): + moose.start(frameruntime) + network.groups["spine"].groups["head"].set("radius", + readValues(diaTab), + lambda x: x * 0.5e6) + network.groups["spine"].groups["head"].set("color", + readValues(psdZ), + mapper) + chem_compt_group.set("color", + readValues(dendZ), + mapper) + if moose.element("/clock").currentTime >= runtime: + view.stop() + + viewer = moogli.Viewer("Viewer") + viewer.attach_shapes(list(network.shapes.values())) + viewer.detach_shape(dendrite) + viewer.attach_shapes(list(chem_compt_group.shapes.values())) + + view = moogli.View("main-view", + prelude=prelude, + interlude=interlude) + cb = moogli.widgets.ColorBar(id="cb", + title="Molecule #", + text_color=moogli.colors.BLACK, + position=moogli.geometry.Vec3f(0.975, 0.5, 0.0), + size=moogli.geometry.Vec3f(0.30, 0.05, 0.0), + text_font="/usr/share/fonts/truetype/ubuntu-font-family/Ubuntu-R.ttf", + orientation=math.pi / 2.0, + text_character_size=20, + label_formatting_precision=0, + colormap=moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow), + color_resolution=100, + scalar_range=moogli.geometry.Vec2f(0.0, + 300.0)) + view.attach_color_bar(cb) + viewer.attach_view(view) + return viewer + + +if __name__ == '__main__': + showVisualization() diff --git a/demos/Fig5_CellMultiscale/Fig5A.py b/demos/Fig5_CellMultiscale/Fig5A.py new file mode 100644 index 0000000..8c7d4d2 --- /dev/null +++ b/demos/Fig5_CellMultiscale/Fig5A.py @@ -0,0 +1,157 @@ +######################################################################## +# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015. +# It is licenced under the GPL 2.1 or higher. +# There is no warranty of any kind. You are welcome to make copies under +# the provisions of the GPL. +# This programme illustrates building a panel of multiscale models to +# test neuronal plasticity in different contexts. The simulation is set +# to settle for 5 seconds, then a 2 second tetanus is delivered, then +# the simulation continues for another 50 seconds. +# By default we set it to run the smallest model, that takes about 4 minutes +# to run 57 seconds of simulation time, on an Intel core I7 at +# 2.2 GHz. The big model, VHC-neuron, takes almost 90 minutes. +# This program dumps data to text files for further analysis. +######################################################################## +import moogli +import numpy +import time +import pylab +import moose +from moose import neuroml +from PyQt5 import Qt, QtCore, QtGui +import matplotlib.pyplot as plt +import sys +import os +from moose.neuroml.ChannelML import ChannelML +sys.path.append('/home/bhalla/moose/trunk/Demos/util') +import rdesigneur as rd + +PI = 3.14159265359 +useGssa = True +combineSegments = False +#### Choose your favourite models here. ################# +#elecFileNames = ( "ca1_minimal.p", ) +#elecFileNames = ( "ca1_minimal.p", "h10.CNG.swc" ) +elecFileNames = ( "CA1.morph.xml", "ca1_minimal.p", "VHC-neuron.CNG.swc", "h10.CNG.swc" ) +synSpineList = [] +synDendList = [] +probeInterval = 0.1 +probeAmplitude = 1.0 +tetanusFrequency = 100.0 +tetanusAmplitude = 1000 +tetanusAmplitudeForSpines = 1000 +baselineTime = 5 +tetTime = 2 +postTetTime = 50 + +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + spineProto = [ \ + ['makeSpineProto()', 'spine' ] + ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + passiveDistrib = [ + [ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \ + "Em", "-58e-3", "initVm", "-65e-3" ], \ + [ ".", "#axon#", "RA", "0.5" ] \ + ] + spineDistrib = [ \ + ["spine", '#apical#', "spineSpacing", "20e-6", \ + "spineSpacingDistrib", "2e-6", \ + "angle", "0", \ + "angleDistrib", str( 2*PI ), \ + "size", "1", \ + "sizeDistrib", "0.5" ] \ + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + + rdes = rd.rdesigneur( + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + passiveDistrib = passiveDistrib, \ + spineDistrib = spineDistrib, \ + spineProto = spineProto \ + ) + + return rdes + +def interlude( view ): + view.yaw( 0.01 ) + +def create_viewer(rdes): + print(' doing viewer for ', rdes.soma.path) + network = moogli.extensions.moose.read(rdes.elecid.path) + normalizer = moogli.utilities.normalizer(-0.08, + 0.02, + clipleft=True, + clipright=True) + colormap = moogli.colors.UniformColorMap([moogli.colors.Color(0.0, + 0.5, + 1.0, + 1.0), + moogli.colors.Color(1.0, + 0.0, + 0.0, + 0.9)]) + mapper = moogli.utilities.mapper(colormap, normalizer) + + vms = [moose.element(x).Vm for x in list(network.shapes.keys())] + network.set("color", vms, mapper) + viewer = moogli.Viewer("vm-viewer") + viewer.attach_shapes(list(network.shapes.values())) + view = moogli.View("vm-view", interlude=interlude ) + viewer.attach_view(view) + viewer.show() + viewer.start() + view.pitch( PI/2.0 ) + return viewer + +def main(): + app = QtGui.QApplication(sys.argv) + numpy.random.seed(1234) + rdes = buildRdesigneur() + viewers = [] + j = 0 + for i in elecFileNames: + print(i) + ename = '/model' + str(j) + rdes.cellProtoList = [ ['./cells/' + i, 'elec' ] ] + rdes.buildModel( ename ) + assert( moose.exists( ename ) ) + moose.reinit() + viewers.append(create_viewer(rdes)) + j = j + 1 + app.exec_() + +if __name__ == '__main__': + main() diff --git a/demos/Fig5_CellMultiscale/Fig5BCD.py b/demos/Fig5_CellMultiscale/Fig5BCD.py new file mode 100644 index 0000000..5a4a9f7 --- /dev/null +++ b/demos/Fig5_CellMultiscale/Fig5BCD.py @@ -0,0 +1,281 @@ +######################################################################## +# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015. +# It is licenced under the GPL 2.1 or higher. +# There is no warranty of any kind. You are welcome to make copies under +# the provisions of the GPL. +# This programme illustrates building a panel of multiscale models to +# test neuronal plasticity in different contexts. The simulation is set +# to settle for 5 seconds, then a 2 second tetanus is delivered, then +# the simulation continues for another 50 seconds. +# By default we set it to run the smallest model, that takes about 4 minutes +# to run 57 seconds of simulation time, on an Intel core I7 at +# 2.2 GHz. The big model, VHC-neuron, takes almost 90 minutes. +# This program dumps data to text files for further analysis. +######################################################################## +import moogli +import numpy +import time +import pylab +import moose +from moose import neuroml +from PyQt5 import Qt, QtCore, QtGui +import matplotlib.pyplot as plt +import sys +import os +from moose.neuroml.ChannelML import ChannelML +sys.path.append('/home/bhalla/moose/trunk/Demos/util') +import rdesigneur as rd + +PI = 3.14159265359 +useGssa = True +combineSegments = False +#### Choose your favourite model here. ################# +#elecFileNames = ( "ca1_minimal.p", ) +#elecFileNames = ( "ca1_minimal.p", "h10.CNG.swc" ) +elecFileNames = ( "CA1.morph.xml", "ca1_minimal.p", "VHC-neuron.CNG.swc", "h10.CNG.swc" ) +synSpineList = [] +synDendList = [] +probeInterval = 0.1 +probeAmplitude = 1.0 +tetanusFrequency = 100.0 +tetanusAmplitude = 1000 +tetanusAmplitudeForSpines = 1000 +baselineTime = 5 +tetTime = 2 +postTetTime = 50 + +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + chanProto = [ + ['./chans/hd.xml'], \ + ['./chans/kap.xml'], \ + ['./chans/kad.xml'], \ + ['./chans/kdr.xml'], \ + ['./chans/na3.xml'], \ + ['./chans/nax.xml'], \ + ['./chans/CaConc.xml'], \ + ['./chans/Ca.xml'], \ + ['./chans/NMDA.xml'], \ + ['./chans/Glu.xml'] \ + ] + spineProto = [ \ + ['makeSpineProto()', 'spine' ] + ] + chemProto = [ \ + ['./chem/' + 'psd53.g', 'ltpModel'] \ + ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + passiveDistrib = [ + [ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \ + "Em", "-58e-3", "initVm", "-65e-3" ], \ + [ ".", "#axon#", "RA", "0.5" ] \ + ] + chanDistrib = [ \ + ["hd", "#dend#,#apical#", "Gbar", "5e-2*(1+(p*3e4))" ], \ + ["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \ + ["na3", "#soma#,#dend#,#apical#", "Gbar", "250" ], \ + ["nax", "#soma#,#axon#", "Gbar", "1250" ], \ + ["kap", "#axon#,#soma#", "Gbar", "300" ], \ + ["kap", "#dend#,#apical#", "Gbar", \ + "300*(H(100-p*1e6)) * (1+(p*1e4))" ], \ + ["Ca_conc", "#dend#,#apical#", "tau", "0.0133" ], \ + ["kad", "#soma#,#dend#,#apical#", "Gbar", \ + "300*H(p - 100e-6)*(1+p*1e4)" ], \ + ["Ca", "#dend#,#apical#", "Gbar", "50" ], \ + ["glu", "#dend#,#apical#", "Gbar", "200*H(p-200e-6)" ], \ + ["NMDA", "#dend#,#apical#", "Gbar", "2*H(p-200e-6)" ] \ + ] + spineDistrib = [ \ + ["spine", '#apical#', "spineSpacing", "20e-6", \ + "spineSpacingDistrib", "2e-6", \ + "angle", "0", \ + "angleDistrib", str( 2*PI ), \ + "size", "1", \ + "sizeDistrib", "0.5" ] \ + ] + chemDistrib = [ \ + [ "ltpModel", "#apical#", "install", "1"] + ] + + ###################################################################### + # Here we define the mappings across scales. Format: + # sourceObj sourceField destObj destField couplingExpr [wildcard][spatialExpn] + # where the coupling expression is anything a muParser can evaluate, + # using the input variable x. For example: 8e-5 + 300*x + # For now, let's use existing adaptors which take an offset and scale. + ###################################################################### + adaptorList = [ + [ 'Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 8e-5, 1 ], + [ 'Ca_conc', 'Ca', 'dend/Ca_dend_input', 'concInit', 8e-5, 1 ], + [ 'psd/tot_PSD_R', 'n', 'glu', 'Gbar', 0, 0.01 ], + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + passiveDistrib = passiveDistrib, \ + spineDistrib = spineDistrib, \ + chanDistrib = chanDistrib, \ + chemDistrib = chemDistrib, \ + spineProto = spineProto, \ + chanProto = chanProto, \ + chemProto = chemProto, \ + adaptorList = adaptorList + ) + + return rdes + +def buildPlots( rdes ): + numPlots = 10 + caPsd = moose.vec( '/model/chem/psd/Ca' ) + caHead = moose.vec( '/model/chem/spine/Ca' ) + psdR = moose.vec( '/model/chem/psd/tot_PSD_R' ) + numSpines = rdes.spineCompt.mesh.num + assert( 2 * numSpines == len( rdes.spineComptElist ) ) + if not moose.exists( '/graphs' ): + moose.Neutral( '/graphs' ) + assert( len( caPsd ) == numSpines ) + assert( len( caHead ) == numSpines ) + if numSpines < numPlots: + caPsdTab = moose.Table2( '/graphs/caPsdTab', numSpines ).vec + caHeadTab = moose.Table2( '/graphs/caHeadTab', numSpines ).vec + psdRtab = moose.Table2( '/graphs/psdRtab', numSpines ).vec + for i in range( numSpines ): + moose.connect( caPsdTab[i], 'requestOut', caPsd[i], 'getConc' ) + moose.connect( caHeadTab[i], 'requestOut', caHead[i], 'getConc') + moose.connect( psdRtab[i], 'requestOut', psdR[i], 'getN' ) + else: + caPsdTab = moose.Table2( '/graphs/caPsdTab', numPlots ).vec + caHeadTab = moose.Table2( '/graphs/caHeadTab', numPlots ).vec + psdRtab = moose.Table2( '/graphs/psdRtab', numPlots ).vec + dx = numSpines / numPlots + for i in range( numPlots ): + moose.connect( caPsdTab[i], 'requestOut', caPsd[i*dx], 'getConc' ) + moose.connect( caHeadTab[i], 'requestOut', caHead[i*dx], 'getConc' ) + moose.connect( psdRtab[i], 'requestOut', psdR[i*dx], 'getN' ) + vtab = moose.Table( '/graphs/vtab' ) + moose.connect( vtab, 'requestOut', rdes.soma, 'getVm' ) + eSpineCaTab = moose.Table( '/graphs/eSpineCaTab' ) + path = rdes.spineComptElist[1].path + "/Ca_conc" + moose.connect( eSpineCaTab, 'requestOut', path, 'getCa' ) + eSpineVmTab = moose.Table( '/graphs/eSpineVmTab' ) + moose.connect( eSpineVmTab, 'requestOut', rdes.spineComptElist[1], 'getVm' ) + eSpineGkTab = moose.Table( '/graphs/eSpineGkTab' ) + path = rdes.spineComptElist[1].path + "/NMDA" + moose.connect( eSpineGkTab, 'requestOut', path, 'getGk' ) + +def saveAndClearPlots( name ): + print('saveAndClearPlots( ', name, ' )') + for i in moose.wildcardFind( "/graphs/#" ): + #plot stuff + i.xplot( name + '.xplot', i.name ) + moose.delete( "/graphs" ) + +def printPsd( name ): + # Print the vol, the path dist from soma, the electrotonic dist, and N + psdR = moose.vec( '/model/chem/psd/tot_PSD_R' ) + neuronVoxel = moose.element( '/model/chem/spine' ).neuronVoxel + elecComptMap = moose.element( '/model/chem/dend' ).elecComptMap + print("len( neuronVoxel = ", len( neuronVoxel), min( neuronVoxel), max( neuronVoxel)) + print(len( elecComptMap), elecComptMap[0], elecComptMap[12]) + neuron = moose.element( '/model/elec' ) + ncompts = neuron.compartments + d = {} + j = 0 + for i in ncompts: + #print i + d[i] = j + j += 1 + + f = open( name + ".txt", 'w' ) + for i in range( len( psdR ) ): + n = psdR[i].n + conc = psdR[i].conc + vol = psdR[i].volume + compt = elecComptMap[ neuronVoxel[i] ] + #print compt + segIndex = d[compt[0]] + p = neuron.geometricalDistanceFromSoma[ segIndex ] + L = neuron.electrotonicDistanceFromSoma[ segIndex ] + s = str( i ) + " " + str(n) + " " + str( conc ) + " " + str(p) + " " + str(L) + "\n" + f.write( s ) + f.close() + + +def probeStimulus( time ): + for t in numpy.arange( 0, time, probeInterval ): + moose.start( probeInterval ) + for i in synSpineList: + i.activation( probeAmplitude ) + +def tetanicStimulus( time ): + tetInterval = 1.0/tetanusFrequency + for t in numpy.arange( 0, time, tetInterval ): + moose.start( tetInterval ) + for i in synDendList: + i.activation( tetanusAmplitude ) + for i in synSpineList: + i.activation( tetanusAmplitudeForSpines ) + +def main(): + global synSpineList + global synDendList + numpy.random.seed( 1234 ) + rdes = buildRdesigneur() + for i in elecFileNames: + print(i) + rdes.cellProtoList = [ ['./cells/' + i, 'elec'] ] + rdes.buildModel( '/model' ) + assert( moose.exists( '/model' ) ) + synSpineList = moose.wildcardFind( "/model/elec/#head#/glu,/model/elec/#head#/NMDA" ) + temp = set( moose.wildcardFind( "/model/elec/#/glu,/model/elec/#/NMDA" ) ) + + synDendList = list( temp - set( synSpineList ) ) + moose.reinit() + buildPlots( rdes ) + # Run for baseline, tetanus, and post-tetanic settling time + t1 = time.time() + probeStimulus( baselineTime ) + tetanicStimulus( tetTime ) + probeStimulus( postTetTime ) + print('real time = ', time.time() - t1) + + printPsd( i + ".fig5" ) + saveAndClearPlots( i + ".fig5" ) + moose.delete( '/model' ) + rdes.elecid = moose.element( '/' ) + +if __name__ == '__main__': + main() diff --git a/demos/Fig5_CellMultiscale/cells/970529c.CNG.swc b/demos/Fig5_CellMultiscale/cells/970529c.CNG.swc new file mode 100644 index 0000000..6b8748e --- /dev/null +++ b/demos/Fig5_CellMultiscale/cells/970529c.CNG.swc @@ -0,0 +1,2493 @@ +# Original file 970529c.out.swc edited by Duncan Donohue using StdSwc version 1.21 on 8/16/05. +# Irregularities and fixes documented in 970529c.out.swc.std. See StdSwc1.21.doc for more information. +# +# Claiborne to SWC conversion from L-Measure. R. 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278.15 407.77 -96.18 0.71 1730 + 1732 4 279.67 409.72 -96.18 0.71 1731 + 1733 4 281.19 411.5 -96.18 0.71 1732 + 1734 4 281.84 413.98 -96.18 0.71 1733 + 1735 4 283.15 415.94 -96.18 0.71 1734 + 1736 4 283.8 418.25 -96.18 0.71 1735 + 1737 4 284.88 419.67 -93.06 0.71 1736 + 1738 4 285.25 421.99 -93.06 0.71 1737 + 1739 4 286.12 424.65 -93.06 0.71 1738 + 1740 4 287.2 426.41 -93.06 0.71 1739 + 1741 4 287.87 427.72 -93.06 0.71 1740 + 1742 4 98.15 132.37 -11.6 1.6 833 + 1743 4 99.89 133.61 -11.6 1.6 1742 + 1744 4 101.63 135.03 -10.04 1.42 1743 + 1745 4 102.89 136.4 -10.04 1.42 1744 + 1746 4 104.84 137.29 -10.04 1.245 1745 + 1747 4 107.01 137.29 -10.04 1.245 1746 + 1748 4 108.32 138.35 -10.04 1.245 1747 + 1749 4 110.7 139.24 -8.42 1.245 1748 + 1750 4 113.09 140.31 -8.42 1.245 1749 + 1751 4 114.4 141.55 -8.42 1.245 1750 + 1752 4 115.92 143.5 -8.42 1.245 1751 + 1753 4 117.44 144.93 -8.42 1.245 1752 + 1754 4 119.17 146.7 -8.42 1.245 1753 + 1755 4 120.91 147.41 -10.38 1.245 1754 + 1756 4 124.01 149.35 -10.38 1.245 1755 + 1757 4 125.09 150.42 -10.38 1.245 1756 + 1758 4 127.03 151.49 -10.38 1.245 1757 + 1759 4 127.9 152.2 -12.32 1.42 1758 + 1760 4 128.12 153.26 -12.32 1.6 1759 + 1761 4 127.66 154.48 -11.34 1.42 1760 + 1762 4 127.01 157.15 -11.34 1.245 1761 + 1763 4 127.23 158.57 -11.34 1.245 1762 + 1764 4 126.14 159.99 -11.34 1.065 1763 + 1765 4 125.93 161.59 -11.34 1.065 1764 + 1766 4 126.14 163.72 -11.34 1.065 1765 + 1767 4 125.71 166.39 -10.09 0.89 1766 + 1768 4 124.99 167.6 -10.74 1.065 1767 + 1769 4 123.69 170.44 -10.74 1.065 1768 + 1770 4 122.61 173.1 -10.74 1.065 1769 + 1771 4 122.39 174.88 -10.74 1.065 1770 + 1772 4 120.43 176.3 -10.74 0.89 1771 + 1773 4 119.57 179.14 -13.15 0.89 1772 + 1774 4 118.48 181.1 -13.15 0.89 1773 + 1775 4 111.53 199.88 -15.63 0.89 1774 + 1776 4 111.09 202.19 -17.74 0.89 1775 + 1777 4 109.57 204.15 -16.32 0.89 1776 + 1778 4 108.05 206.81 -16.32 0.89 1777 + 1779 4 107.4 208.59 -19 0.89 1778 + 1780 4 106.97 210.01 -18.81 0.89 1779 + 1781 4 106.75 212.14 -19.57 0.89 1780 + 1782 4 107.08 214.82 -19.57 0.89 1781 + 1783 4 107.73 217.13 -21.53 0.89 1782 + 1784 4 107.95 219.08 -21.53 0.89 1783 + 1785 4 108.17 220.68 -20.49 0.89 1784 + 1786 4 108.17 222.28 -20.49 0.89 1785 + 1787 4 109.04 224.06 -22.98 0.89 1786 + 1788 4 109.47 225.48 -22.98 0.89 1787 + 1789 4 109.69 227.61 -22.98 0.89 1788 + 1790 4 110.12 229.92 -21.8 0.89 1789 + 1791 4 110.99 232.23 -23.58 0.89 1790 + 1792 4 111.86 233.83 -23.58 0.89 1791 + 1793 4 112.73 235.96 -22.74 0.71 1792 + 1794 4 113.16 238.62 -22.74 0.71 1793 + 1795 4 113.81 240.58 -24.97 0.71 1794 + 1796 4 114.46 241.82 -26.93 0.71 1795 + 1797 4 114.46 245.02 -27.81 0.71 1796 + 1798 4 115.62 246.41 -29.34 0.71 1797 + 1799 4 116.06 248.36 -29.34 0.71 1798 + 1800 4 116.28 249.96 -31.06 0.71 1799 + 1801 4 116.71 253.34 -29.5 0.71 1800 + 1802 4 117.36 256 -29.5 0.71 1801 + 1803 4 118.66 259.91 -29.5 0.71 1802 + 1804 4 119.61 262.45 -31.09 0.71 1803 + 1805 4 120.48 264.76 -31.09 0.71 1804 + 1806 4 121.13 266.71 -31.09 0.71 1805 + 1807 4 121.78 269.02 -31.24 0.71 1806 + 1808 4 122.43 271.16 -31.24 0.71 1807 + 1809 4 123.08 273.47 -31.24 0.71 1808 + 1810 4 123.3 275.77 -31.24 0.71 1809 + 1811 4 124.84 277.36 -31.24 0.71 1810 + 1812 4 124.41 279.85 -31.24 0.71 1811 + 1813 4 124.62 282.16 -31.19 0.71 1812 + 1814 4 124.62 284.65 -31.19 0.89 1813 + 1815 4 123.76 287.84 -31.19 0.89 1814 + 1816 4 123.32 290.15 -29.84 0.89 1815 + 1817 4 122.45 291.76 -29.84 0.89 1816 + 1818 4 122.02 294.07 -29.84 0.89 1817 + 1819 4 121.37 295.85 -27.79 0.89 1818 + 1820 4 120.28 299.4 -27.79 0.89 1819 + 1821 4 119.63 301 -27.79 0.89 1820 + 1822 4 119.41 303.31 -27.79 0.89 1821 + 1823 4 118.76 305.44 -27.79 0.89 1822 + 1824 4 118.3 308.23 -29.7 0.89 1823 + 1825 4 118.3 310.36 -29.7 0.89 1824 + 1826 4 117.87 312.31 -29.35 0.71 1825 + 1827 4 117.65 314.27 -29.35 0.71 1826 + 1828 4 117.22 316.22 -29.35 0.71 1827 + 1829 4 116.78 318.53 -29.44 0.71 1828 + 1830 4 117 320.84 -29.44 0.71 1829 + 1831 4 117.16 323.58 -26.38 0.71 1830 + 1832 4 117.37 326.43 -25.88 0.71 1831 + 1833 4 117.37 328.74 -26.61 0.71 1832 + 1834 4 117.59 331.93 -26.61 0.71 1833 + 1835 4 118.02 333.89 -24.66 0.71 1834 + 1836 4 118.24 336.55 -24.66 0.71 1835 + 1837 4 117.7 339.05 -24.66 0.71 1836 + 1838 4 117.49 341.18 -24.46 0.71 1837 + 1839 4 116.84 343.67 -24.46 0.71 1838 + 1840 4 116.18 345.27 -23.34 0.71 1839 + 1841 4 115.32 347.4 -23.08 0.71 1840 + 1842 4 114.66 349.53 -23.08 0.71 1841 + 1843 4 113.36 351.49 -23.08 0.71 1842 + 1844 4 113.12 352.99 -22.22 0.71 1843 + 1845 4 112.25 354.58 -22.22 0.71 1844 + 1846 4 110.73 355.83 -20.5 0.71 1845 + 1847 4 108.99 357.07 -20.5 0.71 1846 + 1848 4 107.69 359.03 -20.5 0.71 1847 + 1849 4 106.61 361.16 -20.86 0.71 1848 + 1850 4 105.74 362.93 -20.86 0.71 1849 + 1851 4 105.3 365.24 -18.22 0.71 1850 + 1852 4 105.52 367.55 -18.22 0.71 1851 + 1853 4 105.76 369.36 -18.22 0.71 1852 + 1854 4 105.54 370.96 -18.22 0.71 1853 + 1855 4 104.89 372.56 -17.36 0.71 1854 + 1856 4 104.89 375.76 -17.36 0.71 1855 + 1857 4 104.24 377.36 -17.36 0.71 1856 + 1858 4 104.45 378.96 -19.62 0.71 1857 + 1859 4 103.58 380.91 -19.62 0.71 1858 + 1860 4 103.15 382.69 -19.62 0.71 1859 + 1861 4 102.05 384.01 -18.9 0.71 1860 + 1862 4 101.18 385.61 -18.9 0.71 1861 + 1863 4 100.75 387.38 -19.01 0.71 1862 + 1864 4 100.1 389.69 -19.08 0.71 1863 + 1865 4 99.45 391.47 -19.08 0.71 1864 + 1866 4 99.23 393.25 -17.48 0.71 1865 + 1867 4 98.58 395.02 -17.48 0.71 1866 + 1868 4 97.06 397.69 -16.22 0.71 1867 + 1869 4 96.07 399.54 -16.22 0.71 1868 + 1870 4 95.64 401.85 -16.22 0.71 1869 + 1871 4 94.98 403.8 -15.14 0.71 1870 + 1872 4 94.77 406.29 -15.14 0.71 1871 + 1873 4 94.55 408.96 -16.16 0.71 1872 + 1874 4 94.33 411.09 -16.16 0.71 1873 + 1875 4 94.12 412.51 -16.16 0.71 1874 + 1876 4 93.92 414.7 -15.18 0.71 1875 + 1877 4 93.49 416.12 -15.18 0.71 1876 + 1878 4 93.7 418.07 -16.14 0.71 1877 + 1879 4 94.57 420.03 -16.14 0.71 1878 + 1880 4 95.22 422.87 -16.14 0.71 1879 + 1881 4 96.09 424.29 -16.14 0.71 1880 + 1882 4 97.4 426.24 -16.14 0.71 1881 + 1883 4 99.13 428.55 -16.14 0.71 1882 + 1884 4 100.24 429.81 -16.26 0.71 1883 + 1885 4 101.09 431.23 -17.58 0.71 1884 + 1886 4 101.96 433.54 -17.58 0.71 1885 + 1887 4 102.83 435.49 -17.58 0.71 1886 + 1888 4 103.48 437.8 -19.68 0.71 1887 + 1889 4 104.13 439.93 -19.68 0.71 1888 + 1890 4 104.57 441.71 -18.02 0.71 1889 + 1891 4 105.65 444.02 -19.78 0.71 1890 + 1892 4 107.08 445.94 -19.78 0.71 1891 + 1893 4 108.58 449.32 -19.78 0.71 1892 + 1894 4 108.58 451.45 -19.78 0.71 1893 + 1895 4 108.36 453.76 -18.92 0.71 1894 + 1896 4 108.58 455.87 -18.92 0.71 1895 + 1897 4 107.93 457.64 -18.92 0.71 1896 + 1898 4 108.14 459.6 -20.96 0.71 1897 + 1899 4 108.16 462.05 -20.78 0.71 1898 + 1900 4 108.81 464.36 -19.81 0.71 1899 + 1901 4 109.46 466.67 -22.46 0.71 1900 + 1902 4 109.68 469.33 -22.46 0.71 1901 + 1903 4 110.11 471.29 -22.46 0.71 1902 + 1904 4 110.76 473.24 -22.1 0.71 1903 + 1905 4 111.41 475.73 -22.1 0.71 1904 + 1906 4 111.56 477.72 -22.1 0.71 1905 + 1907 4 112.21 480.38 -22.1 0.71 1906 + 1908 4 112.21 482.51 -21.55 0.71 1907 + 1909 4 113.29 483.76 -23.06 0.71 1908 + 1910 4 114.81 485.36 -23.06 0.71 1909 + 1911 4 116.98 487.31 -23.06 0.71 1910 + 1912 4 118.29 488.55 -24.53 0.71 1911 + 1913 4 120.46 489.98 -24.53 0.71 1912 + 1914 4 123.14 491.74 -23.77 0.71 1913 + 1915 4 124.88 493.34 -23.77 0.71 1914 + 1916 4 126.18 494.58 -24.12 0.71 1915 + 1917 4 128.36 495.65 -25.64 0.71 1916 + 1918 4 129.23 496.71 -27.22 0.71 1917 + 1919 4 130.31 499.02 -29.28 0.71 1918 + 1920 4 131.61 501.16 -29.28 0.71 1919 + 1921 4 133.35 503.64 -29.28 0.71 1920 + 1922 4 135.09 505.95 -29.28 0.71 1921 + 1923 4 138.18 507.25 -26.71 0.71 1922 + 1924 4 139.92 507.59 -28.54 0.71 1923 + 1925 4 141.87 508.12 -27.29 0.71 1924 + 1926 4 144.04 509.54 -27.29 0.71 1925 + 1927 4 146.87 510.61 -27.29 0.71 1926 + 1928 4 149.25 512.03 -28.7 0.71 1927 + 1929 4 151.86 512.74 -28.7 0.71 1928 + 1930 4 154.11 513.83 -28.7 0.71 1929 + 1931 4 156.28 514.9 -28.7 0.71 1930 + 1932 4 157.8 515.78 -28.05 0.71 1931 + 1933 4 160.19 515.96 -28.05 0.71 1932 + 1934 4 161.71 517.38 -28.05 0.71 1933 + 1935 4 163.88 518.63 -29.96 0.71 1934 + 1936 4 165.84 518.98 -29.96 0.71 1935 + 1937 4 167.36 519.51 -30.54 0.71 1936 + 1938 4 169.75 520.4 -30.54 0.71 1937 + 1939 4 171.71 521.07 -30.54 0.71 1938 + 1940 4 174.75 522.83 -30.54 0.71 1939 + 1941 4 177.36 523.54 -30.54 0.71 1940 + 1942 4 178.42 525.19 -30.54 0.71 1941 + 1943 4 180.6 526.07 -29.19 0.71 1942 + 1944 4 182.77 527.49 -29.19 0.71 1943 + 1945 4 184.48 528.45 -30.65 0.71 1944 + 1946 4 186.65 529.52 -32.37 0.71 1945 + 1947 4 189.04 531.29 -30.94 0.71 1946 + 1948 4 190.99 532.54 -30.94 0.71 1947 + 1949 4 192.73 534.14 -33.76 0.71 1948 + 1950 4 195.33 536.09 -33.76 0.71 1949 + 1951 4 197.07 537.16 -33.76 0.71 1950 + 1952 4 198.37 539.29 -31.19 0.71 1951 + 1953 4 200.55 541.78 -33.38 0.71 1952 + 1954 4 202.94 543.74 -33.38 0.71 1953 + 1955 4 205.55 545.16 -32.87 0.71 1954 + 1956 4 207.51 546.58 -36.15 0.71 1955 + 1957 4 209.89 547.12 -36.15 0.71 1956 + 1958 4 211.85 547.83 -36.15 0.71 1957 + 1959 4 214.24 549.07 -36.28 0.71 1958 + 1960 4 215.97 550.31 -38.06 0.71 1959 + 1961 4 218.15 551.2 -38.06 0.71 1960 + 1962 4 220.11 552.41 -38.06 0.71 1961 + 1963 4 222.5 553.83 -38.06 0.71 1962 + 1964 4 224.02 555.43 -38.06 0.71 1963 + 1965 4 225.76 556.85 -39.22 0.71 1964 + 1966 4 227.28 558.8 -39.22 0.71 1965 + 1967 4 229.23 560.22 -38.27 0.71 1966 + 1968 4 231.4 562.36 -40.79 0.71 1967 + 1969 4 233.57 564.31 -40.79 0.71 1968 + 1970 4 235.31 565.73 -38.98 0.71 1969 + 1971 4 236.66 567.43 -41.87 0.71 1970 + 1972 4 238.04 568.45 -41.87 0.71 1971 + 1973 4 130.29 153.62 -12.32 1.42 1760 + 1974 4 132.46 154.33 -12.32 1.42 1973 + 1975 4 134.2 155.93 -13 1.42 1974 + 1976 4 135.28 157.35 -13 1.42 1975 + 1977 4 136.8 158.77 -13 1.42 1976 + 1978 4 138.97 160.01 -14.96 1.42 1977 + 1979 4 140.93 160.55 -14.96 1.42 1978 + 1980 4 143.34 162.18 -14.96 1.245 1979 + 1981 4 144.42 163.42 -14.96 1.245 1980 + 1982 4 146.38 165.02 -17.78 1.245 1981 + 1983 4 148.77 166.97 -17.78 1.245 1982 + 1984 4 150.94 168.75 -20.4 1.245 1983 + 1985 4 153.54 170.7 -20.4 1.245 1984 + 1986 4 155.5 171.95 -20.4 1.245 1985 + 1987 4 157.67 173.37 -20.4 1.245 1986 + 1988 4 159.84 174.79 -22.43 1.245 1987 + 1989 4 161.09 176.91 -22.43 1.245 1988 + 1990 4 162.61 179.04 -22.43 1.245 1989 + 1991 4 163.91 181.71 -23.53 1.245 1990 + 1992 4 165.86 184.02 -23.53 1.245 1991 + 1993 4 167.6 186.32 -25.49 1.245 1992 + 1994 4 168.47 187.57 -25.49 1.245 1993 + 1995 4 169.56 189.17 -26.96 1.245 1994 + 1996 4 170.42 190.77 -26.96 1.245 1995 + 1997 4 170.86 192.54 -26.96 1.245 1996 + 1998 4 171.29 193.25 -26.96 1.245 1997 + 1999 4 171.69 196.41 -29.56 1.065 1998 + 2000 4 172.35 200.67 -30.86 0.89 1999 + 2001 4 173 201.91 -32.81 0.89 2000 + 2002 4 172.78 203.16 -30.36 0.71 2001 + 2003 4 173.21 204.56 -33.54 0.71 2002 + 2004 4 173.87 206.51 -33.54 0.71 2003 + 2005 4 173.61 207.99 -36.85 0.71 2004 + 2006 4 174.48 210.47 -39.62 0.71 2005 + 2007 4 176.21 212.6 -41.46 0.71 2006 + 2008 4 176.43 214.2 -44.14 0.71 2007 + 2009 4 178.17 216.34 -44.14 0.71 2008 + 2010 4 179.69 218.64 -44.53 0.71 2009 + 2011 4 181.21 220.95 -46.7 0.71 2010 + 2012 4 184.28 224.14 -48.52 0.71 2011 + 2013 4 186.02 226.09 -50.26 0.71 2012 + 2014 4 187.76 228.76 -50.26 0.71 2013 + 2015 4 189.93 231.07 -49.74 0.71 2014 + 2016 4 191.02 232.84 -49.74 0.71 2015 + 2017 4 192.95 234.8 -53.27 0.71 2016 + 2018 4 193.39 236.4 -52.7 0.71 2017 + 2019 4 193.88 238.3 -56.21 0.71 2018 + 2020 4 195.61 240.25 -56.21 0.71 2019 + 2021 4 196.7 242.03 -55.74 0.71 2020 + 2022 4 198.44 244.16 -55.74 0.71 2021 + 2023 4 200.39 246.47 -60.65 0.71 2022 + 2024 4 202.13 249.13 -60.65 0.71 2023 + 2025 4 203.65 250.55 -62.71 0.71 2024 + 2026 4 204.28 251.96 -63.17 0.71 2025 + 2027 4 205.36 255.16 -63.17 0.71 2026 + 2028 4 205.8 257.29 -65.22 0.71 2027 + 2029 4 206.67 259.78 -68.57 0.71 2028 + 2030 4 207.32 262.09 -68.57 0.71 2029 + 2031 4 208.62 264.4 -70.42 0.71 2030 + 2032 4 208.84 266.89 -70.42 0.71 2031 + 2033 4 209.73 269.1 -70.22 0.71 2032 + 2034 4 210.81 270.7 -73.11 0.71 2033 + 2035 4 211.9 272.83 -73.11 0.71 2034 + 2036 4 213.85 274.96 -76.22 0.71 2035 + 2037 4 215.16 277.45 -76.22 0.71 2036 + 2038 4 216.89 280.47 -79.48 0.71 2037 + 2039 4 218.63 283.31 -79.48 0.71 2038 + 2040 4 220.38 284.94 -80.12 0.71 2039 + 2041 4 221.25 286.54 -82.98 0.71 2040 + 2042 4 224.07 289.92 -82.98 0.71 2041 + 2043 4 222.99 292.22 -84.88 0.71 2042 + 2044 4 224.29 294.89 -84.88 0.71 2043 + 2045 4 226.03 297.2 -87.38 0.71 2044 + 2046 4 227.33 299.15 -87.38 0.71 2045 + 2047 4 228.76 301.1 -89.58 0.71 2046 + 2048 4 230.72 303.76 -89.58 0.71 2047 + 2049 4 232.24 305.72 -88.9 0.71 2048 + 2050 4 233.32 307.14 -91.44 0.71 2049 + 2051 4 234.63 308.74 -91.44 0.71 2050 + 2052 4 235.49 311.04 -92.26 0.71 2051 + 2053 4 237.23 312.82 -92.26 0.71 2052 + 2054 4 239.4 314.42 -94.47 0.71 2053 + 2055 4 241.18 316.12 -94.47 0.71 2054 + 2056 4 242.05 317.72 -94.5 0.71 2055 + 2057 4 243.57 318.78 -94.5 0.71 2056 + 2058 4 245.74 320.03 -94.5 0.71 2057 + 2059 4 247.69 321.45 -94.5 0.71 2058 + 2060 4 249.18 322.23 -94.5 0.71 2059 + 2061 4 249.83 323.3 -94.5 0.71 2060 + 2062 4 250.48 324.18 -94.5 0.89 2061 + 2063 4 250.24 325.41 -92.05 0.71 2062 + 2064 4 251.11 327.16 -92.05 0.71 2063 + 2065 4 252.41 329.12 -92.05 0.71 2064 + 2066 4 254.15 330.72 -91.42 0.71 2065 + 2067 4 255.02 332.67 -88.13 0.71 2066 + 2068 4 256.76 335.69 -88.13 0.71 2067 + 2069 4 258.71 338.89 -88.13 0.71 2068 + 2070 4 260.16 341.07 -86.93 0.71 2069 + 2071 4 261.25 343.03 -86.93 0.71 2070 + 2072 4 261.68 344.8 -86.93 0.71 2071 + 2073 4 262.77 346.94 -89.26 0.71 2072 + 2074 4 265.37 349.6 -89.26 0.71 2073 + 2075 4 265.81 351.91 -88.25 0.71 2074 + 2076 4 267.55 354.93 -88.25 0.71 2075 + 2077 4 269.41 357.07 -87.89 0.71 2076 + 2078 4 270.5 359.56 -90.03 0.71 2077 + 2079 4 272.24 361.16 -90.03 0.71 2078 + 2080 4 273.97 362.76 -91.48 0.71 2079 + 2081 4 275.49 364.71 -91.48 0.71 2080 + 2082 4 277.88 366.13 -91.48 0.71 2081 + 2083 4 280.92 367.73 -91.48 0.71 2082 + 2084 4 282.44 370.04 -93.86 0.71 2083 + 2085 4 283.75 372.07 -93.86 0.71 2084 + 2086 4 286.13 374.38 -93.86 0.71 2085 + 2087 4 288.96 376.52 -93.86 0.71 2086 + 2088 4 290.48 378.47 -93.86 0.71 2087 + 2089 4 291.78 380.25 -95.68 0.71 2088 + 2090 4 294.17 383.62 -95.68 0.71 2089 + 2091 4 296.56 385.75 -95.68 0.71 2090 + 2092 4 297.95 387.52 -93.94 0.71 2091 + 2093 4 299.03 389.65 -93.94 0.71 2092 + 2094 4 300.33 391.78 -93.94 0.71 2093 + 2095 4 300.77 394.45 -91.73 0.71 2094 + 2096 4 301.2 397.29 -91.73 0.71 2095 + 2097 4 301.42 400.31 -91.73 0.71 2096 + 2098 4 300.81 403.01 -91.73 0.71 2097 + 2099 4 300.63 404.39 -91.73 0.71 2098 + 2100 4 299.32 406.87 -91.73 0.71 2099 + 2101 4 299.54 408.63 -87.99 0.71 2100 + 2102 4 299.76 411.47 -87.99 0.71 2101 + 2103 4 299.11 413.6 -84.5 0.71 2102 + 2104 4 299.32 416.27 -84.5 0.71 2103 + 2105 4 299.97 418.93 -84.5 0.71 2104 + 2106 4 298.96 421.78 -84.5 0.71 2105 + 2107 4 298.96 424.09 -84.14 0.71 2106 + 2108 4 299.39 426.23 -84.14 0.71 2107 + 2109 4 300.48 428.89 -84.14 0.71 2108 + 2110 4 301.35 433.33 -80.07 0.71 2109 + 2111 4 302.75 436.18 -80.07 0.71 2110 + 2112 4 304.7 439.92 -80.07 0.71 2111 + 2113 4 306.44 442.4 -80.07 0.71 2112 + 2114 4 307.31 444.71 -77.86 0.71 2113 + 2115 4 308.17 446.67 -77.86 0.71 2114 + 2116 4 309.48 449.86 -74.91 0.71 2115 + 2117 4 310.75 452.41 -74.91 0.71 2116 + 2118 4 312.48 454.89 -74.91 0.71 2117 + 2119 4 314.22 457.03 -74.91 0.71 2118 + 2120 4 315.31 459.34 -73.53 0.71 2119 + 2121 4 316.17 461.11 -73.53 0.71 2120 + 2122 4 317.48 463.78 -73.53 0.71 2121 + 2123 4 318.56 466.97 -75.58 0.71 2122 + 2124 4 319.51 468.92 -75.58 0.71 2123 + 2125 4 319.95 470.87 -74.23 0.71 2124 + 2126 4 321.03 473 -74.23 0.71 2125 + 2127 4 320.38 475.67 -71.43 0.71 2126 + 2128 4 320.16 477.62 -71.43 0.71 2127 + 2129 4 320.81 479.93 -71.43 0.71 2128 + 2130 4 319.95 482.78 -71.67 0.71 2129 + 2131 4 319.61 484.54 -69.26 0.71 2130 + 2132 4 319.83 486.67 -67.86 0.71 2131 + 2133 4 319.83 488.8 -70.26 0.71 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336.16 -37.3 0.71 2233 + 2235 4 220.84 337.58 -38.95 0.71 2234 + 2236 4 221.71 339.89 -38.95 0.71 2235 + 2237 4 222.36 342.38 -37.04 0.71 2236 + 2238 4 223.01 343.8 -37.04 0.71 2237 + 2239 4 223.67 345.76 -37.04 0.71 2238 + 2240 4 224.1 348.42 -37.04 0.71 2239 + 2241 4 224.91 350.14 -37.04 0.71 2240 + 2242 4 224.91 352.27 -37.04 0.71 2241 + 2243 4 225.78 355.12 -35.97 0.71 2242 + 2244 4 226.87 357.42 -37.05 0.71 2243 + 2245 4 228.39 360.27 -37.05 0.71 2244 + 2246 4 229.69 362.75 -37.05 0.71 2245 + 2247 4 230.53 365.23 -37.05 0.71 2246 + 2248 4 232.7 368.6 -37.05 0.71 2247 + 2249 4 234.87 370.18 -37.82 0.71 2248 + 2250 4 236.83 371.96 -37.82 0.71 2249 + 2251 4 239 374.09 -37.82 0.71 2250 + 2252 4 240.52 376.58 -37.82 0.71 2251 + 2253 4 242.26 378.53 -38.21 0.71 2252 + 2254 4 244.18 379.96 -38.21 0.71 2253 + 2255 4 245.92 381.38 -38.21 0.71 2254 + 2256 4 248.31 382.81 -38.21 0.71 2255 + 2257 4 249.17 384.05 -37.32 0.71 2256 + 2258 4 251.56 385.83 -36.91 0.71 2257 + 2259 4 253.95 387.25 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340.72 -13.74 0.71 2437 + 2439 4 313.78 341.97 -12.42 0.71 2438 + 2440 4 316.61 343.03 -12.42 0.71 2439 + 2441 4 318.56 343.56 -9.78 0.71 2440 + 2442 4 321.6 344.1 -9.78 0.71 2441 + 2443 4 323.11 345.44 -9.78 0.71 2442 + 2444 4 326.15 346.15 -9.78 0.71 2443 + 2445 4 328.31 347.03 -5.91 0.71 2444 + 2446 4 331.35 347.57 -5.91 0.71 2445 + 2447 4 333.95 348.81 -5.91 0.71 2446 + 2448 4 336.13 349.88 -5.91 0.71 2447 + 2449 4 338.52 350.23 -6.59 0.71 2448 + 2450 4 340.9 352.01 -3.68 0.71 2449 + 2451 4 342.5 353.26 -3.56 0.71 2450 + 2452 4 345.32 354.86 -3.56 0.71 2451 + 2453 4 347.49 354.86 -4.33 0.71 2452 + 2454 4 350.31 356.63 -2.45 0.71 2453 + 2455 4 351.83 359.12 -2.45 0.71 2454 + 2456 4 353.14 361.43 -2.17 0.71 2455 + 2457 4 353.35 363.38 -2.17 0.71 2456 + 2458 4 353.79 365.16 -1.03 0.71 2457 + 2459 4 354.22 366.94 2.1 0.71 2458 + 2460 4 353.98 368.1 2.1 0.71 2459 + 2461 4 354.19 369.7 2.34 0.71 2460 + 2462 4 355.93 372.01 2.34 0.71 2461 + 2463 4 357.45 374.32 3.12 0.71 2462 + 2464 4 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6755 +6757 4 112.41 129.85 9.3 0.435 6756 diff --git a/demos/Fig5_CellMultiscale/cells/VHC-neuron.CNG.swc b/demos/Fig5_CellMultiscale/cells/VHC-neuron.CNG.swc new file mode 100644 index 0000000..3a7b77c --- /dev/null +++ b/demos/Fig5_CellMultiscale/cells/VHC-neuron.CNG.swc @@ -0,0 +1,3022 @@ +# Original file VHC-neuron.swc edited using StdSwc version 1.31 on 2/28/13. +# Irregularities and fixes documented in VHC-neuron.swc.std. See StdSwc1.31.doc for more information. +# +# Neurolucida to SWC conversion from L-Measure. 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581.94 -11.8 0.54 2789 +2791 4 -0.34 585.61 -11.58 0.54 2790 +2792 4 1.06 590.57 -10.55 0.54 2791 +2793 4 1.36 592.1 -10.43 0.54 2792 +2794 4 2.42 593.18 -10.43 0.54 2793 +2795 4 3.33 594.09 -10.42 0.54 2794 +2796 4 4.09 596.99 -10.21 0.54 2795 +2797 4 5.18 601.67 -9.4 0.54 2796 +2798 4 6.39 605.03 -9.1 0.54 2797 +2799 4 8.17 608.71 -7.63 0.54 2798 +2800 4 8.66 611.57 -6.94 0.54 2799 +2801 4 8.85 612.9 -6.37 0.54 2800 +2802 4 8.73 614.22 -5.85 0.54 2801 +2803 4 8.63 615.53 -5.1 0.54 2802 +2804 4 8.21 617.15 -4.3 0.54 2803 +2805 4 7.77 618.49 -3.91 0.54 2804 +2806 4 -29.22 505.49 -10.91 0.65 2752 +2807 4 -30.38 510.28 -11.25 0.65 2806 +2808 4 -30.54 512.56 -11.01 0.65 2807 +2809 4 -31.88 517.53 -11.53 0.65 2808 +2810 4 -32.81 520.25 -11.18 0.65 2809 +2811 4 -34.59 524.5 -10.76 0.65 2810 +2812 4 -35.11 527.47 -11.17 0.65 2811 +2813 4 -36.54 531.0 -11.15 0.65 2812 +2814 4 -37.46 534.04 -12.51 0.65 2813 +2815 4 -38.11 536.8 -12.49 0.65 2814 +2816 4 -39.15 539.05 -13.45 0.65 2815 +2817 4 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402.74 7.15 0.65 2918 +2920 4 -31.79 405.45 7.68 0.65 2919 +2921 4 -34.06 407.7 6.67 0.65 2920 +2922 4 -35.9 409.5 7.01 0.65 2921 +2923 4 -38.35 411.92 7.41 0.65 2922 +2924 4 -41.44 414.68 7.43 0.65 2923 +2925 4 -46.14 419.63 7.14 0.65 2924 +2926 4 -48.43 422.49 7.62 0.65 2925 +2927 4 -48.54 425.34 6.78 0.65 2926 +2928 4 -48.64 428.77 6.22 0.65 2927 +2929 4 -48.07 430.64 5.89 0.65 2928 +2930 4 -47.63 433.53 6.06 0.54 2929 +2931 4 -47.99 435.73 5.77 0.54 2930 +2932 4 -48.6 437.55 4.35 0.54 2931 +2933 4 -49.3 438.85 3.63 0.54 2932 +2934 4 -49.29 439.74 5.46 0.54 2933 +2935 4 -50.1 440.54 5.16 0.54 2934 +2936 4 -50.96 441.39 4.26 0.54 2935 +2937 4 -51.52 442.86 3.39 0.54 2936 +2938 4 -52.49 444.74 3.07 0.54 2937 +2939 4 -53.85 447.31 1.86 0.54 2938 +2940 4 -54.82 448.87 1.56 0.54 2939 +2941 4 -54.78 450.35 0.58 0.54 2940 +2942 4 -55.02 452.7 0.0 0.54 2941 +2943 4 -55.12 454.94 -0.91 0.54 2942 +2944 4 -55.78 456.2 -1.17 0.54 2943 +2945 4 -57.93 457.42 -1.09 0.54 2944 +2946 4 -60.72 460.18 -1.02 0.54 2945 +2947 4 -61.87 463.13 -1.44 0.54 2946 +2948 4 -62.44 464.91 -2.35 0.54 2947 +2949 4 -62.81 466.19 -2.88 0.54 2948 +2950 4 -62.67 466.98 -3.04 0.54 2949 +2951 4 -5.99 292.26 22.29 0.865 2088 +2952 4 -5.25 294.24 22.42 0.865 2951 +2953 4 -4.94 296.38 22.6 0.865 2952 +2954 4 -3.89 299.58 22.82 0.865 2953 +2955 4 -1.99 302.56 22.11 0.865 2954 +2956 4 -0.94 304.26 22.18 0.865 2955 +2957 4 -0.79 306.85 22.41 0.865 2956 +2958 4 -1.4 310.18 22.8 0.865 2957 +2959 4 -2.07 313.26 24.29 0.865 2958 +2960 4 -1.92 315.84 24.61 0.865 2959 +2961 4 -2.08 318.11 24.91 0.865 2960 +2962 4 -2.39 321.15 25.24 0.865 2961 +2963 4 -3.31 324.17 25.7 0.865 2962 +2964 4 -4.07 326.74 26.09 0.65 2963 +2965 4 -6.04 328.69 26.61 0.65 2964 +2966 4 -7.57 332.02 27.16 0.65 2965 +2967 4 -8.07 332.51 28.39 0.65 2966 +2968 4 -9.45 333.87 28.64 0.65 2967 +2969 4 -11.59 335.97 29.04 0.65 2968 +2970 4 -12.81 339.01 29.46 0.65 2969 +2971 4 -14.35 342.33 29.92 0.65 2970 +2972 4 -16.34 344.9 30.36 0.65 2971 +2973 4 -18.01 346.25 30.64 0.65 2972 +2974 4 -19.26 348.09 32.3 0.65 2973 +2975 4 -19.83 349.85 33.05 0.65 2974 +2976 4 -20.38 351.0 33.9 0.65 2975 +2977 4 -21.41 352.01 34.62 0.65 2976 +2978 4 -21.71 352.9 34.81 0.65 2977 +2979 4 -21.97 353.78 35.37 0.65 2978 +2980 4 -21.82 356.05 35.65 0.65 2979 +2981 4 -21.83 358.78 35.92 0.65 2980 +2982 4 -21.29 360.38 36.93 0.65 2981 +2983 4 -20.75 362.49 38.54 0.65 2982 +2984 4 -19.8 363.97 39.11 0.65 2983 +2985 4 -19.08 364.47 40.23 0.65 2984 +2986 4 -18.66 364.64 41.56 0.65 2985 +2987 4 -18.04 365.84 41.93 0.65 2986 +2988 4 -17.67 365.79 42.5 0.65 2987 +2989 4 -17.2 365.91 44.37 0.65 2988 +2990 4 -6.61 91.18 9.77 0.435 1189 +2991 4 -7.98 91.62 9.94 0.435 2990 +2992 4 -8.7 91.42 10.44 0.435 2991 +2993 4 -8.69 91.11 10.56 0.65 2992 +2994 4 -8.95 90.75 11.08 0.65 2993 +2995 4 -8.89 90.09 11.62 0.65 2994 +2996 4 -9.16 89.43 11.96 0.65 2995 +2997 4 -9.56 88.31 12.41 0.65 2996 +2998 4 -9.55 87.99 12.53 0.65 2997 +2999 4 -9.83 87.06 12.69 0.65 2998 +3000 4 -9.81 86.44 12.78 0.65 2999 +3001 4 -9.77 86.09 13.2 0.65 3000 +3002 4 -9.87 85.27 13.65 0.65 3001 +3003 4 -9.68 84.79 13.89 0.65 3002 +3004 4 -9.21 84.32 13.95 0.65 3003 +3005 4 -8.85 83.96 14.57 0.65 3004 +3006 4 -8.62 83.72 15.35 0.65 3005 +3007 4 -8.21 83.31 16.42 0.65 3006 +3008 4 -7.9 82.7 16.39 0.65 3007 +3009 4 -7.85 82.04 16.93 0.65 3008 +3010 4 -7.79 81.68 17.42 0.65 3009 +3011 4 -7.91 80.57 17.78 0.435 3010 +3012 4 -7.99 80.05 18.49 0.435 3011 +3013 4 -7.97 79.73 18.53 0.435 3012 +3014 4 -8.26 79.11 18.65 0.435 3013 +3015 4 -8.4 78.63 18.84 0.435 3014 +3016 4 -8.68 78.0 18.96 0.435 3015 diff --git a/demos/Fig5_CellMultiscale/cells/ca1_minimal.p b/demos/Fig5_CellMultiscale/cells/ca1_minimal.p new file mode 100644 index 0000000..4395d62 --- /dev/null +++ b/demos/Fig5_CellMultiscale/cells/ca1_minimal.p @@ -0,0 +1,58 @@ +// genesis +// cell parameter file for the 1991 Traub CA1 hippocampal cell +// "phi" parameter reduced by e-3 +*cartesian +*relative + +*set_global RM 1.0 //ohm*m^2 +*set_global RA 1.0 //ohm*m +*set_global CM 0.03 //F/m^2 +*set_global EREST_ACT -0.06 // volts + +// The format for each compartment parameter line is : +// name parent x y z d ch dens ... +// For channels, "dens" = maximum conductance per unit area of compartment + + +dend_3 none 0 220 0 3.84 +dend_5 . 0 220 0 3.84 +dend_6 . 0 220 0 3.84 +dend_8 . 0 110 0 3.84 + +soma dend_8 0 125 0 8.46 + + +apical_10 soma 0 120 0 4.0 +apical_11 apical_10 0 120 0 3 +apical_12 apical_11 0 120 0 3 +apical_13 apical_12 0 120 0 2.6 +apical_14 apical_13 0 120 0 2.6 +apical_15 apical_14 0 120 0 2.6 +apical_16 apical_15 0 120 0 2.6 +apical_17 apical_16 0 120 0 2.6 +apical_18 apical_17 0 120 0 2.6 +apical_19 apical_18 0 120 0 2.6 + +apical_11_1 apical_10 -60 60 0 2 +apical_11_2 apical_11_1 -60 60 0 1.8 +apical_11_3 apical_11_2 0 80 0 1.5 +apical_11_4 apical_11_3 0 80 0 1.5 + +apical_13_1 apical_12 40 40 0 1.0 +apical_13_2 apical_13_1 40 40 0 1.0 + +apical_14_1 apical_13_2 0 10 0 1.0 +apical_14_2 . 0 10 0 1.0 +apical_14_3 . 0 10 0 1.0 +apical_14_4 . 0 10 0 1.0 +apical_14_5 . 0 10 0 1.0 +apical_14_6 . 0 10 0 1.0 +apical_14_7 . 0 10 0 1.0 +apical_14_8 . 0 10 0 1.0 +apical_14_9 . 0 10 0 1.0 +apical_14_10 . 0 10 0 1.0 +apical_14_11 . 0 10 0 1.0 +apical_14_12 . 0 10 0 1.0 +apical_14_13 . 0 10 0 1.0 +apical_15_1 . 0 30 0 1.0 +apical_15_2 . 0 60 0 1.0 diff --git a/demos/Fig5_CellMultiscale/cells/h10.CNG.swc b/demos/Fig5_CellMultiscale/cells/h10.CNG.swc new file mode 100644 index 0000000..554dbe2 --- /dev/null +++ b/demos/Fig5_CellMultiscale/cells/h10.CNG.swc @@ -0,0 +1,226 @@ +# Original file h10.swc edited by Duncan Donohue using StdSwc version 1.21 on 9/6/05. +# Irregularities and fixes documented in h10.swc.std. See StdSwc1.21.doc for more information. +# +#---------------------------------------------------------------------- +# This file was obtained using ban2swc.pl on file h10.txt +# (Jose Ambros-Ingerson, jose@kiubo.net): Sun Oct 19 18:38:56 2003 +#---------------------------------------------------------------------- +# ORIGINAL_SOURCE +# CREATURE +# REGION +# FIELD/LAYER +# TYPE +# CONTRIBUTOR +# REFERENCE +# RAW +# EXTRAS +# SOMA_AREA +# SHRINKAGE_CORRECTION +# VERSION_NUMBER +# VERSION_DATE +# ********************************************* +# SCALE 1.0 1.0 1.0 + 1 1 0. 23. 0. 3.35 -1 + 2 1 0. 18. 0. 2.5 1 + 3 1 0. 0. 0. 1.058 2 + 4 3 -4.157 -2.778 0. 0.6 3 + 5 3 -5.925 -3.510 -4.62 0.55 4 + 6 3 -15.47 -7.464 -29.560 0.4 5 + 7 3 -23.89 -9.139 -72.72 0.4 6 + 8 3 -24.39 -13.43 -83.51 0.350 6 + 9 3 -9.814 -5.121 -14.780 0.5 5 + 10 3 -15.81 -6.313 -23.93 0.5 9 + 11 3 -65.94 -16.29 -100.4 0.4 10 + 12 3 -54.5 -14.01 -82.960 0.4 10 + 13 3 -17.2 -10.06 -28.09 0.4 9 + 14 3 -78.64 -51.11 -138.70 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ModelViewParmSubset_5 + + + + ModelViewParmSubset_5 + + + + + + soma_group + + + + soma_group + + + + + + ModelViewParmSubset_7 + + + + ModelViewParmSubset_7 + + + + + + axon_group + soma_group + + + + + + all + + + + + + ModelViewParmSubset_2 + + + + ModelViewParmSubset_2 + + + + + + OneSecGrp_SectionRef_5 + + + + + + all + + + all + + + + + + + + dendrite_group + + + + + + + + + + dendrite_group + + + + + + + + + + dendrite_group + + + + + + + + all + + + + + + ModelViewParmSubset_2 + + + + OneSecGrp_SectionRef_5 + + + + + + all + + + + + + all + + + + + + + all + + + + + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chans/Ca.xml b/demos/Fig5_CellMultiscale/chans/Ca.xml new file mode 100644 index 0000000..645161c --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/Ca.xml @@ -0,0 +1,62 @@ + + + + + A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a + Detailed Network Model of the Cerebellar Granule Cell Layer + + + + + + + Voltage-gated Ca2+ channel, based on Traub + + + + Traub, R. + + + Upi Bhalla + NCBS + bhalla - at - ncbs.res.in + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/demos/Fig5_CellMultiscale/chans/CaConc.xml b/demos/Fig5_CellMultiscale/chans/CaConc.xml new file mode 100644 index 0000000..fe10a98 --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/CaConc.xml @@ -0,0 +1,36 @@ + + + + Ca pool + + + Signifies that the ion is involved in a process which alters its concentration + + + + + + + Upi Bhalla + + + + An expontially decaying pool of calcium + + + + Upi Bhalla + National Centre for Biological Sciences, Bangalore, India. + bhalla - at - ncbs.res.in + + + + + + + + + + + + diff --git a/demos/Fig5_CellMultiscale/chans/DoubExpSyn.xml b/demos/Fig5_CellMultiscale/chans/DoubExpSyn.xml new file mode 100644 index 0000000..58cc74e --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/DoubExpSyn.xml @@ -0,0 +1,32 @@ + + + + ChannelML file describing a single synaptic mechanism + + + + + + + Simple example of a synaptic mechanism, which consists of a postsynaptic conductance which changes as + double exponential function of time. Mappings exist for NEURON and GENESIS. + + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Receptor properties + http://senselab.med.yale.edu/senselab/NeuronDB/receptors2.asp + + + + + + + + diff --git a/demos/Fig5_CellMultiscale/chans/Generated.net.xml b/demos/Fig5_CellMultiscale/chans/Generated.net.xml new file mode 100644 index 0000000..d2f3f34 --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/Generated.net.xml @@ -0,0 +1,59 @@ + + + + + +Network structure (NeuroML 1.x) for project: CA1PyramidalCell saved with neuroConstruct v1.7.1 on: 11:29:49, 18-Jul-14 + +Cell Group: CA1_CG contains 1 cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chans/Glu.xml b/demos/Fig5_CellMultiscale/chans/Glu.xml new file mode 100644 index 0000000..c1a7d7c --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/Glu.xml @@ -0,0 +1,16 @@ + + + + + Glutamate receptor synchan, 2 ms tau. + + + + Simple double exponential waveform glu synapse + + + diff --git a/demos/Fig5_CellMultiscale/chans/HChannel.xml b/demos/Fig5_CellMultiscale/chans/HChannel.xml new file mode 100644 index 0000000..c1c91b4 --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/HChannel.xml @@ -0,0 +1,73 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and l traces on single comp with current pulse + + Padraig Gleeson + + + + H current. Comment from original mod: I-h channel from Magee 1998 for distal dendrites + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + diff --git a/demos/Fig5_CellMultiscale/chans/NMDA.xml b/demos/Fig5_CellMultiscale/chans/NMDA.xml new file mode 100644 index 0000000..ce7e3dd --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/NMDA.xml @@ -0,0 +1,16 @@ + + + + + NMDA receptor synchan, 20 ms tau. + + + + Simple double exponential waveform NMDA synapse + + + diff --git a/demos/Fig5_CellMultiscale/chans/hd.xml b/demos/Fig5_CellMultiscale/chans/hd.xml new file mode 100644 index 0000000..a882baa --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/hd.xml @@ -0,0 +1,73 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and l traces on single comp with current pulse + + Padraig Gleeson + + + + H current. Comment from original mod: I-h channel from Magee 1998 for distal dendrites + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chans/kad.xml b/demos/Fig5_CellMultiscale/chans/kad.xml new file mode 100644 index 0000000..bb7c5af --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/kad.xml @@ -0,0 +1,84 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + A type K channel for distal dendrites. Comment from original mod: K-A channel from Klee Ficker and Heinemann, modified to account for Dax A Current, M.Migliore Jun 1997 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chans/kap.xml b/demos/Fig5_CellMultiscale/chans/kap.xml new file mode 100644 index 0000000..58fdea0 --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/kap.xml @@ -0,0 +1,86 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + A type K channel. Comment from original mod: K-A channel from Klee Ficker and Heinemann, + modified to account for Dax A Current --- M.Migliore Jun 1997, + modified to be used with cvode M.Migliore 2001 + + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chans/kdr.xml b/demos/Fig5_CellMultiscale/chans/kdr.xml new file mode 100644 index 0000000..180c563 --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/kdr.xml @@ -0,0 +1,75 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + Delayed rectifier K channel. Comment from original mod: K-DR channel, from Klee Ficker and Heinemann, + modified to account for Dax et al., M.Migliore 1997 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chans/na3.xml b/demos/Fig5_CellMultiscale/chans/na3.xml new file mode 100644 index 0000000..94e9713 --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/na3.xml @@ -0,0 +1,107 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + Note: the inactivation gate s is not included here as it was disabled in original mod file for Migliore et al. Changing the parameter below ar from 1 will not enable s! + + Padraig Gleeson + + + + Na channel. Comment from original mod: Na current, modified from Jeff Magee. M.Migliore may97, + added sh to account for higher threshold M.Migliore, Apr.2002 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + Na channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chans/nax.xml b/demos/Fig5_CellMultiscale/chans/nax.xml new file mode 100644 index 0000000..1225d6a --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/nax.xml @@ -0,0 +1,88 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + Na channel for axon. Comment from original mod: Na current for axon. No slow inact. M.Migliore Jul. 1997, + added sh to account for higher threshold M.Migliore, Apr.2002 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + Na channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + + + diff --git a/demos/Fig5_CellMultiscale/chans/pas.xml b/demos/Fig5_CellMultiscale/chans/pas.xml new file mode 100644 index 0000000..9abffeb --- /dev/null +++ b/demos/Fig5_CellMultiscale/chans/pas.xml @@ -0,0 +1,17 @@ + + + + ChannelML file containing a single Channel description + + + + + + Simple example of a leak/passive conductance. Note: for GENESIS cells with a single leak conductance, + it is better to use the Rm and Em variables for a passive current. + + + + + + \ No newline at end of file diff --git a/demos/Fig5_CellMultiscale/chem/psd53.g b/demos/Fig5_CellMultiscale/chem/psd53.g new file mode 100644 index 0000000..e120a6a --- /dev/null +++ b/demos/Fig5_CellMultiscale/chem/psd53.g @@ -0,0 +1,477 @@ +//genesis +// kkit Version 11 flat dumpfile + +// Saved on Fri Jun 5 09:12:59 2015 + +include kkit {argv 1} + +FASTDT = 1e-05 +SIMDT = 0.0001 +CONTROLDT = 1 +PLOTDT = 0.2 +MAXTIME = 200 +TRANSIENT_TIME = 2 +VARIABLE_DT_FLAG = 1 +DEFAULT_VOL = 1e-19 +VERSION = 11.0 +setfield /file/modpath value /home2/bhalla/scripts/modules +kparms + +//genesis + +initdump -version 3 -ignoreorphans 1 +simobjdump doqcsinfo filename accessname accesstype transcriber developer \ + citation species tissue cellcompartment methodology sources \ + model_implementation model_validation x y z +simobjdump table input output alloced step_mode stepsize x y z +simobjdump xtree path script namemode sizescale +simobjdump xcoredraw xmin xmax ymin ymax +simobjdump xtext editable +simobjdump xgraph xmin xmax ymin ymax overlay +simobjdump xplot pixflags script fg ysquish do_slope wy +simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ + link savename file version md5sum mod_save_flag x y z +simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \ + z +simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \ + geomname xtree_fg_req xtree_textfg_req x y z +simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z +simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ + keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z +simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ + trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z +simobjdump xtab input output alloced step_mode stepsize notes editfunc \ + xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z +simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ + xtree_textfg_req x y z +simobjdump transport input output alloced step_mode stepsize dt delay clock \ + kf xtree_fg_req xtree_textfg_req x y z +simobjdump proto x y z +simobjdump text str +simundump geometry /kinetics/geometry 0 1.6667e-21 3 sphere "" white black 5 \ + -4 0 +simundump geometry /kinetics/geometry[1] 0 1e-19 3 sphere "" white black 5 -2 \ + 0 +simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black 2 2 \ + 0 +simundump geometry /kinetics/geometry[3] 0 1e-20 3 sphere "" white black 4 8 \ + 0 +simundump geometry /kinetics/geometry[4] 0 1e-20 3 sphere "" white black 2 \ + -17 0 +simundump geometry /kinetics/geometry[5] 0 1e-20 3 sphere "" white black 5 \ + -13 0 +simundump geometry /kinetics/geometry[6] 0 1e-19 3 sphere "" white black 0 7 \ + 0 +simundump geometry /kinetics/geometry[7] 0 1e-20 3 sphere "" white black 0 -3 \ + 0 +simundump geometry /kinetics/geometry[8] 0 1e-20 3 sphere "" white black -1 \ + -18 0 +simundump geometry /kinetics/geometry[9] 0 1e-18 3 sphere "" white black 0 0 \ + 0 +simundump text /kinetics/notes 0 "" +call /kinetics/notes LOAD \ +"" +simundump text /kinetics/geometry/notes 0 "" +call /kinetics/geometry/notes LOAD \ +"" +simundump text /kinetics/geometry[1]/notes 0 "" +call /kinetics/geometry[1]/notes LOAD \ +"" +simundump text /kinetics/geometry[2]/notes 0 "" +call /kinetics/geometry[2]/notes LOAD \ +"" +simundump text /kinetics/geometry[3]/notes 0 "" +call /kinetics/geometry[3]/notes LOAD \ +"" +simundump text /kinetics/geometry[4]/notes 0 "" +call /kinetics/geometry[4]/notes LOAD \ +"" +simundump text /kinetics/geometry[5]/notes 0 "" +call /kinetics/geometry[5]/notes LOAD \ +"" +simundump text /kinetics/geometry[6]/notes 0 "" +call /kinetics/geometry[6]/notes LOAD \ +"" +simundump text /kinetics/geometry[7]/notes 0 "" +call /kinetics/geometry[7]/notes LOAD \ +"" +simundump text /kinetics/geometry[8]/notes 0 "" +call /kinetics/geometry[8]/notes LOAD \ +"" +simundump text /kinetics/geometry[9]/notes 0 "" +call /kinetics/geometry[9]/notes LOAD \ +"" +simundump kreac /kinetics/exocytosis 0 0.01 0 "" white black 4 -5 0 +simundump text /kinetics/exocytosis/notes 0 "" +call /kinetics/exocytosis/notes LOAD \ +"" +simundump kreac /kinetics/endocytosis 0 0 4 "" white black -7 -5 0 +simundump text /kinetics/endocytosis/notes 0 "" +call /kinetics/endocytosis/notes LOAD \ +"" +simundump group /kinetics/PSD 0 0 black x 0 1 "" PSD defaultfile.g 0 0 0 -10 \ + -3 0 +simundump text /kinetics/PSD/notes 0 "" +call /kinetics/PSD/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Rp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] \ + blue 0 -4 1 0 +simundump text /kinetics/PSD/Rp/notes 0 "" +call /kinetics/PSD/Rp/notes LOAD \ +"" +simundump kpool /kinetics/PSD/P 0 0 1 1 6 6 0 0 6 0 /kinetics/geometry[1] 61 \ + 0 -4 -2 0 +simundump text /kinetics/PSD/P/notes 0 "" +call /kinetics/PSD/P/notes LOAD \ +"" +simundump kenz /kinetics/PSD/P/P1 0 0 0 0 0 60 10.417 20 5 0 0 "" red 61 "" \ + -6 -1 0 +simundump text /kinetics/PSD/P/P1/notes 0 "" +call /kinetics/PSD/P/P1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/P/P2 0 0 0 0 0 60 10.417 20 5 0 0 "" red 61 "" \ + -2 -1 0 +simundump text /kinetics/PSD/P/P2/notes 0 "" +call /kinetics/PSD/P/P2/notes LOAD \ +"" +simundump kpool /kinetics/PSD/KK 0 0 3 3 18 18 0 0 6 0 /kinetics/geometry[1] \ + 49 0 -4 4 0 +simundump text /kinetics/PSD/KK/notes 0 "" +call /kinetics/PSD/KK/notes LOAD \ +"" +simundump kenz /kinetics/PSD/KK/KK1 0 0 0 0 0 60 4.1667 40 10 0 0 "" red 49 \ + "" -6 3 0 +simundump text /kinetics/PSD/KK/KK1/notes 0 "" +call /kinetics/PSD/KK/KK1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/KK/KK2 0 0 0 0 0 60 4.1667 40 10 0 0 "" red 49 \ + "" -2 3 0 +simundump text /kinetics/PSD/KK/KK2/notes 0 "" +call /kinetics/PSD/KK/KK2/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Rpp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] \ + 28 0 0 1 0 +simundump text /kinetics/PSD/Rpp/notes 0 "" +call /kinetics/PSD/Rpp/notes LOAD \ +"" +simundump kpool /kinetics/PSD/R 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] 4 0 \ + -8 1 0 +simundump text /kinetics/PSD/R/notes 0 "" +call /kinetics/PSD/R/notes LOAD \ +"" +simundump kpool /kinetics/PSD/tot_PSD_R 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry[4] blue 0 -4 7 0 +simundump text /kinetics/PSD/tot_PSD_R/notes 0 "" +call /kinetics/PSD/tot_PSD_R/notes LOAD \ +"" +simundump kpool /kinetics/PSD/psd_inact_CaN 0 0 1 1 6 6 0 0 6 0 \ + /kinetics/geometry[7] blue 0 -12 5 0 +simundump text /kinetics/PSD/psd_inact_CaN/notes 0 "" +call /kinetics/PSD/psd_inact_CaN/notes LOAD \ +"" +simundump kreac /kinetics/PSD/psd_activate_CaN 0 0.27778 1 "" white 0 -11 1 0 +simundump text /kinetics/PSD/psd_activate_CaN/notes 0 "" +call /kinetics/PSD/psd_activate_CaN/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Ca.P 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[7] \ + blue 0 -4 -4 0 +simundump text /kinetics/PSD/Ca.P/notes 0 "" +call /kinetics/PSD/Ca.P/notes LOAD \ +"" +simundump kenz /kinetics/PSD/Ca.P/Ca.P2 0 0 0 0 0 6 1.6667 40 10 0 0 "" red \ + blue "" -2 -3 0 +simundump text /kinetics/PSD/Ca.P/Ca.P2/notes 0 "" +call /kinetics/PSD/Ca.P/Ca.P2/notes LOAD \ +"" +simundump kenz /kinetics/PSD/Ca.P/Ca.P1 0 0 0 0 0 6 1.6667 40 10 0 0 "" red \ + blue "" -6 -3 0 +simundump text /kinetics/PSD/Ca.P/Ca.P1/notes 0 "" +call /kinetics/PSD/Ca.P/Ca.P1/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Ca_input 0 0 0.1 0.1 0.6 0.6 0 0 6 4 \ + /kinetics/geometry[8] 60 black -12 9 0 +simundump text /kinetics/PSD/Ca_input/notes 0 "" +call /kinetics/PSD/Ca_input/notes LOAD \ +"" +simundump kreac /kinetics/PSD/Ca_reac 0 100 100 "" white black -17 6 0 +simundump text /kinetics/PSD/Ca_reac/notes 0 "" +call /kinetics/PSD/Ca_reac/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Ca 0 1e-11 0.1 0.1 0.6 0.6 0 0 6 0 \ + /kinetics/geometry[5] 53 0 -15 2 0 +simundump text /kinetics/PSD/Ca/notes 0 "" +call /kinetics/PSD/Ca/notes LOAD \ +"" +simundump group /kinetics/Bulk 0 yellow black x 0 0 "" Bulk defaultfile.g 0 0 \ + 0 -6 -16 0 +simundump text /kinetics/Bulk/notes 0 "" +call /kinetics/Bulk/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iRpp 0 0 0 0 0 0 0 0 59.999 0 \ + /kinetics/geometry 29 yellow 2 -11 0 +simundump text /kinetics/Bulk/iRpp/notes 0 "" +call /kinetics/Bulk/iRpp/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iRp 0 0 0 0 0 0 0 0 59.999 0 \ + /kinetics/geometry blue yellow -2 -11 0 +simundump text /kinetics/Bulk/iRp/notes 0 "" +call /kinetics/Bulk/iRp/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iR 0 0 4.0001 4.0001 240 240 0 0 59.999 0 \ + /kinetics/geometry 0 yellow -6 -11 0 +simundump text /kinetics/Bulk/iR/notes 0 "Same as Fus3\n" +call /kinetics/Bulk/iR/notes LOAD \ +"Same as Fus3" \ +"" +simundump kpool /kinetics/Bulk/iKK 0 0 1 1 59.999 59.999 0 0 59.999 0 \ + /kinetics/geometry 50 yellow -2 -8 0 +simundump text /kinetics/Bulk/iKK/notes 0 "Same as Ste7\n" +call /kinetics/Bulk/iKK/notes LOAD \ +"Same as Ste7" \ +"" +simundump kenz /kinetics/Bulk/iKK/iKK1 0 0 0 0 0 59.999 0.83335 40 10 0 0 "" \ + red 50 "" -4 -9 0 +simundump text /kinetics/Bulk/iKK/iKK1/notes 0 "" +call /kinetics/Bulk/iKK/iKK1/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/iKK/iKK2 0 0 0 0 0 59.999 0.83335 40 10 0 0 "" \ + red 50 "" 0 -9 0 +simundump text /kinetics/Bulk/iKK/iKK2/notes 0 "" +call /kinetics/Bulk/iKK/iKK2/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iP 0 0 0.50001 0.50001 30 30 0 0 59.999 0 \ + /kinetics/geometry 62 yellow -2 -14 0 +simundump text /kinetics/Bulk/iP/notes 0 "Same as Msg5\n" +call /kinetics/Bulk/iP/notes LOAD \ +"Same as Msg5" \ +"" +simundump kenz /kinetics/Bulk/iP/iP1 0 0 0 0 0 59.999 6.2501 60 15 0 0 "" red \ + 62 "" -4 -13 0 +simundump text /kinetics/Bulk/iP/iP1/notes 0 "" +call /kinetics/Bulk/iP/iP1/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/iP/iP2 0 0 0 0 0 59.999 6.2501 60 15 0 0 "" red \ + 62 "" 0 -13 0 +simundump text /kinetics/Bulk/iP/iP2/notes 0 "" +call /kinetics/Bulk/iP/iP2/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/PKA 0 0 0 0 0 0 0 0 60 0 /kinetics/geometry[3] \ + 43 yellow -3 -5 0 +simundump text /kinetics/Bulk/PKA/notes 0 "" +call /kinetics/Bulk/PKA/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/PKA/PKA1 0 0 0 0 0 60 0.41667 40 10 0 0 "" red \ + 43 "" -4 -7 0 +simundump text /kinetics/Bulk/PKA/PKA1/notes 0 "" +call /kinetics/Bulk/PKA/PKA1/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/PKA/PKA2 0 0 0 0 0 60 0.41667 40 10 0 0 "" red \ + 43 "" 0 -7 0 +simundump text /kinetics/Bulk/PKA/PKA2/notes 0 "" +call /kinetics/Bulk/PKA/PKA2/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/PKA/PKA_exo 0 0 0 0 0 60 0.016667 8 2 0 0 "" \ + red 43 "" 1 -5 0 +simundump text /kinetics/Bulk/PKA/PKA_exo/notes 0 "" +call /kinetics/Bulk/PKA/PKA_exo/notes LOAD \ +"" +simundump kreac /kinetics/Bulk/activate_PKA 0 0.0016667 5 "" white yellow -11 \ + -10 0 +simundump text /kinetics/Bulk/activate_PKA/notes 0 "" +call /kinetics/Bulk/activate_PKA/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/inact_PKA 0 0 1.6 1.6 96 96 0 0 60 0 \ + /kinetics/geometry[2] 51 yellow -12 -6 0 +simundump text /kinetics/Bulk/inact_PKA/notes 0 "" +call /kinetics/Bulk/inact_PKA/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/inact_CaN 0 0 0.2 0.2 12 12 0 0 60 0 \ + /kinetics/geometry[6] blue yellow -13 -18 0 +simundump text /kinetics/Bulk/inact_CaN/notes 0 "" +call /kinetics/Bulk/inact_CaN/notes LOAD \ +"" +simundump kreac /kinetics/Bulk/activate_CaN 0 0.0055556 1 "" white yellow -10 \ + -16 0 +simundump text /kinetics/Bulk/activate_CaN/notes 0 "" +call /kinetics/Bulk/activate_CaN/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/Ca 0 1e-11 0.1 0.1 6 6 0 0 60 0 \ + /kinetics/geometry[2] 50 yellow -15 -13 0 +simundump text /kinetics/Bulk/Ca/notes 0 "" +call /kinetics/Bulk/Ca/notes LOAD \ +"" +simundump kpool /kinetics/Ca_dend_input 0 0 0 0 0 0 0 0 600 0 \ + /kinetics/geometry[9] 60 black -12 -28 0 +simundump text /kinetics/Ca_dend_input/notes 0 "" +call /kinetics/Ca_dend_input/notes LOAD \ +"" +simundump kreac /kinetics/dend_Ca_reac 0 100 100 "" white black -16 -27 0 +simundump text /kinetics/dend_Ca_reac/notes 0 "" +call /kinetics/dend_Ca_reac/notes LOAD \ +"" +simundump kpool /kinetics/Ca 0 1e-11 0 0 0 0 0 0 600 0 /kinetics/geometry[9] \ + 1 black -19 -25 0 +simundump text /kinetics/Ca/notes 0 "" +call /kinetics/Ca/notes LOAD \ +"" +simundump xgraph /graphs/conc1 0 0 800 9.6002e-07 0.10547 0 +simundump xgraph /graphs/conc2 0 0 800 0 18.128 0 +simundump xplot /graphs/conc1/Ca_PSD.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 53 0 0 1 +simundump xplot /graphs/conc1/Ca_Bulk.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 41 0 0 1 +simundump xplot /graphs/conc1/PKA.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 43 0 0 1 +simundump xplot /graphs/conc1/Ca.P.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xplot /graphs/conc1/Ca_dend.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 1 0 0 1 +simundump xplot /graphs/conc2/tot_PSD_R.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xplot /graphs/conc2/Rpp.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 28 0 0 1 +simundump xgraph /moregraphs/conc3 0 0 800 0 33.241 0 +simundump xgraph /moregraphs/conc4 0 0 800 0 2 0 +simundump xcoredraw /edit/draw 0 -21 7 -30 11 +simundump xtree /edit/draw/tree 0 \ + /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ + "edit_elm.D ; drag_from_edit.w " auto 0.6 +simundump xtext /file/notes 0 1 +xtextload /file/notes \ +"26 Nov 2014. psd51.g: based on psd50.g which was" \ +"based on psd41_back_dend.g." \ +"07 Dec 2014. psd52.g: based on psd51. Slowed down Ca_to_dend by " \ +"10x while retaining Keq." \ +"04 June 2015. psd53.g: Removed the reacts between dend, head and" \ +"psd. Will use diffusion instead." \ +"05 June 2015. psd53.g updated further to use the same name (Ca)" \ +"for Ca_dend, Ca_spine and Ca_PSD so as to get them to diffuse." \ +"" +addmsg /kinetics/Bulk/iRpp /kinetics/exocytosis SUBSTRATE n +addmsg /kinetics/PSD/Rpp /kinetics/exocytosis PRODUCT n +addmsg /kinetics/Bulk/iR /kinetics/endocytosis SUBSTRATE n +addmsg /kinetics/PSD/R /kinetics/endocytosis PRODUCT n +addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/Rp MM_PRD pA +addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/Rp REAC sA B +addmsg /kinetics/PSD/P/P2 /kinetics/PSD/Rp MM_PRD pA +addmsg /kinetics/PSD/P/P1 /kinetics/PSD/Rp REAC sA B +addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Rp MM_PRD pA +addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/Rp REAC sA B +addmsg /kinetics/PSD/P/P1 /kinetics/PSD/P REAC eA B +addmsg /kinetics/PSD/P/P2 /kinetics/PSD/P REAC eA B +addmsg /kinetics/PSD/P /kinetics/PSD/P/P1 ENZYME n +addmsg /kinetics/PSD/Rp /kinetics/PSD/P/P1 SUBSTRATE n +addmsg /kinetics/PSD/P /kinetics/PSD/P/P2 ENZYME n +addmsg /kinetics/PSD/Rpp /kinetics/PSD/P/P2 SUBSTRATE n +addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/KK REAC eA B +addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/KK REAC eA B +addmsg /kinetics/PSD/KK /kinetics/PSD/KK/KK1 ENZYME n +addmsg /kinetics/PSD/R /kinetics/PSD/KK/KK1 SUBSTRATE n +addmsg /kinetics/PSD/KK /kinetics/PSD/KK/KK2 ENZYME n +addmsg /kinetics/PSD/Rp /kinetics/PSD/KK/KK2 SUBSTRATE n +addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/Rpp MM_PRD pA +addmsg /kinetics/PSD/P/P2 /kinetics/PSD/Rpp REAC sA B +addmsg /kinetics/exocytosis /kinetics/PSD/Rpp REAC B A +addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/PSD/Rpp MM_PRD pA +addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Rpp REAC sA B +addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/R REAC sA B +addmsg /kinetics/PSD/P/P1 /kinetics/PSD/R MM_PRD pA +addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/R MM_PRD pA +addmsg /kinetics/endocytosis /kinetics/PSD/R REAC B A +addmsg /kinetics/PSD/R /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/Rp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/Rpp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/psd_inact_CaN REAC A B +addmsg /kinetics/PSD/psd_inact_CaN /kinetics/PSD/psd_activate_CaN SUBSTRATE n +addmsg /kinetics/PSD/Ca /kinetics/PSD/psd_activate_CaN SUBSTRATE n +addmsg /kinetics/PSD/Ca /kinetics/PSD/psd_activate_CaN SUBSTRATE n +addmsg /kinetics/PSD/Ca.P /kinetics/PSD/psd_activate_CaN PRODUCT n +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca.P REAC B A +addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Ca.P REAC eA B +addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/Ca.P REAC eA B +addmsg /kinetics/PSD/Ca.P /kinetics/PSD/Ca.P/Ca.P2 ENZYME n +addmsg /kinetics/PSD/Rpp /kinetics/PSD/Ca.P/Ca.P2 SUBSTRATE n +addmsg /kinetics/PSD/Ca.P /kinetics/PSD/Ca.P/Ca.P1 ENZYME n +addmsg /kinetics/PSD/Rp /kinetics/PSD/Ca.P/Ca.P1 SUBSTRATE n +addmsg /kinetics/PSD/Ca_reac /kinetics/PSD/Ca_input REAC A B +addmsg /kinetics/PSD/Ca_input /kinetics/PSD/Ca_reac SUBSTRATE n +addmsg /kinetics/PSD/Ca /kinetics/PSD/Ca_reac PRODUCT n +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca REAC A B +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca REAC A B +addmsg /kinetics/PSD/Ca_reac /kinetics/PSD/Ca REAC B A +addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iRpp MM_PRD pA +addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iRpp REAC sA B +addmsg /kinetics/exocytosis /kinetics/Bulk/iRpp REAC A B +addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/iRpp MM_PRD pA +addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/Bulk/iRpp REAC sA B +addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iRp MM_PRD pA +addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iRp REAC sA B +addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iRp MM_PRD pA +addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iRp REAC sA B +addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/iRp MM_PRD pA +addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/iRp REAC sA B +addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iR REAC sA B +addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iR MM_PRD pA +addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/iR REAC sA B +addmsg /kinetics/endocytosis /kinetics/Bulk/iR REAC A B +addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iKK REAC eA B +addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iKK REAC eA B +addmsg /kinetics/Bulk/iKK /kinetics/Bulk/iKK/iKK1 ENZYME n +addmsg /kinetics/Bulk/iR /kinetics/Bulk/iKK/iKK1 SUBSTRATE n +addmsg /kinetics/Bulk/iKK /kinetics/Bulk/iKK/iKK2 ENZYME n +addmsg /kinetics/Bulk/iRp /kinetics/Bulk/iKK/iKK2 SUBSTRATE n +addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iP REAC eA B +addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iP REAC eA B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/iP REAC B A +addmsg /kinetics/Bulk/iP /kinetics/Bulk/iP/iP1 ENZYME n +addmsg /kinetics/Bulk/iRp /kinetics/Bulk/iP/iP1 SUBSTRATE n +addmsg /kinetics/Bulk/iP /kinetics/Bulk/iP/iP2 ENZYME n +addmsg /kinetics/Bulk/iRpp /kinetics/Bulk/iP/iP2 SUBSTRATE n +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/PKA REAC B A +addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/PKA REAC eA B +addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/PKA REAC eA B +addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/Bulk/PKA REAC eA B +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA1 ENZYME n +addmsg /kinetics/Bulk/iR /kinetics/Bulk/PKA/PKA1 SUBSTRATE n +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA2 ENZYME n +addmsg /kinetics/Bulk/iRp /kinetics/Bulk/PKA/PKA2 SUBSTRATE n +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA_exo ENZYME n +addmsg /kinetics/Bulk/iRpp /kinetics/Bulk/PKA/PKA_exo SUBSTRATE n +addmsg /kinetics/Bulk/inact_PKA /kinetics/Bulk/activate_PKA SUBSTRATE n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_PKA SUBSTRATE n +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/activate_PKA PRODUCT n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_PKA SUBSTRATE n +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/inact_PKA REAC A B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/inact_CaN REAC A B +addmsg /kinetics/Bulk/inact_CaN /kinetics/Bulk/activate_CaN SUBSTRATE n +addmsg /kinetics/Bulk/iP /kinetics/Bulk/activate_CaN PRODUCT n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_CaN SUBSTRATE n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_CaN SUBSTRATE n +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/dend_Ca_reac /kinetics/Ca_dend_input REAC A B +addmsg /kinetics/Ca_dend_input /kinetics/dend_Ca_reac SUBSTRATE n +addmsg /kinetics/Ca /kinetics/dend_Ca_reac PRODUCT n +addmsg /kinetics/dend_Ca_reac /kinetics/Ca REAC B A +addmsg /kinetics/PSD/Ca /graphs/conc1/Ca_PSD.Co PLOT Co *Ca_PSD.Co *53 +addmsg /kinetics/Bulk/Ca /graphs/conc1/Ca_Bulk.Co PLOT Co *Ca_Bulk.Co *41 +addmsg /kinetics/Bulk/PKA /graphs/conc1/PKA.Co PLOT Co *PKA.Co *43 +addmsg /kinetics/PSD/Ca.P /graphs/conc1/Ca.P.Co PLOT Co *Ca.P.Co *blue +addmsg /kinetics/Ca /graphs/conc1/Ca_dend.Co PLOT Co *Ca_dend.Co *1 +addmsg /kinetics/PSD/tot_PSD_R /graphs/conc2/tot_PSD_R.Co PLOT Co *tot_PSD_R.Co *blue +addmsg /kinetics/PSD/Rpp /graphs/conc2/Rpp.Co PLOT Co *Rpp.Co *28 +enddump +// End of dump + +call /kinetics/Bulk/iR/notes LOAD \ +"Same as Fus3" \ +"" +call /kinetics/Bulk/iKK/notes LOAD \ +"Same as Ste7" \ +"" +call /kinetics/Bulk/iP/notes LOAD \ +"Same as Msg5" \ +"" +complete_loading diff --git a/demos/Fig6_NetMultiscale/Fig6A.py b/demos/Fig6_NetMultiscale/Fig6A.py new file mode 100644 index 0000000..b8646bc --- /dev/null +++ b/demos/Fig6_NetMultiscale/Fig6A.py @@ -0,0 +1,503 @@ +#!/usr/bin/env python +#/********************************************************************** +#** This program is part of 'MOOSE', the +#** Messaging Object Oriented Simulation Environment. +#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS +#** It is made available under the terms of the +#** GNU Lesser General Public License version 2.1 +#** See the file COPYING.LIB for the full notice. +#**********************************************************************/ + +''' +This LIF network with Ca plasticity is based on: +David Higgins, Michael Graupner, Nicolas Brunel + Memory Maintenance in Synapses with Calcium-Based + Plasticity in the Presence of Background Activity + PLOS Computational Biology, 2014. + +Implemented by: Aditya Gilra, NCBS, Bangalore, October, 2014. +This variant has 2500 LIF neurons + +Upi Bhalla, Nov 2014: Appended single neuron model. +This script generates Panel A from Figure 6. It is a dummy for showing +the layout, and loads in about 20 seconds. +''' + +## import modules and functions to be used +import numpy as np +import matplotlib.pyplot as plt +import random +import time +import moose +from PyQt5 import Qt, QtCore, QtGui +from numpy import random as nprand +from moose.neuroml.NeuroML import NeuroML +import sys +sys.path.append( "/home/bhalla/moose/trunk/Demos/util" ) +import rdesigneur as rd +import moogli +cellname = "./cells_channels/CA1_nochans.morph.xml" +#cellname = "./ca1_minimal.p" +fname = "fig6bcde" + +############################################# +np.random.seed(100) # set seed for reproducibility of simulations +random.seed(100) # set seed for reproducibility of simulations +moose.seed(100) # set seed for reproducibility of simulations + +############################################# +# All parameters as per: +# David Higgins, Michael Graupner, Nicolas Brunel +# Memory Maintenance in Synapses with Calcium-Based +# Plasticity in the Presence of Background Activity +# PLOS Computational Biology, 2014. +############################################# + +############################################# +# Neuron model +############################################# + +# equation: dv/dt = (1/taum)*(-(v-el)) + inp +# with spike when v>vt, reset to vr + +PI = 3.14159265358979 +useGssa = True +combineSegments = False + +el = -70e-3 #V # Resting potential +vt = -50e-3 #V # Spiking threshold +Rm = 20e6 #Ohm # Only taum is needed, but LIF neuron accepts +Cm = 1e-9 #F # Rm and Cm and constructs taum=Rm*Cm +taum = Rm*Cm #s # Membrane time constant is 20 ms +vr = -60e-3 #V # Reset potential +Iinject = 10e-3/Rm # constant current injection into LIF neuron + # same as setting el=-70+15=-55 mV and inp=0 +noiseInj = True # inject noisy current into each cell: boolean +noiseInjSD = 5e-3/Rm #A # SD of noise added to 'current' + # SD*sqrt(taum) is used as noise current SD + +############################################# +# Network parameters: numbers +############################################# + +N = 2500 # Total number of neurons +fexc = 0.8 # Fraction of exc neurons +NE = int(fexc*N) # Number of excitatory cells +NI = N-NE # Number of inhibitory cells + +############################################# +# Simulation parameters +############################################# + +simtime = 30 #s # Simulation time +interTetInterval = 5.0 # sec +updateDt = 0.2 #s: time to update live display +dt = 1e-3 #s # time step + +############################################# +# Network parameters: synapses (not for ExcInhNetBase) +############################################# + +## With each presynaptic spike in exc / inh neuron, +## J / -g*J is added to post-synaptic Vm -- delta-fn synapse +## Since LIF neuron used below is derived from Compartment class, +## conductance-based synapses (SynChan class) can also be used. + +C = 100 # Number of incoming connections on each neuron (exc or inh) +fC = fexc # fraction fC incoming connections are exc, rest inhibitory +J = 0.2e-3 #V # exc strength is J (in V as we add to voltage) + # Critical J is ~ 0.45e-3 V in paper for N = 10000, C = 1000 + # See what happens for J = 0.2e-3 V versus J = 0.8e-3 V +g = 4.0 # -gJ is the inh strength. For exc-inh balance g >~ f(1-f)=4 +syndelay = dt # synaptic delay: +refrT = 0.0 # s # absolute refractory time + +############################################# +# Ca Plasticity parameters: synapses (not for ExcInhNetBase) +############################################# + +CaPlasticity = True # set it True or False to turn on/off plasticity +tauCa = 22.6936e-3 # s # Ca decay time scale +tauSyn = 346.3615 # s # synaptic plasticity time scale +## in vitro values in Higgins et al 2014, faster plasticity +CaPre = 0.56175 # mM + +CaPost = 1.2964 # mM +## in vivo values in Higgins et al 2014, slower plasticity +#CaPre = 0.33705 # mM +#CaPost = 0.74378 # mM +delayD = 4.6098e-3 # s # CaPre is added to Ca after this delay + # proxy for rise-time of NMDA +thetaD = 1.0 # mM # depression threshold for Ca +thetaP = 1.3 # mM # potentiation threshold for Ca +gammaD = 331.909 # factor for depression term +gammaP = 725.085 # factor for potentiation term + +eqWeight = 0.5 # initial synaptic weight + # gammaP/(gammaP+gammaD) = eq weight w/o noise + # but see eqn (22), noiseSD also appears + +bistable = True # if bistable is True, use bistable potential for weights +noisy = True # use noisy weight updates given by noiseSD +noiseSD = 3.3501 # if noisy, use noiseSD (3.3501 from Higgins et al 2014) +#noiseSD = 0.1 # if bistable==False, use a smaller noise than in Higgins et al 2014 + +############################################# +# Here we set up a single neuron to fit in this network +############################################# + +diffDt = 0.005 +chemDt = 0.005 +ePlotDt = 0.5e-3 +cPlotDt = 0.005 + +############################################# +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + cellProto = [ [cellname, 'elec'] ] + chanProto = [ + ['./cells_channels/hd.xml'], \ + ['./cells_channels/kap.xml'], \ + ['./cells_channels/kad.xml'], \ + ['./cells_channels/kdr.xml'], \ + ['./cells_channels/na3.xml'], \ + ['./cells_channels/nax.xml'], \ + ['./cells_channels/CaConc.xml'], \ + ['./cells_channels/Ca.xml'], \ + ['./cells_channels/NMDA.xml'], \ + ['./cells_channels/Glu.xml'], \ + ['./cells_channels/GABA.xml'] \ + ] + spineProto = [ \ + ['makeSpineProto()', 'spine' ] + ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + passiveDistrib = [ + [ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \ + "Em", "-58e-3", "initVm", "-65e-3" ], \ + [ ".", "#axon#", "RA", "0.5" ] \ + ] + chanDistrib = [ \ + ["hd", "#dend#,#apical#,#user#", "Gbar", "5e-2*(1+(p*3e4))" ], \ + ["kdr", "#", "Gbar", "100" ], \ + ["na3", "#soma#,#dend#,#apical#,#user#", "Gbar", "250" ], \ + ["nax", "#axon#", "Gbar", "1250" ], \ + ["nax", "#soma#", "Gbar", "100" ], \ + ["kap", "#axon#,#soma#", "Gbar", "300" ], \ + ["kap", "#dend#,#apical#,#user#", "Gbar", \ + "300*(H(100-p*1e6)) * (1+(p*1e4))" ], \ + ["Ca_conc", "#soma#,#dend#,#apical#,#user#", "tau", "0.0133" ], \ + ["kad", "#dend#,#apical#,#user#", "Gbar", \ + "300*H(p*1e6-100)*(1+p*1e4)" ], \ + ["Ca", "#soma#", "Gbar", "10e-3" ], \ + ["Ca", "#dend#,#apical#,#user#", "Gbar", "50e-3" ], \ + ["GABA", "#dend#,#apical#,#user#", "Gbar", "100*H(250e-6 - p)" ], \ + ] + spineDistrib = [ \ + ["spine", '#apical#,#dend#,#user#', "spineSpacing", "6.2e-6", \ + "spineSpacingDistrib", "1e-6", \ + "angle", "0", \ + "angleDistrib", str( 2*PI ), \ + "size", "1", \ + "sizeDistrib", "0.5" ] \ + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + passiveDistrib = passiveDistrib, \ + spineDistrib = spineDistrib, \ + chanDistrib = chanDistrib, \ + cellProto = cellProto, \ + spineProto = spineProto, \ + chanProto = chanProto, \ + ) + + return rdes + + +############################################# + +def makeDetailedNeuron(): + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + #bcs.addAllPlots() + + +############################################# +# Exc-Inh network base class without connections +############################################# + +class ExcInhNetBase: + """Simulates and plots LIF neurons (exc and inh separate). + Author: Aditya Gilra, NCBS, Bangalore, India, October 2014 + """ + + def __init__(self,N=N,fexc=fexc,el=el,vt=vt,Rm=Rm,Cm=Cm,vr=vr,\ + refrT=refrT,Iinject=Iinject): + """ Constructor of the class """ + + self.N = N # Total number of neurons + self.fexc = fexc # Fraction of exc neurons + self.NmaxExc = int(fexc*N) # max idx of exc neurons, rest inh + + self.el = el # Resting potential + self.vt = vt # Spiking threshold + self.taum = taum # Membrane time constant + self.vr = vr # Reset potential + self.refrT = refrT # Absolute refractory period + self.Rm = Rm # Membrane resistance + self.Cm = Cm # Membrane capacitance + self.Iinject = Iinject # constant input current + self.noiseInjSD = noiseInjSD # SD of injected noise + + self.simif = False # whether the simulation is complete + + self._setup_network() + + def __str__(self): + return "LIF network of %d neurons "\ + "having %d exc." % (self.N,self.NmaxExc) + + def _setup_network(self): + """Sets up the network (_init_network is enough)""" + self.network = moose.LIF( 'network', self.N ); + moose.le( '/network' ) + self.network.vec.Em = self.el + self.network.vec.thresh = self.vt + self.network.vec.refractoryPeriod = self.refrT + self.network.vec.Rm = self.Rm + self.network.vec.vReset = self.vr + self.network.vec.Cm = self.Cm + if not noiseInj: + self.network.vec.inject = self.Iinject + else: + ## inject a constant + noisy current + ## values are set in self.simulate() + self.noiseTables = moose.StimulusTable('noiseTables',self.N) + moose.connect( self.noiseTables, 'output', \ + self.network, 'setInject', 'OneToOne') + + def _init_network(self,v0=el): + """Initialises the network variables before simulation""" + self.network.vec.initVm = v0 + + def _init_plots(self): + ## make a few tables to store a few Vm-s + numVms = 10 + self.plots = moose.Table( '/plotVms', numVms ) + ## draw numVms out of N neurons + nrnIdxs = random.sample(list(range(self.N)),numVms) + for i in range( numVms ): + moose.connect( self.network.vec[nrnIdxs[i]], 'VmOut', \ + self.plots.vec[i], 'input') + + ## make self.N tables to store spikes of all neurons + self.spikes = moose.Table( '/plotSpikes', self.N ) + moose.connect( self.network, 'spikeOut', \ + self.spikes, 'input', 'OneToOne' ) + + ## make 2 tables to store spikes of all exc and all inh neurons + self.spikesExc = moose.Table( '/plotSpikesAllExc' ) + for i in range(self.NmaxExc): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesExc, 'input' ) + self.spikesInh = moose.Table( '/plotSpikesAllInh' ) + for i in range(self.NmaxExc,self.N): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesInh, 'input' ) + + def _plot(self, fig): + """ plots the spike raster for the simulated net""" + plt.figure(1) + + ax = plt.subplot(221) + cleanAx( ax, 'B' ) + plt.ylabel( 'Neuron #', fontsize = 16 ) + for i in range(0,self.NmaxExc): + if i==0: label = 'Exc. spike trains' + else: label = '' + spikes = self.spikes.vec[i].vector + ax.plot(spikes,[i]*len(spikes),\ + 'b.',marker='.', markersize = 2, label=label) + for i in range(self.NmaxExc,self.N): + if i==self.NmaxExc: label = 'Inh. spike trains' + else: label = '' + spikes = self.spikes.vec[i].vector + ax.plot(spikes,[i]*len(spikes),\ + 'r.',marker='.', markersize = 2, label=label) + +############################################# +# Exc-Inh network class with Ca plasticity based connections +# (inherits from ExcInhNetBase) +############################################# + +class ExcInhNet(ExcInhNetBase): + """ Recurrent network simulation """ + + def __init__(self,J=J,incC=C,fC=fC,scaleI=g,syndelay=syndelay,**kwargs): + """Overloads base (parent) class""" + self.J = J # exc connection weight + self.incC = incC # number of incoming connections per neuron + self.fC = fC # fraction of exc incoming connections + self.excC = int(fC*incC)# number of exc incoming connections + self.scaleI = scaleI # inh weight is scaleI*J + self.syndelay = syndelay# synaptic delay + + # call the parent class constructor + ExcInhNetBase.__init__(self,**kwargs) + + def __str__(self): + return "LIF network of %d neurons "\ + "of which %d are exc." % (self.N,self.NmaxExc) + + def _init_network(self,**args): + ExcInhNetBase._init_network(self,**args) + + def _init_plots(self): + ExcInhNetBase._init_plots(self) + + def _setup_network(self): + ## Set up the neurons without connections + ExcInhNetBase._setup_network(self) + + ## Now, add in the connections... + ## Each pre-synaptic spike cause Vm of post-neuron to rise by + ## synaptic weight in one time step i.e. delta-fn synapse. + ## Since LIF neuron is derived from Compartment class, + ## conductance-based synapses (SynChan class) can also be used. + + ## E to E synapses can be plastic + ## Two ways to do this: + ## 1) Each LIF neuron has one incoming postsynaptic SynHandler, + ## which collects the activation from all presynaptic neurons, + ## but then a common Ca pool is used. + ## 2) Each LIF neuron has multiple postsyanptic SynHandlers, + ## one for each pre-synaptic neuron, i.e. one per synapse, + ## then each synapse has a different Ca pool. + ## Here we go with option 2) as per Higgins et al 2014 (Brunel private email) + ## separate SynHandler per EE synapse, thus NmaxExc*excC + if CaPlasticity: + self.synsEE = moose.GraupnerBrunel2012CaPlasticitySynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + else: + self.synsEE = moose.SimpleSynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + moose.useClock( 0, '/network/synsEE', 'process' ) + + ## I to E synapses are not plastic + self.synsIE = moose.SimpleSynHandler( '/network/synsIE', self.NmaxExc ) + ## all synapses to I neurons are not plastic + self.synsI = moose.SimpleSynHandler( '/network/synsI', self.N-self.NmaxExc ) + ## connect all SynHandlers to their respective neurons + + moose.useClock( 0, '/network/synsIE', 'process' ) + moose.useClock( 0, '/network/synsI', 'process' ) + +############################################# +# Make plots +############################################# + +def interlude( view ): + view.yaw( 0.005 ) + +def create_viewer(rdes): + # print "Creating 3D Viewer" + network = moogli.extensions.moose.read(path=rdes.elecid.path, + vertices=10) + # print "Read Network" + network.set("color", moogli.colors.LIGHT_BLUE) + network.groups["spine"].set("color", moogli.colors.ORANGE) + # for dendrite in dendrites.values(): + # dendrite.set_colors(moogli.core.Vec4f(173 / 255.0, 216 / 255.0, 230 / 255.0, 1.0)) + + [shape.set_radius(shape.get_apex_radius() * 4.0) for shape in + list(network.groups["spine"].groups["head"].shapes.values())] + # print "Creating LIFS" + soma = network.shapes[rdes.soma.path] + + center = soma.get_center() + row_axis = moogli.geometry.X_AXIS + row_count = 50 + row_separation = soma.get_base_radius() * 5.0 + col_axis = moogli.geometry.Z_AXIS + col_count = 50 + col_separation = row_separation + radii = soma.get_base_radius() + colors = moogli.colors.GREEN + vertices = 20 + lifs = moogli.shapes.Sphere.grid("LIF", + center, + row_axis, + row_count, + row_separation, + col_axis, + col_count, + col_separation, + radii, + colors, + vertices) + # print "Created LIFS" + # morphology.create_group("dendrites", dendrites, 0.0, 300.0, colormap) + # print "Creating Viewer" + viewer = moogli.Viewer("viewer") # prelude = prelude, interlude = interlude) + # print "Created Viewer" + viewer.attach_shapes(list(network.shapes.values())) + viewer.attach_shapes(list(lifs.shapes.values())) + # print "Attached Shapes" + view = moogli.View("view", interlude=interlude) + viewer.attach_view(view) + # print "Attached View" + viewer.showMaximized() + viewer.start() + view.zoom( 0.4 ) + view.pitch( PI/2.5 ) + return viewer + +if __name__=='__main__': + ## ExcInhNetBase has unconnected neurons, + ## ExcInhNet connects them + ## Instantiate either ExcInhNetBase or ExcInhNet below + #net = ExcInhNetBase(N=N) + net = ExcInhNet(N=N) + print(net) + moose.le( '/' ) + moose.le( '/network' ) + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + + app = QtGui.QApplication(sys.argv) + viewer = create_viewer(rdes) + app.exec_() diff --git a/demos/Fig6_NetMultiscale/Fig6BCDE.py b/demos/Fig6_NetMultiscale/Fig6BCDE.py new file mode 100644 index 0000000..876be18 --- /dev/null +++ b/demos/Fig6_NetMultiscale/Fig6BCDE.py @@ -0,0 +1,941 @@ +#/********************************************************************** +#** This program is part of 'MOOSE', the +#** Messaging Object Oriented Simulation Environment. +#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS +#** It is made available under the terms of the +#** GNU Lesser General Public License version 2.1 +#** See the file COPYING.LIB for the full notice. +#**********************************************************************/ + +''' +This LIF network with Ca plasticity is based on: +David Higgins, Michael Graupner, Nicolas Brunel + Memory Maintenance in Synapses with Calcium-Based + Plasticity in the Presence of Background Activity + PLOS Computational Biology, 2014. + +Implemented by: Aditya Gilra, NCBS, Bangalore, October, 2014. +This variant has 2500 LIF neurons + +Upi Bhalla, Nov 2014: Appended single neuron model. +This script generates the panels in Figure 6. It takes a long time, +about 65 minutes to run 30 seconds of simulation time. +''' + +from __future__ import print_function + +## import modules and functions to be used +import numpy as np +import matplotlib.pyplot as plt +import random +import time +import moose +from PyQt5 import Qt, QtCore, QtGui +from numpy import random as nprand +from moose.neuroml.NeuroML import NeuroML +import sys +sys.path.append( "/home/bhalla/moose/trunk/Demos/util" ) +import rdesigneur as rd +import moogli +cellname = "./cells_channels/CA1_nochans.morph.xml" +#cellname = "./ca1_minimal.p" +fname = "fig6bcde" + +############################################# +np.random.seed(100) # set seed for reproducibility of simulations +random.seed(100) # set seed for reproducibility of simulations +moose.seed(100) # set seed for reproducibility of simulations + +############################################# +# All parameters as per: +# David Higgins, Michael Graupner, Nicolas Brunel +# Memory Maintenance in Synapses with Calcium-Based +# Plasticity in the Presence of Background Activity +# PLOS Computational Biology, 2014. +############################################# + +############################################# +# Neuron model +############################################# + +# equation: dv/dt = (1/taum)*(-(v-el)) + inp +# with spike when v>vt, reset to vr + +PI = 3.14159265358979 +useGssa = True +combineSegments = False + +el = -70e-3 #V # Resting potential +vt = -50e-3 #V # Spiking threshold +Rm = 20e6 #Ohm # Only taum is needed, but LIF neuron accepts +Cm = 1e-9 #F # Rm and Cm and constructs taum=Rm*Cm +taum = Rm*Cm #s # Membrane time constant is 20 ms +vr = -60e-3 #V # Reset potential +Iinject = 10e-3/Rm # constant current injection into LIF neuron + # same as setting el=-70+15=-55 mV and inp=0 +noiseInj = True # inject noisy current into each cell: boolean +noiseInjSD = 5e-3/Rm #A # SD of noise added to 'current' + # SD*sqrt(taum) is used as noise current SD + +############################################# +# Network parameters: numbers +############################################# + +N = 2500 # Total number of neurons +fexc = 0.8 # Fraction of exc neurons +NE = int(fexc*N) # Number of excitatory cells +NI = N-NE # Number of inhibitory cells + +############################################# +# Simulation parameters +############################################# + +simtime = 30 #s # Simulation time +interTetInterval = 5.0 # sec +updateDt = 0.2 #s: time to update live display +dt = 1e-3 #s # time step + +############################################# +# Network parameters: synapses (not for ExcInhNetBase) +############################################# + +## With each presynaptic spike in exc / inh neuron, +## J / -g*J is added to post-synaptic Vm -- delta-fn synapse +## Since LIF neuron used below is derived from Compartment class, +## conductance-based synapses (SynChan class) can also be used. + +C = 100 # Number of incoming connections on each neuron (exc or inh) +fC = fexc # fraction fC incoming connections are exc, rest inhibitory +J = 0.2e-3 #V # exc strength is J (in V as we add to voltage) + # Critical J is ~ 0.45e-3 V in paper for N = 10000, C = 1000 + # See what happens for J = 0.2e-3 V versus J = 0.8e-3 V +g = 4.0 # -gJ is the inh strength. For exc-inh balance g >~ f(1-f)=4 +syndelay = dt # synaptic delay: +refrT = 0.0 # s # absolute refractory time + +############################################# +# Ca Plasticity parameters: synapses (not for ExcInhNetBase) +############################################# + +CaPlasticity = True # set it True or False to turn on/off plasticity +tauCa = 22.6936e-3 # s # Ca decay time scale +tauSyn = 346.3615 # s # synaptic plasticity time scale +## in vitro values in Higgins et al 2014, faster plasticity +CaPre = 0.56175 # mM + +CaPost = 1.2964 # mM +## in vivo values in Higgins et al 2014, slower plasticity +#CaPre = 0.33705 # mM +#CaPost = 0.74378 # mM +delayD = 4.6098e-3 # s # CaPre is added to Ca after this delay + # proxy for rise-time of NMDA +thetaD = 1.0 # mM # depression threshold for Ca +thetaP = 1.3 # mM # potentiation threshold for Ca +gammaD = 331.909 # factor for depression term +gammaP = 725.085 # factor for potentiation term + +eqWeight = 0.5 # initial synaptic weight + # gammaP/(gammaP+gammaD) = eq weight w/o noise + # but see eqn (22), noiseSD also appears + +bistable = True # if bistable is True, use bistable potential for weights +noisy = True # use noisy weight updates given by noiseSD +noiseSD = 3.3501 # if noisy, use noiseSD (3.3501 from Higgins et al 2014) +#noiseSD = 0.1 # if bistable==False, use a smaller noise than in Higgins et al 2014 + +############################################# +# Here we set up a single neuron to fit in this network +############################################# + +diffDt = 0.005 +chemDt = 0.005 +ePlotDt = 0.5e-3 +cPlotDt = 0.005 + +############################################# +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + cellProto = [ [cellname, 'elec'] ] + chanProto = [ + ['./cells_channels/hd.xml'], \ + ['./cells_channels/kap.xml'], \ + ['./cells_channels/kad.xml'], \ + ['./cells_channels/kdr.xml'], \ + ['./cells_channels/na3.xml'], \ + ['./cells_channels/nax.xml'], \ + ['./cells_channels/CaConc.xml'], \ + ['./cells_channels/Ca.xml'], \ + ['./cells_channels/NMDA.xml'], \ + ['./cells_channels/Glu.xml'], \ + ['./cells_channels/GABA.xml'] \ + ] + spineProto = [ \ + ['makeSpineProto()', 'spine' ] + ] + chemProto = [ \ + [ 'psd53.g', 'ltpModel'] \ + ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + passiveDistrib = [ + [ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \ + "Em", "-58e-3", "initVm", "-65e-3" ], \ + [ ".", "#axon#", "RA", "0.5" ] \ + ] + chanDistrib = [ \ + ["hd", "#dend#,#apical#,#user#", "Gbar", "5e-2*(1+(p*3e4))" ], \ + ["kdr", "#", "Gbar", "100" ], \ + ["na3", "#soma#,#dend#,#apical#,#user#", "Gbar", "250" ], \ + ["nax", "#axon#", "Gbar", "1250" ], \ + ["nax", "#soma#", "Gbar", "100" ], \ + ["kap", "#axon#,#soma#", "Gbar", "300" ], \ + ["kap", "#dend#,#apical#,#user#", "Gbar", \ + "300*(H(100-p*1e6)) * (1+(p*1e4))" ], \ + ["Ca_conc", "#soma#,#dend#,#apical#,#user#", "tau", "0.0133" ], \ + ["kad", "#dend#,#apical#,#user#", "Gbar", \ + "300*H(p*1e6-100)*(1+p*1e4)" ], \ + ["Ca", "#soma#", "Gbar", "10e-3" ], \ + ["Ca", "#dend#,#apical#,#user#", "Gbar", "50e-3" ], \ + ["GABA", "#dend#,#apical#,#user#", "Gbar", "100*H(250e-6 - p)" ], \ + ] + spineDistrib = [ \ + ["spine", '#apical#,#dend#,#user#', "spineSpacing", "6.2e-6", \ + "spineSpacingDistrib", "1e-6", \ + "angle", "0", \ + "angleDistrib", str( 2*PI ), \ + "size", "1", \ + "sizeDistrib", "0.5" ] \ + ] + chemDistrib = [ \ + [ "ltpModel", "#apical#,#dend#,#user#", "install", "1" ] \ + ] + + ''' + ''' + ###################################################################### + # Here we define the mappings across scales. Format: + # sourceObj sourceField destObj destField couplingExpr [wildcard][spatialExpn] + # where the coupling expression is anything a muParser can evaluate, + # using the input variable x. For example: 8e-5 + 300*x + # For now, let's use existing adaptors which take an offset and scale. + ###################################################################### + adaptorList = [ + [ 'Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 8e-5, 1 ], + [ 'Ca_conc', 'Ca', 'dend/Ca_dend_input', 'concInit', 8e-5, 1 ], + [ 'psd/tot_PSD_R', 'n', 'glu', 'modulation', 0.5, 0.002 ], + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + passiveDistrib = passiveDistrib, \ + spineDistrib = spineDistrib, \ + chanDistrib = chanDistrib, \ + chemDistrib = chemDistrib, \ + cellProto = cellProto, \ + spineProto = spineProto, \ + chanProto = chanProto, \ + chemProto = chemProto, \ + adaptorList = adaptorList + ) + + return rdes + + +############################################# + +def makeDetailedNeuron(): + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + #bcs.addAllPlots() + +def connectDetailedNeuron(): + excProb = 0.00042 + excSeed = 1234 + inhProb = 0.00013 + inhSeed = 4567 + numExc = 0 + numNMDA = 0 + numInh = 0 + delayMax = 0.010 + delayMin = 0.002 + excWeightMax = 360 + nmdaWeightMax = 1 + inhWeightMax = 100 + # Note we use the same seed for all 3 exc connections, to make sure + # they are all equivalent. + seed = excSeed + totGluWt = 0.0 + totNMDAWt = 0.0 + totGABAWt = 0.0 + for x in moose.wildcardFind( '/model/elec/#/glu/##[ISA=Synapse]' ): + exc = moose.connect( '/network', 'spikeOut', x, 'addSpike','sparse') + exc.setRandomConnectivity( excProb, seed ) + seed = seed + 1 + if exc.numEntries > 0: + numExc += exc.numEntries + assert( exc.numEntries == x.numField ) + x.vec.delay = delayMin + nprand.rand( exc.numEntries ) * ( delayMax - delayMin ) + x.vec.weight = nprand.rand( exc.numEntries ) * excWeightMax + #x.parent.tick = 4 + x.parent.parent.tick = 4 + print('+', end=' ') + totGluWt += sum(x.vec.weight) * x.parent.parent.Gbar + + seed = excSeed + for x in moose.wildcardFind( '/model/elec/#/NMDA/##[ISA=Synapse]' ): + #print " x = ", x + exc = moose.connect( '/network', 'spikeOut', x, 'addSpike','sparse') + exc.setRandomConnectivity( excProb, seed ) + seed = seed + 1 + if exc.numEntries > 0: + numNMDA += exc.numEntries + assert( exc.numEntries == x.numField ) + x.vec.delay = delayMin + nprand.rand( exc.numEntries ) * ( delayMax - delayMin ) + x.vec.weight = nprand.rand( exc.numEntries ) * nmdaWeightMax + #x.parent.tick = 4 + x.parent.parent.tick = 4 + print('*', end=' ') + totNMDAWt += sum(x.vec.weight) * x.parent.parent.Gbar + + seed = inhSeed + for x in moose.wildcardFind( '/model/elec/#/GABA/##[ISA=Synapse]' ): + #print x + inh = moose.connect( '/network', 'spikeOut', x, 'addSpike','sparse') + inh.setRandomConnectivity( inhProb, seed ) + seed = seed + 1 + if inh.numEntries > 0: + numInh += inh.numEntries + x.vec.delay = delayMin + nprand.rand( inh.numEntries ) * ( delayMax - delayMin ) + x.vec.weight = nprand.rand( inh.numEntries ) * inhWeightMax + #x.parent.tick = 4 + x.parent.parent.tick = 4 + print('-', end=' ') + totGABAWt += sum(x.vec.weight) * x.parent.parent.Gbar + + print('connectDetailedNeuron: numExc = ', numExc, ', numNMDA=', numNMDA, ', numInh = ', numInh) + print('connectDetailedNeuron: totWts Glu = ', totGluWt, ', NMDA = ', totNMDAWt, ', GABA = ', totGABAWt) + +############################################# +# Exc-Inh network base class without connections +############################################# + +class ExcInhNetBase: + """Simulates and plots LIF neurons (exc and inh separate). + Author: Aditya Gilra, NCBS, Bangalore, India, October 2014 + """ + + def __init__(self,N=N,fexc=fexc,el=el,vt=vt,Rm=Rm,Cm=Cm,vr=vr,\ + refrT=refrT,Iinject=Iinject): + """ Constructor of the class """ + + self.N = N # Total number of neurons + self.fexc = fexc # Fraction of exc neurons + self.NmaxExc = int(fexc*N) # max idx of exc neurons, rest inh + + self.el = el # Resting potential + self.vt = vt # Spiking threshold + self.taum = taum # Membrane time constant + self.vr = vr # Reset potential + self.refrT = refrT # Absolute refractory period + self.Rm = Rm # Membrane resistance + self.Cm = Cm # Membrane capacitance + self.Iinject = Iinject # constant input current + self.noiseInjSD = noiseInjSD # SD of injected noise + + self.simif = False # whether the simulation is complete + + self._setup_network() + + def __str__(self): + return "LIF network of %d neurons "\ + "having %d exc." % (self.N,self.NmaxExc) + + def _setup_network(self): + """Sets up the network (_init_network is enough)""" + self.network = moose.LIF( 'network', self.N ); + moose.le( '/network' ) + self.network.vec.Em = self.el + self.network.vec.thresh = self.vt + self.network.vec.refractoryPeriod = self.refrT + self.network.vec.Rm = self.Rm + self.network.vec.vReset = self.vr + self.network.vec.Cm = self.Cm + if not noiseInj: + self.network.vec.inject = self.Iinject + else: + ## inject a constant + noisy current + ## values are set in self.simulate() + self.noiseTables = moose.StimulusTable('noiseTables',self.N) + moose.connect( self.noiseTables, 'output', \ + self.network, 'setInject', 'OneToOne') + + def _init_network(self,v0=el): + """Initialises the network variables before simulation""" + self.network.vec.initVm = v0 + + def simulate(self,simtime=simtime,dt=dt,plotif=False,**kwargs): + + self.dt = dt + self.simtime = simtime + self.T = np.ceil(simtime/dt) + self.trange = np.arange(0,self.simtime,dt) + + # Build in the LTP stimulus + offset = Iinject * 0.5 + injBaseline = np.repeat( self.Iinject, self.T ) + start = np.ceil( simtime / (interTetInterval * dt) ) + for i in range( 3 ): + end = start + np.ceil( 0.5 / dt ) + injBaseline[ start:end ] += offset + start = start + np.ceil( interTetInterval / dt ) + + for i in range(self.N): + if noiseInj: + ## Gaussian white noise SD added every dt interval should be + ## divided by sqrt(dt), as the later numerical integration + ## will multiply it by dt. + ## See the Euler-Maruyama method, numerical integration in + ## http://www.scholarpedia.org/article/Stochastic_dynamical_systems + self.noiseTables.vec[i].vector = injBaseline + \ + np.random.normal( \ + scale=self.noiseInjSD*np.sqrt(self.Rm*self.Cm/self.dt), \ + size=self.T ) # scale = SD + self.noiseTables.vec[i].stepSize = 0 # use current time + # as x value for interpolation + + + self.noiseTables.vec[i].stopTime = self.simtime + + self._init_network(**kwargs) + if plotif: + self._init_plots() + + + def _init_plots(self): + ## make a few tables to store a few Vm-s + numVms = 10 + self.plots = moose.Table( '/plotVms', numVms ) + ## draw numVms out of N neurons + nrnIdxs = random.sample(list(range(self.N)),numVms) + for i in range( numVms ): + moose.connect( self.network.vec[nrnIdxs[i]], 'VmOut', \ + self.plots.vec[i], 'input') + + ## make self.N tables to store spikes of all neurons + self.spikes = moose.Table( '/plotSpikes', self.N ) + moose.connect( self.network, 'spikeOut', \ + self.spikes, 'input', 'OneToOne' ) + + ## make 2 tables to store spikes of all exc and all inh neurons + self.spikesExc = moose.Table( '/plotSpikesAllExc' ) + for i in range(self.NmaxExc): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesExc, 'input' ) + self.spikesInh = moose.Table( '/plotSpikesAllInh' ) + for i in range(self.NmaxExc,self.N): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesInh, 'input' ) + + def _plot(self, fig): + """ plots the spike raster for the simulated net""" + plt.figure(1) + + ax = plt.subplot(221) + cleanAx( ax, 'B' ) + plt.ylabel( 'Neuron #', fontsize = 16 ) + for i in range(0,self.NmaxExc): + if i==0: label = 'Exc. spike trains' + else: label = '' + spikes = self.spikes.vec[i].vector + ax.plot(spikes,[i]*len(spikes),\ + 'b.',marker='.', markersize = 2, label=label) + for i in range(self.NmaxExc,self.N): + if i==self.NmaxExc: label = 'Inh. spike trains' + else: label = '' + spikes = self.spikes.vec[i].vector + ax.plot(spikes,[i]*len(spikes),\ + 'r.',marker='.', markersize = 2, label=label) + +############################################# +# Exc-Inh network class with Ca plasticity based connections +# (inherits from ExcInhNetBase) +############################################# + +class ExcInhNet(ExcInhNetBase): + """ Recurrent network simulation """ + + def __init__(self,J=J,incC=C,fC=fC,scaleI=g,syndelay=syndelay,**kwargs): + """Overloads base (parent) class""" + self.J = J # exc connection weight + self.incC = incC # number of incoming connections per neuron + self.fC = fC # fraction of exc incoming connections + self.excC = int(fC*incC)# number of exc incoming connections + self.scaleI = scaleI # inh weight is scaleI*J + self.syndelay = syndelay# synaptic delay + + # call the parent class constructor + ExcInhNetBase.__init__(self,**kwargs) + + def __str__(self): + return "LIF network of %d neurons "\ + "of which %d are exc." % (self.N,self.NmaxExc) + + def _init_network(self,**args): + ExcInhNetBase._init_network(self,**args) + + def _init_plots(self): + ExcInhNetBase._init_plots(self) + self.recN = 5 # number of neurons for which to record weights and Ca + if CaPlasticity: + ## make tables to store weights of recN exc synapses + ## for each post-synaptic exc neuron + self.weights = moose.Table( '/plotWeights', self.excC*self.recN ) + for i in range(self.recN): # range(self.N) is too large + for j in range(self.excC): + moose.connect( self.weights.vec[self.excC*i+j], 'requestOut', + self.synsEE.vec[i*self.excC+j].synapse[0], 'getWeight') + + def _setup_network(self): + ## Set up the neurons without connections + ExcInhNetBase._setup_network(self) + + ## Now, add in the connections... + ## Each pre-synaptic spike cause Vm of post-neuron to rise by + ## synaptic weight in one time step i.e. delta-fn synapse. + ## Since LIF neuron is derived from Compartment class, + ## conductance-based synapses (SynChan class) can also be used. + + ## E to E synapses can be plastic + ## Two ways to do this: + ## 1) Each LIF neuron has one incoming postsynaptic SynHandler, + ## which collects the activation from all presynaptic neurons, + ## but then a common Ca pool is used. + ## 2) Each LIF neuron has multiple postsyanptic SynHandlers, + ## one for each pre-synaptic neuron, i.e. one per synapse, + ## then each synapse has a different Ca pool. + ## Here we go with option 2) as per Higgins et al 2014 (Brunel private email) + ## separate SynHandler per EE synapse, thus NmaxExc*excC + if CaPlasticity: + self.synsEE = moose.GraupnerBrunel2012CaPlasticitySynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + else: + self.synsEE = moose.SimpleSynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + moose.useClock( 0, '/network/synsEE', 'process' ) + + ## I to E synapses are not plastic + self.synsIE = moose.SimpleSynHandler( '/network/synsIE', self.NmaxExc ) + ## all synapses to I neurons are not plastic + self.synsI = moose.SimpleSynHandler( '/network/synsI', self.N-self.NmaxExc ) + ## connect all SynHandlers to their respective neurons + for i in range(self.NmaxExc): + moose.connect( self.synsIE.vec[i], 'activationOut', \ + self.network.vec[i], 'activation' ) + for i in range(self.NmaxExc,self.N): + moose.connect( self.synsI.vec[i-self.NmaxExc], 'activationOut', \ + self.network.vec[i], 'activation' ) + + ## Connections from some Exc/Inh neurons to each Exc neuron + for i in range(0,self.NmaxExc): + self.synsIE.vec[i].numSynapses = self.incC-self.excC + + ## Connections from some Exc neurons to each Exc neuron + ## draw excC number of neuron indices out of NmaxExc neurons + preIdxs = random.sample(list(range(self.NmaxExc)),self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synidx = i*self.excC+synnum + synHand = self.synsEE.vec[synidx] + + ## connect each synhandler to the post-synaptic neuron + moose.connect( synHand, 'activationOut', \ + self.network.vec[i], 'activation' ) + ## important to set numSynapses = 1 for each synHandler, + ## doesn't create synapses if you set the full array of SynHandlers + synHand.numSynapses = 1 + + synij = synHand.synapse[0] + connectExcId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + if CaPlasticity: + ## set parameters for the Ca Plasticity SynHandler + ## have to be set for each SynHandler + ## doesn't set for full array at a time + synHand.CaInit = 0.0 + synHand.tauCa = tauCa + synHand.tauSyn = tauSyn + synHand.CaPre = CaPre + synHand.CaPost = CaPost + synHand.delayD = delayD + synHand.thetaD = thetaD + synHand.thetaP = thetaP + synHand.gammaD = gammaD + synHand.gammaP = gammaP + synHand.weightMax = 1.0 # bounds on the weight + synHand.weightMin = 0.0 + synHand.weightScale = \ + self.J*2.0 # 0.2 mV, weight*weightScale is activation + # typically weight <~ 0.5, so activation <~ J + synHand.noisy = noisy + synHand.noiseSD = noiseSD + synHand.bistable = bistable + + moose.connect( self.network.vec[i], \ + 'spikeOut', synHand, 'addPostSpike') + synij.weight = eqWeight # activation = weight*weightScale + # weightScale = 2*J + # weight <~ 0.5 + ## Randomly set 5% of them to be 1.0 + if np.random.uniform()<0.05: + synij.weight = 1.0 + else: + synij.weight = self.J # no weightScale here, activation = weight + + ## Connections from some Inh neurons to each Exc neuron + ## draw inhC=incC-excC number of neuron indices out of inhibitory neurons + preIdxs = random.sample(list(range(self.NmaxExc,self.N)),self.incC-self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsIE.vec[i].synapse[synnum] + connectInhId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = -self.scaleI*self.J # activation = weight + + ## Connections from some Exc/Inh neurons to each Inh neuron + for i in range(self.N-self.NmaxExc): + ## each neuron has incC number of synapses + self.synsI.vec[i].numSynapses = self.incC + + ## draw excC number of neuron indices out of NmaxExc neurons + preIdxs = random.sample(list(range(self.NmaxExc)),self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsI.vec[i].synapse[synnum] + connectExcId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = self.J # activation = weight + + ## draw inhC=incC-excC number of neuron indices out of inhibitory neurons + preIdxs = random.sample(list(range(self.NmaxExc,self.N)),self.incC-self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsI.vec[i].synapse[ self.excC + synnum ] + connectInhId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = -self.scaleI*self.J # activation = weight + + moose.useClock( 0, '/network/synsIE', 'process' ) + moose.useClock( 0, '/network/synsI', 'process' ) + +############################################# +# Analysis functions +############################################# + +def rate_from_spiketrain(spiketimes,fulltime,dt,tau=50e-3): + """ + Returns a rate series of spiketimes convolved with a Gaussian kernel; + all times must be in SI units. + """ + sigma = tau/2. + ## normalized Gaussian kernel, integral with dt is normed to 1 + ## to count as 1 spike smeared over a finite interval + norm_factor = 1./(np.sqrt(2.*np.pi)*sigma) + gauss_kernel = np.array([norm_factor*np.exp(-x**2/(2.*sigma**2))\ + for x in np.arange(-5.*sigma,5.*sigma+dt,dt)]) + kernel_len = len(gauss_kernel) + ## need to accommodate half kernel_len on either side of fulltime + rate_full = np.zeros(int(fulltime/dt)+kernel_len) + for spiketime in spiketimes: + idx = int(spiketime/dt) + rate_full[idx:idx+kernel_len] += gauss_kernel + ## only the middle fulltime part of the rate series + ## This is already in Hz, + ## since should have multiplied by dt for above convolution + ## and divided by dt to get a rate, so effectively not doing either. + return rate_full[kernel_len/2:kernel_len/2+int(fulltime/dt)] + +############################################# +# Make plots +############################################# + +def extra_plots(net): + ## extra plots apart from the spike rasters + timeseries = net.trange + ## individual neuron firing rates + fig3 = plt.figure() + plt.subplot(221) + num_to_plot = 10 + #rates = [] + for nrni in range(num_to_plot): + rate = rate_from_spiketrain(\ + net.spikes.vec[nrni].vector,simtime,dt, 1.0 ) + plt.plot(timeseries,rate) + plt.title("Rates of "+str(num_to_plot)+" exc nrns") + plt.ylabel("Hz") + plt.ylim(0,100) + plt.subplot(222) + for nrni in range(num_to_plot): + rate = rate_from_spiketrain(\ + net.spikes.vec[net.NmaxExc+nrni].vector,simtime,dt, 1.0 ) + plt.plot(timeseries,rate) + plt.title("Rates of "+str(num_to_plot)+" inh nrns") + plt.ylim(0,100) + + ## population firing rates + plt.subplot(223) + rate = rate_from_spiketrain(net.spikesExc.vector,simtime,dt)\ + /float(net.NmaxExc) # per neuron + plt.plot(timeseries,rate) + plt.ylim(0,100) + plt.title("Exc population rate") + plt.ylabel("Hz") + plt.xlabel("Time (s)") + plt.subplot(224) + rate = rate_from_spiketrain(net.spikesInh.vector,simtime,dt)\ + /float(net.N-net.NmaxExc) # per neuron + plt.plot(timeseries,rate) + plt.ylim(0,100) + plt.title("Inh population rate") + plt.xlabel("Time (s)") + + fig3.tight_layout() + +def makeScatterPlot( m, n, v ): + fig4 = plt.figure() + + dx = 100e-6 + dy = 100e-6 + x = np.arange( m ) * dx + x = np.tile( x, n ) + y = np.arange( n ) * dy + y = y.repeat( m ) + #z = np.arange( m * n ) + #ret = plt.scatter( x, y, s = 64, c = v, vmin = -0.065, vmax = -0.055 ) + cmap = plt.get_cmap('afmhot') + ret = plt.scatter( x, y, s = 64, c = v, vmin = 0.5, vmax = 1.0, cmap = cmap ) + plt.xlim( -dx, dx * m ) + plt.ylim( -dy, dy * n ) + return fig4, ret + +def buildNeuronPlots( rdes ): + if not moose.exists( '/graphs' ): + graphs = moose.Neutral( '/graphs' ) + vtab = moose.Table( '/graphs/vtab' ) + catab = moose.Table( '/graphs/catab' ) + moose.connect( vtab, "requestOut", rdes.soma, "getVm" ) + caSoma = moose.element( rdes.soma.path + "/Ca_conc" ) + moose.connect( catab, "requestOut", caSoma, "getCa" ) + elist = moose.wildcardFind( '/model/chem/psd/tot_PSD_R[]' ) + rtab = moose.Table2( '/graphs/rtab', len( elist ) ).vec + for i in zip( elist, rtab ): + moose.connect( i[1], "requestOut", i[0], "getN" ) + elist = moose.wildcardFind( '/model/chem/spine/Ca[]' ) + pcatab = moose.Table2( '/graphs/pcatab', len( elist ) ).vec + for i in zip( elist, pcatab ): + moose.connect( i[1], "requestOut", i[0], "getConc" ) + +def cleanAx( ax, label, showXlabel = False ): + ax.spines['top'].set_visible( False ) + ax.spines['right'].set_visible( False ) + ax.tick_params( direction = 'out' ) + if not showXlabel: + ax.set_xticklabels( [] ) + for tick in ax.xaxis.get_major_ticks(): + tick.tick2On = False + for tick in ax.yaxis.get_major_ticks(): + tick.tick2On = False + ax.text( -0.18, 1.0, label, fontsize = 18, weight = 'bold', transform=ax.transAxes ) + + +def saveNeuronPlots( fig, rdes ): + #fig = plt.figure( figsize=(12, 10), facecolor='white' ) + #fig.subplots_adjust( left = 0.18 ) + plt.figure(1) + + ax = plt.subplot(222) + cleanAx( ax, 'C' ) + plt.ylabel( 'Vm (mV)', fontsize = 16 ) + vtab = moose.element( '/graphs/vtab' ) + t = np.arange( 0, len( vtab.vector ), 1 ) * vtab.dt + plt.plot( t, vtab.vector * 1000, label="Vm" ) + #plt.legend() + + ax = plt.subplot(223) + cleanAx( ax, 'D', showXlabel = True ) + pcatab = list( moose.vec( '/graphs/pcatab' ) )[0::50] + t = np.arange( 0, len( pcatab[0].vector ), 1 ) * pcatab[0].dt + for i in pcatab: + plt.plot( t, i.vector * 1000 ) + plt.ylabel( '[Ca] (uM)', fontsize = 16 ) + plt.xlabel( 'Time (s)', fontsize = 16 ) + + ax = plt.subplot(224) + cleanAx( ax, 'E', showXlabel = True ) + rtab = list( moose.vec( '/graphs/rtab' ) )[0::50] + t = np.arange( 0, len( rtab[0].vector ), 1 ) * rtab[0].dt + for i in rtab: + plt.plot( t, i.vector ) + plt.ylabel( '# of inserted GluRs', fontsize = 16 ) + plt.xlabel( 'Time (s)', fontsize = 16 ) + ''' + for i in moose.wildcardFind( '/graphs/#' ): + i.xplot( fname + '.xplot', i.name ) + ''' + +def create_viewer(rdes): + # print "Creating 3D Viewer" + network = moogli.extensions.moose.read(path=rdes.elecid.path, + vertices=10) + # print "Read Network" + network.set("color", moogli.colors.LIGHT_BLUE) + network.groups["spine"].set("color", moogli.colors.ORANGE) + # for dendrite in dendrites.values(): + # dendrite.set_colors(moogli.core.Vec4f(173 / 255.0, 216 / 255.0, 230 / 255.0, 1.0)) + + [shape.set_radius(shape.get_apex_radius() * 4.0) for shape in + list(network.groups["spine"].groups["head"].shapes.values())] + # print "Creating LIFS" + soma = network.shapes[rdes.soma.path] + + center = soma.get_center() + row_axis = moogli.geometry.X_AXIS + row_count = 25 + row_separation = soma.get_base_radius() * 5.0 + col_axis = moogli.geometry.Z_AXIS + col_count = 25 + col_separation = row_separation + radii = soma.get_base_radius() + colors = moogli.colors.GREEN + vertices = 20 + lifs = moogli.shapes.Sphere.grid("LIF", + center, + row_axis, + row_count, + row_separation, + col_axis, + col_count, + col_separation, + radii, + colors, + vertices) + # print "Created LIFS" + # morphology.create_group("dendrites", dendrites, 0.0, 300.0, colormap) + # print "Creating Viewer" + viewer = moogli.Viewer("viewer") # prelude = prelude, interlude = interlude) + # print "Created Viewer" + viewer.attach_shapes(list(network.shapes.values())) + viewer.attach_shapes(list(lifs.shapes.values())) + # print "Attached Shapes" + view = moogli.View("view") + viewer.attach_view(view) + # print "Attached View" + return viewer + +if __name__=='__main__': + plt.ion() + ## ExcInhNetBase has unconnected neurons, + ## ExcInhNet connects them + ## Instantiate either ExcInhNetBase or ExcInhNet below + #net = ExcInhNetBase(N=N) + net = ExcInhNet(N=N) + print(net) + moose.le( '/' ) + moose.le( '/network' ) + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + buildNeuronPlots( rdes ) + connectDetailedNeuron() + + app = QtGui.QApplication(sys.argv) + viewer = create_viewer(rdes) + viewer.showMaximized() + viewer.start() + app.exec_() + + ## Important to distribute the initial Vm-s + ## else weak coupling gives periodic synchronous firing + plotif = True + net.simulate(simtime,plotif=plotif,\ + v0=np.random.uniform(el-20e-3,vt,size=N)) + + # moose simulation + moose.useClock( 1, '/network', 'process' ) + moose.useClock( 2, '/plotSpikes', 'process' ) + moose.useClock( 3, '/plotVms', 'process' ) + if CaPlasticity: + moose.useClock( 3, '/plotWeights', 'process' ) + moose.useClock( 3, '/plotCa', 'process' ) + moose.setClock( 0, dt ) + moose.setClock( 1, dt ) + moose.setClock( 2, dt ) + moose.setClock( 3, dt ) + #moose.setClock( moose.element( '/cell/hsolve' ), dt ) + moose.setClock( 9, dt ) + + if plotif: + Vm = net.network.vec.Vm + fig = plt.figure( 1, figsize=(12, 10), facecolor='white' ) + fig.subplots_adjust( left = 0.18 ) + fig2, ret = makeScatterPlot( 50, 50, Vm ) + #cellFig = bcs.neuronPlot( '/model/elec', '/model/chem/psd/tot_PSD_R[]' ) + + moose.reinit() + t1 = time.time() + print('starting') + #moose.start(simtime) + for currTime in np.arange( 0, simtime, updateDt ): + moose.start(updateDt) + lastt = net.network.vec.lastEventTime + lastt = np.exp( 2 * (lastt - currTime ) ) + print(currTime, time.time() - t1) + ret.set_array( lastt ) + fig2.canvas.draw() + + print('runtime, t = ', time.time() - t1) + + if plotif: + net._plot( fig ) + + extra_plots(net) + #bcs.displayCellPlots( plt ) + saveNeuronPlots( fig, rdes ) + plt.show() + plt.savefig( fname + '.svg', bbox_inches='tight') + print( "Hit 'enter' to exit" ) + input() diff --git a/demos/Fig6_NetMultiscale/ReducedModel.py b/demos/Fig6_NetMultiscale/ReducedModel.py new file mode 100644 index 0000000..1b73043 --- /dev/null +++ b/demos/Fig6_NetMultiscale/ReducedModel.py @@ -0,0 +1,888 @@ +#/********************************************************************** +#** This program is part of 'MOOSE', the +#** Messaging Object Oriented Simulation Environment. +#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS +#** It is made available under the terms of the +#** GNU Lesser General Public License version 2.1 +#** See the file COPYING.LIB for the full notice. +#**********************************************************************/ + +''' +This LIF network with Ca plasticity is based on: +David Higgins, Michael Graupner, Nicolas Brunel + Memory Maintenance in Synapses with Calcium-Based + Plasticity in the Presence of Background Activity + PLOS Computational Biology, 2014. + +Implemented by: Aditya Gilra, NCBS, Bangalore, October, 2014. +This variant has 400 LIF neurons + +Upi Bhalla, Nov 2014: Appended single neuron model. + +This script is a reduced version of the model that generates the panels +in Figure 6. It takes just a couple of minutes to run 30 seconds of +simulation time. That is, 400 neurons, 1 detailed model with 36 +compartments plus 16 spines each having 2 compartments and 34 molecules, +and lots of synapses. +''' + +from __future__ import print_function + +## import modules and functions to be used +import numpy as np +import matplotlib.pyplot as plt +import random +import time +import moose +from numpy import random as nprand +from moose.neuroml.NeuroML import NeuroML +import sys +sys.path.append( "/home/bhalla/moose/trunk/Demos/util" ) +import rdesigneur as rd +#cellname = "./cells_channels/CA1_nochans.morph.xml" +cellname = "./cells_channels/ca1_minimal.p" +fname = "reduced" + +############################################# +np.random.seed(100) # set seed for reproducibility of simulations +random.seed(100) # set seed for reproducibility of simulations +moose.seed(100) # set seed for reproducibility of simulations + +############################################# +# All parameters as per: +# David Higgins, Michael Graupner, Nicolas Brunel +# Memory Maintenance in Synapses with Calcium-Based +# Plasticity in the Presence of Background Activity +# PLOS Computational Biology, 2014. +############################################# + +############################################# +# Neuron model +############################################# + +# equation: dv/dt = (1/taum)*(-(v-el)) + inp +# with spike when v>vt, reset to vr + +PI = 3.14159265358979 +useGssa = True +combineSegments = False + +el = -70e-3 #V # Resting potential +vt = -50e-3 #V # Spiking threshold +Rm = 20e6 #Ohm # Only taum is needed, but LIF neuron accepts +Cm = 1e-9 #F # Rm and Cm and constructs taum=Rm*Cm +taum = Rm*Cm #s # Membrane time constant is 20 ms +vr = -60e-3 #V # Reset potential +Iinject = 10e-3/Rm # constant current injection into LIF neuron + # same as setting el=-70+15=-55 mV and inp=0 +noiseInj = True # inject noisy current into each cell: boolean +noiseInjSD = 5e-3/Rm #A # SD of noise added to 'current' + # SD*sqrt(taum) is used as noise current SD + +############################################# +# Network parameters: numbers +############################################# + +N = 400 # Total number of neurons +fexc = 0.8 # Fraction of exc neurons +NE = int(fexc*N) # Number of excitatory cells +NI = N-NE # Number of inhibitory cells + +############################################# +# Simulation parameters +############################################# + +simtime = 30 #s # Simulation time +interTetInterval = 5.0 # sec +updateDt = 0.2 #s: time to update live display +dt = 1e-3 #s # time step + +############################################# +# Network parameters: synapses (not for ExcInhNetBase) +############################################# + +## With each presynaptic spike in exc / inh neuron, +## J / -g*J is added to post-synaptic Vm -- delta-fn synapse +## Since LIF neuron used below is derived from Compartment class, +## conductance-based synapses (SynChan class) can also be used. + +C = 100 # Number of incoming connections on each neuron (exc or inh) +fC = fexc # fraction fC incoming connections are exc, rest inhibitory +J = 0.2e-3 #V # exc strength is J (in V as we add to voltage) + # Critical J is ~ 0.45e-3 V in paper for N = 10000, C = 1000 + # See what happens for J = 0.2e-3 V versus J = 0.8e-3 V +g = 4.0 # -gJ is the inh strength. For exc-inh balance g >~ f(1-f)=4 +syndelay = dt # synaptic delay: +refrT = 0.0 # s # absolute refractory time + +############################################# +# Ca Plasticity parameters: synapses (not for ExcInhNetBase) +############################################# + +CaPlasticity = True # set it True or False to turn on/off plasticity +tauCa = 22.6936e-3 # s # Ca decay time scale +tauSyn = 346.3615 # s # synaptic plasticity time scale +## in vitro values in Higgins et al 2014, faster plasticity +CaPre = 0.56175 # mM + +CaPost = 1.2964 # mM +## in vivo values in Higgins et al 2014, slower plasticity +#CaPre = 0.33705 # mM +#CaPost = 0.74378 # mM +delayD = 4.6098e-3 # s # CaPre is added to Ca after this delay + # proxy for rise-time of NMDA +thetaD = 1.0 # mM # depression threshold for Ca +thetaP = 1.3 # mM # potentiation threshold for Ca +gammaD = 331.909 # factor for depression term +gammaP = 725.085 # factor for potentiation term + +eqWeight = 0.5 # initial synaptic weight + # gammaP/(gammaP+gammaD) = eq weight w/o noise + # but see eqn (22), noiseSD also appears + +bistable = True # if bistable is True, use bistable potential for weights +noisy = True # use noisy weight updates given by noiseSD +noiseSD = 3.3501 # if noisy, use noiseSD (3.3501 from Higgins et al 2014) +#noiseSD = 0.1 # if bistable==False, use a smaller noise than in Higgins et al 2014 + +############################################# +# Here we set up a single neuron to fit in this network +############################################# + +diffDt = 0.005 +chemDt = 0.005 +ePlotDt = 0.5e-3 +cPlotDt = 0.005 + +############################################# +def buildRdesigneur(): + ################################################################## + # Here we define which prototypes are to be loaded in to the system. + # Each specification has the format + # source [localName] + # source can be any of + # filename.extension, # Identify type of file by extension, load it. + # function(), # func( name ) builds object of specified name + # file.py:function() , # load Python file, run function(name) in it. + # moose.Classname # Make obj moose.Classname, assign to name. + # path # Already loaded into library or on path. + # After loading the prototypes, there should be an object called 'name' + # in the library. + ################################################################## + cellProto = [ [cellname, 'elec'] ] + chanProto = [ + ['./cells_channels/hd.xml'], \ + ['./cells_channels/kap.xml'], \ + ['./cells_channels/kad.xml'], \ + ['./cells_channels/kdr.xml'], \ + ['./cells_channels/na3.xml'], \ + ['./cells_channels/nax.xml'], \ + ['./cells_channels/CaConc.xml'], \ + ['./cells_channels/Ca.xml'], \ + ['./cells_channels/NMDA.xml'], \ + ['./cells_channels/Glu.xml'], \ + ['./cells_channels/GABA.xml'] \ + ] + spineProto = [ \ + ['makeSpineProto()', 'spine' ] + ] + chemProto = [ \ + [ 'psd53.g', 'ltpModel'] \ + ] + + ################################################################## + # Here we define what goes where, and any parameters. Each distribution + # has the format + # protoName, path, field, expr, [field, expr]... + # where + # protoName identifies the prototype to be placed on the cell + # path is a MOOSE wildcard path specifying where to put things + # field is the field to assign. + # expr is a math expression to define field value. This uses the + # muParser. Built-in variables are p, g, L, len, dia. + # The muParser provides most math functions, and the Heaviside + # function H(x) = 1 for x > 0 is also provided. + ################################################################## + passiveDistrib = [ + [ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \ + "Em", "-58e-3", "initVm", "-65e-3" ], \ + [ ".", "#axon#", "RA", "0.5" ] \ + ] + chanDistrib = [ \ + ["hd", "#dend#,#apical#,#user#", "Gbar", "5e-2*(1+(p*3e4))" ], \ + ["kdr", "#", "Gbar", "100" ], \ + ["na3", "#soma#,#dend#,#apical#,#user#", "Gbar", "250" ], \ + ["nax", "#axon#", "Gbar", "1250" ], \ + ["nax", "#soma#", "Gbar", "100" ], \ + ["kap", "#axon#,#soma#", "Gbar", "300" ], \ + ["kap", "#dend#,#apical#,#user#", "Gbar", \ + "300*(H(100-p*1e6)) * (1+(p*1e4))" ], \ + ["Ca_conc", "#soma#,#dend#,#apical#,#user#", "tau", "0.0133" ], \ + ["kad", "#dend#,#apical#,#user#", "Gbar", \ + "300*H(p*1e6-100)*(1+p*1e4)" ], \ + ["Ca", "#soma#", "Gbar", "10e-3" ], \ + ["Ca", "#dend#,#apical#,#user#", "Gbar", "50e-3" ], \ + ["glu", "#dend#,#apical#", "Gbar", "50" ], \ + ["NMDA", "#dend#,#apical#", "Gbar", "20" ], \ + ["GABA", "#dend#,#apical#,#user#", "Gbar", "100*H(250e-6 - p)" ], \ + ] + spineDistrib = [ \ + ["spine", '#apical#', \ + "spineSpacing", "H(p-400e-6)*H(800e-6-p)*10e-6", \ + "spineSpacingDistrib", "1e-6", \ + "angle", "0", \ + "angleDistrib", str( 2*PI ), \ + "size", "1", \ + "sizeDistrib", "0.5" ] \ + ] + chemDistrib = [ \ + [ "ltpModel", "#apical#", "install", "1" ] \ + ] + + ''' + ''' + ###################################################################### + # Here we define the mappings across scales. Format: + # sourceObj sourceField destObj destField couplingExpr [wildcard][spatialExpn] + # where the coupling expression is anything a muParser can evaluate, + # using the input variable x. For example: 8e-5 + 300*x + # For now, let's use existing adaptors which take an offset and scale. + ###################################################################### + adaptorList = [ + [ 'Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 8e-5, 1 ], + [ 'Ca_conc', 'Ca', 'dend/Ca_dend_input', 'concInit', 8e-5, 1 ], + [ 'psd/tot_PSD_R', 'n', 'glu', 'modulation', 0.5, 0.002 ], + ] + + ###################################################################### + # Having defined everything, now to create the rdesigneur and proceed + # with creating the model. + ###################################################################### + + + rdes = rd.rdesigneur( + useGssa = useGssa, \ + combineSegments = combineSegments, \ + stealCellFromLibrary = True, \ + passiveDistrib = passiveDistrib, \ + spineDistrib = spineDistrib, \ + chanDistrib = chanDistrib, \ + chemDistrib = chemDistrib, \ + cellProto = cellProto, \ + spineProto = spineProto, \ + chanProto = chanProto, \ + chemProto = chemProto, \ + adaptorList = adaptorList + ) + + return rdes + + +############################################# + +def makeDetailedNeuron(): + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + #bcs.addAllPlots() + +def connectDetailedNeuron(): + excProb = 0.005 + excSeed = 1234 + inhProb = 0.005 + inhSeed = 4567 + numExc = 0 + numNMDA = 0 + numInh = 0 + delayMax = 0.010 + delayMin = 0.002 + excWeightMax = 5 + nmdaWeightMax = 2 + inhWeightMax = 50 + # Note we use the same seed for all 3 exc connections, to make sure + # they are all equivalent. + seed = excSeed + totGluWt = 0.0 + totNMDAWt = 0.0 + totGABAWt = 0.0 + for x in moose.wildcardFind( '/model/elec/#/glu/##[ISA=Synapse]' ): + exc = moose.connect( '/network', 'spikeOut', x, 'addSpike','sparse') + exc.setRandomConnectivity( excProb, seed ) + seed = seed + 1 + if exc.numEntries > 0: + numExc += exc.numEntries + assert( exc.numEntries == x.numField ) + x.vec.delay = delayMin + nprand.rand( exc.numEntries ) * ( delayMax - delayMin ) + x.vec.weight = nprand.rand( exc.numEntries ) * excWeightMax + #x.parent.tick = 4 + x.parent.parent.tick = 4 + print('+', end=' ') + totGluWt += sum(x.vec.weight) * x.parent.parent.Gbar + + seed = excSeed + for x in moose.wildcardFind( '/model/elec/#/NMDA/##[ISA=Synapse]' ): + #print " x = ", x + exc = moose.connect( '/network', 'spikeOut', x, 'addSpike','sparse') + exc.setRandomConnectivity( excProb, seed ) + seed = seed + 1 + if exc.numEntries > 0: + numNMDA += exc.numEntries + assert( exc.numEntries == x.numField ) + x.vec.delay = delayMin + nprand.rand( exc.numEntries ) * ( delayMax - delayMin ) + x.vec.weight = nprand.rand( exc.numEntries ) * nmdaWeightMax + #x.parent.tick = 4 + x.parent.parent.tick = 4 + print('*', end=' ') + totNMDAWt += sum(x.vec.weight) * x.parent.parent.Gbar + + seed = inhSeed + for x in moose.wildcardFind( '/model/elec/#/GABA/##[ISA=Synapse]' ): + #print x + inh = moose.connect( '/network', 'spikeOut', x, 'addSpike','sparse') + inh.setRandomConnectivity( inhProb, seed ) + seed = seed + 1 + if inh.numEntries > 0: + numInh += inh.numEntries + x.vec.delay = delayMin + nprand.rand( inh.numEntries ) * ( delayMax - delayMin ) + x.vec.weight = nprand.rand( inh.numEntries ) * inhWeightMax + #x.parent.tick = 4 + x.parent.parent.tick = 4 + print('-', end=' ') + totGABAWt += sum(x.vec.weight) * x.parent.parent.Gbar + + print('connectDetailedNeuron: numExc = ', numExc, ', numNMDA=', numNMDA, ', numInh = ', numInh) + print('connectDetailedNeuron: totWts Glu = ', totGluWt, ', NMDA = ', totNMDAWt, ', GABA = ', totGABAWt) + +############################################# +# Exc-Inh network base class without connections +############################################# + +class ExcInhNetBase: + """Simulates and plots LIF neurons (exc and inh separate). + Author: Aditya Gilra, NCBS, Bangalore, India, October 2014 + """ + + def __init__(self,N=N,fexc=fexc,el=el,vt=vt,Rm=Rm,Cm=Cm,vr=vr,\ + refrT=refrT,Iinject=Iinject): + """ Constructor of the class """ + + self.N = N # Total number of neurons + self.fexc = fexc # Fraction of exc neurons + self.NmaxExc = int(fexc*N) # max idx of exc neurons, rest inh + + self.el = el # Resting potential + self.vt = vt # Spiking threshold + self.taum = taum # Membrane time constant + self.vr = vr # Reset potential + self.refrT = refrT # Absolute refractory period + self.Rm = Rm # Membrane resistance + self.Cm = Cm # Membrane capacitance + self.Iinject = Iinject # constant input current + self.noiseInjSD = noiseInjSD # SD of injected noise + + self.simif = False # whether the simulation is complete + + self._setup_network() + + def __str__(self): + return "LIF network of %d neurons "\ + "having %d exc." % (self.N,self.NmaxExc) + + def _setup_network(self): + """Sets up the network (_init_network is enough)""" + self.network = moose.LIF( 'network', self.N ); + moose.le( '/network' ) + self.network.vec.Em = self.el + self.network.vec.thresh = self.vt + self.network.vec.refractoryPeriod = self.refrT + self.network.vec.Rm = self.Rm + self.network.vec.vReset = self.vr + self.network.vec.Cm = self.Cm + if not noiseInj: + self.network.vec.inject = self.Iinject + else: + ## inject a constant + noisy current + ## values are set in self.simulate() + self.noiseTables = moose.StimulusTable('noiseTables',self.N) + moose.connect( self.noiseTables, 'output', \ + self.network, 'setInject', 'OneToOne') + + def _init_network(self,v0=el): + """Initialises the network variables before simulation""" + self.network.vec.initVm = v0 + + def simulate(self,simtime=simtime,dt=dt,plotif=False,**kwargs): + + self.dt = dt + self.simtime = simtime + self.T = np.ceil(simtime/dt) + self.trange = np.arange(0,self.simtime,dt) + + # Build in the LTP stimulus + offset = Iinject * 0.5 + injBaseline = np.repeat( self.Iinject, self.T ) + start = np.ceil( simtime / (interTetInterval * dt) ) + for i in range( 3 ): + end = start + np.ceil( 0.5 / dt ) + injBaseline[ start:end ] += offset + start = start + np.ceil( interTetInterval / dt ) + + for i in range(self.N): + if noiseInj: + ## Gaussian white noise SD added every dt interval should be + ## divided by sqrt(dt), as the later numerical integration + ## will multiply it by dt. + ## See the Euler-Maruyama method, numerical integration in + ## http://www.scholarpedia.org/article/Stochastic_dynamical_systems + self.noiseTables.vec[i].vector = injBaseline + \ + np.random.normal( \ + scale=self.noiseInjSD*np.sqrt(self.Rm*self.Cm/self.dt), \ + size=self.T ) # scale = SD + self.noiseTables.vec[i].stepSize = 0 # use current time + # as x value for interpolation + + + self.noiseTables.vec[i].stopTime = self.simtime + + self._init_network(**kwargs) + if plotif: + self._init_plots() + + + def _init_plots(self): + ## make a few tables to store a few Vm-s + numVms = 10 + self.plots = moose.Table( '/plotVms', numVms ) + ## draw numVms out of N neurons + nrnIdxs = random.sample(list(range(self.N)),numVms) + for i in range( numVms ): + moose.connect( self.network.vec[nrnIdxs[i]], 'VmOut', \ + self.plots.vec[i], 'input') + + ## make self.N tables to store spikes of all neurons + self.spikes = moose.Table( '/plotSpikes', self.N ) + moose.connect( self.network, 'spikeOut', \ + self.spikes, 'input', 'OneToOne' ) + + ## make 2 tables to store spikes of all exc and all inh neurons + self.spikesExc = moose.Table( '/plotSpikesAllExc' ) + for i in range(self.NmaxExc): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesExc, 'input' ) + self.spikesInh = moose.Table( '/plotSpikesAllInh' ) + for i in range(self.NmaxExc,self.N): + moose.connect( self.network.vec[i], 'spikeOut', \ + self.spikesInh, 'input' ) + + def _plot(self, fig): + """ plots the spike raster for the simulated net""" + plt.figure(1) + + ax = plt.subplot(221) + cleanAx( ax, 'B' ) + plt.ylabel( 'Neuron #', fontsize = 16 ) + for i in range(0,self.NmaxExc): + if i==0: label = 'Exc. spike trains' + else: label = '' + spikes = self.spikes.vec[i].vector + ax.plot(spikes,[i]*len(spikes),\ + 'b.',marker='.', markersize = 2, label=label) + for i in range(self.NmaxExc,self.N): + if i==self.NmaxExc: label = 'Inh. spike trains' + else: label = '' + spikes = self.spikes.vec[i].vector + ax.plot(spikes,[i]*len(spikes),\ + 'r.',marker='.', markersize = 2, label=label) + +############################################# +# Exc-Inh network class with Ca plasticity based connections +# (inherits from ExcInhNetBase) +############################################# + +class ExcInhNet(ExcInhNetBase): + """ Recurrent network simulation """ + + def __init__(self,J=J,incC=C,fC=fC,scaleI=g,syndelay=syndelay,**kwargs): + """Overloads base (parent) class""" + self.J = J # exc connection weight + self.incC = incC # number of incoming connections per neuron + self.fC = fC # fraction of exc incoming connections + self.excC = int(fC*incC)# number of exc incoming connections + self.scaleI = scaleI # inh weight is scaleI*J + self.syndelay = syndelay# synaptic delay + + # call the parent class constructor + ExcInhNetBase.__init__(self,**kwargs) + + def __str__(self): + return "LIF network of %d neurons "\ + "of which %d are exc." % (self.N,self.NmaxExc) + + def _init_network(self,**args): + ExcInhNetBase._init_network(self,**args) + + def _init_plots(self): + ExcInhNetBase._init_plots(self) + self.recN = 5 # number of neurons for which to record weights and Ca + if CaPlasticity: + ## make tables to store weights of recN exc synapses + ## for each post-synaptic exc neuron + self.weights = moose.Table( '/plotWeights', self.excC*self.recN ) + for i in range(self.recN): # range(self.N) is too large + for j in range(self.excC): + moose.connect( self.weights.vec[self.excC*i+j], 'requestOut', + self.synsEE.vec[i*self.excC+j].synapse[0], 'getWeight') + + def _setup_network(self): + ## Set up the neurons without connections + ExcInhNetBase._setup_network(self) + + ## Now, add in the connections... + ## Each pre-synaptic spike cause Vm of post-neuron to rise by + ## synaptic weight in one time step i.e. delta-fn synapse. + ## Since LIF neuron is derived from Compartment class, + ## conductance-based synapses (SynChan class) can also be used. + + ## E to E synapses can be plastic + ## Two ways to do this: + ## 1) Each LIF neuron has one incoming postsynaptic SynHandler, + ## which collects the activation from all presynaptic neurons, + ## but then a common Ca pool is used. + ## 2) Each LIF neuron has multiple postsyanptic SynHandlers, + ## one for each pre-synaptic neuron, i.e. one per synapse, + ## then each synapse has a different Ca pool. + ## Here we go with option 2) as per Higgins et al 2014 (Brunel private email) + ## separate SynHandler per EE synapse, thus NmaxExc*excC + if CaPlasticity: + self.synsEE = moose.GraupnerBrunel2012CaPlasticitySynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + else: + self.synsEE = moose.SimpleSynHandler( \ + '/network/synsEE', self.NmaxExc*self.excC ) + moose.useClock( 0, '/network/synsEE', 'process' ) + + ## I to E synapses are not plastic + self.synsIE = moose.SimpleSynHandler( '/network/synsIE', self.NmaxExc ) + ## all synapses to I neurons are not plastic + self.synsI = moose.SimpleSynHandler( '/network/synsI', self.N-self.NmaxExc ) + ## connect all SynHandlers to their respective neurons + for i in range(self.NmaxExc): + moose.connect( self.synsIE.vec[i], 'activationOut', \ + self.network.vec[i], 'activation' ) + for i in range(self.NmaxExc,self.N): + moose.connect( self.synsI.vec[i-self.NmaxExc], 'activationOut', \ + self.network.vec[i], 'activation' ) + + ## Connections from some Exc/Inh neurons to each Exc neuron + for i in range(0,self.NmaxExc): + self.synsIE.vec[i].numSynapses = self.incC-self.excC + + ## Connections from some Exc neurons to each Exc neuron + ## draw excC number of neuron indices out of NmaxExc neurons + preIdxs = random.sample(list(range(self.NmaxExc)),self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synidx = i*self.excC+synnum + synHand = self.synsEE.vec[synidx] + + ## connect each synhandler to the post-synaptic neuron + moose.connect( synHand, 'activationOut', \ + self.network.vec[i], 'activation' ) + ## important to set numSynapses = 1 for each synHandler, + ## doesn't create synapses if you set the full array of SynHandlers + synHand.numSynapses = 1 + + synij = synHand.synapse[0] + connectExcId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + if CaPlasticity: + ## set parameters for the Ca Plasticity SynHandler + ## have to be set for each SynHandler + ## doesn't set for full array at a time + synHand.CaInit = 0.0 + synHand.tauCa = tauCa + synHand.tauSyn = tauSyn + synHand.CaPre = CaPre + synHand.CaPost = CaPost + synHand.delayD = delayD + synHand.thetaD = thetaD + synHand.thetaP = thetaP + synHand.gammaD = gammaD + synHand.gammaP = gammaP + synHand.weightMax = 1.0 # bounds on the weight + synHand.weightMin = 0.0 + synHand.weightScale = \ + self.J*2.0 # 0.2 mV, weight*weightScale is activation + # typically weight <~ 0.5, so activation <~ J + synHand.noisy = noisy + synHand.noiseSD = noiseSD + synHand.bistable = bistable + + moose.connect( self.network.vec[i], \ + 'spikeOut', synHand, 'addPostSpike') + synij.weight = eqWeight # activation = weight*weightScale + # weightScale = 2*J + # weight <~ 0.5 + ## Randomly set 5% of them to be 1.0 + if np.random.uniform()<0.05: + synij.weight = 1.0 + else: + synij.weight = self.J # no weightScale here, activation = weight + + ## Connections from some Inh neurons to each Exc neuron + ## draw inhC=incC-excC number of neuron indices out of inhibitory neurons + preIdxs = random.sample(list(range(self.NmaxExc,self.N)),self.incC-self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsIE.vec[i].synapse[synnum] + connectInhId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = -self.scaleI*self.J # activation = weight + + ## Connections from some Exc/Inh neurons to each Inh neuron + for i in range(self.N-self.NmaxExc): + ## each neuron has incC number of synapses + self.synsI.vec[i].numSynapses = self.incC + + ## draw excC number of neuron indices out of NmaxExc neurons + preIdxs = random.sample(list(range(self.NmaxExc)),self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsI.vec[i].synapse[synnum] + connectExcId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = self.J # activation = weight + + ## draw inhC=incC-excC number of neuron indices out of inhibitory neurons + preIdxs = random.sample(list(range(self.NmaxExc,self.N)),self.incC-self.excC) + ## connect these presynaptically to i-th post-synaptic neuron + for synnum,preIdx in enumerate(preIdxs): + synij = self.synsI.vec[i].synapse[ self.excC + synnum ] + connectInhId = moose.connect( self.network.vec[preIdx], \ + 'spikeOut', synij, 'addSpike') + synij.delay = syndelay + synij.weight = -self.scaleI*self.J # activation = weight + + moose.useClock( 0, '/network/synsIE', 'process' ) + moose.useClock( 0, '/network/synsI', 'process' ) + +############################################# +# Analysis functions +############################################# + +def rate_from_spiketrain(spiketimes,fulltime,dt,tau=50e-3): + """ + Returns a rate series of spiketimes convolved with a Gaussian kernel; + all times must be in SI units. + """ + sigma = tau/2. + ## normalized Gaussian kernel, integral with dt is normed to 1 + ## to count as 1 spike smeared over a finite interval + norm_factor = 1./(np.sqrt(2.*np.pi)*sigma) + gauss_kernel = np.array([norm_factor*np.exp(-x**2/(2.*sigma**2))\ + for x in np.arange(-5.*sigma,5.*sigma+dt,dt)]) + kernel_len = len(gauss_kernel) + ## need to accommodate half kernel_len on either side of fulltime + rate_full = np.zeros(int(fulltime/dt)+kernel_len) + for spiketime in spiketimes: + idx = int(spiketime/dt) + rate_full[idx:idx+kernel_len] += gauss_kernel + ## only the middle fulltime part of the rate series + ## This is already in Hz, + ## since should have multiplied by dt for above convolution + ## and divided by dt to get a rate, so effectively not doing either. + return rate_full[kernel_len/2:kernel_len/2+int(fulltime/dt)] + +############################################# +# Make plots +############################################# + +def extra_plots(net): + ## extra plots apart from the spike rasters + timeseries = net.trange + ## individual neuron firing rates + fig3 = plt.figure() + plt.subplot(221) + num_to_plot = 10 + #rates = [] + for nrni in range(num_to_plot): + rate = rate_from_spiketrain(\ + net.spikes.vec[nrni].vector,simtime,dt, 1.0 ) + plt.plot(timeseries,rate) + plt.title("Rates of "+str(num_to_plot)+" exc nrns") + plt.ylabel("Hz") + plt.ylim(0,100) + plt.subplot(222) + for nrni in range(num_to_plot): + rate = rate_from_spiketrain(\ + net.spikes.vec[net.NmaxExc+nrni].vector,simtime,dt, 1.0 ) + plt.plot(timeseries,rate) + plt.title("Rates of "+str(num_to_plot)+" inh nrns") + plt.ylim(0,100) + + ## population firing rates + plt.subplot(223) + rate = rate_from_spiketrain(net.spikesExc.vector,simtime,dt)\ + /float(net.NmaxExc) # per neuron + plt.plot(timeseries,rate) + plt.ylim(0,100) + plt.title("Exc population rate") + plt.ylabel("Hz") + plt.xlabel("Time (s)") + plt.subplot(224) + rate = rate_from_spiketrain(net.spikesInh.vector,simtime,dt)\ + /float(net.N-net.NmaxExc) # per neuron + plt.plot(timeseries,rate) + plt.ylim(0,100) + plt.title("Inh population rate") + plt.xlabel("Time (s)") + + fig3.tight_layout() + +def makeScatterPlot( m, n, v ): + fig4 = plt.figure() + + dx = 100e-6 + dy = 100e-6 + x = np.arange( m ) * dx + x = np.tile( x, n ) + y = np.arange( n ) * dy + y = y.repeat( m ) + #z = np.arange( m * n ) + #ret = plt.scatter( x, y, s = 64, c = v, vmin = -0.065, vmax = -0.055 ) + cmap = plt.get_cmap('afmhot') + ret = plt.scatter( x, y, s = 64, c = v, vmin = 0.5, vmax = 1.0, cmap = cmap ) + plt.xlim( -dx, dx * m ) + plt.ylim( -dy, dy * n ) + return fig4, ret + +def buildNeuronPlots( rdes ): + if not moose.exists( '/graphs' ): + graphs = moose.Neutral( '/graphs' ) + vtab = moose.Table( '/graphs/vtab' ) + catab = moose.Table( '/graphs/catab' ) + moose.connect( vtab, "requestOut", rdes.soma, "getVm" ) + caSoma = moose.element( rdes.soma.path + "/Ca_conc" ) + moose.connect( catab, "requestOut", caSoma, "getCa" ) + elist = moose.wildcardFind( '/model/chem/psd/tot_PSD_R[]' ) + rtab = moose.Table2( '/graphs/rtab', len( elist ) ).vec + for i in zip( elist, rtab ): + moose.connect( i[1], "requestOut", i[0], "getN" ) + elist = moose.wildcardFind( '/model/chem/spine/Ca[]' ) + pcatab = moose.Table2( '/graphs/pcatab', len( elist ) ).vec + for i in zip( elist, pcatab ): + moose.connect( i[1], "requestOut", i[0], "getConc" ) + +def cleanAx( ax, label, showXlabel = False ): + ax.spines['top'].set_visible( False ) + ax.spines['right'].set_visible( False ) + ax.tick_params( direction = 'out' ) + if not showXlabel: + ax.set_xticklabels( [] ) + for tick in ax.xaxis.get_major_ticks(): + tick.tick2On = False + for tick in ax.yaxis.get_major_ticks(): + tick.tick2On = False + ax.text( -0.18, 1.0, label, fontsize = 18, weight = 'bold', transform=ax.transAxes ) + + +def saveNeuronPlots( fig, rdes ): + #fig = plt.figure( figsize=(12, 10), facecolor='white' ) + #fig.subplots_adjust( left = 0.18 ) + plt.figure(1) + + ax = plt.subplot(222) + cleanAx( ax, 'C' ) + plt.ylabel( 'Vm (mV)', fontsize = 16 ) + vtab = moose.element( '/graphs/vtab' ) + t = np.arange( 0, len( vtab.vector ), 1 ) * vtab.dt + plt.plot( t, vtab.vector * 1000, label="Vm" ) + #plt.legend() + + ax = plt.subplot(223) + cleanAx( ax, 'D', showXlabel = True ) + pcatab = list( moose.vec( '/graphs/pcatab' ) )[0::2] + t = np.arange( 0, len( pcatab[0].vector ), 1 ) * pcatab[0].dt + for i in pcatab: + plt.plot( t, i.vector * 1000 ) + plt.ylabel( '[Ca] (uM)', fontsize = 16 ) + plt.xlabel( 'Time (s)', fontsize = 16 ) + + ax = plt.subplot(224) + cleanAx( ax, 'E', showXlabel = True ) + rtab = list( moose.vec( '/graphs/rtab' ) )[0::2] + t = np.arange( 0, len( rtab[0].vector ), 1 ) * rtab[0].dt + for i in rtab: + plt.plot( t, i.vector ) + plt.ylabel( '# of inserted GluRs', fontsize = 16 ) + plt.xlabel( 'Time (s)', fontsize = 16 ) + ''' + for i in moose.wildcardFind( '/graphs/#' ): + i.xplot( fname + '.xplot', i.name ) + ''' + +if __name__=='__main__': + plt.ion() + ## ExcInhNetBase has unconnected neurons, + ## ExcInhNet connects them + ## Instantiate either ExcInhNetBase or ExcInhNet below + #net = ExcInhNetBase(N=N) + net = ExcInhNet(N=N) + print(net) + moose.le( '/' ) + moose.le( '/network' ) + rdes = buildRdesigneur() + rdes.buildModel( '/model' ) + buildNeuronPlots( rdes ) + connectDetailedNeuron() + + ## Important to distribute the initial Vm-s + ## else weak coupling gives periodic synchronous firing + plotif = True + net.simulate(simtime,plotif=plotif,\ + v0=np.random.uniform(el-20e-3,vt,size=N)) + + # moose simulation + moose.useClock( 1, '/network', 'process' ) + moose.useClock( 2, '/plotSpikes', 'process' ) + moose.useClock( 3, '/plotVms', 'process' ) + if CaPlasticity: + moose.useClock( 3, '/plotWeights', 'process' ) + moose.useClock( 3, '/plotCa', 'process' ) + moose.setClock( 0, dt ) + moose.setClock( 1, dt ) + moose.setClock( 2, dt ) + moose.setClock( 3, dt ) + moose.setClock( 9, dt ) + + if plotif: + Vm = net.network.vec.Vm + fig = plt.figure( 1, figsize=(12, 10), facecolor='white' ) + fig.subplots_adjust( left = 0.18 ) + fig2, ret = makeScatterPlot( 20, 20, Vm ) + title = fig2.text( 0.1, 0.95, "Simulation starting..." ) + + moose.reinit() + t1 = time.time() + print('starting') + for currTime in np.arange( 0, simtime, updateDt ): + moose.start(updateDt) + lastt = net.network.vec.lastEventTime + lastt = np.exp( 2 * (lastt - currTime ) ) + title.set_text( "t = " + str( currTime ) ) + ret.set_array( lastt ) + fig2.canvas.draw() + + print('runtime, t = ', time.time() - t1) + + if plotif: + net._plot( fig ) + + extra_plots(net) + saveNeuronPlots( fig, rdes ) + plt.show() + plt.savefig( fname + '.svg', bbox_inches='tight') + print( "Hit 'enter' to exit" ) + input() diff --git a/demos/Fig6_NetMultiscale/cells_channels/CA1.morph.spines.xml b/demos/Fig6_NetMultiscale/cells_channels/CA1.morph.spines.xml new file mode 100644 index 0000000..028852a --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/CA1.morph.spines.xml @@ -0,0 +1,12658 @@ + + + + + + + Cell exported from NEURON ModelView in NeuroML Level 2 format and imported into neuroConstruct. The densities of hd, kap, kad have been replaced with variable mechanisms recreating the densities as used in the original model from ModelDB. + MOOSE NeuroML importer still does not support changing channel parameters post load and inhomogenous tags. Thus this model has been modified. + All inhomogeneous tags have been removed. All changed channel parameters have been hardcoded into modified channels. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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allButSpineShaft + + + SomaPlusProxDend + + + axon_group + soma_group + + + + + + + + SomaPlusProxDend + + + axon_group + soma_group + + + + + + SomaPlusProxDend + + + axon_group + soma_group + + + + + + + + all + + + all + + + + + + + This opaque name OneSecGrp_SectionRef_5 means the axon. + + + OneSecGrp_SectionRef_5 + soma_group + + + + + + SomaPlusProxDend + + + axon_group + soma_group + + + + + + allButSpineShaft + + + + + allButShaft + + + + + + all + + + + + + all + + + + OneSecGrp_SectionRef_5 + + + + + + all + + + + + + all + + + + + + + all + + + + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/Ca.xml b/demos/Fig6_NetMultiscale/cells_channels/Ca.xml new file mode 100644 index 0000000..645161c --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/Ca.xml @@ -0,0 +1,62 @@ + + + + + A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a + Detailed Network Model of the Cerebellar Granule Cell Layer + + + + + + + Voltage-gated Ca2+ channel, based on Traub + + + + Traub, R. + + + Upi Bhalla + NCBS + bhalla - at - ncbs.res.in + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/CaConc.xml b/demos/Fig6_NetMultiscale/cells_channels/CaConc.xml new file mode 100644 index 0000000..fe10a98 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/CaConc.xml @@ -0,0 +1,36 @@ + + + + Ca pool + + + Signifies that the ion is involved in a process which alters its concentration + + + + + + + Upi Bhalla + + + + An expontially decaying pool of calcium + + + + Upi Bhalla + National Centre for Biological Sciences, Bangalore, India. + bhalla - at - ncbs.res.in + + + + + + + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/Ca_conc.xml b/demos/Fig6_NetMultiscale/cells_channels/Ca_conc.xml new file mode 100644 index 0000000..29da3e8 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/Ca_conc.xml @@ -0,0 +1,31 @@ + + + + Ca pool. + + + Signifies that the ion is involved in a process which alters its concentration + + + + + + + + An expontially decaying pool of calcium + + + + + + + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/GABA.xml b/demos/Fig6_NetMultiscale/cells_channels/GABA.xml new file mode 100644 index 0000000..306dd9e --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/GABA.xml @@ -0,0 +1,16 @@ + + + + + GABA receptor synchan, 2 ms tau. + + + + Simple double exponential waveform GABA synapse + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/Glu.xml b/demos/Fig6_NetMultiscale/cells_channels/Glu.xml new file mode 100644 index 0000000..c1a7d7c --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/Glu.xml @@ -0,0 +1,16 @@ + + + + + Glutamate receptor synchan, 2 ms tau. + + + + Simple double exponential waveform glu synapse + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/NMDA.xml b/demos/Fig6_NetMultiscale/cells_channels/NMDA.xml new file mode 100644 index 0000000..ce7e3dd --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/NMDA.xml @@ -0,0 +1,16 @@ + + + + + NMDA receptor synchan, 20 ms tau. + + + + Simple double exponential waveform NMDA synapse + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/Pyramidal_KM.xml b/demos/Fig6_NetMultiscale/cells_channels/Pyramidal_KM.xml new file mode 100644 index 0000000..09239c3 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/Pyramidal_KM.xml @@ -0,0 +1,92 @@ + + + + + Voltage-gated K channel + + + + + + Matteo Farinella + + + + Channel translated from the original .mod file used in Kole MH, Ilschner SU, Kampa BM, Williams SR, Ruben PC, Stuart GJ, Action potential generation requires a high sodium channel density in the axon initial segment. Nat Neurosci. 2008 Feb;11(2):178-86. + Based on I-M (muscarinic K channel) Slow, noninactivating + + + + + Zach Mainen + Salk Institute + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + Matteo Farinella + UCL + m.farinella - at - ucl.ac.uk + + + + + + + Rothman JS, Cathala L, Steuber V, Silver RA, Synaptic depression enables neuronal gain control. Nature. 2009 Jan 14 + http://www.ncbi.nlm.nih.gov/pubmed/19145233?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum + + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/Traub_KA.xml b/demos/Fig6_NetMultiscale/cells_channels/Traub_KA.xml new file mode 100644 index 0000000..9e507d0 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/Traub_KA.xml @@ -0,0 +1,109 @@ + + + + ChannelML file based on Traub et al. 2003 + + + + + Verified equivalence of NEURON and GENESIS mapping to orig NEURON mod impl at 0.02ms dt with current pulse + In original mod, m is initialised to 0, as opposed to minf at t=0. ChannelML impl corrects this + + Yoana Dimitrova + + + Padraig Gleeson + + + + Potasium A-type conductance (transient, inactivating). Based on NEURON port of FRB L2/3 model from Traub et al 2003. Same channel used in Traub et al 2005 + + + + Maciej Lazarewicz + Conversion of FORTRAN model to NEURON. See Traub et al 2003 for detailed origin of channels + + + Roger D Traub + Conversion of FORTRAN model to NEURON. See Traub et al 2003 for detailed origin of channels + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + Yoana Dimitrova + UCL + + + + + Roger D. Traub, Eberhard H. Buhl, Tengis Gloveli, and Miles A. Whittington +Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na+ Conductance or by Blocking BK Channels +J Neurophysiol 89: 909-921, 2003 + http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12574468 + + + + Roger D. Traub, Diego Contreras, Mark O. Cunningham, Hilary Murray, Fiona E. N. LeBeau, Anita Roopun, Andrea Bibbig, W. Bryan Wilent, Michael J. Higley, and Miles A. Whittington +Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. +J. Neurophysiol. 93, 2194-2232, 2005 + http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + Mechanisms of fast rhythmic bursting in a layer 2/3 cortical neuron (Traub et al 2003) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=20756 + + + + A single column thalamocortical network model (Traub et al 2005) + http://senselab.med.yale.edu/ModelDb/ShowModel.asp?model=45539 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Using broad range of voltages for sufficient coverage + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/Traub_KCaAHP.xml b/demos/Fig6_NetMultiscale/cells_channels/Traub_KCaAHP.xml new file mode 100644 index 0000000..bc5e1b5 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/Traub_KCaAHP.xml @@ -0,0 +1,105 @@ + + + + ChannelML file based on Traub et al. 2003 + + + + + Verified equivalence of NEURON and GENESIS mapping to orig NEURON mod impl at 0.02ms dt with current pulse on single comp incl CaD + In original mod, m is initialised to 0, as opposed to minf at t=0. ChannelML impl corrects this + + + Padraig Gleeson + + + Yoana Dimitrova + + + + [Ca2+] dependent K AHP (afterhyperpolarization) conductance. Based on NEURON port of FRB L2/3 model from Traub et al 2003. Same channel used in Traub et al 2005 + + + + Maciej Lazarewicz + Conversion of FORTRAN model to NEURON. See Traub et al 2003 for detailed origin of channels + + + Roger D Traub + Conversion of FORTRAN model to NEURON. See Traub et al 2003 for detailed origin of channels + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + Yoana Dimitrova + UCL + + + + + Roger D. Traub, Eberhard H. Buhl, Tengis Gloveli, and Miles A. Whittington +Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na+ Conductance or by Blocking BK Channels +J Neurophysiol 89: 909-921, 2003 + http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12574468 + + + + Roger D. Traub, Diego Contreras, Mark O. Cunningham, Hilary Murray, Fiona E. N. LeBeau, Anita Roopun, Andrea Bibbig, W. Bryan Wilent, Michael J. Higley, and Miles A. Whittington +Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. +J. Neurophysiol. 93, 2194-2232, 2005 + http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + Mechanisms of fast rhythmic bursting in a layer 2/3 cortical neuron (Traub et al 2003) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=20756 + + + + A single column thalamocortical network model (Traub et al 2005) + http://senselab.med.yale.edu/ModelDb/ShowModel.asp?model=45539 + + + + + + + + + + + + + + + + + + + + + + + + + This will ensure more points in calcium dependence table + + + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/ca1_minimal.p b/demos/Fig6_NetMultiscale/cells_channels/ca1_minimal.p new file mode 100644 index 0000000..4395d62 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/ca1_minimal.p @@ -0,0 +1,58 @@ +// genesis +// cell parameter file for the 1991 Traub CA1 hippocampal cell +// "phi" parameter reduced by e-3 +*cartesian +*relative + +*set_global RM 1.0 //ohm*m^2 +*set_global RA 1.0 //ohm*m +*set_global CM 0.03 //F/m^2 +*set_global EREST_ACT -0.06 // volts + +// The format for each compartment parameter line is : +// name parent x y z d ch dens ... +// For channels, "dens" = maximum conductance per unit area of compartment + + +dend_3 none 0 220 0 3.84 +dend_5 . 0 220 0 3.84 +dend_6 . 0 220 0 3.84 +dend_8 . 0 110 0 3.84 + +soma dend_8 0 125 0 8.46 + + +apical_10 soma 0 120 0 4.0 +apical_11 apical_10 0 120 0 3 +apical_12 apical_11 0 120 0 3 +apical_13 apical_12 0 120 0 2.6 +apical_14 apical_13 0 120 0 2.6 +apical_15 apical_14 0 120 0 2.6 +apical_16 apical_15 0 120 0 2.6 +apical_17 apical_16 0 120 0 2.6 +apical_18 apical_17 0 120 0 2.6 +apical_19 apical_18 0 120 0 2.6 + +apical_11_1 apical_10 -60 60 0 2 +apical_11_2 apical_11_1 -60 60 0 1.8 +apical_11_3 apical_11_2 0 80 0 1.5 +apical_11_4 apical_11_3 0 80 0 1.5 + +apical_13_1 apical_12 40 40 0 1.0 +apical_13_2 apical_13_1 40 40 0 1.0 + +apical_14_1 apical_13_2 0 10 0 1.0 +apical_14_2 . 0 10 0 1.0 +apical_14_3 . 0 10 0 1.0 +apical_14_4 . 0 10 0 1.0 +apical_14_5 . 0 10 0 1.0 +apical_14_6 . 0 10 0 1.0 +apical_14_7 . 0 10 0 1.0 +apical_14_8 . 0 10 0 1.0 +apical_14_9 . 0 10 0 1.0 +apical_14_10 . 0 10 0 1.0 +apical_14_11 . 0 10 0 1.0 +apical_14_12 . 0 10 0 1.0 +apical_14_13 . 0 10 0 1.0 +apical_15_1 . 0 30 0 1.0 +apical_15_2 . 0 60 0 1.0 diff --git a/demos/Fig6_NetMultiscale/cells_channels/hd.xml b/demos/Fig6_NetMultiscale/cells_channels/hd.xml new file mode 100644 index 0000000..141c1ac --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/hd.xml @@ -0,0 +1,73 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and l traces on single comp with current pulse + + Padraig Gleeson + + + + H current. Comment from original mod: I-h channel from Magee 1998 for distal dendrites + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/hd_minus73.xml b/demos/Fig6_NetMultiscale/cells_channels/hd_minus73.xml new file mode 100644 index 0000000..38815ff --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/hd_minus73.xml @@ -0,0 +1,73 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and l traces on single comp with current pulse + + Padraig Gleeson + + + + H current. Comment from original mod: I-h channel from Magee 1998 for distal dendrites + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/kad.xml b/demos/Fig6_NetMultiscale/cells_channels/kad.xml new file mode 100644 index 0000000..bb7c5af --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/kad.xml @@ -0,0 +1,84 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + A type K channel for distal dendrites. Comment from original mod: K-A channel from Klee Ficker and Heinemann, modified to account for Dax A Current, M.Migliore Jun 1997 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig6_NetMultiscale/cells_channels/kap.xml b/demos/Fig6_NetMultiscale/cells_channels/kap.xml new file mode 100644 index 0000000..58fdea0 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/kap.xml @@ -0,0 +1,86 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + A type K channel. Comment from original mod: K-A channel from Klee Ficker and Heinemann, + modified to account for Dax A Current --- M.Migliore Jun 1997, + modified to be used with cvode M.Migliore 2001 + + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig6_NetMultiscale/cells_channels/kdr.xml b/demos/Fig6_NetMultiscale/cells_channels/kdr.xml new file mode 100644 index 0000000..180c563 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/kdr.xml @@ -0,0 +1,75 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + Delayed rectifier K channel. Comment from original mod: K-DR channel, from Klee Ficker and Heinemann, + modified to account for Dax et al., M.Migliore 1997 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + K channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + \ No newline at end of file diff --git a/demos/Fig6_NetMultiscale/cells_channels/na3.xml b/demos/Fig6_NetMultiscale/cells_channels/na3.xml new file mode 100644 index 0000000..5684d19 --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/na3.xml @@ -0,0 +1,107 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + Note: the inactivation gate s is not included here as it was disabled in original mod file for Migliore et al. Changing the parameter below ar from 1 will not enable s! + + Padraig Gleeson + + + + Na channel. Comment from original mod: Na current, modified from Jeff Magee. M.Migliore may97, + added sh to account for higher threshold M.Migliore, Apr.2002 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + Na channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/nax.xml b/demos/Fig6_NetMultiscale/cells_channels/nax.xml new file mode 100644 index 0000000..3ca589c --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/nax.xml @@ -0,0 +1,88 @@ + + + + ChannelML file containing a single Channel description + + + + + Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse + + Padraig Gleeson + + + + Na channel for axon. Comment from original mod: Na current for axon. No slow inact. M.Migliore Jul. 1997, + added sh to account for higher threshold M.Migliore, Apr.2002 + + + + Michele Migliore + Cited implementer according to ModelDB + + + Padraig Gleeson + UCL + p.gleeson - at - ucl.ac.uk + + + + + Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155 + http://www.ncbi.nlm.nih.gov/pubmed/16293591 + + + + Na channels + http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2 + + + + CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005) + http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values + + + + + + + + diff --git a/demos/Fig6_NetMultiscale/cells_channels/pas.xml b/demos/Fig6_NetMultiscale/cells_channels/pas.xml new file mode 100644 index 0000000..9abffeb --- /dev/null +++ b/demos/Fig6_NetMultiscale/cells_channels/pas.xml @@ -0,0 +1,17 @@ + + + + ChannelML file containing a single Channel description + + + + + + Simple example of a leak/passive conductance. Note: for GENESIS cells with a single leak conductance, + it is better to use the Rm and Em variables for a passive current. + + + + + + \ No newline at end of file diff --git a/demos/Fig6_NetMultiscale/psd53.g b/demos/Fig6_NetMultiscale/psd53.g new file mode 100644 index 0000000..e120a6a --- /dev/null +++ b/demos/Fig6_NetMultiscale/psd53.g @@ -0,0 +1,477 @@ +//genesis +// kkit Version 11 flat dumpfile + +// Saved on Fri Jun 5 09:12:59 2015 + +include kkit {argv 1} + +FASTDT = 1e-05 +SIMDT = 0.0001 +CONTROLDT = 1 +PLOTDT = 0.2 +MAXTIME = 200 +TRANSIENT_TIME = 2 +VARIABLE_DT_FLAG = 1 +DEFAULT_VOL = 1e-19 +VERSION = 11.0 +setfield /file/modpath value /home2/bhalla/scripts/modules +kparms + +//genesis + +initdump -version 3 -ignoreorphans 1 +simobjdump doqcsinfo filename accessname accesstype transcriber developer \ + citation species tissue cellcompartment methodology sources \ + model_implementation model_validation x y z +simobjdump table input output alloced step_mode stepsize x y z +simobjdump xtree path script namemode sizescale +simobjdump xcoredraw xmin xmax ymin ymax +simobjdump xtext editable +simobjdump xgraph xmin xmax ymin ymax overlay +simobjdump xplot pixflags script fg ysquish do_slope wy +simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ + link savename file version md5sum mod_save_flag x y z +simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \ + z +simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \ + geomname xtree_fg_req xtree_textfg_req x y z +simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z +simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ + keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z +simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ + trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z +simobjdump xtab input output alloced step_mode stepsize notes editfunc \ + xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z +simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ + xtree_textfg_req x y z +simobjdump transport input output alloced step_mode stepsize dt delay clock \ + kf xtree_fg_req xtree_textfg_req x y z +simobjdump proto x y z +simobjdump text str +simundump geometry /kinetics/geometry 0 1.6667e-21 3 sphere "" white black 5 \ + -4 0 +simundump geometry /kinetics/geometry[1] 0 1e-19 3 sphere "" white black 5 -2 \ + 0 +simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black 2 2 \ + 0 +simundump geometry /kinetics/geometry[3] 0 1e-20 3 sphere "" white black 4 8 \ + 0 +simundump geometry /kinetics/geometry[4] 0 1e-20 3 sphere "" white black 2 \ + -17 0 +simundump geometry /kinetics/geometry[5] 0 1e-20 3 sphere "" white black 5 \ + -13 0 +simundump geometry /kinetics/geometry[6] 0 1e-19 3 sphere "" white black 0 7 \ + 0 +simundump geometry /kinetics/geometry[7] 0 1e-20 3 sphere "" white black 0 -3 \ + 0 +simundump geometry /kinetics/geometry[8] 0 1e-20 3 sphere "" white black -1 \ + -18 0 +simundump geometry /kinetics/geometry[9] 0 1e-18 3 sphere "" white black 0 0 \ + 0 +simundump text /kinetics/notes 0 "" +call /kinetics/notes LOAD \ +"" +simundump text /kinetics/geometry/notes 0 "" +call /kinetics/geometry/notes LOAD \ +"" +simundump text /kinetics/geometry[1]/notes 0 "" +call /kinetics/geometry[1]/notes LOAD \ +"" +simundump text /kinetics/geometry[2]/notes 0 "" +call /kinetics/geometry[2]/notes LOAD \ +"" +simundump text /kinetics/geometry[3]/notes 0 "" +call /kinetics/geometry[3]/notes LOAD \ +"" +simundump text /kinetics/geometry[4]/notes 0 "" +call /kinetics/geometry[4]/notes LOAD \ +"" +simundump text /kinetics/geometry[5]/notes 0 "" +call /kinetics/geometry[5]/notes LOAD \ +"" +simundump text /kinetics/geometry[6]/notes 0 "" +call /kinetics/geometry[6]/notes LOAD \ +"" +simundump text /kinetics/geometry[7]/notes 0 "" +call /kinetics/geometry[7]/notes LOAD \ +"" +simundump text /kinetics/geometry[8]/notes 0 "" +call /kinetics/geometry[8]/notes LOAD \ +"" +simundump text /kinetics/geometry[9]/notes 0 "" +call /kinetics/geometry[9]/notes LOAD \ +"" +simundump kreac /kinetics/exocytosis 0 0.01 0 "" white black 4 -5 0 +simundump text /kinetics/exocytosis/notes 0 "" +call /kinetics/exocytosis/notes LOAD \ +"" +simundump kreac /kinetics/endocytosis 0 0 4 "" white black -7 -5 0 +simundump text /kinetics/endocytosis/notes 0 "" +call /kinetics/endocytosis/notes LOAD \ +"" +simundump group /kinetics/PSD 0 0 black x 0 1 "" PSD defaultfile.g 0 0 0 -10 \ + -3 0 +simundump text /kinetics/PSD/notes 0 "" +call /kinetics/PSD/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Rp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] \ + blue 0 -4 1 0 +simundump text /kinetics/PSD/Rp/notes 0 "" +call /kinetics/PSD/Rp/notes LOAD \ +"" +simundump kpool /kinetics/PSD/P 0 0 1 1 6 6 0 0 6 0 /kinetics/geometry[1] 61 \ + 0 -4 -2 0 +simundump text /kinetics/PSD/P/notes 0 "" +call /kinetics/PSD/P/notes LOAD \ +"" +simundump kenz /kinetics/PSD/P/P1 0 0 0 0 0 60 10.417 20 5 0 0 "" red 61 "" \ + -6 -1 0 +simundump text /kinetics/PSD/P/P1/notes 0 "" +call /kinetics/PSD/P/P1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/P/P2 0 0 0 0 0 60 10.417 20 5 0 0 "" red 61 "" \ + -2 -1 0 +simundump text /kinetics/PSD/P/P2/notes 0 "" +call /kinetics/PSD/P/P2/notes LOAD \ +"" +simundump kpool /kinetics/PSD/KK 0 0 3 3 18 18 0 0 6 0 /kinetics/geometry[1] \ + 49 0 -4 4 0 +simundump text /kinetics/PSD/KK/notes 0 "" +call /kinetics/PSD/KK/notes LOAD \ +"" +simundump kenz /kinetics/PSD/KK/KK1 0 0 0 0 0 60 4.1667 40 10 0 0 "" red 49 \ + "" -6 3 0 +simundump text /kinetics/PSD/KK/KK1/notes 0 "" +call /kinetics/PSD/KK/KK1/notes LOAD \ +"" +simundump kenz /kinetics/PSD/KK/KK2 0 0 0 0 0 60 4.1667 40 10 0 0 "" red 49 \ + "" -2 3 0 +simundump text /kinetics/PSD/KK/KK2/notes 0 "" +call /kinetics/PSD/KK/KK2/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Rpp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] \ + 28 0 0 1 0 +simundump text /kinetics/PSD/Rpp/notes 0 "" +call /kinetics/PSD/Rpp/notes LOAD \ +"" +simundump kpool /kinetics/PSD/R 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] 4 0 \ + -8 1 0 +simundump text /kinetics/PSD/R/notes 0 "" +call /kinetics/PSD/R/notes LOAD \ +"" +simundump kpool /kinetics/PSD/tot_PSD_R 0 0 0 0 0 0 0 0 6 0 \ + /kinetics/geometry[4] blue 0 -4 7 0 +simundump text /kinetics/PSD/tot_PSD_R/notes 0 "" +call /kinetics/PSD/tot_PSD_R/notes LOAD \ +"" +simundump kpool /kinetics/PSD/psd_inact_CaN 0 0 1 1 6 6 0 0 6 0 \ + /kinetics/geometry[7] blue 0 -12 5 0 +simundump text /kinetics/PSD/psd_inact_CaN/notes 0 "" +call /kinetics/PSD/psd_inact_CaN/notes LOAD \ +"" +simundump kreac /kinetics/PSD/psd_activate_CaN 0 0.27778 1 "" white 0 -11 1 0 +simundump text /kinetics/PSD/psd_activate_CaN/notes 0 "" +call /kinetics/PSD/psd_activate_CaN/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Ca.P 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[7] \ + blue 0 -4 -4 0 +simundump text /kinetics/PSD/Ca.P/notes 0 "" +call /kinetics/PSD/Ca.P/notes LOAD \ +"" +simundump kenz /kinetics/PSD/Ca.P/Ca.P2 0 0 0 0 0 6 1.6667 40 10 0 0 "" red \ + blue "" -2 -3 0 +simundump text /kinetics/PSD/Ca.P/Ca.P2/notes 0 "" +call /kinetics/PSD/Ca.P/Ca.P2/notes LOAD \ +"" +simundump kenz /kinetics/PSD/Ca.P/Ca.P1 0 0 0 0 0 6 1.6667 40 10 0 0 "" red \ + blue "" -6 -3 0 +simundump text /kinetics/PSD/Ca.P/Ca.P1/notes 0 "" +call /kinetics/PSD/Ca.P/Ca.P1/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Ca_input 0 0 0.1 0.1 0.6 0.6 0 0 6 4 \ + /kinetics/geometry[8] 60 black -12 9 0 +simundump text /kinetics/PSD/Ca_input/notes 0 "" +call /kinetics/PSD/Ca_input/notes LOAD \ +"" +simundump kreac /kinetics/PSD/Ca_reac 0 100 100 "" white black -17 6 0 +simundump text /kinetics/PSD/Ca_reac/notes 0 "" +call /kinetics/PSD/Ca_reac/notes LOAD \ +"" +simundump kpool /kinetics/PSD/Ca 0 1e-11 0.1 0.1 0.6 0.6 0 0 6 0 \ + /kinetics/geometry[5] 53 0 -15 2 0 +simundump text /kinetics/PSD/Ca/notes 0 "" +call /kinetics/PSD/Ca/notes LOAD \ +"" +simundump group /kinetics/Bulk 0 yellow black x 0 0 "" Bulk defaultfile.g 0 0 \ + 0 -6 -16 0 +simundump text /kinetics/Bulk/notes 0 "" +call /kinetics/Bulk/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iRpp 0 0 0 0 0 0 0 0 59.999 0 \ + /kinetics/geometry 29 yellow 2 -11 0 +simundump text /kinetics/Bulk/iRpp/notes 0 "" +call /kinetics/Bulk/iRpp/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iRp 0 0 0 0 0 0 0 0 59.999 0 \ + /kinetics/geometry blue yellow -2 -11 0 +simundump text /kinetics/Bulk/iRp/notes 0 "" +call /kinetics/Bulk/iRp/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iR 0 0 4.0001 4.0001 240 240 0 0 59.999 0 \ + /kinetics/geometry 0 yellow -6 -11 0 +simundump text /kinetics/Bulk/iR/notes 0 "Same as Fus3\n" +call /kinetics/Bulk/iR/notes LOAD \ +"Same as Fus3" \ +"" +simundump kpool /kinetics/Bulk/iKK 0 0 1 1 59.999 59.999 0 0 59.999 0 \ + /kinetics/geometry 50 yellow -2 -8 0 +simundump text /kinetics/Bulk/iKK/notes 0 "Same as Ste7\n" +call /kinetics/Bulk/iKK/notes LOAD \ +"Same as Ste7" \ +"" +simundump kenz /kinetics/Bulk/iKK/iKK1 0 0 0 0 0 59.999 0.83335 40 10 0 0 "" \ + red 50 "" -4 -9 0 +simundump text /kinetics/Bulk/iKK/iKK1/notes 0 "" +call /kinetics/Bulk/iKK/iKK1/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/iKK/iKK2 0 0 0 0 0 59.999 0.83335 40 10 0 0 "" \ + red 50 "" 0 -9 0 +simundump text /kinetics/Bulk/iKK/iKK2/notes 0 "" +call /kinetics/Bulk/iKK/iKK2/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/iP 0 0 0.50001 0.50001 30 30 0 0 59.999 0 \ + /kinetics/geometry 62 yellow -2 -14 0 +simundump text /kinetics/Bulk/iP/notes 0 "Same as Msg5\n" +call /kinetics/Bulk/iP/notes LOAD \ +"Same as Msg5" \ +"" +simundump kenz /kinetics/Bulk/iP/iP1 0 0 0 0 0 59.999 6.2501 60 15 0 0 "" red \ + 62 "" -4 -13 0 +simundump text /kinetics/Bulk/iP/iP1/notes 0 "" +call /kinetics/Bulk/iP/iP1/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/iP/iP2 0 0 0 0 0 59.999 6.2501 60 15 0 0 "" red \ + 62 "" 0 -13 0 +simundump text /kinetics/Bulk/iP/iP2/notes 0 "" +call /kinetics/Bulk/iP/iP2/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/PKA 0 0 0 0 0 0 0 0 60 0 /kinetics/geometry[3] \ + 43 yellow -3 -5 0 +simundump text /kinetics/Bulk/PKA/notes 0 "" +call /kinetics/Bulk/PKA/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/PKA/PKA1 0 0 0 0 0 60 0.41667 40 10 0 0 "" red \ + 43 "" -4 -7 0 +simundump text /kinetics/Bulk/PKA/PKA1/notes 0 "" +call /kinetics/Bulk/PKA/PKA1/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/PKA/PKA2 0 0 0 0 0 60 0.41667 40 10 0 0 "" red \ + 43 "" 0 -7 0 +simundump text /kinetics/Bulk/PKA/PKA2/notes 0 "" +call /kinetics/Bulk/PKA/PKA2/notes LOAD \ +"" +simundump kenz /kinetics/Bulk/PKA/PKA_exo 0 0 0 0 0 60 0.016667 8 2 0 0 "" \ + red 43 "" 1 -5 0 +simundump text /kinetics/Bulk/PKA/PKA_exo/notes 0 "" +call /kinetics/Bulk/PKA/PKA_exo/notes LOAD \ +"" +simundump kreac /kinetics/Bulk/activate_PKA 0 0.0016667 5 "" white yellow -11 \ + -10 0 +simundump text /kinetics/Bulk/activate_PKA/notes 0 "" +call /kinetics/Bulk/activate_PKA/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/inact_PKA 0 0 1.6 1.6 96 96 0 0 60 0 \ + /kinetics/geometry[2] 51 yellow -12 -6 0 +simundump text /kinetics/Bulk/inact_PKA/notes 0 "" +call /kinetics/Bulk/inact_PKA/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/inact_CaN 0 0 0.2 0.2 12 12 0 0 60 0 \ + /kinetics/geometry[6] blue yellow -13 -18 0 +simundump text /kinetics/Bulk/inact_CaN/notes 0 "" +call /kinetics/Bulk/inact_CaN/notes LOAD \ +"" +simundump kreac /kinetics/Bulk/activate_CaN 0 0.0055556 1 "" white yellow -10 \ + -16 0 +simundump text /kinetics/Bulk/activate_CaN/notes 0 "" +call /kinetics/Bulk/activate_CaN/notes LOAD \ +"" +simundump kpool /kinetics/Bulk/Ca 0 1e-11 0.1 0.1 6 6 0 0 60 0 \ + /kinetics/geometry[2] 50 yellow -15 -13 0 +simundump text /kinetics/Bulk/Ca/notes 0 "" +call /kinetics/Bulk/Ca/notes LOAD \ +"" +simundump kpool /kinetics/Ca_dend_input 0 0 0 0 0 0 0 0 600 0 \ + /kinetics/geometry[9] 60 black -12 -28 0 +simundump text /kinetics/Ca_dend_input/notes 0 "" +call /kinetics/Ca_dend_input/notes LOAD \ +"" +simundump kreac /kinetics/dend_Ca_reac 0 100 100 "" white black -16 -27 0 +simundump text /kinetics/dend_Ca_reac/notes 0 "" +call /kinetics/dend_Ca_reac/notes LOAD \ +"" +simundump kpool /kinetics/Ca 0 1e-11 0 0 0 0 0 0 600 0 /kinetics/geometry[9] \ + 1 black -19 -25 0 +simundump text /kinetics/Ca/notes 0 "" +call /kinetics/Ca/notes LOAD \ +"" +simundump xgraph /graphs/conc1 0 0 800 9.6002e-07 0.10547 0 +simundump xgraph /graphs/conc2 0 0 800 0 18.128 0 +simundump xplot /graphs/conc1/Ca_PSD.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 53 0 0 1 +simundump xplot /graphs/conc1/Ca_Bulk.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 41 0 0 1 +simundump xplot /graphs/conc1/PKA.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 43 0 0 1 +simundump xplot /graphs/conc1/Ca.P.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xplot /graphs/conc1/Ca_dend.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 1 0 0 1 +simundump xplot /graphs/conc2/tot_PSD_R.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " blue 0 0 1 +simundump xplot /graphs/conc2/Rpp.Co 3 524288 \ + "delete_plot.w ; edit_plot.D " 28 0 0 1 +simundump xgraph /moregraphs/conc3 0 0 800 0 33.241 0 +simundump xgraph /moregraphs/conc4 0 0 800 0 2 0 +simundump xcoredraw /edit/draw 0 -21 7 -30 11 +simundump xtree /edit/draw/tree 0 \ + /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ + "edit_elm.D ; drag_from_edit.w " auto 0.6 +simundump xtext /file/notes 0 1 +xtextload /file/notes \ +"26 Nov 2014. psd51.g: based on psd50.g which was" \ +"based on psd41_back_dend.g." \ +"07 Dec 2014. psd52.g: based on psd51. Slowed down Ca_to_dend by " \ +"10x while retaining Keq." \ +"04 June 2015. psd53.g: Removed the reacts between dend, head and" \ +"psd. Will use diffusion instead." \ +"05 June 2015. psd53.g updated further to use the same name (Ca)" \ +"for Ca_dend, Ca_spine and Ca_PSD so as to get them to diffuse." \ +"" +addmsg /kinetics/Bulk/iRpp /kinetics/exocytosis SUBSTRATE n +addmsg /kinetics/PSD/Rpp /kinetics/exocytosis PRODUCT n +addmsg /kinetics/Bulk/iR /kinetics/endocytosis SUBSTRATE n +addmsg /kinetics/PSD/R /kinetics/endocytosis PRODUCT n +addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/Rp MM_PRD pA +addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/Rp REAC sA B +addmsg /kinetics/PSD/P/P2 /kinetics/PSD/Rp MM_PRD pA +addmsg /kinetics/PSD/P/P1 /kinetics/PSD/Rp REAC sA B +addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Rp MM_PRD pA +addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/Rp REAC sA B +addmsg /kinetics/PSD/P/P1 /kinetics/PSD/P REAC eA B +addmsg /kinetics/PSD/P/P2 /kinetics/PSD/P REAC eA B +addmsg /kinetics/PSD/P /kinetics/PSD/P/P1 ENZYME n +addmsg /kinetics/PSD/Rp /kinetics/PSD/P/P1 SUBSTRATE n +addmsg /kinetics/PSD/P /kinetics/PSD/P/P2 ENZYME n +addmsg /kinetics/PSD/Rpp /kinetics/PSD/P/P2 SUBSTRATE n +addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/KK REAC eA B +addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/KK REAC eA B +addmsg /kinetics/PSD/KK /kinetics/PSD/KK/KK1 ENZYME n +addmsg /kinetics/PSD/R /kinetics/PSD/KK/KK1 SUBSTRATE n +addmsg /kinetics/PSD/KK /kinetics/PSD/KK/KK2 ENZYME n +addmsg /kinetics/PSD/Rp /kinetics/PSD/KK/KK2 SUBSTRATE n +addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/Rpp MM_PRD pA +addmsg /kinetics/PSD/P/P2 /kinetics/PSD/Rpp REAC sA B +addmsg /kinetics/exocytosis /kinetics/PSD/Rpp REAC B A +addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/PSD/Rpp MM_PRD pA +addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Rpp REAC sA B +addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/R REAC sA B +addmsg /kinetics/PSD/P/P1 /kinetics/PSD/R MM_PRD pA +addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/R MM_PRD pA +addmsg /kinetics/endocytosis /kinetics/PSD/R REAC B A +addmsg /kinetics/PSD/R /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/Rp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/Rpp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/psd_inact_CaN REAC A B +addmsg /kinetics/PSD/psd_inact_CaN /kinetics/PSD/psd_activate_CaN SUBSTRATE n +addmsg /kinetics/PSD/Ca /kinetics/PSD/psd_activate_CaN SUBSTRATE n +addmsg /kinetics/PSD/Ca /kinetics/PSD/psd_activate_CaN SUBSTRATE n +addmsg /kinetics/PSD/Ca.P /kinetics/PSD/psd_activate_CaN PRODUCT n +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca.P REAC B A +addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Ca.P REAC eA B +addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/Ca.P REAC eA B +addmsg /kinetics/PSD/Ca.P /kinetics/PSD/Ca.P/Ca.P2 ENZYME n +addmsg /kinetics/PSD/Rpp /kinetics/PSD/Ca.P/Ca.P2 SUBSTRATE n +addmsg /kinetics/PSD/Ca.P /kinetics/PSD/Ca.P/Ca.P1 ENZYME n +addmsg /kinetics/PSD/Rp /kinetics/PSD/Ca.P/Ca.P1 SUBSTRATE n +addmsg /kinetics/PSD/Ca_reac /kinetics/PSD/Ca_input REAC A B +addmsg /kinetics/PSD/Ca_input /kinetics/PSD/Ca_reac SUBSTRATE n +addmsg /kinetics/PSD/Ca /kinetics/PSD/Ca_reac PRODUCT n +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca REAC A B +addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca REAC A B +addmsg /kinetics/PSD/Ca_reac /kinetics/PSD/Ca REAC B A +addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iRpp MM_PRD pA +addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iRpp REAC sA B +addmsg /kinetics/exocytosis /kinetics/Bulk/iRpp REAC A B +addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/iRpp MM_PRD pA +addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/Bulk/iRpp REAC sA B +addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iRp MM_PRD pA +addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iRp REAC sA B +addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iRp MM_PRD pA +addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iRp REAC sA B +addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/iRp MM_PRD pA +addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/iRp REAC sA B +addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iR REAC sA B +addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iR MM_PRD pA +addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/iR REAC sA B +addmsg /kinetics/endocytosis /kinetics/Bulk/iR REAC A B +addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iKK REAC eA B +addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iKK REAC eA B +addmsg /kinetics/Bulk/iKK /kinetics/Bulk/iKK/iKK1 ENZYME n +addmsg /kinetics/Bulk/iR /kinetics/Bulk/iKK/iKK1 SUBSTRATE n +addmsg /kinetics/Bulk/iKK /kinetics/Bulk/iKK/iKK2 ENZYME n +addmsg /kinetics/Bulk/iRp /kinetics/Bulk/iKK/iKK2 SUBSTRATE n +addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iP REAC eA B +addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iP REAC eA B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/iP REAC B A +addmsg /kinetics/Bulk/iP /kinetics/Bulk/iP/iP1 ENZYME n +addmsg /kinetics/Bulk/iRp /kinetics/Bulk/iP/iP1 SUBSTRATE n +addmsg /kinetics/Bulk/iP /kinetics/Bulk/iP/iP2 ENZYME n +addmsg /kinetics/Bulk/iRpp /kinetics/Bulk/iP/iP2 SUBSTRATE n +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/PKA REAC B A +addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/PKA REAC eA B +addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/PKA REAC eA B +addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/Bulk/PKA REAC eA B +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA1 ENZYME n +addmsg /kinetics/Bulk/iR /kinetics/Bulk/PKA/PKA1 SUBSTRATE n +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA2 ENZYME n +addmsg /kinetics/Bulk/iRp /kinetics/Bulk/PKA/PKA2 SUBSTRATE n +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA_exo ENZYME n +addmsg /kinetics/Bulk/iRpp /kinetics/Bulk/PKA/PKA_exo SUBSTRATE n +addmsg /kinetics/Bulk/inact_PKA /kinetics/Bulk/activate_PKA SUBSTRATE n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_PKA SUBSTRATE n +addmsg /kinetics/Bulk/PKA /kinetics/Bulk/activate_PKA PRODUCT n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_PKA SUBSTRATE n +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/inact_PKA REAC A B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/inact_CaN REAC A B +addmsg /kinetics/Bulk/inact_CaN /kinetics/Bulk/activate_CaN SUBSTRATE n +addmsg /kinetics/Bulk/iP /kinetics/Bulk/activate_CaN PRODUCT n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_CaN SUBSTRATE n +addmsg /kinetics/Bulk/Ca /kinetics/Bulk/activate_CaN SUBSTRATE n +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/Ca REAC A B +addmsg /kinetics/dend_Ca_reac /kinetics/Ca_dend_input REAC A B +addmsg /kinetics/Ca_dend_input /kinetics/dend_Ca_reac SUBSTRATE n +addmsg /kinetics/Ca /kinetics/dend_Ca_reac PRODUCT n +addmsg /kinetics/dend_Ca_reac /kinetics/Ca REAC B A +addmsg /kinetics/PSD/Ca /graphs/conc1/Ca_PSD.Co PLOT Co *Ca_PSD.Co *53 +addmsg /kinetics/Bulk/Ca /graphs/conc1/Ca_Bulk.Co PLOT Co *Ca_Bulk.Co *41 +addmsg /kinetics/Bulk/PKA /graphs/conc1/PKA.Co PLOT Co *PKA.Co *43 +addmsg /kinetics/PSD/Ca.P /graphs/conc1/Ca.P.Co PLOT Co *Ca.P.Co *blue +addmsg /kinetics/Ca /graphs/conc1/Ca_dend.Co PLOT Co *Ca_dend.Co *1 +addmsg /kinetics/PSD/tot_PSD_R /graphs/conc2/tot_PSD_R.Co PLOT Co *tot_PSD_R.Co *blue +addmsg /kinetics/PSD/Rpp /graphs/conc2/Rpp.Co PLOT Co *Rpp.Co *28 +enddump +// End of dump + +call /kinetics/Bulk/iR/notes LOAD \ +"Same as Fus3" \ +"" +call /kinetics/Bulk/iKK/notes LOAD \ +"Same as Ste7" \ +"" +call /kinetics/Bulk/iP/notes LOAD \ +"Same as Msg5" \ +"" +complete_loading diff --git a/demos/README b/demos/README new file mode 100644 index 0000000..bd856f3 --- /dev/null +++ b/demos/README @@ -0,0 +1,33 @@ +Here we have Python scripts that replicate most of the figures in the MOOSE +paper. Most of these can be accessed through the MooseGUI startup screen. +Some of these take a very long time. Approximate runtimes for a 2.2 GHz +core I7 processor are listed here. +Some of these figures/demos depend on the 3-D graphics visualization, which +may not be compiled into your distribution. + +The figure scripts are in the directories Fig_ +and are named Fig2A, Fig3D etc. + +Figure panel Runtime(s) Uses 3-D? Notes +2A 1500 No Generates 2 xplot files for + analysis by Fig2A_analysis.py +2C 6 Yes +2D 35 Yes +2E 5 Yes + +3ABC 2 No This is a GENESIS/KKIT model + definition file loaded by MOOSE. +3D 1 No There is a corresponding + Fig3_NEURON.py for the same + model in NEURON. + +4B 10 Yes +4CDEF 370 No +4GHIJ 300 No + +5A 20 Yes Pops up four windows. +5BCDE 240 No Text only output. + +6A 60 Yes Spines exaggerated for display +6BCDE 3900 No Dumps to SVG. + diff --git a/demos/README.md b/demos/README.md new file mode 100644 index 0000000..30797ae --- /dev/null +++ b/demos/README.md @@ -0,0 +1,3 @@ +[![Build Status](https://travis-ci.org/BhallaLab/moose-examples.svg)](https://travis-ci.org/BhallaLab/moose-examples). + +Examples, tutorial and demo scripts. diff --git a/demos/__init__.py b/demos/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/demos/rxdSpineSize.py b/demos/rxdSpineSize.py new file mode 100644 index 0000000..aa61446 --- /dev/null +++ b/demos/rxdSpineSize.py @@ -0,0 +1,293 @@ +################################################################## +## This program is part of 'MOOSE', the +## Messaging Object Oriented Simulation Environment. +## Copyright (C) 2015 Upinder S. Bhalla. and NCBS +## It is made available under the terms of the +## GNU Lesser General Public License version 2.1 +## See the file COPYING.LIB for the full notice. +## +## rxdSpineSize.py: Builds a cell with spines and a propagating reaction +## wave. Products diffuse into the spine and cause it to get bigger. +################################################################## +import math +import pylab +import numpy +import matplotlib.pyplot as plt +import moose +import sys +sys.path.append( '../util' ) +import rdesigneur as rd +from PyQt5 import QtGui +import moogli +import moogli.extensions.moose +import matplotlib + +PI = 3.141592653 +ScalingForTesting = 10 +RM = 1.0 / ScalingForTesting +RA = 1.0 * ScalingForTesting +CM = 0.01 * ScalingForTesting +runtime = 100.0 +frameruntime = 1.0 +diffConst = 5e-12 +dendLen = 100e-6 +diffLen = 1.0e-6 +dendDia = 2e-6 +somaDia = 5e-6 +concInit = 0.001 # 1 millimolar +spineSpacing = 10e-6 +spineSpacingDistrib = 1e-6 +spineSize = 1.0 +spineSizeDistrib = 0.5 +spineAngle= numpy.pi / 2.0 +spineAngleDistrib = 0.0 + +def makeCellProto( name ): + elec = moose.Neuron( '/library/' + name ) + ecompt = [] + soma = rd.buildCompt( elec, 'soma', somaDia, somaDia, -somaDia, RM, RA, CM ) + dend = rd.buildCompt( elec, 'dend', dendLen, dendDia, 0, RM, RA, CM ) + moose.connect( soma, 'axial', dend, 'raxial' ) + elec.buildSegmentTree() + +def makeChemProto( name ): + chem = moose.Neutral( '/library/' + name ) + comptVol = diffLen * dendDia * dendDia * PI / 4.0 + for i in ( ['dend', comptVol], ['spine', 1e-19], ['psd', 1e-20] ): + print(('making ', i)) + compt = moose.CubeMesh( chem.path + '/' + i[0] ) + compt.volume = i[1] + #x = moose.Pool( compt.path + '/x' ) + #y = moose.BufPool( compt.path + '/y' ) + z = moose.Pool( compt.path + '/z' ) + #x.concInit = 0.0 + #x.diffConst = diffConst + #y.concInit = concInit + z.concInit = 0.0 + z.diffConst = diffConst + nInit = comptVol * 6e23 * concInit + nstr = str( 1/nInit) + + x = moose.Pool( chem.path + '/dend/x' ) + x.diffConst = diffConst + func = moose.Function( x.path + '/func' ) + func.expr = "-x0 * (0.3 - " + nstr + " * x0) * ( 1 - " + nstr + " * x0)" + print((func.expr)) + func.x.num = 1 + moose.connect( x, 'nOut', func.x[0], 'input' ) + moose.connect( func, 'valueOut', x, 'increment' ) + z = moose.element( '/library/' + name + '/dend/z' ) + reac = moose.Reac( '/library/' + name + '/dend/reac' ) + reac.Kf = 1 + reac.Kb = 10 + moose.connect( reac, 'sub', x, 'reac' ) + moose.connect( reac, 'prd', z, 'reac' ) + +def makeSpineProto2( name ): + spine = moose.Neutral( '/library/' + name ) + shaft = rd.buildCompt( spine, 'shaft', 0.5e-6, 0.4e-6, 0, RM, RA, CM ) + head = rd.buildCompt( spine, 'head', 0.5e-6, 0.5e-6, 0.5e-6, RM, RA, CM ) + moose.connect( shaft, 'axial', head, 'raxial' ) + +def makeModel(): + moose.Neutral( '/library' ) + makeCellProto( 'cellProto' ) + makeChemProto( 'cProto' ) + makeSpineProto2( 'spine' ) + rdes = rd.rdesigneur( useGssa = False, \ + combineSegments = False, \ + stealCellFromLibrary = True, \ + meshLambda = 1e-6, \ + cellProto = [['cellProto', 'elec' ]] ,\ + spineProto = [['spineProto', 'spine' ]] ,\ + chemProto = [['cProto', 'chem' ]] ,\ + spineDistrib = [ \ + ['spine', '#', \ + 'spacing', str( spineSpacing ), \ + 'spacingDistrib', str( spineSpacingDistrib ), \ + 'angle', str( spineAngle ), \ + 'angleDistrib', str( spineAngleDistrib ), \ + 'size', str( spineSize ), \ + 'sizeDistrib', str( spineSizeDistrib ) ] \ + ], \ + chemDistrib = [ \ + [ "chem", "dend", "install", "1" ] \ + ], + adaptorList = [ \ + [ 'psd/z', 'n', 'spine', 'psdArea', 10.0e-15, 300e-15 ], \ + ] \ + ) + rdes.buildModel( '/model' ) + x = moose.vec( '/model/chem/dend/x' ) + x.concInit = 0.0 + for i in range( 0,20 ): + x[i].concInit = concInit + +def makePlot( name, srcVec, field ): + tab = moose.Table2('/graphs/' + name + 'Tab', len( srcVec ) ).vec + for i in zip(srcVec, tab): + moose.connect(i[1], 'requestOut', i[0], field) + return tab + + +def displayPlots(): + for x in moose.wildcardFind( '/graphs/#[0]' ): + tab = moose.vec( x ) + for i in range( len( tab ) ): + pylab.plot( tab[i].vector, label=x.name[:-3] + " " + str( i ) ) + pylab.legend() + pylab.figure() + +def main(): + """ + This illustrates the use of rdesigneur to build a simple dendrite with + spines, and then to resize them using spine fields. These are the + fields that would be changed dynamically in a simulation with reactions + that affect spine geometry. + In this simulation there is a propagating reaction wave using a + highly abstracted equation, whose product diffuses into the spines and + makes them bigger. + """ + makeModel() + elec = moose.element( '/model/elec' ) + elec.setSpineAndPsdMesh( moose.element('/model/chem/spine'), moose.element('/model/chem/psd') ) + + eHead = moose.wildcardFind( '/model/elec/#head#' ) + oldDia = [ i.diameter for i in eHead ] + graphs = moose.Neutral( '/graphs' ) + #makePlot( 'psd_x', moose.vec( '/model/chem/psd/x' ), 'getN' ) + #makePlot( 'head_x', moose.vec( '/model/chem/spine/x' ), 'getN' ) + makePlot( 'dend_x', moose.vec( '/model/chem/dend/x' ), 'getN' ) + makePlot( 'dend_z', moose.vec( '/model/chem/dend/z' ), 'getN' ) + makePlot( 'head_z', moose.vec( '/model/chem/spine/z' ), 'getN' ) + makePlot( 'psd_z', moose.vec( '/model/chem/psd/z' ), 'getN' ) + makePlot( 'headDia', eHead, 'getDiameter' ) + + ''' + debug = moose.PyRun( '/pyrun' ) + debug.tick = 10 + debug.runString = """print "RUNNING: ", moose.element( '/model/chem/psd/z' ).n, moose.element( '/model/elec/head0' ).diameter""" + ''' + moose.reinit() + moose.start( runtime ) + + displayPlots() + pylab.plot( oldDia, label = 'old Diameter' ) + pylab.plot( [ i.diameter for i in eHead ], label = 'new Diameter' ) + pylab.legend() + pylab.show() + + app = QtGui.QApplication(sys.argv) + #widget = mv.MoogliViewer( '/model' ) + morphology = moogli.read_morphology_from_moose( name="", path = '/model/elec' ) + widget = moogli.MorphologyViewerWidget( morphology ) + widget.show() + return app.exec_() + quit() + +# Run the 'main' if this script is executed standalone. + +def showVisualization(): + makeModel() + elec = moose.element( '/model/elec' ) + elec.setSpineAndPsdMesh( moose.element('/model/chem/spine'), moose.element('/model/chem/psd') ) + + eHead = moose.wildcardFind( '/model/elec/#head#' ) + oldDia = [ i.diameter for i in eHead ] + graphs = moose.Neutral( '/graphs' ) + #makePlot( 'psd_x', moose.vec( '/model/chem/psd/x' ), 'getN' ) + #makePlot( 'head_x', moose.vec( '/model/chem/spine/x' ), 'getN' ) + makePlot( 'dend_x', moose.vec( '/model/chem/dend/x' ), 'getN' ) + dendZ = makePlot( 'dend_z', moose.vec( '/model/chem/dend/z' ), 'getN' ) + makePlot( 'head_z', moose.vec( '/model/chem/spine/z' ), 'getN' ) + psdZ = makePlot( 'psd_z', moose.vec( '/model/chem/psd/z' ), 'getN' ) + diaTab = makePlot( 'headDia', eHead, 'getDiameter' ) + # print diaTab[0].vector[-1] + # return + dendrite = moose.element("/model/elec/dend") + dendrites = [dendrite.path + "/" + str(i) for i in range(len(dendZ))] + # print dendrites + moose.reinit() + + spineHeads = moose.wildcardFind( '/model/elec/#head#') + # print moose.wildcardFind( '/model/elec/##') + + # print "dendZ", readValues(dendZ) + # print dendrite + + app = QtGui.QApplication(sys.argv) + viewer = create_viewer("/model/elec", dendrite, dendZ, diaTab, psdZ) + viewer.showMaximized() + viewer.start() + return app.exec_() + + +def create_viewer(path, moose_dendrite, dendZ, diaTab, psdZ): + network = moogli.extensions.moose.read(path=path, + vertices=15) + + dendrite = network.groups["dendrite"].shapes[moose_dendrite.path] + chem_compt_group = dendrite.subdivide(len(dendZ)) + normalizer = moogli.utilities.normalizer(0.0, + 300.0, + clipleft=True, + clipright=True) + colormap = moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow) + mapper = moogli.utilities.mapper(colormap, normalizer) + + def readValues(tables): + values = [] + for i in range(len(tables)): + values.append(tables[i].vector[-1]) + return values + + def prelude(view): + view.home() + view.pitch(math.pi / 3.0) + view.zoom(0.3) + network.groups["soma"].set("color", moogli.colors.RED) + network.groups["spine"].groups["shaft"].set("color", + moogli.colors.RED) + + def interlude(view): + moose.start(frameruntime) + network.groups["spine"].groups["head"].set("radius", + readValues(diaTab), + lambda x: x * 0.5e6) + network.groups["spine"].groups["head"].set("color", + readValues(psdZ), + mapper) + chem_compt_group.set("color", + readValues(dendZ), + mapper) + if moose.element("/clock").currentTime >= runtime: + view.stop() + + viewer = moogli.Viewer("Viewer") + viewer.attach_shapes(list(network.shapes.values())) + viewer.detach_shape(dendrite) + viewer.attach_shapes(list(chem_compt_group.shapes.values())) + + view = moogli.View("main-view", + prelude=prelude, + interlude=interlude) + cb = moogli.widgets.ColorBar(id="cb", + title="Molecule #", + text_color=moogli.colors.BLACK, + position=moogli.geometry.Vec3f(0.975, 0.5, 0.0), + size=moogli.geometry.Vec3f(0.30, 0.05, 0.0), + text_font="/usr/share/fonts/truetype/ubuntu-font-family/Ubuntu-R.ttf", + orientation=math.pi / 2.0, + text_character_size=20, + label_formatting_precision=0, + colormap=moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow), + color_resolution=100, + scalar_range=moogli.geometry.Vec2f(0.0, + 300.0)) + view.attach_color_bar(cb) + viewer.attach_view(view) + return viewer + + +if __name__ == '__main__': + showVisualization() diff --git a/demos/squid/README.txt b/demos/squid/README.txt new file mode 100644 index 0000000..221cc0a --- /dev/null +++ b/demos/squid/README.txt @@ -0,0 +1,14 @@ +This is the port of Hodgkin-Huxley Squid Giant Axon demo from +GENESIS. Run `python squid_demo.py` to start the GUI. Open help.org in +a text editor or help.html in a web-browser (or click `Help` button in +the GUI) to read the tutorial. + +The biophysical model is in `squid.py`. The electronics setup is in +`electronics.py`. The combination of squid axon model and the +electronics is in squid_setup.py. All these can be run without any GUI +dependency. To run squid_demo.py you need PyQt and matplotlib with Qt +backend installed. + +Author: Subhasis Ray +Place: NCBS, Bangalore, INDIA +Date: 21 September 2012 diff --git a/demos/squid/channeleditor.py b/demos/squid/channeleditor.py new file mode 100644 index 0000000..09ac719 --- /dev/null +++ b/demos/squid/channeleditor.py @@ -0,0 +1,147 @@ +# channeleditor.py --- +# +# Filename: channeleditor.py +# Description: +# Author: Subhasis Ray +# Maintainer: +# Created: Wed Jul 18 19:06:39 2012 (+0530) +# Version: +# Last-Updated: Wed Aug 8 16:36:10 2012 (+0530) +# By: Subhasis Ray +# Update #: 179 +# URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# +# A widget for editing Hodgkin-Huxley type ion channels. +# +# + +# Change log: +# +# +# + +# Code: + +import sys +from PyQt5 import QtGui, QtCore +from numpy import * +import ast + +class GateEditor(QtGui.QWidget): + """Utility to edit gate equations. + + It provides two line edits to enter the alpha and beta equations + directly. + """ + def __init__(self, *args): + QtGui.QWidget.__init__(self, *args) + self.useVButton = QtGui.QRadioButton('Use V', self) + self.useVButton.setChecked(True) + self.useCaButton = QtGui.QRadioButton('Use Ca', self) + self.useCaButton.setChecked(False) + self.symbolGroup = QtGui.QGroupBox(self) + layout = QtGui.QHBoxLayout() + # self.symbolGroup.setExclusive(True) + layout.addWidget(self.useVButton) + layout.addWidget(self.useCaButton) + self.symbolGroup.setLayout(layout) + self.inputPanel = QtGui.QFrame(self) + self.minVLabel = QtGui.QLabel('Minimum', self) + self.maxVLabel = QtGui.QLabel('Maximum', self) + self.divsVLabel = QtGui.QLabel('Number of divisions', self) + self.minVEdit = QtGui.QLineEdit(self) + self.maxVEdit = QtGui.QLineEdit(self) + self.divsVEdit = QtGui.QLineEdit(self) + self.equation = '(A + B * V) / (C + exp((V + D)/F))' + self.alphaText = 'Equation for forward rate \u03B1 ' + self.betaText = 'Equation for backward rate \u03B2 ' + self.minfText = 'Equation for m\u221E ' + self.taumText = 'Equation for \u03C4m ' + self.alphaLabel = QtGui.QLabel(self.minfText, self) + self.betaLabel = QtGui.QLabel(self.taumText, self) + self.alphaEdit = QtGui.QLineEdit(self) + self.betaEdit = QtGui.QLineEdit(self) + self.formCombo = QtGui.QComboBox(self) + self.formCombo.addItem('m\u221E - \u03C4m') + self.formCombo.addItem('\u03B1 - \u03B2') + self.okButton = QtGui.QPushButton('OK', self) + layout = QtGui.QGridLayout(self.inputPanel) + layout.addWidget(self.minVLabel, 0, 0) + layout.addWidget(self.minVEdit, 0, 1) + layout.addWidget(self.maxVLabel, 0, 3) + layout.addWidget(self.maxVEdit, 0, 4) + layout.addWidget(self.divsVLabel, 0, 6) + layout.addWidget(self.divsVEdit, 0, 7) + layout.addWidget(self.formCombo, 1, 0, 1, 4) + layout.addWidget(self.alphaLabel, 2, 0, 1, 2) + layout.addWidget(self.alphaEdit, 2, 2, 1, 7) + layout.addWidget(self.betaLabel, 3, 0, 1, 2) + layout.addWidget(self.betaEdit, 3, 2, 1, 7) + self.inputPanel.setLayout(layout) + layout = QtGui.QVBoxLayout(self) + layout.addWidget(self.symbolGroup) + layout.addWidget(self.inputPanel) + layout.addWidget(self.okButton) + self.setLayout(layout) + self.connect(self.okButton, QtCore.SIGNAL('clicked()'), self.evalGateExpressions) + # self.connect(self.useVButton, QtCore.SIGNAL('toggled(bool)'), self.toggleInputPanel) + self.connect(self.formCombo, QtCore.SIGNAL('currentIndexChanged(int)'), self.switchEquationForm) + + def toggleInputPanel(self, on): + self.inputPanel.setVisible(on) + self.adjustSize() + + def switchEquationForm(self, index): + if index == 1: + self.alphaLabel.setText(self.alphaText) + self.betaLabel.setText(self.betaText) + elif index == 0: + self.alphaLabel.setText(self.minfText) + self.betaLabel.setText(self.taumText) + + def evalGateExpressions(self): + """Evaluate the expressions supplied by user to obtain the + arrays for the gate tables.""" + vmin = float(str(self.minVEdit.text())) + vmax = float(str(self.maxVEdit.text())) + vdivs = float(str(self.divsVEdit.text())) + vrange = linspace(vmin, vmax, vdivs+1) + a_expr = str(self.alphaEdit.text()) + b_expr = str(self.betaEdit.text()) + a = zeros(vdivs+1) + b = zeros(vdivs+1) + if self.useVButton.isChecked(): + symbol = 'V' + elif self.useCaButton.isChecked(): + symbol = 'Ca' + code = """for ii in range(len(vrange)): + %s = vrange[ii] + a[ii] = %s + b[ii] = %s + """ % (symbol, a_expr, b_expr) + print(code) + tree = compile(code, '', 'exec') + exec(tree) + print(a, b) + return {'min': vmin, + 'max': vmax, + 'divs': vdivs, + 'a': a, + 'b': b} + + # 0.5 * (1-exp(-(V-10)/10)) +if __name__ == '__main__': + app = QtGui.QApplication(sys.argv) + QtGui.qApp = app + editor = GateEditor() + editor.show() + sys.exit(app.exec_()) + +# +# channeleditor.py ends here diff --git a/demos/squid/electronics.py b/demos/squid/electronics.py new file mode 100644 index 0000000..2f356e3 --- /dev/null +++ b/demos/squid/electronics.py @@ -0,0 +1,116 @@ +# electronics.py --- +# +# Filename: electronics.py +# Description: +# Author: Subhasis Ray +# Maintainer: +# Created: Wed Feb 22 00:53:38 2012 (+0530) +# Version: +# Last-Updated: Tue Jul 10 10:28:40 2012 (+0530) +# By: subha +# Update #: 221 +# URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# +# +# +# + +# Change log: +# +# 2012-02-22 23:22:30 (+0530) Subha - the circuitry put in a class. +# + +# Code: + +import numpy +import moose + +class ClampCircuit(moose.Neutral): + """Container for a Voltage-Clamp/Current clamp circuit.""" + defaults = { + 'level1': 25.0, + 'width1': 50.0, + 'delay1': 2.0, + 'delay2': 1e6, + 'trigMode': 0, + 'delay3': 1e9 + } + def __init__(self, path, compartment): + moose.Neutral.__init__(self, path) + self.pulsegen = moose.PulseGen(path+"/pulse") # holding voltage/current generator + self.pulsegen.count = 2 + self.pulsegen.firstLevel = 25.0 + self.pulsegen.firstWidth = 50.0 + self.pulsegen.firstDelay = 2.0 + self.pulsegen.secondDelay = 0.0 + self.pulsegen.trigMode = 2 + self.gate = moose.PulseGen(path+"/gate") # holding voltage/current generator + self.gate.level[0] = 1.0 + self.gate.delay[0] = 0.0 + self.gate.width[0] = 1e9 + moose.connect(self.gate, 'output', self.pulsegen, 'input') + self.lowpass = moose.RC(path+"/lowpass") # lowpass filter + self.lowpass.R = 1.0 + self.lowpass.C = 0.03 + self.vclamp = moose.DiffAmp(path+"/vclamp") + self.vclamp.gain = 0.0 + self.vclamp.saturation = 1e10 + self.iclamp = moose.DiffAmp(path+"/iclamp") + self.iclamp.gain = 0.0 + self.iclamp.saturation = 1e10 + self.pid = moose.PIDController(path+"/pid") + self.pid.gain = 0.5 + self.pid.tauI = 0.02 + self.pid.tauD = 0.005 + self.pid.saturation = 1e10 + # Connect current clamp circuitry + moose.connect(self.pulsegen, "output", self.iclamp, "plusIn") + moose.connect(self.iclamp, "output", compartment, "injectMsg") + # Connect voltage clamp circuitry + moose.connect(self.pulsegen, "output", self.lowpass, "injectIn") + moose.connect(self.lowpass, "output", self.vclamp, "plusIn") + moose.connect(self.vclamp, "output", self.pid, "commandIn") + moose.connect(compartment, "VmOut", self.pid, "sensedIn") + moose.connect(self.pid, "output", compartment, "injectMsg") + current_table = moose.Table("/data/Im") + moose.connect(current_table, "requestOut", compartment, "getIm") + + def configure_pulses(self, baseLevel=0.0, firstLevel=0.1, firstDelay=5.0, firstWidth=40.0, secondLevel=0.0, secondDelay=1e6, secondWidth=0.0, singlePulse=True): + """Set up the pulse generator.""" + self.pulsegen.baseLevel = baseLevel + self.pulsegen.firstLevel = firstLevel + self.pulsegen.firstWidth = firstWidth + self.pulsegen.firstDelay = firstDelay + self.pulsegen.secondLevel = secondLevel + self.pulsegen.secondDelay = secondDelay + self.pulsegen.secondWidth = secondWidth + if singlePulse: + self.pulsegen.trigMode = 1 + else: + self.pulsegen.trigMode = 0 + + def do_voltage_clamp(self): + """Switch to voltage clamp circuitry. After this the simdt may + need to be changed for correct performance.""" + self.vclamp.gain = 1.0 + self.iclamp.gain = 0.0 + self.pid.gain = 0.5 + self.pid.tauD = 0.005 + self.pid.tauI = 0.02 + + def do_current_clamp(self): + """Switch to current clamp circuitry. After this the simdt may + need to be changed for correct performance.""" + self.iclamp.gain = 1.0 + self.vclamp.gain = 0.0 + self.pid.gain = 0.0 + + +# +# electronics.py ends here diff --git a/demos/squid/help.html b/demos/squid/help.html new file mode 100644 index 0000000..617a710 --- /dev/null +++ b/demos/squid/help.html @@ -0,0 +1,587 @@ + + + + +Simulation of squid axon with Hodgkin-Huxley ion channels + + + + + + + + + + + + + +
+ +
+ +
+

Simulation of squid axon with Hodgkin-Huxley ion channels

+ + + + +
+

1 Navigation: navigation toolbar is located at bottom of the plots

+
+ +

This uses the built-in navigation toolbar of matplotlib [click to + open in your default web-browser]. +

+ +
+

./images/navigationtoolbar.jpg

+

Navigation toolbar for plots

+
+ +

+ You can hover the mouse cursor on any icon on this toolbar to get a + brief tool-tip. To summarize: +

+ +
+ +
+

1.1 Zoom

+
+ +
    +
  1. Zoom-in: +
      +
    1. Zoom-in both X and Y axes: +
        +
      • click on the subplot you want to zoom and scroll mouse + wheel down, or +
        • +
      • click magnifier icon and press left mouse button on the + subplot and drag. This will zoom the subplot to the + rectangle you cover by this. +
        • +
      • click compass icon and press right mouse button on the plot + and drag towards top-right. +
        • +
      + +
      2. +
    2. Zoom-in along X-axis: +
        +
      • click compass icon and press right mouse button on the plot + and drag towards right. +
        • +
      + +
      3. +
    3. Zoom-in along Y-axis: +
        +
      • click compass icon and press right mouse button on the plot + and drag upwards. +
        • +
      + +
      4. +
    + +
    2. +
  2. Zoom-out: +
      +
    1. Zoom-out both X and Y axes: +
        +
      • click on the subplot you want to zoom and scroll mouse wheel up, or +
        • +
      • click magnifier icon and press right mouse button on the + plot and drag. The whole visible axis area will fit into + the rectangle you cover by this. +
        • +
      • click compass icon and press right mouse button on the plot + and drag towards bottom-left. +
        • +
      + +
      2. +
    2. Zoom-out whole plot window along X-axis: +
        +
      • click compass icon and press right mouse button on the plot + and drag towards left. +
        • +
      + +
      3. +
    3. Zoom-out Y-axis: +
        +
      • click compass icon and press right mouse button on the plot + and drag downwards. +
        • +
      + +
      4. +
    + +
    3. +
  3. Go forward/backward in zoom stack: + click right/left arrow icon. +
    4. +
+ +
+ +
+ +
+

1.2 Pan:

+
+ +

click compass-icon and left click-and-drag +

+ +
+ +
+

1.3 Reset to initial plot state:

+
+ +

click home icon. +

+ +
+ +
+

1.4 Change spacing and position of subplots:

+
+ +

click button with four green arrow-heads pointing (this is called + the Subplot-Configuration button). +

+ +
+ +
+

1.5 Configure axes:

+
+ +

click green tick-mark. In the pop-up dialog select the axis you want + to modify and click OK. In the next dialog you can set the range of + X and Y values for the axes and modify several other properties. +

+ +
+ +
+

1.6 Save plot:

+
+ +

click floppy-disk icon. +

+
+
+ +
+ +
+

2 Rearranging the frames on small screens

+
+ +

The default layout of the squid demo may exceed available screen + size on your system. But you can always undock the control panels + and put them one over the other to save screen space. To undock all + panels in one go, click the "Undock all" button in the tool bar. +

+

+ To move or float a single panel, click the left mouse button on its + title bar (in the same horizontal line with the expand buttons) of + any of the panels and drag. You can choose to leave it floating or + drop it somewhere (top, left, bottom or right of the plot window) in + the main window to reposition it. You can drop multiple panels in + the same location. Then they will be put as multiple tabs over one + another. +

+

+ An undocked panel will be always on top of the main window. If this + is a problem, you can close it by clicking the close button. You can + make it visible again by clicking "Show all" button on the tool bar. +

+
+ +
+ +
+

3 The SQUID tutorial

+
+ +

The following is adapted from the GENESIS squid demo notes with + modifications for MOOSE by Subhasis Ray, September 2012. +

+

+ The original header was: +

+ +
+ +

+ SQUID +

+

+ An Introductory Tutorial for GENESIS, XODUS, and the HODGKIN-HUXLEY model +

+

+ By M. Nelson, Caltech, April 1989 - Modified by D. Beeman, June 1991, Dec 1994 + ­ Modified by E. Vigmond, September 1993 +

+ +
+ +

+ In the process of working through this tutorial, you will learn + something about the Hodgkin-Huxley model. This program may serve as + a good starting point for those of you who plan to work on + single-cell models for a course project. +

+ +
+ +
+

3.1 The Model

+
+ +

For the time being, we are going to simulate a single axon + compartment with active Na and K conductances, as described by Hodgkin + and Huxley for the squid giant axon. In other tutorials we will link + compartments together to form a simple model of an entire neuron with + a soma and dendrites (the Neuron tutorial), model a cable with many + compartments (the cable tutorial), and build neural circuits with + connected neurons (MultiCell and tritonia). For now, we confine + ourselves to a single axon compartment. +

+
+ +
+ +
+

3.2 Running the Simulation

+
+ +

The model has already been initialized with some reasonable + parameter values, so all you have to do to run the simulation is: +

+

+ click on the ``Run`` button in the toolbar. +

+

+ The simulation which you just observed was for a constant current + pulse, which is shown in the lower left graph panel. The upper left + graph shows the membrane potential. You can see that 3 action + potentials were generated during this 50 msec simulation. Now let's + change the injection current and see what happens. +

+

+ At the bottom of the left panel is a widget labeled "Electronics" + and inside it there are two tabs labeled ``Current clamp`` and + ``Voltage clamp``. Select the ``Current clamp`` tab and you will + see a series of labeled text boxes with default values. In order + to change the injection current: +

+

+ position the cursor to the right of the last digit in the "First + Pulse Current" field and click in the text box with the left mouse + button. +

+

+ Let's change the peak injection current from 0.1 to 1.0. +

+

+ type <BACKSPACE> to delete the 0.1 and then type 1.0 +

+

+ The value in the dialog field should now be 1.0. +

+

+ Now we'll run the simulation again. +

+

+ click the "Run" button on the toolbar again. +

+

+ There should be a dramatic change in the time-course of the + membrane potential at this higher current injection level. + Experiment with the injection level to see what happens to the + axon at higher injection currents. Also try decreasing the + injection level until an action potential is no longer elicited by + the stimulus. What is the threshold for producing an action + potential in this compartment? +

+

+ You may also experiment with trains of short pulses. Set the + "First Pulse Width" dialog field to 1 msec and click on the + "Single Pulse" drop down box and select "Pulse Train". Now vary + "First Onset Delay". What is the minimum interval between action + potentials that you can achieve? +

+
+ +
+ +
+

3.3 Voltage Clamping

+
+ +

You can also perform voltage clamp experiments in this simulation. +

+

+ click on the "Voltage clamp" tab header at the bottom of the + control form under "Electronics". +

+

+ Again, reasonable default values have been selected , so all you + have to do to run the voltage clamp simulation is: +

+

+ click the "Run" button on the control form +

+
+ +
+ +
+

3.4 Changing Extracellular Concentrations

+
+ +

You can alter the extracellular concentrations of the ions through + the "Channels" panel. Any changes in concentration will cause the + reversal potentials to be recalculated. To reset the values back + to the initial ones, just click on the "Restore defaults" button + in the top tool bar. +

+
+ +
+ +
+

3.5 Controlling Graphs

+
+ +

The graph of the clamp current (lower left panel) has gone off + scale. In order to rescale the graph: +

+

+ click on the button with green tick mark in the navigation toolbar + at the bottom of the plots. +

+

+ A dialog containing drop-down to select the subplot should appear. + Select the "Injection current" and click OK. Another dialog box + will appear with text boxes for `Min` and `Max` values for X-Axis + and Y-Axis. Adjust for Y axis to bring the graph into range and + press "Apply". +

+ +

+ The top toolbar has an "Overlay plots" button. When it is + checked, any existing plots in the graph will be held and new + simulation results will be overlayed. Try this now. +

+

+ Click "Overlay plots" and run the simulation at several values of + the clamp voltage. Do the first run with "Overlay plots" button + unchecked so that all previous graphs are cleared at this + run. Then click this button to checked state and do the subsequent + runs. +

+
+ +
+ +
+

3.6 State Plots

+
+ +

One can learn a great deal by studying plots in which one of the + Hodgkin-Huxley channel activation parameters (the K activation + "n", the Na activation "m", or the Na inactivation "h") is plotted + as a function of the membrane potential, V. (See, for example, + Chapter 5 of "Methods in Neuronal Modeling", by Koch and Segev.) +

+

+ In order to view such a plot, click the left mouse button on the + button labeled "State plot" in the top toolbar. The label will + change to "State Plot Visible", and a state plot graph will + appear. Clicking the button again will hide the graph. The + default plot is to show the K channel "n" parameter on the y-axis + and the membrane potential on the x-axis. The drop-down menus at + the top of the window allow you to change these defaults. +

+
+ +
+ +
+

3.7 Channel Blocking

+
+ +

In order to explore the effects of blocking one of the channels, + you may click on one of the check boxes in the "Channels" panel + for blocking and unblocking a channel. When a channel is blocked, + its conductance is set to zero. Activation parameters for a + blocked channel are still calculated and may be plotted, but are + relatively meaningless because they will have no effect on the + membrane potential. +

+
+ +
+ +
+

3.8 Saving Graphs

+
+ +

You can save a graph to file by clicking the save button in the + navigation toolbar. In the file dialog you can select from several + formats including PDF, JPEG, PNG and SVG. +

+
+ +
+ +
+

3.9 Units used in the simulation

+
+ +

Units: +

+ ++ + + + + + + + + + + + + + + +
quantityunit
timemsec
lengthum (microns)
potentialmV
conductancemS (mmho)
resistancekohm
capacitanceuF
specific axial resistancekohm-cm
specific membrane conductancemS/cm2
specific membrane capacitanceuF/cm2
+ + +
+
+
+
+ +
+

Date: 2012-09-25 17:03:29 IST

+

Author: Subhasis Ray

+

Org version 7.8.11 with Emacs version 23

+Validate XHTML 1.0 + +
+ + diff --git a/demos/squid/help.org b/demos/squid/help.org new file mode 100644 index 0000000..2b47b4e --- /dev/null +++ b/demos/squid/help.org @@ -0,0 +1,242 @@ +Simulation of squid axon with Hodgkin-Huxley ion channels + +#+AUTHOR: Subhasis Ray + +* Navigation: navigation toolbar is located at bottom of the plots + This uses the built-in navigation toolbar of [[http://matplotlib.org/users/navigation_toolbar.html][matplotlib]] [click to + open in your default web-browser]. + +#+CAPTION: Navigation toolbar for plots +#+LABEL: fignavigationtoolbar +[[./images/navigationtoolbar.jpg]] + + You can hover the mouse cursor on any icon on this toolbar to get a + brief tool-tip. To summarize: + +** Zoom + 1. Zoom-in: + 1) Zoom-in both X and Y axes: + - click on the subplot you want to zoom and scroll mouse + wheel down, or + - click magnifier icon and press left mouse button on the + subplot and drag. This will zoom the subplot to the + rectangle you cover by this. + - click compass icon and press right mouse button on the plot + and drag towards top-right. + 2) Zoom-in along X-axis: + - click compass icon and press right mouse button on the plot + and drag towards right. + 3) Zoom-in along Y-axis: + - click compass icon and press right mouse button on the plot + and drag upwards. + 2. Zoom-out: + 1) Zoom-out both X and Y axes: + - click on the subplot you want to zoom and scroll mouse wheel up, or + - click magnifier icon and press right mouse button on the + plot and drag. The whole visible axis area will fit into + the rectangle you cover by this. + - click compass icon and press right mouse button on the plot + and drag towards bottom-left. + 2) Zoom-out whole plot window along X-axis: + - click compass icon and press right mouse button on the plot + and drag towards left. + 3) Zoom-out Y-axis: + - click compass icon and press right mouse button on the plot + and drag downwards. + 3. Go forward/backward in zoom stack: + click right/left arrow icon. +** Pan: + click compass-icon and left click-and-drag +** Reset to initial plot state: + click home icon. +** Change spacing and position of subplots: + click button with four green arrow-heads pointing (this is called + the Subplot-Configuration button). +** Configure axes: + click green tick-mark. In the pop-up dialog select the axis you want + to modify and click OK. In the next dialog you can set the range of + X and Y values for the axes and modify several other properties. +** Save plot: + click floppy-disk icon. + +* Rearranging the frames on small screens + The default layout of the squid demo may exceed available screen + size on your system. But you can always undock the control panels + and put them one over the other to save screen space. To undock all + panels in one go, click the "Undock all" button in the tool bar. + + To move or float a single panel, click the left mouse button on its + title bar (in the same horizontal line with the expand buttons) of + any of the panels and drag. You can choose to leave it floating or + drop it somewhere (top, left, bottom or right of the plot window) in + the main window to reposition it. You can drop multiple panels in + the same location. Then they will be put as multiple tabs over one + another. + + An undocked panel will be always on top of the main window. If this + is a problem, you can close it by clicking the close button. You can + make it visible again by clicking "Show all" button on the tool bar. + +* The SQUID tutorial + The following is adapted from the GENESIS squid demo notes with + modifications for MOOSE by Subhasis Ray, September 2012. + + The original header was: + + ----------------------------------------------------------------------------- + + SQUID + + An Introductory Tutorial for GENESIS, XODUS, and the HODGKIN-HUXLEY model + + By M. Nelson, Caltech, April 1989 - Modified by D. Beeman, June 1991, Dec 1994 + \- Modified by E. Vigmond, September 1993 + + ----------------------------------------------------------------------------- + + In the process of working through this tutorial, you will learn + something about the Hodgkin-Huxley model. This program may serve as + a good starting point for those of you who plan to work on + single-cell models for a course project. + +** The Model + For the time being, we are going to simulate a single axon + compartment with active Na and K conductances, as described by Hodgkin + and Huxley for the squid giant axon. In other tutorials we will link + compartments together to form a simple model of an entire neuron with + a soma and dendrites (the Neuron tutorial), model a cable with many + compartments (the cable tutorial), and build neural circuits with + connected neurons (MultiCell and tritonia). For now, we confine + ourselves to a single axon compartment. + +** Running the Simulation + The model has already been initialized with some reasonable + parameter values, so all you have to do to run the simulation is: + + click on the ``Run`` button in the toolbar. + + The simulation which you just observed was for a constant current + pulse, which is shown in the lower left graph panel. The upper left + graph shows the membrane potential. You can see that 3 action + potentials were generated during this 50 msec simulation. Now let's + change the injection current and see what happens. + + At the bottom of the left panel is a widget labeled "Electronics" + and inside it there are two tabs labeled ``Current clamp`` and + ``Voltage clamp``. Select the ``Current clamp`` tab and you will + see a series of labeled text boxes with default values. In order + to change the injection current: + + position the cursor to the right of the last digit in the "First + Pulse Current" field and click in the text box with the left mouse + button. + + Let's change the peak injection current from 0.1 to 1.0. + + type to delete the 0.1 and then type 1.0 + + The value in the dialog field should now be 1.0. + + Now we'll run the simulation again. + + click the "Run" button on the toolbar again. + + There should be a dramatic change in the time-course of the + membrane potential at this higher current injection level. + Experiment with the injection level to see what happens to the + axon at higher injection currents. Also try decreasing the + injection level until an action potential is no longer elicited by + the stimulus. What is the threshold for producing an action + potential in this compartment? + + You may also experiment with trains of short pulses. Set the + "First Pulse Width" dialog field to 1 msec and click on the + "Single Pulse" drop down box and select "Pulse Train". Now vary + "First Onset Delay". What is the minimum interval between action + potentials that you can achieve? + +** Voltage Clamping + You can also perform voltage clamp experiments in this simulation. + + click on the "Voltage clamp" tab header at the bottom of the + control form under "Electronics". + + Again, reasonable default values have been selected , so all you + have to do to run the voltage clamp simulation is: + + click the "Run" button on the control form + +** Changing Extracellular Concentrations + You can alter the extracellular concentrations of the ions through + the "Channels" panel. Any changes in concentration will cause the + reversal potentials to be recalculated. To reset the values back + to the initial ones, just click on the "Restore defaults" button + in the top tool bar. + +** Controlling Graphs + The graph of the clamp current (lower left panel) has gone off + scale. In order to rescale the graph: + + click on the button with green tick mark in the navigation toolbar + at the bottom of the plots. + + A dialog containing drop-down to select the subplot should appear. + Select the "Injection current" and click OK. Another dialog box + will appear with text boxes for `Min` and `Max` values for X-Axis + and Y-Axis. Adjust for Y axis to bring the graph into range and + press "Apply". + + + The top toolbar has an "Overlay plots" button. When it is + checked, any existing plots in the graph will be held and new + simulation results will be overlayed. Try this now. + + Click "Overlay plots" and run the simulation at several values of + the clamp voltage. Do the first run with "Overlay plots" button + unchecked so that all previous graphs are cleared at this + run. Then click this button to checked state and do the subsequent + runs. + +** State Plots + One can learn a great deal by studying plots in which one of the + Hodgkin-Huxley channel activation parameters (the K activation + "n", the Na activation "m", or the Na inactivation "h") is plotted + as a function of the membrane potential, V. (See, for example, + Chapter 5 of "Methods in Neuronal Modeling", by Koch and Segev.) + + In order to view such a plot, click the left mouse button on the + button labeled "State plot" in the top toolbar. The label will + change to "State Plot Visible", and a state plot graph will + appear. Clicking the button again will hide the graph. The + default plot is to show the K channel "n" parameter on the y-axis + and the membrane potential on the x-axis. The drop-down menus at + the top of the window allow you to change these defaults. + +** Channel Blocking + In order to explore the effects of blocking one of the channels, + you may click on one of the check boxes in the "Channels" panel + for blocking and unblocking a channel. When a channel is blocked, + its conductance is set to zero. Activation parameters for a + blocked channel are still calculated and may be plotted, but are + relatively meaningless because they will have no effect on the + membrane potential. + +** Saving Graphs + You can save a graph to file by clicking the save button in the + navigation toolbar. In the file dialog you can select from several + formats including PDF, JPEG, PNG and SVG. + +** Units used in the simulation + Units: + | quantity | unit | + |-------------------------------+--------------| + | time | msec | + | length | um (microns) | + | potential | mV | + | conductance | mS (mmho) | + | resistance | kohm | + | capacitance | uF | + | specific axial resistance | kohm-cm | + | specific membrane conductance | mS/cm^2 | + | specific membrane capacitance | uF/cm^2 | + diff --git a/demos/squid/images/navigationtoolbar.jpg b/demos/squid/images/navigationtoolbar.jpg new file mode 100644 index 0000000..a7ba52a Binary files /dev/null and b/demos/squid/images/navigationtoolbar.jpg differ diff --git a/demos/squid/squid.py b/demos/squid/squid.py new file mode 100644 index 0000000..a8a75c7 --- /dev/null +++ b/demos/squid/squid.py @@ -0,0 +1,376 @@ +# squid.py --- +# +# Filename: squid.py +# Description: +# Author: Subhasis Ray +# Maintainer: +# Created: Mon Feb 13 11:35:11 2012 (+0530) +# Version: +# Last-Updated: Thu Sep 20 14:05:27 2012 (+0530) +# By: subha +# Update #: 771 +# URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# +# Rewrite of the squid demo for new moose. +# +# + +# Change log: +# +# +# + +# Code: +import sys +sys.path.append('../../python') + +import numpy +import moose + +GAS_CONSTANT = 8.314 +FARADAY = 9.65e4 +CELSIUS_TO_KELVIN = 273.15 + +class IonChannel(moose.HHChannel): + """Enhanced version of HHChannel with setupAlpha that takes a dict + of parameters.""" + def __init__(self, name, compartment, specific_gbar, e_rev, Xpower, Ypower=0.0, Zpower=0.0): + """Instantuate an ion channel. + + name -- name of the channel. + + compartment -- moose.Compartment object that contains the channel. + + specific_gbar -- specific value of maximum conductance. + + e_rev -- reversal potential of the channel. + + Xpower -- exponent for the first gating parameter. + + Ypower -- exponent for the second gatinmg component. + """ + moose.HHChannel.__init__(self, '%s/%s' % (compartment.path, name)) + self.Gbar = specific_gbar * compartment.area + self.Ek = e_rev + self.Xpower = Xpower + self.Ypower = Ypower + self.Zpower = Zpower + moose.connect(self, 'channel', compartment, 'channel') + + def setupAlpha(self, gate, params, vdivs, vmin, vmax): + """Setup alpha and beta parameters of specified gate. + + gate -- 'X'/'Y'/'Z' string initial of the gate. + + params -- dict of parameters to compute alpha and beta, the rate constants for gates. + + vdivs -- number of divisions in the interpolation tables for alpha and beta parameters. + + vmin -- minimum voltage value for the alpha/beta lookup tables. + + vmax -- maximum voltage value for the alpha/beta lookup tables. + """ + if gate == 'X' and self.Xpower > 0: + gate = moose.HHGate(self.path + '/gateX') + elif gate == 'Y' and self.Ypower > 0: + gate = moose.HHGate(self.path + '/gateY') + else: + return False + gate.setupAlpha([params['A_A'], + params['A_B'], + params['A_C'], + params['A_D'], + params['A_F'], + params['B_A'], + params['B_B'], + params['B_C'], + params['B_D'], + params['B_F'], + vdivs, vmin, vmax]) + return True + + @property + def alpha_m(self): + if self.Xpower == 0: + return numpy.array([]) + return numpy.array(moose.HHGate('%s/gateX' % (self.path)).tableA) + @property + def beta_m(self): + if self.Xpower == 0: + return numpy.array([]) + return numpy.array(moose.HHGate('%s/gateX' % (self.path)).tableB) - numpy.array(moose.HHGate('%s/gateX' % (self.path)).tableA) + @property + def alpha_h(self): + if self.Ypower == 0: + return numpy.array([]) + return numpy.array(moose.HHGate('%s/gateY' % (self.path)).tableA) + @property + def beta_h(self): + if self.Ypower == 0: + return numpy.array([]) + return numpy.array(moose.HHGate('%s/gateY' % (self.path)).tableB) - numpy.array(moose.HHGate('%s/gateY' % (self.path)).tableA) + +class SquidAxon(moose.Compartment): + EREST_ACT = 0.0 # can be -70 mV if not following original HH convention + VMIN = -30.0 + VMAX = 120.0 + VDIVS = 150 + defaults = { + 'temperature': CELSIUS_TO_KELVIN + 6.3, + 'K_out': 10.0, + 'Na_out': 460.0, + 'K_in': 301.4, + 'Na_in': 70.96, + 'Cl_out': 540.0, + 'Cl_in': 100.0, + 'length': 500, # um + 'diameter': 500, # um + 'Em': EREST_ACT + 10.613, + 'initVm': EREST_ACT, + 'specific_cm': 1.0, # uF/cm^2 + 'specific_gl': 0.3, # mmho/cm^2 + 'specific_ra': 0.030, # kohm-cm + 'specific_gNa': 120.0, # mmho/cm^2 + 'specific_gK': 36.0 # mmho/cm^2 + } + + Na_m_params = {'A_A':0.1 * (25.0 + EREST_ACT), + 'A_B': -0.1, + 'A_C': -1.0, + 'A_D': -25.0 - EREST_ACT, + 'A_F':-10.0, + 'B_A': 4.0, + 'B_B': 0.0, + 'B_C': 0.0, + 'B_D': 0.0 - EREST_ACT, + 'B_F': 18.0} + Na_h_params = {'A_A': 0.07, + 'A_B': 0.0, + 'A_C': 0.0, + 'A_D': 0.0 - EREST_ACT, + 'A_F': 20.0, + 'B_A': 1.0, + 'B_B': 0.0, + 'B_C': 1.0, + 'B_D': -30.0 - EREST_ACT, + 'B_F': -10.0} + K_n_params = {'A_A': 0.01*(10.0 + EREST_ACT), + 'A_B': -0.01, + 'A_C': -1.0, + 'A_D': -10.0 - EREST_ACT, + 'A_F': -10.0, + 'B_A': 0.125, + 'B_B': 0.0, + 'B_C': 0.0, + 'B_D': 0.0 - EREST_ACT, + 'B_F': 80.0} + """Compartment class enhanced with specific values of passive + electrical properties set and calculated using dimensions.""" + def __init__(self, path): + moose.Compartment.__init__(self, path) + self.temperature = SquidAxon.defaults['temperature'] + self.K_out = SquidAxon.defaults['K_out'] + self.Na_out = SquidAxon.defaults['Na_out'] + # Modified internal concentrations used to give HH values of + # equilibrium constants from the Nernst equation at 6.3 deg C. + # HH 1952a, p. 455 + self.K_in = SquidAxon.defaults['K_in'] + self.Na_in = SquidAxon.defaults['Na_in'] + self.Cl_out = SquidAxon.defaults['Cl_out'] + self.Cl_in = SquidAxon.defaults['Cl_in'] + + self.length = SquidAxon.defaults['length'] + self.diameter = SquidAxon.defaults['diameter'] + self.Em = SquidAxon.defaults['Em'] + self.initVm = SquidAxon.defaults['initVm'] + self.specific_cm = SquidAxon.defaults['specific_cm'] + self.specific_gl = SquidAxon.defaults['specific_gl'] + self.specific_ra = SquidAxon.defaults['specific_ra'] + + self.Na_channel = IonChannel('Na', self, + 0.0, + self.VNa, + Xpower=3.0, + Ypower=1.0) + self.Na_channel.setupAlpha('X', SquidAxon.Na_m_params, + SquidAxon.VDIVS, + SquidAxon.VMIN, + SquidAxon.VMAX) + self.Na_channel.setupAlpha('Y', SquidAxon.Na_h_params, + SquidAxon.VDIVS, + SquidAxon.VMIN, + SquidAxon.VMAX) + self.K_channel = IonChannel('K', self, + 0.0, + self.VK, + Xpower=4.0) + self.K_channel.setupAlpha('X', SquidAxon.K_n_params, + SquidAxon.VDIVS, + SquidAxon.VMIN, + SquidAxon.VMAX) + self.specific_gNa = SquidAxon.defaults['specific_gNa'] + self.specific_gK = SquidAxon.defaults['specific_gK'] + + @classmethod + def reversal_potential(cls, temp, c_out, c_in): + """Compute the reversal potential based on Nernst equation.""" + # NOTE the 70 mV added for compatibility with original HH + return (GAS_CONSTANT * temp / FARADAY) * 1000.0 * numpy.log(c_out/c_in) + 70.0 + cls.EREST_ACT + + + @property + def xarea(self): + """Area of cross section in cm^2 when length and diameter are in um""" + return 1e-8 * numpy.pi * self.diameter * self.diameter / 4.0 # cm^2 + + @property + def area(self): + """Area in cm^2 when length and diameter are in um""" + return 1e-8 * self.length * numpy.pi * self.diameter # cm^2 + + @property + def specific_ra(self): + return self.Ra * self.xarea / self.length + @specific_ra.setter + def specific_ra(self, value): + self.Ra = value * self.length / self.xarea + + @property + def specific_cm(self): + return self.Cm / self.area + @specific_cm.setter + def specific_cm(self, value): + self.Cm = value * self.area + + @property + def specific_gl(self): + return 1.0/(self.Rm * self.area) + @specific_gl.setter + def specific_gl(self, value): + self.Rm = 1.0/(value * self.area) + + @property + def specific_rm(self): + return self.Rm * self.area + @specific_rm.setter + def specific_rm(self, value): + self.Rm = value / self.area + + @property + def specific_gNa(self): + return self.Na_channel.Gbar / self.area + + @specific_gNa.setter + def specific_gNa(self, value): + self.Na_channel.Gbar = value * self.area + + @property + def specific_gK(self): + return self.K_channel.Gbar / self.area + + @specific_gK.setter + def specific_gK(self, value): + self.K_channel.Gbar = value * self.area + + @property + def VK(self): + """Reversal potential of K+ channels""" + return SquidAxon.reversal_potential(self.temperature, self.K_out, self.K_in) + + @property + def VNa(self): + """Reversal potential of Na+ channels""" + return SquidAxon.reversal_potential(self.temperature, self.Na_out, self.Na_in) + + def updateEk(self): + """Update the channels' Ek""" + self.Na_channel.Ek = self.VNa + self.K_channel.Ek = self.VK + + + @property + def celsius(self): + return self.temperature - CELSIUS_TO_KELVIN + + @celsius.setter + def celsius(self, celsius): + self.temperature = celsius + CELSIUS_TO_KELVIN + + def use_defaults(self): + for field, value in list(SquidAxon.defaults.items()): + setattr(self, field, value) + +class SquidModel(moose.Neutral): + """Container for squid demo.""" + def __init__(self, path): + moose.Neutral.__init__(self, path) + self.squid_axon = SquidAxon(path+'/squid_axon') + print(self.squid_axon.Na_channel.Gbar, self.squid_axon.K_channel.Gbar) + self.current_clamp = moose.PulseGen(path+'/pulsegen') + self.current_clamp.firstDelay = 5.0 # ms + self.current_clamp.firstWidth = 40 # ms + self.current_clamp.firstLevel = 0.1 # uA + self.current_clamp.secondDelay = 1e9 + print('Current clamp connected:', moose.connect(self.current_clamp, 'output', self.squid_axon, 'injectMsg')) + + self.Vm_table = moose.Table('%s/Vm' % (self.path)) + moose.connect(self.Vm_table, 'requestOut', self.squid_axon, 'getVm') + self.gK_table = moose.Table('%s/gK' % (self.path)) + moose.connect(self.gK_table, 'requestOut', self.squid_axon.K_channel, 'getGk') + self.gNa_table = moose.Table('%s/gNa' % (self.path)) + moose.connect(self.gNa_table, 'requestOut', self.squid_axon.Na_channel, 'getGk') + self.clocks_assigned = False + + def run(self, runtime, simdt=1e-6): + self.squid_axon.updateEk() + moose.setClock(0, simdt) + moose.setClock(1, simdt) + moose.setClock(2, simdt) + moose.setClock(3, simdt) + if not self.clocks_assigned: + moose.useClock(0, '%s/#[TYPE=Compartment]' % (self.path), 'init') + moose.useClock(0, '%s/#[TYPE=PulseGen]' % (self.path), 'process') + moose.useClock(1, '%s/#[TYPE=Compartment]' % (self.path), 'process') + moose.useClock(2, '%s/#[TYPE=HHChannel]' % (self.squid_axon.path), 'process') + moose.useClock(3, '%s/#[TYPE=Table]' % (self.path), 'process') + self.clocks_assigned = True + moose.reinit() + moose.start(runtime) + + def save_data(self): + self.Vm_table.xplot('Vm.dat', 'Vm') + print('Vm saved to Vm.dat') + if hasattr(self, 'gK_table'): + self.gK_table.xplot('gK.dat', 'gK') + numpy.savetxt('K_alpha_n.dat', self.squid_axon.K_channel.alpha_m) + numpy.savetxt('K_beta_n.dat', self.squid_axon.K_channel.beta_m) + print('K conductance saved to gK.dat') + if hasattr(self, 'gNa_table'): + self.gNa_table.xplot('gNa.dat', 'gNa') + numpy.savetxt('Na_alpha_m.dat', self.squid_axon.Na_channel.alpha_m) + numpy.savetxt('Na_beta_m.dat', self.squid_axon.Na_channel.beta_m) + numpy.savetxt('Na_alpha_h.dat', self.squid_axon.Na_channel.alpha_h) + numpy.savetxt('Na_beta_h.dat', self.squid_axon.Na_channel.beta_h) + print('Na conductance saved to gNa.dat') + + + +def test(runtime=100.0, simdt=1e-2): + model = SquidModel('model') + model.run(runtime, simdt) + model.save_data() + +if __name__ == '__main__': + # unittest.main() + test() + + + +# +# squid.py ends here diff --git a/demos/squid/squid_demo.py b/demos/squid/squid_demo.py new file mode 100644 index 0000000..9e9344a --- /dev/null +++ b/demos/squid/squid_demo.py @@ -0,0 +1,899 @@ +#!/usr/bin/env python + # -*- coding: utf-8 -*- +# squidgui.py --- +# +# Filename: squidgui.py +# Description: +# Author: +# Maintainer: +# Created: Mon Jul 9 18:23:55 2012 (+0530) +# Version: +# Last-Updated: Tue May 3 00:18:47 2016 (-0400) +# By: subha +# Update #: 1078 +# URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# +# +# +# + +# Change log: +# +# +# +# +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License as +# published by the Free Software Foundation; either version 3, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; see the file COPYING. If not, write to +# the Free Software Foundation, Inc., 51 Franklin Street, Fifth +# Floor, Boston, MA 02110-1301, USA. +# +# + +# Code: + +import sys +sys.path.append('../../python') +import os +os.environ['NUMPTHREADS'] = '1' + +from collections import defaultdict +import time + +from PyQt5 import QtGui +from PyQt5 import QtCore +import numpy +from matplotlib.figure import Figure +from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas, NavigationToolbar2QT as NavigationToolbar + +import moose + +from squid import * +from squid_setup import SquidSetup +from electronics import ClampCircuit + + +tooltip_Nernst = """

Ionic equilibrium potential

+

+The equilibrium potential for ion C is given by Nernst equation: +

+EC = (RT/zF) * ln([C]out / [C]in) +

+where R is the ideal gas constant (8.3145 J/mol K),
+ T is absolute temperature,
+ z is the valence of the ion,
+ F is Faraday's constant 96480 C/mol,
+ [C]out is concentration of C outside the membrane,
+ [C]in is concentration of C inside the membrane.""" + +tooltip_Erest = """

Resting membrane potential

+

+The resting membrane potential is determined by the ionic +concentrations inside and outside the cell membrane and is given by +the Goldman-Hodgkin-Katz equation: +

+ +V = (RT/F) * ln((PK[K+]out + PNa[Na+]out + PCl[Cl-]in) / (PK[K+]in + PNa[Na+]in + PCl[Cl-]out)) + +

+where PC is the permeability of the membrane to ion C. + +""" + +tooltip_NaChan = """

Na+ channel conductance

+

+The Na+ channel conductance in squid giant axon is given by: + +

GNa = GÌ„Na * m3 * h

+ +and the current through this channel is: +

+INa = GNa * (V - ENa) = GÌ„Na * m3 * h * (V - ENa) +

+ +where GÌ„Na is the peak conductance of Na+ channel, m is +the fraction of activation gates open and h is the fraction of +deactivation gates open. The transition from open to closed state has +first order kinetics: +

dm/dt = αm * ( 1 - m) - βm * m

+and similarly for h. + +The steady state values are: +

m∞ = αm/(αm + βm)

+and time constant for steady state is: +

τm = 1/ (αm + βm)

+and similarly for h. +""" + +tooltip_KChan = """

K+ channel conductance

+

The K+ channel conductance in squid giant axon is given by: + +

GK = GÌ„K * n4

+ +and the current through this channel is: +

+IK = GK * (V - EK) = GÌ„K * n4 * (V - EK) +

+where GÌ„K is the peak conductance of K+ channel, +n is the fraction of activation gates open. The transition from open +to closed state has first order kinetics:

dn/dt = αn * +( 1 - n) - βn * n

. + +The steady state values are: +

+n∞ = αn/(αn + βn) +

+and time constant for steady state is: +

+τn = 1/ (αn + βn) + +

+and similarly for h. +""" + +tooltip_Im = """

Membrane current

+

+The current through the membrane is given by: +

+Im = Cm dV/dt + IK + INa + IL +

+ = Cm dV/dt + GK(V, t) * (V - EK) + GNa * (V - ENa) + GL * (V - EL) +

+where GL is the leak current and EL is the leak reversal potential. + +""" + +default_line_edit_size = QtCore.QSize(80, 25) +def set_default_line_edit_size(widget): + widget.setMinimumSize(default_line_edit_size) + widget.setMaximumSize(default_line_edit_size) + + +class SquidGui(QtGui.QMainWindow): + defaults = {} + defaults.update(SquidAxon.defaults) + defaults.update(ClampCircuit.defaults) + defaults.update({'runtime': 50.0, + 'simdt': 0.01, + 'plotdt': 0.1, + 'vclamp.holdingV': 0.0, + 'vclamp.holdingT': 10.0, + 'vclamp.prepulseV': 0.0, + 'vclamp.prepulseT': 0.0, + 'vclamp.clampV': 50.0, + 'vclamp.clampT': 20.0, + 'iclamp.baseI': 0.0, + 'iclamp.firstI': 0.1, + 'iclamp.firstT': 40.0, + 'iclamp.firstD': 5.0, + 'iclamp.secondI': 0.0, + 'iclamp.secondT': 0.0, + 'iclamp.secondD': 0.0 + }) + def __init__(self, *args): + QtGui.QMainWindow.__init__(self, *args) + self.squid_setup = SquidSetup() + self._plotdt = SquidGui.defaults['plotdt'] + self._plot_dict = defaultdict(list) + self.setWindowTitle('Squid Axon simulation') + self.setDockNestingEnabled(True) + self._createRunControl() + self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._runControlDock) + self._runControlDock.setFeatures(QtGui.QDockWidget.AllDockWidgetFeatures) + self._createChannelControl() + self._channelCtrlBox.setWindowTitle('Channel properties') + self._channelControlDock.setFeatures(QtGui.QDockWidget.AllDockWidgetFeatures) + self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._channelControlDock) + self._createElectronicsControl() + self._electronicsDock.setFeatures(QtGui.QDockWidget.AllDockWidgetFeatures) + self._electronicsDock.setWindowTitle('Electronics') + self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._electronicsDock) + self._createPlotWidget() + self.setCentralWidget(self._plotWidget) + self._createStatePlotWidget() + self._createHelpMessage() + self._helpWindow.setVisible(False) + self._statePlotWidget.setWindowFlags(QtCore.Qt.Window) + self._statePlotWidget.setWindowTitle('State plot') + self._initActions() + self._createRunToolBar() + self._createPlotToolBar() + + def getFloatInput(self, widget, name): + try: + return float(str(widget.text())) + except ValueError: + QtGui.QMessageBox.critical(self, 'Invalid input', 'Please enter a valid number for {}'.format(name)) + raise + + + def _createPlotWidget(self): + self._plotWidget = QtGui.QWidget() + self._plotFigure = Figure() + self._plotCanvas = FigureCanvas(self._plotFigure) + self._plotCanvas.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding) + self._plotCanvas.updateGeometry() + self._plotCanvas.setParent(self._plotWidget) + self._plotCanvas.mpl_connect('scroll_event', self._onScroll) + self._plotFigure.set_canvas(self._plotCanvas) + # Vm and command voltage go in the same subplot + self._vm_axes = self._plotFigure.add_subplot(2,2,1, title='Membrane potential') + self._vm_axes.set_ylim(-20.0, 120.0) + # Channel conductances go to the same subplot + self._g_axes = self._plotFigure.add_subplot(2,2,2, title='Channel conductance') + self._g_axes.set_ylim(0.0, 0.5) + # Injection current for Vclamp/Iclamp go to the same subplot + self._im_axes = self._plotFigure.add_subplot(2,2,3, title='Injection current') + self._im_axes.set_ylim(-0.5, 0.5) + # Channel currents go to the same subplot + self._i_axes = self._plotFigure.add_subplot(2,2,4, title='Channel current') + self._i_axes.set_ylim(-10, 10) + for axis in self._plotFigure.axes: + axis.set_autoscale_on(False) + layout = QtGui.QVBoxLayout() + layout.addWidget(self._plotCanvas) + self._plotNavigator = NavigationToolbar(self._plotCanvas, self._plotWidget) + layout.addWidget(self._plotNavigator) + self._plotWidget.setLayout(layout) + + def _createStatePlotWidget(self): + self._statePlotWidget = QtGui.QWidget() + self._statePlotFigure = Figure() + self._statePlotCanvas = FigureCanvas(self._statePlotFigure) + self._statePlotCanvas.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding) + self._statePlotCanvas.updateGeometry() + self._statePlotCanvas.setParent(self._statePlotWidget) + self._statePlotFigure.set_canvas(self._statePlotCanvas) + self._statePlotFigure.subplots_adjust(hspace=0.5) + self._statePlotAxes = self._statePlotFigure.add_subplot(2,1,1, title='State plot') + self._state_plot, = self._statePlotAxes.plot([], [], label='state') + self._activationParamAxes = self._statePlotFigure.add_subplot(2,1,2, title='H-H activation parameters vs time') + self._activationParamAxes.set_xlabel('Time (ms)') + #for axis in self._plotFigure.axes: + # axis.autoscale(False) + self._stateplot_xvar_label = QtGui.QLabel('Variable on X-axis') + self._stateplot_xvar_combo = QtGui.QComboBox() + self._stateplot_xvar_combo.addItems(['V', 'm', 'n', 'h']) + self._stateplot_xvar_combo.setCurrentIndex(0) + self._stateplot_xvar_combo.setEditable(False) + self.connect(self._stateplot_xvar_combo, + QtCore.SIGNAL('currentIndexChanged(const QString&)'), + self._statePlotXSlot) + self._stateplot_yvar_label = QtGui.QLabel('Variable on Y-axis') + self._stateplot_yvar_combo = QtGui.QComboBox() + self._stateplot_yvar_combo.addItems(['V', 'm', 'n', 'h']) + self._stateplot_yvar_combo.setCurrentIndex(2) + self._stateplot_yvar_combo.setEditable(False) + self.connect(self._stateplot_yvar_combo, + QtCore.SIGNAL('currentIndexChanged(const QString&)'), + self._statePlotYSlot) + self._statePlotNavigator = NavigationToolbar(self._statePlotCanvas, self._statePlotWidget) + frame = QtGui.QFrame() + frame.setFrameStyle(QtGui.QFrame.StyledPanel + QtGui.QFrame.Raised) + layout = QtGui.QHBoxLayout() + layout.addWidget(self._stateplot_xvar_label) + layout.addWidget(self._stateplot_xvar_combo) + layout.addWidget(self._stateplot_yvar_label) + layout.addWidget(self._stateplot_yvar_combo) + frame.setLayout(layout) + self._closeStatePlotAction = QtGui.QAction('Close', self) + self.connect(self._closeStatePlotAction, QtCore.SIGNAL('triggered()'), self._statePlotWidget.close) + self._closeStatePlotButton = QtGui.QToolButton() + self._closeStatePlotButton.setDefaultAction(self._closeStatePlotAction) + layout = QtGui.QVBoxLayout() + layout.addWidget(frame) + layout.addWidget(self._statePlotCanvas) + layout.addWidget(self._statePlotNavigator) + layout.addWidget(self._closeStatePlotButton) + self._statePlotWidget.setLayout(layout) + # Setting the close event so that when the help window is + # closed the ``State plot`` button becomes unchecked + self._statePlotWidget.closeEvent = lambda event: self._showStatePlotAction.setChecked(False) + + def _createRunControl(self): + self._runControlBox = QtGui.QGroupBox(self) + self._runControlBox.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred) + self._runTimeLabel = QtGui.QLabel("Run time (ms)", self._runControlBox) + self._simTimeStepLabel = QtGui.QLabel("Simulation time step (ms)", self._runControlBox) + self._runTimeEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['runtime']), self._runControlBox) + set_default_line_edit_size(self._runTimeEdit) + self._simTimeStepEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['simdt']), self._runControlBox) + set_default_line_edit_size(self._simTimeStepEdit) + layout = QtGui.QGridLayout() + layout.addWidget(self._runTimeLabel, 0, 0) + layout.addWidget(self._runTimeEdit, 0, 1) + layout.addWidget(self._simTimeStepLabel, 1, 0) + layout.addWidget(self._simTimeStepEdit, 1, 1) + layout.setColumnStretch(2, 1.0) + layout.setRowStretch(2, 1.0) + self._runControlBox.setLayout(layout) + self._runControlDock = QtGui.QDockWidget('Simulation', self) + self._runControlDock.setWidget(self._runControlBox) + + def _createChannelControl(self): + self._channelControlDock = QtGui.QDockWidget('Channels', self) + self._channelCtrlBox = QtGui.QGroupBox(self) + self._naConductanceToggle = QtGui.QCheckBox('Block Na+ channel', self._channelCtrlBox) + self._naConductanceToggle.setToolTip('%s' % (tooltip_NaChan)) + self._kConductanceToggle = QtGui.QCheckBox('Block K+ channel', self._channelCtrlBox) + self._kConductanceToggle.setToolTip('%s' % (tooltip_KChan)) + self._kOutLabel = QtGui.QLabel('[K+]out (mM)', self._channelCtrlBox) + self._kOutEdit = QtGui.QLineEdit('%g' % (self.squid_setup.squid_axon.K_out), + self._channelCtrlBox) + self._kOutLabel.setToolTip('%s' % (tooltip_Nernst)) + self._kOutEdit.setToolTip('%s' % (tooltip_Nernst)) + set_default_line_edit_size(self._kOutEdit) + self._naOutLabel = QtGui.QLabel('[Na+]out (mM)', self._channelCtrlBox) + self._naOutEdit = QtGui.QLineEdit('%g' % (self.squid_setup.squid_axon.Na_out), + self._channelCtrlBox) + self._naOutLabel.setToolTip('%s' % (tooltip_Nernst)) + self._naOutEdit.setToolTip('%s' % (tooltip_Nernst)) + set_default_line_edit_size(self._naOutEdit) + self._kInLabel = QtGui.QLabel('[K+]in (mM)', self._channelCtrlBox) + self._kInEdit = QtGui.QLineEdit('%g' % (self.squid_setup.squid_axon.K_in), + self._channelCtrlBox) + self._kInEdit.setToolTip(tooltip_Nernst) + self._naInLabel = QtGui.QLabel('[Na+]in (mM)', self._channelCtrlBox) + self._naInEdit = QtGui.QLineEdit('%g' % (self.squid_setup.squid_axon.Na_in), + self._channelCtrlBox) + self._naInEdit.setToolTip('%s' % (tooltip_Nernst)) + self._temperatureLabel = QtGui.QLabel('Temperature (C)', self._channelCtrlBox) + self._temperatureEdit = QtGui.QLineEdit('%g' % (self.defaults['temperature'] - CELSIUS_TO_KELVIN), + self._channelCtrlBox) + self._temperatureEdit.setToolTip('%s' % (tooltip_Nernst)) + set_default_line_edit_size(self._temperatureEdit) + for child in self._channelCtrlBox.children(): + if isinstance(child, QtGui.QLineEdit): + set_default_line_edit_size(child) + layout = QtGui.QGridLayout(self._channelCtrlBox) + layout.addWidget(self._naConductanceToggle, 0, 0) + layout.addWidget(self._kConductanceToggle, 1, 0) + layout.addWidget(self._naOutLabel, 2, 0) + layout.addWidget(self._naOutEdit, 2, 1) + layout.addWidget(self._naInLabel, 3, 0) + layout.addWidget(self._naInEdit, 3, 1) + layout.addWidget(self._kOutLabel, 4, 0) + layout.addWidget(self._kOutEdit, 4, 1) + layout.addWidget(self._kInLabel, 5, 0) + layout.addWidget(self._kInEdit, 5, 1) + layout.addWidget(self._temperatureLabel, 6, 0) + layout.addWidget(self._temperatureEdit, 6, 1) + layout.setRowStretch(7, 1.0) + self._channelCtrlBox.setLayout(layout) + self._channelControlDock.setWidget(self._channelCtrlBox) + return self._channelCtrlBox + + def __get_stateplot_data(self, name): + data = [] + if name == 'V': + data = self.squid_setup.vm_table.vector + elif name == 'm': + data = self.squid_setup.m_table.vector + elif name == 'h': + data = self.squid_setup.h_table.vector + elif name == 'n': + data = self.squid_setup.n_table.vector + else: + raise ValueError('Unrecognized selection: %s' % (name)) + return numpy.asarray(data) + + def _statePlotYSlot(self, selectedItem): + ydata = self.__get_stateplot_data(str(selectedItem)) + self._state_plot.set_ydata(ydata) + self._statePlotAxes.set_ylabel(selectedItem) + if str(selectedItem) == 'V': + self._statePlotAxes.set_ylim(-20, 120) + else: + self._statePlotAxes.set_ylim(0, 1) + self._statePlotCanvas.draw() + + def _statePlotXSlot(self, selectedItem): + xdata = self.__get_stateplot_data(str(selectedItem)) + self._state_plot.set_xdata(xdata) + self._statePlotAxes.set_xlabel(selectedItem) + if str(selectedItem) == 'V': + self._statePlotAxes.set_xlim(-20, 120) + else: + self._statePlotAxes.set_xlim(0, 1) + self._statePlotCanvas.draw() + + def _createElectronicsControl(self): + """Creates a tabbed widget of voltage clamp and current clamp controls""" + self._electronicsTab = QtGui.QTabWidget(self) + self._electronicsTab.addTab(self._getIClampCtrlBox(), 'Current clamp') + self._electronicsTab.addTab(self._getVClampCtrlBox(), 'Voltage clamp') + self._electronicsDock = QtGui.QDockWidget(self) + self._electronicsDock.setWidget(self._electronicsTab) + + def _getVClampCtrlBox(self): + vClampPanel = QtGui.QGroupBox(self) + self._vClampCtrlBox = vClampPanel + self._holdingVLabel = QtGui.QLabel("Holding Voltage (mV)", vClampPanel) + self._holdingVEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['vclamp.holdingV']), vClampPanel) + self._holdingTimeLabel = QtGui.QLabel("Holding Time (ms)", vClampPanel) + self._holdingTimeEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['vclamp.holdingT']), vClampPanel) + self._prePulseVLabel = QtGui.QLabel("Pre-pulse Voltage (mV)", vClampPanel) + self._prePulseVEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['vclamp.prepulseV']), vClampPanel) + self._prePulseTimeLabel = QtGui.QLabel("Pre-pulse Time (ms)", vClampPanel) + self._prePulseTimeEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['vclamp.prepulseT']), vClampPanel) + self._clampVLabel = QtGui.QLabel("Clamp Voltage (mV)", vClampPanel) + self._clampVEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['vclamp.clampV']), vClampPanel) + self._clampTimeLabel = QtGui.QLabel("Clamp Time (ms)", vClampPanel) + self._clampTimeEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['vclamp.clampT']), vClampPanel) + for child in vClampPanel.children(): + if isinstance(child, QtGui.QLineEdit): + set_default_line_edit_size(child) + layout = QtGui.QGridLayout(vClampPanel) + layout.addWidget(self._holdingVLabel, 0, 0) + layout.addWidget(self._holdingVEdit, 0, 1) + layout.addWidget(self._holdingTimeLabel, 1, 0) + layout.addWidget(self._holdingTimeEdit, 1, 1) + layout.addWidget(self._prePulseVLabel, 2, 0) + layout.addWidget(self._prePulseVEdit, 2, 1) + layout.addWidget(self._prePulseTimeLabel,3,0) + layout.addWidget(self._prePulseTimeEdit, 3, 1) + layout.addWidget(self._clampVLabel, 4, 0) + layout.addWidget(self._clampVEdit, 4, 1) + layout.addWidget(self._clampTimeLabel, 5, 0) + layout.addWidget(self._clampTimeEdit, 5, 1) + layout.setRowStretch(6, 1.0) + vClampPanel.setLayout(layout) + return self._vClampCtrlBox + + def _getIClampCtrlBox(self): + iClampPanel = QtGui.QGroupBox(self) + self._iClampCtrlBox = iClampPanel + self._baseCurrentLabel = QtGui.QLabel("Base Current Level (uA)",iClampPanel) + self._baseCurrentEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['iclamp.baseI']),iClampPanel) + self._firstPulseLabel = QtGui.QLabel("First Pulse Current (uA)", iClampPanel) + self._firstPulseEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['iclamp.firstI']), iClampPanel) + self._firstDelayLabel = QtGui.QLabel("First Onset Delay (ms)", iClampPanel) + self._firstDelayEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['iclamp.firstD']),iClampPanel) + self._firstPulseWidthLabel = QtGui.QLabel("First Pulse Width (ms)", iClampPanel) + self._firstPulseWidthEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['iclamp.firstT']), iClampPanel) + self._secondPulseLabel = QtGui.QLabel("Second Pulse Current (uA)", iClampPanel) + self._secondPulseEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['iclamp.secondI']), iClampPanel) + self._secondDelayLabel = QtGui.QLabel("Second Onset Delay (ms)", iClampPanel) + self._secondDelayEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['iclamp.secondD']),iClampPanel) + self._secondPulseWidthLabel = QtGui.QLabel("Second Pulse Width (ms)", iClampPanel) + self._secondPulseWidthEdit = QtGui.QLineEdit('%g' % (SquidGui.defaults['iclamp.secondT']), iClampPanel) + self._pulseMode = QtGui.QComboBox(iClampPanel) + self._pulseMode.addItem("Single Pulse") + self._pulseMode.addItem("Pulse Train") + for child in iClampPanel.children(): + if isinstance(child, QtGui.QLineEdit): + set_default_line_edit_size(child) + layout = QtGui.QGridLayout(iClampPanel) + layout.addWidget(self._baseCurrentLabel, 0, 0) + layout.addWidget(self._baseCurrentEdit, 0, 1) + layout.addWidget(self._firstPulseLabel, 1, 0) + layout.addWidget(self._firstPulseEdit, 1, 1) + layout.addWidget(self._firstDelayLabel, 2, 0) + layout.addWidget(self._firstDelayEdit, 2, 1) + layout.addWidget(self._firstPulseWidthLabel, 3, 0) + layout.addWidget(self._firstPulseWidthEdit, 3, 1) + layout.addWidget(self._secondPulseLabel, 4, 0) + layout.addWidget(self._secondPulseEdit, 4, 1) + layout.addWidget(self._secondDelayLabel, 5, 0) + layout.addWidget(self._secondDelayEdit, 5, 1) + layout.addWidget(self._secondPulseWidthLabel, 6, 0) + layout.addWidget(self._secondPulseWidthEdit, 6, 1) + layout.addWidget(self._pulseMode, 7, 0, 1, 2) + layout.setRowStretch(8, 1.0) + # layout.setSizeConstraint(QtGui.QLayout.SetFixedSize) + iClampPanel.setLayout(layout) + return self._iClampCtrlBox + + def _overlayPlots(self, overlay): + if not overlay: + for axis in (self._plotFigure.axes + self._statePlotFigure.axes): + title = axis.get_title() + axis.clear() + axis.set_title(title) + suffix = '' + else: + suffix = '_%d' % (len(self._plot_dict['vm'])) + self._vm_axes.set_xlim(0.0, self._runtime) + self._g_axes.set_xlim(0.0, self._runtime) + self._im_axes.set_xlim(0.0, self._runtime) + self._i_axes.set_xlim(0.0, self._runtime) + self._vm_plot, = self._vm_axes.plot([], [], label='Vm%s'%(suffix)) + self._plot_dict['vm'].append(self._vm_plot) + self._command_plot, = self._vm_axes.plot([], [], label='command%s'%(suffix)) + self._plot_dict['command'].append(self._command_plot) + # Channel conductances go to the same subplot + self._gna_plot, = self._g_axes.plot([], [], label='Na%s'%(suffix)) + self._plot_dict['gna'].append(self._gna_plot) + self._gk_plot, = self._g_axes.plot([], [], label='K%s'%(suffix)) + self._plot_dict['gk'].append(self._gk_plot) + # Injection current for Vclamp/Iclamp go to the same subplot + self._iclamp_plot, = self._im_axes.plot([], [], label='Iclamp%s'%(suffix)) + self._vclamp_plot, = self._im_axes.plot([], [], label='Vclamp%s'%(suffix)) + self._plot_dict['iclamp'].append(self._iclamp_plot) + self._plot_dict['vclamp'].append(self._vclamp_plot) + # Channel currents go to the same subplot + self._ina_plot, = self._i_axes.plot([], [], label='Na%s'%(suffix)) + self._plot_dict['ina'].append(self._ina_plot) + self._ik_plot, = self._i_axes.plot([], [], label='K%s'%(suffix)) + self._plot_dict['ik'].append(self._ik_plot) + # self._i_axes.legend() + # State plots + self._state_plot, = self._statePlotAxes.plot([], [], label='state%s'%(suffix)) + self._plot_dict['state'].append(self._state_plot) + self._m_plot, = self._activationParamAxes.plot([],[], label='m%s'%(suffix)) + self._h_plot, = self._activationParamAxes.plot([], [], label='h%s'%(suffix)) + self._n_plot, = self._activationParamAxes.plot([], [], label='n%s'%(suffix)) + self._plot_dict['m'].append(self._m_plot) + self._plot_dict['h'].append(self._h_plot) + self._plot_dict['n'].append(self._n_plot) + if self._showLegendAction.isChecked(): + for axis in (self._plotFigure.axes + self._statePlotFigure.axes): + axis.legend() + + def _updateAllPlots(self): + self._updatePlots() + self._updateStatePlot() + + def _updatePlots(self): + if len(self.squid_setup.vm_table.vector) <= 0: + return + vm = numpy.asarray(self.squid_setup.vm_table.vector) + cmd = numpy.asarray(self.squid_setup.cmd_table.vector) + ik = numpy.asarray(self.squid_setup.ik_table.vector) + ina = numpy.asarray(self.squid_setup.ina_table.vector) + iclamp = numpy.asarray(self.squid_setup.iclamp_table.vector) + vclamp = numpy.asarray(self.squid_setup.vclamp_table.vector) + gk = numpy.asarray(self.squid_setup.gk_table.vector) + gna = numpy.asarray(self.squid_setup.gna_table.vector) + time_series = numpy.linspace(0, self._plotdt * len(vm), len(vm)) + self._vm_plot.set_data(time_series, vm) + time_series = numpy.linspace(0, self._plotdt * len(cmd), len(cmd)) + self._command_plot.set_data(time_series, cmd) + time_series = numpy.linspace(0, self._plotdt * len(ik), len(ik)) + self._ik_plot.set_data(time_series, ik) + time_series = numpy.linspace(0, self._plotdt * len(ina), len(ina)) + self._ina_plot.set_data(time_series, ina) + time_series = numpy.linspace(0, self._plotdt * len(iclamp), len(iclamp)) + self._iclamp_plot.set_data(time_series, iclamp) + time_series = numpy.linspace(0, self._plotdt * len(vclamp), len(vclamp)) + self._vclamp_plot.set_data(time_series, vclamp) + time_series = numpy.linspace(0, self._plotdt * len(gk), len(gk)) + self._gk_plot.set_data(time_series, gk) + time_series = numpy.linspace(0, self._plotdt * len(gna), len(gna)) + self._gna_plot.set_data(time_series, gna) + # self._vm_axes.margins(y=0.1) + # self._g_axes.margin(y=0.1) + # self._im_axes.margins(y=0.1) + # self._i_axes.margins(y=0.1) + if self._autoscaleAction.isChecked(): + for axis in self._plotFigure.axes: + axis.relim() + axis.margins(0.1, 0.1) + axis.autoscale_view(tight=True) + else: + self._vm_axes.set_ylim(-20.0, 120.0) + self._g_axes.set_ylim(0.0, 0.5) + self._im_axes.set_ylim(-0.5, 0.5) + self._i_axes.set_ylim(-10, 10) + self._vm_axes.set_xlim(0.0, time_series[-1]) + self._g_axes.set_xlim(0.0, time_series[-1]) + self._im_axes.set_xlim(0.0, time_series[-1]) + self._i_axes.set_xlim(0.0, time_series[-1]) + self._plotCanvas.draw() + + def _updateStatePlot(self): + if len(self.squid_setup.vm_table.vector) <= 0: + return + sx = str(self._stateplot_xvar_combo.currentText()) + sy = str(self._stateplot_yvar_combo.currentText()) + xdata = self.__get_stateplot_data(sx) + ydata = self.__get_stateplot_data(sy) + minlen = min(len(xdata), len(ydata)) + self._state_plot.set_data(xdata[:minlen], ydata[:minlen]) + self._statePlotAxes.set_xlabel(sx) + self._statePlotAxes.set_ylabel(sy) + if sx == 'V': + self._statePlotAxes.set_xlim(-20, 120) + else: + self._statePlotAxes.set_xlim(0, 1) + if sy == 'V': + self._statePlotAxes.set_ylim(-20, 120) + else: + self._statePlotAxes.set_ylim(0, 1) + self._activationParamAxes.set_xlim(0, self._runtime) + m = self.__get_stateplot_data('m') + n = self.__get_stateplot_data('n') + h = self.__get_stateplot_data('h') + time_series = numpy.linspace(0, self._plotdt*len(m), len(m)) + self._m_plot.set_data(time_series, m) + time_series = numpy.linspace(0, self._plotdt*len(h), len(h)) + self._h_plot.set_data(time_series, h) + time_series = numpy.linspace(0, self._plotdt*len(n), len(n)) + self._n_plot.set_data(time_series, n) + if self._autoscaleAction.isChecked(): + for axis in self._statePlotFigure.axes: + axis.relim() + axis.set_autoscale_on(True) + axis.autoscale_view(True) + self._statePlotCanvas.draw() + + def _runSlot(self): + if moose.isRunning(): + print('Stopping simulation in progress ...') + moose.stop() + self._runtime = self.getFloatInput(self._runTimeEdit, self._runTimeLabel.text()) + self._overlayPlots(self._overlayAction.isChecked()) + self._simdt = self.getFloatInput(self._simTimeStepEdit, self._simTimeStepLabel.text()) + clampMode = None + singlePulse = True + if self._electronicsTab.currentWidget() == self._vClampCtrlBox: + clampMode = 'vclamp' + baseLevel = self.getFloatInput(self._holdingVEdit, self._holdingVLabel.text()) + firstDelay = self.getFloatInput(self._holdingTimeEdit, self._holdingTimeLabel.text()) + firstWidth = self.getFloatInput(self._prePulseTimeEdit, self._prePulseTimeLabel.text()) + firstLevel = self.getFloatInput(self._prePulseVEdit, self._prePulseVLabel.text()) + secondDelay = firstWidth + secondWidth = self.getFloatInput(self._clampTimeEdit, self._clampTimeLabel.text()) + secondLevel = self.getFloatInput(self._clampVEdit, self._clampVLabel.text()) + if not self._autoscaleAction.isChecked(): + self._im_axes.set_ylim(-10.0, 10.0) + else: + clampMode = 'iclamp' + baseLevel = self.getFloatInput(self._baseCurrentEdit, self._baseCurrentLabel.text()) + firstDelay = self.getFloatInput(self._firstDelayEdit, self._firstDelayLabel.text()) + firstWidth = self.getFloatInput(self._firstPulseWidthEdit, self._firstPulseWidthLabel.text()) + firstLevel = self.getFloatInput(self._firstPulseEdit, self._firstPulseLabel.text()) + secondDelay = self.getFloatInput(self._secondDelayEdit, self._secondDelayLabel.text()) + secondLevel = self.getFloatInput(self._secondPulseEdit, self._secondPulseLabel.text()) + secondWidth = self.getFloatInput(self._secondPulseWidthEdit, self._secondPulseWidthLabel.text()) + singlePulse = (self._pulseMode.currentIndex() == 0) + if not self._autoscaleAction.isChecked(): + self._im_axes.set_ylim(-0.4, 0.4) + self.squid_setup.clamp_ckt.configure_pulses(baseLevel=baseLevel, + firstDelay=firstDelay, + firstWidth=firstWidth, + firstLevel=firstLevel, + secondDelay=secondDelay, + secondWidth=secondWidth, + secondLevel=secondLevel, + singlePulse=singlePulse) + if self._kConductanceToggle.isChecked(): + self.squid_setup.squid_axon.specific_gK = 0.0 + else: + self.squid_setup.squid_axon.specific_gK = SquidAxon.defaults['specific_gK'] + if self._naConductanceToggle.isChecked(): + self.squid_setup.squid_axon.specific_gNa = 0.0 + else: + self.squid_setup.squid_axon.specific_gNa = SquidAxon.defaults['specific_gNa'] + self.squid_setup.squid_axon.celsius = self.getFloatInput(self._temperatureEdit, self._temperatureLabel.text()) + self.squid_setup.squid_axon.K_out = self.getFloatInput(self._kOutEdit, self._kOutLabel.text()) + self.squid_setup.squid_axon.Na_out = self.getFloatInput(self._naOutEdit, self._naOutLabel.text()) + self.squid_setup.squid_axon.K_in = self.getFloatInput(self._kInEdit, self._kInLabel.text()) + self.squid_setup.squid_axon.Na_in = self.getFloatInput(self._naInEdit, self._naInLabel.text()) + self.squid_setup.squid_axon.updateEk() + self.squid_setup.schedule(self._simdt, self._plotdt, clampMode) + # The following line is for use with Qthread + self.squid_setup.run(self._runtime) + self._updateAllPlots() + + def _toggleDocking(self, on): + self._channelControlDock.setFloating(on) + self._electronicsDock.setFloating(on) + self._runControlDock.setFloating(on) + + def _restoreDocks(self): + self._channelControlDock.setVisible(True) + self._electronicsDock.setVisible(True) + self._runControlDock.setVisible(True) + + def _initActions(self): + self._runAction = QtGui.QAction(self.tr('Run'), self) + self._runAction.setShortcut(self.tr('F5')) + self._runAction.setToolTip('Run simulation (F5)') + self.connect(self._runAction, QtCore.SIGNAL('triggered()'), self._runSlot) + self._resetToDefaultsAction = QtGui.QAction(self.tr('Restore defaults'), self) + self._resetToDefaultsAction.setToolTip('Reset all settings to their default values') + self.connect(self._resetToDefaultsAction, QtCore.SIGNAL('triggered()'), self._useDefaults) + self._showLegendAction = QtGui.QAction(self.tr('Display legend'), self) + self._showLegendAction.setCheckable(True) + self.connect(self._showLegendAction, QtCore.SIGNAL('toggled(bool)'), self._showLegend) + self._showStatePlotAction = QtGui.QAction(self.tr('State plot'), self) + self._showStatePlotAction.setCheckable(True) + self._showStatePlotAction.setChecked(False) + self.connect(self._showStatePlotAction, QtCore.SIGNAL('toggled(bool)'), self._statePlotWidget.setVisible) + self._autoscaleAction = QtGui.QAction(self.tr('Auto-scale plots'), self) + self._autoscaleAction.setCheckable(True) + self._autoscaleAction.setChecked(False) + self.connect(self._autoscaleAction, QtCore.SIGNAL('toggled(bool)'), self._autoscale) + self._overlayAction = QtGui.QAction('Overlay plots', self) + self._overlayAction.setCheckable(True) + self._overlayAction.setChecked(False) + self._dockAction = QtGui.QAction('Undock all', self) + self._dockAction.setCheckable(True) + self._dockAction.setChecked(False) + self.connect(self._dockAction, QtCore.SIGNAL('toggled(bool)'), self._toggleDocking) + self._restoreDocksAction = QtGui.QAction('Show all', self) + self.connect(self._restoreDocksAction, QtCore.SIGNAL('triggered()'), self._restoreDocks) + self._quitAction = QtGui.QAction(self.tr('&Quit'), self) + self._quitAction.setShortcut(self.tr('Ctrl+Q')) + self.connect(self._quitAction, QtCore.SIGNAL('triggered()'), QtGui.qApp.closeAllWindows) + + + + def _createRunToolBar(self): + self._simToolBar = self.addToolBar(self.tr('Simulation control')) + self._simToolBar.addAction(self._quitAction) + self._simToolBar.addAction(self._runAction) + self._simToolBar.addAction(self._resetToDefaultsAction) + self._simToolBar.addAction(self._dockAction) + self._simToolBar.addAction(self._restoreDocksAction) + + def _createPlotToolBar(self): + self._plotToolBar = self.addToolBar(self.tr('Plotting control')) + self._plotToolBar.addAction(self._showLegendAction) + self._plotToolBar.addAction(self._autoscaleAction) + self._plotToolBar.addAction(self._overlayAction) + self._plotToolBar.addAction(self._showStatePlotAction) + self._plotToolBar.addAction(self._helpAction) + self._plotToolBar.addAction(self._helpBiophysicsAction) + + def _showLegend(self, on): + if on: + for axis in (self._plotFigure.axes + self._statePlotFigure.axes): + axis.legend().set_visible(True) + else: + for axis in (self._plotFigure.axes + self._statePlotFigure.axes): + axis.legend().set_visible(False) + self._plotCanvas.draw() + self._statePlotCanvas.draw() + + def _autoscale(self, on): + if on: + for axis in (self._plotFigure.axes + self._statePlotFigure.axes): + axis.relim() + axis.set_autoscale_on(True) + axis.autoscale_view(True) + else: + for axis in self._plotFigure.axes: + axis.set_autoscale_on(False) + self._vm_axes.set_ylim(-20.0, 120.0) + self._g_axes.set_ylim(0.0, 0.5) + self._im_axes.set_ylim(-0.5, 0.5) + self._i_axes.set_ylim(-10, 10) + self._plotCanvas.draw() + self._statePlotCanvas.draw() + + def _useDefaults(self): + self._runTimeEdit.setText('%g' % (self.defaults['runtime'])) + self._simTimeStepEdit.setText('%g' % (self.defaults['simdt'])) + self._overlayAction.setChecked(False) + self._naConductanceToggle.setChecked(False) + self._kConductanceToggle.setChecked(False) + self._kOutEdit.setText('%g' % (SquidGui.defaults['K_out'])) + self._naOutEdit.setText('%g' % (SquidGui.defaults['Na_out'])) + self._kInEdit.setText('%g' % (SquidGui.defaults['K_in'])) + self._naInEdit.setText('%g' % (SquidGui.defaults['Na_in'])) + self._temperatureEdit.setText('%g' % (SquidGui.defaults['temperature'] - CELSIUS_TO_KELVIN)) + self._holdingVEdit.setText('%g' % (SquidGui.defaults['vclamp.holdingV'])) + self._holdingTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.holdingT'])) + self._prePulseVEdit.setText('%g' % (SquidGui.defaults['vclamp.prepulseV'])) + self._prePulseTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.prepulseT'])) + self._clampVEdit.setText('%g' % (SquidGui.defaults['vclamp.clampV'])) + self._clampTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.clampT'])) + self._baseCurrentEdit.setText('%g' % (SquidGui.defaults['iclamp.baseI'])) + self._firstPulseEdit.setText('%g' % (SquidGui.defaults['iclamp.firstI'])) + self._firstDelayEdit.setText('%g' % (SquidGui.defaults['iclamp.firstD'])) + self._firstPulseWidthEdit.setText('%g' % (SquidGui.defaults['iclamp.firstT'])) + self._secondPulseEdit.setText('%g' % (SquidGui.defaults['iclamp.secondI'])) + self._secondDelayEdit.setText('%g' % (SquidGui.defaults['iclamp.secondD'])) + self._secondPulseWidthEdit.setText('%g' % (SquidGui.defaults['iclamp.secondT'])) + self._pulseMode.setCurrentIndex(0) + + def _onScroll(self, event): + if event.inaxes is None: + return + axes = event.inaxes + zoom = 0.0 + if event.button == 'up': + zoom = -1.0 + elif event.button == 'down': + zoom = 1.0 + if zoom != 0.0: + self._plotNavigator.push_current() + axes.get_xaxis().zoom(zoom) + axes.get_yaxis().zoom(zoom) + self._plotCanvas.draw() + + def closeEvent(self, event): + QtGui.qApp.closeAllWindows() + + def _showBioPhysicsHelp(self): + self._createHelpMessage() + self._helpMessageText.setText('

%s

%s

%s

%s

%s

' % + (tooltip_Nernst, + tooltip_Erest, + tooltip_KChan, + tooltip_NaChan, + tooltip_Im)) + self._helpWindow.setVisible(True) + + def _showRunningHelp(self): + self._createHelpMessage() + self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL)) + self._helpWindow.setVisible(True) + + def _createHelpMessage(self): + if hasattr(self, '_helpWindow'): + return + self._helpWindow = QtGui.QWidget() + self._helpWindow.setWindowFlags(QtCore.Qt.Window) + layout = QtGui.QVBoxLayout() + self._helpWindow.setLayout(layout) + self._helpMessageArea = QtGui.QScrollArea() + self._helpMessageText = QtGui.QTextBrowser() + self._helpMessageText.setOpenExternalLinks(True) + self._helpMessageArea.setWidget(self._helpMessageText) + layout.addWidget(self._helpMessageText) + self._squidGuiPath = os.path.dirname(os.path.abspath(__file__)) + self._helpBaseURL = os.path.join(self._squidGuiPath,'help.html') + self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL)) + self._helpMessageText.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding) + self._helpMessageArea.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding) + self._helpMessageText.setMinimumSize(800, 600) + self._closeHelpAction = QtGui.QAction('Close', self) + self.connect(self._closeHelpAction, QtCore.SIGNAL('triggered()'), self._helpWindow.close) + # Setting the close event so that the ``Help`` button is + # unchecked when the help window is closed + self._helpWindow.closeEvent = lambda event: self._helpAction.setChecked(False) + self._helpTOCAction = QtGui.QAction('Help running demo', self) + self.connect(self._helpTOCAction, QtCore.SIGNAL('triggered()'), self._jumpToHelpTOC) + # This panel is for putting two buttons using horizontal + # layout + panel = QtGui.QFrame() + panel.setFrameStyle(QtGui.QFrame.StyledPanel + QtGui.QFrame.Raised) + layout.addWidget(panel) + layout = QtGui.QHBoxLayout() + panel.setLayout(layout) + self._helpAction = QtGui.QAction('Help running', self) + self.connect(self._helpAction, QtCore.SIGNAL('triggered()'), self._showRunningHelp) + self._helpBiophysicsAction = QtGui.QAction('Help biophysics', self) + self.connect(self._helpBiophysicsAction, QtCore.SIGNAL('triggered()'), self._showBioPhysicsHelp) + self._helpTOCButton = QtGui.QToolButton() + self._helpTOCButton.setDefaultAction(self._helpTOCAction) + self._helpBiophysicsButton = QtGui.QToolButton() + self._helpBiophysicsButton.setDefaultAction(self._helpBiophysicsAction) + layout.addWidget(self._helpTOCButton) + layout.addWidget(self._helpBiophysicsButton) + self._closeHelpButton = QtGui.QToolButton() + self._closeHelpButton.setDefaultAction(self._closeHelpAction) + layout.addWidget(self._closeHelpButton) + + def _jumpToHelpTOC(self): + self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL)) + +if __name__ == '__main__': + app = QtGui.QApplication(sys.argv) + app.connect(app, QtCore.SIGNAL('lastWindowClosed()'), app, QtCore.SLOT('quit()')) + QtGui.qApp = app + squid_gui = SquidGui() + squid_gui.show() + print(squid_gui.size()) + sys.exit(app.exec_()) + +# +# squidgui.py ends here diff --git a/demos/squid/squid_setup.py b/demos/squid/squid_setup.py new file mode 100644 index 0000000..6f24e46 --- /dev/null +++ b/demos/squid/squid_setup.py @@ -0,0 +1,118 @@ +# squid_demo.py --- +# +# Filename: squid_demo.py +# Description: +# Author: Subhasis Ray +# Maintainer: +# Created: Wed Feb 22 23:24:21 2012 (+0530) +# Version: +# Last-Updated: Tue Mar 6 23:25:50 2012 (+0530) +# By: Subhasis Ray +# Update #: 162 +# URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# +# +# +# + +# Change log: +# +# +# + +# Code: + +import moose + +from squid import SquidAxon +from electronics import ClampCircuit + +class SquidSetup(object): + def __init__(self): + self.scheduled = False + self.model_container = moose.Neutral('/model') + self.data_container = moose.Neutral('/data') + self.squid_axon = SquidAxon('/model/squid_axon') + self.clamp_ckt = ClampCircuit('/model/electronics', self.squid_axon) + self.simdt = 0.0 + self.plotdt = 0.0 + self.setup_recording() + + def setup_recording(self): + # Setup data collection + self.vm_table = moose.Table('/data/Vm') + moose.connect(self.vm_table, 'requestOut', self.squid_axon, 'getVm') + self.cmd_table = moose.Table('/data/command') + moose.connect(self.cmd_table, 'requestOut', self.clamp_ckt.vclamp, 'getOutputValue') + self.iclamp_table = moose.Table('/data/Iclamp') + moose.connect(self.iclamp_table, 'requestOut', self.clamp_ckt.iclamp, 'getOutputValue') + self.vclamp_table = moose.Table('/data/Vclamp') + moose.connect(self.vclamp_table, 'requestOut', self.clamp_ckt.pid, 'getOutputValue') + self.m_table = moose.Table('/data/m') + moose.connect(self.m_table, 'requestOut', self.squid_axon.Na_channel, 'getX') + self.h_table = moose.Table('/data/h') + moose.connect(self.h_table, 'requestOut', self.squid_axon.Na_channel, 'getY') + self.n_table = moose.Table('/data/n') + moose.connect(self.n_table, 'requestOut', self.squid_axon.K_channel, 'getX') + self.ina_table = moose.Table('/data/INa') + moose.connect(self.ina_table, 'requestOut', self.squid_axon.Na_channel, 'getIk') + self.ik_table = moose.Table('/data/IK') + moose.connect(self.ik_table, 'requestOut', self.squid_axon.K_channel, 'getIk') + self.gna_table = moose.Table('/data/GNa') + moose.connect(self.gna_table, 'requestOut', self.squid_axon.Na_channel, 'getGk') + self.gk_table = moose.Table('/data/GK') + moose.connect(self.gk_table, 'requestOut', self.squid_axon.K_channel, 'getGk') + + def schedule(self, simdt, plotdt, clampmode): + self.simdt = simdt + self.plotdt = plotdt + if clampmode == 'vclamp': + self.clamp_ckt.do_voltage_clamp() + else: + self.clamp_ckt.do_current_clamp() + moose.setClock(0, simdt) + moose.setClock(1, simdt) + moose.setClock(2, simdt) + moose.setClock(3, plotdt) + # Ensure we do not create multiple scheduling + if not self.scheduled: + moose.useClock(0, '%s/#[TYPE=Compartment]' % (self.model_container.path), 'init') + moose.useClock(0, '%s/##' % (self.clamp_ckt.path), 'process') + moose.useClock(1, '%s/#[TYPE=Compartment]' % (self.model_container.path), 'process') + moose.useClock(2, '%s/#[TYPE=HHChannel]' % (self.squid_axon.path), 'process') + moose.useClock(3, '%s/#[TYPE=Table]' % (self.data_container.path), 'process') + self.scheduled = True + moose.reinit() + + def run(self, runtime): + moose.start(runtime) + + def save_data(self): + for child in self.data_container.children: + tab = moose.Table(child) + tab.xplot('%s.dat' % (tab.name), tab.name) + +import sys +clamp_mode = 'vclamp' +if __name__ == '__main__': + demo = SquidSetup() + if len(sys.argv) > 1: + clamp_mode = sys.argv[1] + # The pulsegen object needs different values for different clamp modes + if clamp_mode == 'iclamp': + demo.clamp_ckt.configure_pulses() + else: + demo.clamp_ckt.configure_pulses(baseLevel=0.0, firstDelay=10.0, firstLevel=SquidAxon.EREST_ACT, firstWidth=0.0, secondDelay=0.0, secondLevel=50.0+SquidAxon.EREST_ACT, secondWidth=20.0) + demo.schedule(1e-2, 0.01, clamp_mode) + + demo.run(50.0) + demo.save_data() + +# +# squid_demo.py ends here diff --git a/demos/squid/test_squid.py b/demos/squid/test_squid.py new file mode 100644 index 0000000..005cb16 --- /dev/null +++ b/demos/squid/test_squid.py @@ -0,0 +1,117 @@ +# test_squid.py --- +# +# Filename: test_squid.py +# Description: +# Author: Subhasis Ray +# Maintainer: +# Created: Wed Feb 22 00:41:36 2012 (+0530) +# Version: +# Last-Updated: Wed Feb 22 00:41:51 2012 (+0530) +# By: Subhasis Ray +# Update #: 2 +# URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# +# +# +# + +# Change log: +# +# +# + +# Code: + +import unittest +import pylab +from squid import SquidModel + +class SquidAxonTest(unittest.TestCase): + def setUp(self): + self.vrange = numpy.linspace(SquidModel.VMIN, SquidModel.VMAX, SquidModel.VDIVS+1) + self.model = SquidModel('testSquidAxon') + + def calc_alpha_beta(self, params, table='A'): + denominator = params[table+'_C'] + numpy.exp((self.vrange+params[table+'_D'])/params[table+'_F']) + numerator = params[table+'_A'] + params[table+'_B'] * self.vrange + y = numpy.zeros(len(self.vrange)) + singularities = numpy.nonzero(denominator == 0.0)[0] + self.assertLessEqual(len(singularities), 1) + if len(singularities) == 1: + y[:singularities[0]] = numerator[:singularities[0]]/denominator[:singularities[0]] + y[singularities[0]] = params[table+'_B'] * params[table+'_F'] + y[singularities[0]+1:] = numerator[singularities[0]+1:]/denominator[singularities[0]+1:] + elif len(singularities) == 0: + y[:] = numerator[:]/denominator[:] + return y + + def test_Na_alpha_m(self): + alpha_m = self.calc_alpha_beta(SquidModel.Na_m_params, 'A') + difference = numpy.sqrt(numpy.mean((alpha_m - self.model.Na_channel.alpha_m)**2)) + pylab.title('Na_alpha_m') + pylab.plot(alpha_m, label='python') + pylab.plot(self.model.Na_channel.alpha_m, label='moose') + pylab.legend() + pylab.show() + self.assertLessEqual(difference, numpy.mean(alpha_m)*1e-6) + + def test_Na_beta_m(self): + beta_m = self.calc_alpha_beta(SquidModel.Na_m_params, 'B') + difference = numpy.sqrt(numpy.mean((beta_m - self.model.Na_channel.beta_m)**2)) + pylab.title('Na_beta_m') + pylab.plot(beta_m, label='python') + pylab.plot(self.model.Na_channel.beta_m, label='moose') + pylab.legend() + pylab.show() + self.assertLessEqual(difference, numpy.mean(beta_m)*1e-6) + + def test_Na_alpha_h(self): + alpha_h = self.calc_alpha_beta(SquidModel.Na_h_params, 'A') + difference = numpy.sqrt(numpy.mean((alpha_h - self.model.Na_channel.alpha_h)**2)) + pylab.title('Na_alpha_h') + pylab.plot(alpha_h, label='python') + pylab.plot(self.model.Na_channel.alpha_h, label='moose') + pylab.legend() + pylab.show() + self.assertLessEqual(difference, numpy.mean(alpha_h)*1e-6) + + def test_Na_beta_h(self): + beta_h = self.calc_alpha_beta(SquidModel.Na_h_params, 'B') + difference = numpy.sqrt(numpy.mean((beta_h - self.model.Na_channel.beta_h)**2)) + pylab.title('Na_beta_h') + pylab.plot(beta_h, label='python') + pylab.plot(self.model.Na_channel.beta_h, label='moose') + pylab.legend() + pylab.show() + self.assertLessEqual(difference, numpy.mean(beta_h)*1e-6) + + def test_K_alpha_m(self): + alpha_m = self.calc_alpha_beta(SquidModel.K_n_params, 'A') + difference = numpy.sqrt(numpy.mean((alpha_m - self.model.K_channel.alpha_m)**2)) + pylab.title('K_alpha_n') + pylab.plot(alpha_m, label='python') + pylab.plot(self.model.K_channel.alpha_m, label='moose') + pylab.legend() + pylab.show() + self.assertLessEqual(difference, numpy.mean(alpha_m)*1e-6) + + def test_K_beta_m(self): + beta_m = self.calc_alpha_beta(SquidModel.K_n_params, 'B') + difference = numpy.sqrt(numpy.mean((beta_m - self.model.K_channel.beta_m)**2)) + pylab.title('K_beta_n') + pylab.plot(beta_m, label='python') + pylab.plot(self.model.K_channel.beta_m, label='moose') + pylab.legend() + pylab.show() + self.assertLessEqual(difference, numpy.mean(beta_m)*1e-6) + + + +# +# test_squid.py ends here diff --git a/drawsbml b/drawsbml new file mode 160000 index 0000000..3805a2d --- /dev/null +++ b/drawsbml @@ -0,0 +1 @@ +Subproject commit 3805a2dd2b5bc218df3300bb36631a1059c5e895 diff --git a/global_constants.py b/global_constants.py deleted file mode 100644 index 247b5cb..0000000 --- a/global_constants.py +++ /dev/null @@ -1,3 +0,0 @@ -from PreferencesPresenter import PreferencesPresenter - -preferences = PreferencesPresenter() diff --git a/loaderdialog.py b/loaderdialog.py deleted file mode 100644 index d49e1ce..0000000 --- a/loaderdialog.py +++ /dev/null @@ -1,112 +0,0 @@ -# fileloader.py --- -# -# Filename: fileloader.py -# Description: -# Author: -# Maintainer: -# Created: Mon Feb 25 15:59:54 2013 (+0530) -# Version: -# Last-Updated: Wed May 22 12:30:14 2013 (+0530) -# By: subha -# Update #: 106 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# Dialog for loading model files -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: - -import sys -from PyQt4 import QtGui,QtCore,Qt -import moose -import os -import posixpath - -class LoaderDialog(QtGui.QFileDialog): - # Update ftypes to include new file types - ftypes='All Supported Files (*.cspace *.g *.xml *.p);; CSPACE (*.cspace);; GENESIS (*.g);; GENESIS Prototype (*.p);; NeuroML/SBML (*.xml)' - target_default = '' # The default target when loading a model - def __init__(self, *args): - self.modelpath = None - super(LoaderDialog, self).__init__(*args) - self.setNameFilter(self.tr(self.ftypes)) - self.setNameFilterDetailsVisible(True) - self.setReadOnly(True) - self.setFileMode(self.ExistingFile) - # self.targetPanel = QtGui.QFrame() - # self.targetLabel = QtGui.QLabel('Model name') - # self.targetText = QtGui.QLineEdit(self.target_default) - # form = QtGui.QFormLayout() - # form.addRow(self.targetLabel, self.targetText) - # self.modelChoiceBox = QtGui.QGroupBox('Model name') - # self.replaceExistingButton = QtGui.QRadioButton('&Replace current model') - # self.mergeExistingButton = QtGui.QRadioButton('&Keep current model') - # self.replaceExistingButton.setChecked(True) - # vbox = QtGui.QVBoxLayout() - # vbox.addWidget(self.replaceExistingButton) - # vbox.addWidget(self.mergeExistingButton) - # self.modelChoiceBox.setLayout(vbox) - # self.targetPanel.setLayout(form) - # self.layout().addWidget(self.targetPanel) - # self.layout().addWidget(self.modelChoiceBox) - self.fileSelected.connect(self.fileSelectedSlot) - - def fileSelectedSlot(self, fpath): - """On selecting a file, this function will cause the target location to change to: - - /model/filename_minus_extension - - """ - self.modelpath = os.path.splitext(os.path.basename(str(fpath)))[0] - - # def isReplace(self): - # return self.replaceExistingButton.isChecked() - - # def isMerge(self): - # return self.mergeExistingButton.isChecked() - - def getTargetPath(self): - return self.modelpath - - -if __name__ == '__main__': - app = QtGui.QApplication(sys.argv) - QtGui.qApp = app - mw = LoaderDialog() - mw.show() - # mw.exec_() - sys.exit(app.exec_()) - - - -# -# fileloader.py ends here diff --git a/moose b/moose new file mode 100755 index 0000000..d4b51ed --- /dev/null +++ b/moose @@ -0,0 +1,5 @@ +#!/usr/bin/env python + +import moosegui +print( moosegui.__file__ ) +moosegui.main( ) diff --git a/moosegui/GenericTypes.py b/moosegui/GenericTypes.py new file mode 100644 index 0000000..c4ef7ab --- /dev/null +++ b/moosegui/GenericTypes.py @@ -0,0 +1,34 @@ +"""GenericTypes + +This class fixes the pytho2 and python3 related issues with PyQt5 + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import sys +import os + +from PyQt5 import QtCore + +if sys.version_info >= (3, 0): + + class QVariant(str): + """docstring for QVariant""" + def __init__(self, val): + super(QVariant, self).__init__() + self.val = val + + def toString( self ): + return "%s" % self.val + +else: + QVariant = QtCore.QVariant + diff --git a/mgui.py b/moosegui/MWindow.py similarity index 60% rename from mgui.py rename to moosegui/MWindow.py index 0ecb96f..379957c 100644 --- a/mgui.py +++ b/moosegui/MWindow.py @@ -1,123 +1,63 @@ -# mgui.py --- -# -# Filename: mgui.py -# Description: +# -*- coding: utf-8 -*- + # Author: "Subhasis", "HarshaRani","Aviral Goel" -# Maintainer: HarshaRani +# Maintainer: HarshaRani, Dilawar Singh # Created: Mon Nov 12 09:38:09 2012 (+0530) -# Version: -# Last-Updated: Fri Sep 20 00:54:33 2018 (+0530) -# By: Harsha -# Update #: -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# The gui driver -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -'''' -2018 -Sep 20 : Lot of duplicate code removed - Function call made when filename or filepath is passed in command line -Sep 19 : From the cmd line if a directory is passed, then Gui opens up the dialog file for the folder, - window is resized to maximum width, clean warning message if filename or path is wrong - Added model info QmessageBox -Sep 7 : popup is closed if exist -2017 -Aug 31 : Pass file from the command to load into gui - : added dsolver in disableModel function is used to unset the solver for the model - into moose-gui which are not to be run. - -Oct 5 : clean up with round trip of dialog_exe - -''' -# Code: + +import os import imp import inspect -import code import traceback -import sys -sys.path.append('../python') -#sys.path.append('utils') -import os -from collections import defaultdict -import posixpath # We use this to create MOOSE paths -from PyQt4 import QtGui, QtCore, Qt -import config -import mplugin -import moose -import mexception -from moose import utils -from mload import loadFile -from loaderdialog import LoaderDialog -from shell import get_shell_class -from objectedit import ObjectEditDockWidget -from newmodeldialog import DialogWidget import re -from biomodelsclient import BioModelsClientWidget -from PyQt4 import Qt, QtCore, QtGui -from PyQt4.QtGui import * -from MdiArea import MdiArea -import os -from moose.chemUtil.add_Delete_ChemicalSolver import * -#from setsolver import * -from defines import * +import sys +import code + from collections import OrderedDict +from PyQt5 import QtGui, QtCore, Qt +from PyQt5.QtWidgets import QMainWindow, QAction, QApplication +from PyQt5.QtWidgets import QDockWidget, QMdiArea, QMenu +from PyQt5.QtWidgets import QActionGroup, QSizePolicy, QDialog +from PyQt5.QtWidgets import QGridLayout, QPushButton +from PyQt5.QtWidgets import QHBoxLayout, QMessageBox + +# moose +import moose -__author__ = 'Subhasis Ray , HarshaRani, Aviral Goel, NCBS' +# moosegui +from moosegui import config +from moosegui import mplugin +from moosegui import mexception +from moosegui import mload +from moosegui.loaderdialog import LoaderDialog +from moosegui.shell import get_shell_class +from moosegui.objectedit import ObjectEditDockWidget +from moosegui.newmodeldialog import DialogWidget +from moosegui.biomodelsclient import BioModelsClientWidget +from moosegui.MdiArea import MdiArea +from moosegui.plugins import defines + +# Logger +import logging +logger_ = logging.getLogger("moosegui.window") # This maps model subtypes to corresponding plugin names. Should be # moved to a separate property file perhaps -subtype_plugin_map = { 'genesis/kkit': 'kkit' - , 'cspace/': 'kkit' - , 'xml/sbml': 'kkit' - , 'xml/neuroml': 'NeuroKit' - } - -#APPLICATION_ICON_PATH = os.path.join( os.path.dirname(os.path.realpath(__file__)) -# , "icons/moose_icon.png" -# ) - +subtype_plugin_map = { + 'genesis/kkit': 'kkit' + , 'cspace/': 'kkit' + , 'xml/sbml': 'kkit' + , 'xml/neuroml': 'NeuroKit' + } def busyCursor(): app = QtGui.qApp - app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow + app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) def freeCursor(): app = QtGui.qApp app.restoreOverrideCursor() - - -class MWindow(QtGui.QMainWindow): +class MWindow(QMainWindow): """The main window for MOOSE GUI. This is the driver class that uses the mplugin API. mplugin based @@ -150,7 +90,7 @@ class MWindow(QtGui.QMainWindow): """ def __init__(self, *args): - QtGui.QMainWindow.__init__(self, *args) + QMainWindow.__init__(self, *args) self.setWindowTitle('MOOSE') self.pluginNames = None self.plugin = None @@ -170,26 +110,13 @@ def __init__(self, *args): self.setDockOptions(self.AnimatedDocks and self.AllowNestedDocks and self.AllowTabbedDocks) self.mdiArea = MdiArea() - self.quitAction = QtGui.QAction('&Quit', self) - self.connect(self.quitAction, QtCore.SIGNAL('triggered()'), self.quit) - self.quitAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+Q", None, QtGui.QApplication.UnicodeUTF8)) + self.quitAction = QAction('&Quit', self) + self.quitAction.triggered.connect(self.quit) + self.quitAction.setShortcut("Ctrl+Q") self.getMyDockWidgets() self.setCentralWidget(self.mdiArea) - #self.setWindowIcon(QIcon(APPLICATION_ICON_PATH)) - - # pixmap = QPixmap("icons/moose_icon.png") - # pixmap = pixmap.scaled(self.mdiArea.size()) - # self.mdiArea.setStyleSheet("QMdiArea { background-image: url(icons/moose_icon_large.png); }") - # palette = QPalette() - # palette.setBrush(QPalette.Background, QBrush(pixmap)) - # self.setPalette(palette) - - - # self.mdiArea.setStyleSheet("border-image: url(icons/moose_icon_large.png)") - # self.mdiArea.setBackground(QBrush(pixmap)) - - self.mdiArea.setViewMode(QtGui.QMdiArea.TabbedView) + self.mdiArea.setViewMode(QMdiArea.TabbedView) self.mdiArea.subWindowActivated.connect(self.switchSubwindowSlot) self.setPlugin('default', '/') self.plugin.getEditorView().getCentralWidget().parent().close() @@ -217,17 +144,17 @@ def __init__(self, *args): self.show() self.createPopup() freeCursor() - reply = QtGui.QMessageBox.information(self,"Model file can not open","At present python file cann\'t be laoded into GUI",QtGui.QMessageBox.Ok) - if reply == QtGui.QMessageBox.Ok: - QtGui.QApplication.restoreOverrideCursor() + reply = QMessageBox.information(self,"Model file can not open","At present python file cann\'t be laoded into GUI", QMessageBox.Ok) + if reply == QMessageBox.Ok: + QApplication.restoreOverrideCursor() return if not os.path.exists(cmdfilepath): self.setWindowState(QtCore.Qt.WindowMaximized) self.show() self.createPopup() - reply = QtGui.QMessageBox.information(self,"Model file can not open","File Not Found \n \nCheck filename or filepath\n ",QtGui.QMessageBox.Ok) - if reply == QtGui.QMessageBox.Ok: - QtGui.QApplication.restoreOverrideCursor() + reply = QMessageBox.information(self,"Model file can not open","File Not Found \n \nCheck filename or filepath\n ", QMessageBox.Ok) + if reply == QMessageBox.Ok: + QApplication.restoreOverrideCursor() return if os.path.isdir(cmdfilepath): self.setWindowState(QtCore.Qt.WindowMaximized) @@ -271,36 +198,31 @@ def __init__(self, *args): self.createPopup() def createPopup(self): - self.popup = dialog = QDialog(self) - #dialog.setWindowFlags(Qt.Qt.Dialog | Qt.Qt.FramelessWindowHint) - dialog.setWindowFlags(Qt.Qt.Dialog | Qt.Qt.CustomizeWindowHint) - #dialog.setStyleSheet("border:1px solid rgb(0, 0, 0); ") - qapp = QApplication.desktop().screenGeometry(); - dialog.setGeometry((qapp.bottomLeft().x()+100),(qapp.bottomLeft().y()-250),100,100) - #dialog.move(qapp.bottomLeft().x()+10,qapp.bottomLeft().y()-10) - layout = QGridLayout() - self.setStyleSheet("QPushButton{border-radius: 5px; border-color: rgb(0,0,0); border-width: 2px; border-style: outset; padding-top: 2px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px}") - #self.setStyleSheet("QToolTip{border-radius: 5px; border-width: 2px; border-style: outset; padding-top: 2px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; color: black}") + self.popup = dialog = QDialog() createKineticModelButton = QPushButton("Create Kinetic Model") loadKineticModelButton = QPushButton("Load Model") loadNeuronalModelButton = QPushButton("Load Neuronal Model") - layout.setContentsMargins(QtCore.QMargins(20,20,20,20)) - - self.menuitems = OrderedDict([("Fig2C" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2C.py"), - ("Fig2D (35s)", "../moose-examples/paper-2015/Fig2_elecModels/Fig2D.py"), - ("Fig2E" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2E.py"), - ("Fig3B_Gssa", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), - ("Fig3C_Gsl", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), - ("Fig3D", "../moose-examples/paper-2015/Fig3_chemModels/Fig3D.py"), - ("Fig4B", "../moose-examples/paper-2015/Fig4_ReacDiff/Fig4B.py" ), - ("Fig4K", "../moose-examples/paper-2015/Fig4_ReacDiff/rxdSpineSize.py"), - ("Fig5A (20s)", "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py"), - ("Fig5BCD (240s)" , "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py"), - ("Fig6A (60s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py" ), - ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"), - ("Squid" , "../moose-examples/squid/squid_demo.py") - ]) - layout.setContentsMargins(QtCore.QMargins(20,20,20,20)) + + # setup layout. + layout = QGridLayout() + _m = 15 + layout.setContentsMargins(QtCore.QMargins(_m, _m, _m, _m)) + + self.menuitems = [ + ("Fig2C" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2C.py"), + ("Fig2D (35s)", "../moose-examples/paper-2015/Fig2_elecModels/Fig2D.py"), + ("Fig2E" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2E.py"), + ("Fig3B_Gssa", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), + ("Fig3C_Gsl", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), + ("Fig3D", "../moose-examples/paper-2015/Fig3_chemModels/Fig3D.py"), + ("Fig4B", "../moose-examples/paper-2015/Fig4_ReacDiff/Fig4B.py" ), + ("Fig4K", "../moose-examples/paper-2015/Fig4_ReacDiff/rxdSpineSize.py"), + ("Fig5A (20s)", "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py"), + ("Fig5BCD (240s)" , "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py"), + ("Fig6A (60s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py" ), + ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"), + ("Squid" , "../moose-examples/squid/squid_demo.py") + ] layout1 = QHBoxLayout() layout1.addWidget(createKineticModelButton) layout1.addWidget(loadKineticModelButton) @@ -310,10 +232,7 @@ def createPopup(self): layout5 = QHBoxLayout() layout6 = QHBoxLayout() layout7 = QHBoxLayout() - listofButtons = {} - for i in range(0,len(self.menuitems)): - k = self.menuitems.popitem(0) - t = k[0] + for i, k in enumerate( self.menuitems ): button = QPushButton(k[0]) if k[0] == "Fig2E": button.setToolTip("Illustrates loading a model from an SWC file, inserting channels, and running it") @@ -368,35 +287,44 @@ def createPopup(self): layout.addLayout(layout5,4,0) layout.addLayout(layout6,5,0) layout.addLayout(layout7,6,0) - dialog.setStyleSheet("border:1px solid rgb(0, 0, 0); ") - dialog.setLayout(layout) + self.popup.setStyleSheet("border:1px solid rgb(0, 0, 0); ") + self.popup.setLayout(layout) createKineticModelButton.clicked.connect(self.newModelDialogSlot) loadKineticModelButton.clicked.connect(self.loadModelDialogSlot) loadNeuronalModelButton.clicked.connect(self.loadModelDialogSlot) - - dialog.show() - freeCursor() - return dialog - def run_genesis_script(self,filepath,solver): - self.popup.hide() + # Create the popup and move to the middle of destop app. + qApp = QApplication.desktop() + qAppScreen = qApp.screenGeometry(); + self.popup.setGeometry((qAppScreen.bottomLeft().x()+100),(qAppScreen.bottomLeft().y()-250),100,100) + self.popup.move( qApp.availableGeometry().center() ) + self.popup.setWindowFlags( Qt.Qt.WindowStaysOnTopHint | + Qt.Qt.X11BypassWindowManagerHint # else it wont go on top. + ) + self.popup.show() + + def run_genesis_script(self, filepath, solver): + if self.popup: + self.popup.hide() abspath = os.path.abspath(filepath) directory, modulename = os.path.split(abspath) modelName = os.path.splitext(modulename)[0] - ret = loadFile(str(abspath),'%s' %(modelName),solver,merge=False) + ret = mload.loadFile(str(abspath),'%s' %(modelName),solver,merge=False) self.setPlugin("kkit", ret["model"].path) self.setCurrentView("run") widget = self.plugin.view.getSchedulingDockWidget().widget() widget.runSimulation() def run_python_script(self, filepath): + """ Execute a python script """ busyCursor() import subprocess, shlex t = os.path.abspath(filepath) directory, filename = os.path.split(t) - p = subprocess.Popen(["python", filename], cwd=directory) + logger_.info( "Executing %s" % filepath ) + p = subprocess.Popen([ sys.executable, filename], cwd=directory) p.wait() freeCursor() @@ -404,16 +332,15 @@ def quit(self): QtGui.qApp.closeAllWindows() def handleException(self, t, v, s): - """This handler will show warning messages for error exceptions. Show + """ + This handler will show warning messages for error exceptions. Show info at status bar for non-error exceptions. It will replace sys.excepthook and has the same signature (except being bound to this object). - t : exception type - - v : exception value - - s: traceback object. + t : exception type + v : exception value + s: traceback object. """ traceback.print_exception(t, v, s) @@ -422,43 +349,50 @@ def handleException(self, t, v, s): if isinstance(v, mexception.MooseInfo): self.statusBar().showMessage(title, 5000) elif isinstance(v, mexception.MooseWarning): - QtGui.QMessageBox.warning(self, title, '\n'.join((title, trace))) + QMessageBox.warning(self, title, '\n'.join((title, trace))) else: - QtGui.QMessageBox.critical(self, title, '\n'.join((title, trace))) + QMessageBox.critical(self, title, '\n'.join((title, trace))) def getPluginNames(self): - """Return pluginNames attribute or create it by retrieving + """ + Return pluginNames attribute or create it by retrieving available plugin names from plugin/list.txt file. - """ if self.pluginNames is None: - with open(os.path.join(config.MOOSE_GUI_DIR, - 'plugins', - 'list.txt')) as lfile: + pluginF = os.path.join( config.MOOSE_GUI_DIR, 'plugins', 'list.txt' ) + with open( pluginF, 'r' ) as lfile: self.pluginNames = [line.strip() for line in lfile] self.pluginNames = [name for name in self.pluginNames if name] - return self.pluginNames - def loadPluginModule(self, name, re=False): + def loadPluginModule(self, name, _reload=False): """Load a plugin module by name. First check if the plugin is already loaded. If so return the existing one. Otherwise, search load the plugin as a python module from {MOOSE_GUI_DIRECTORY}/plugins directory. - If re is True, the plugin is reloaded. + If re is True, the plugin is _reloaded. + """ - if (not re) and name in sys.modules: + logger_.info("Loading plugin '%s' from %s" % (name, config.MOOSE_PLUGIN_DIR)) + if (not _reload) and name in sys.modules: + logger_.debug( "\tThis plugin is already loaded" ) return sys.modules[name] + fp, pathname, description = imp.find_module(name, [config.MOOSE_PLUGIN_DIR]) try: module = imp.load_module(name, fp, pathname, description) - finally: - if fp: - fp.close() + except Exception as e: + module = "" + extra = traceback.format_exc() + logger_.warn( "Could not load module %s: '%s'" % (fp, extra)) + + if fp: + fp.close() return module + def getMyDockWidgets(self): """Return a list of dockwidgets that belong to the top level. This is needed to keep them separate from those @@ -467,7 +401,7 @@ def getMyDockWidgets(self): Currently we only have shell for this.""" if not hasattr(self, 'dockWidgets') or self.dockWidgets is None: self.dockWidgets = {} - dockWidget = QtGui.QDockWidget('Python') + dockWidget = QDockWidget('Python') dockWidget.setWidget(self.getShellWidget()) self.dockWidgets[dockWidget] = True self.addDockWidget(Qt.Qt.BottomDockWidgetArea, dockWidget) @@ -477,48 +411,51 @@ def getMyDockWidgets(self): self.objectEditDockWidget = dockWidget self.addDockWidget(Qt.Qt.RightDockWidgetArea, dockWidget) dockWidget.setVisible(False) - return self.dockWidgets.keys() + return list(self.dockWidgets.keys()) def getShellWidget(self): - """Create an instance of shell widget. This can be either a + """ + Create an instance of shell widget. This can be either a QSciQScintialla widget or a PyCute widget (extends QTextArea) - if the first is not available""" + if the first is not available. + """ + + # raise DeprecationWarning("ShellWidget is no longer supported.") if not hasattr(self, 'shellWidget') or self.shellWidget is None: - self.shellWidget = get_shell_class()( code.InteractiveInterpreter() - , message='MOOSE version %s' % (moose._moose.__version__) - ) + self.shellWidget = get_shell_class()( + code.InteractiveInterpreter() + , message='MOOSE version %s' % (moose._moose.__version__) + ) self.shellWidget.interpreter.runsource('from moose import *') self.shellWidget.setVisible(False) return self.shellWidget - def loadPluginClass(self, name, re=False): + def loadPluginClass(self, name, _reload=False): """Load the plugin class from a plugin module. A plugin module should have only one subclass of MoosePluginBase. Otherwise the first such class found will be loaded. """ - try: + if name in self._loadedPlugins: return self._loadedPlugins[name] - except KeyError: - pluginModule = self.loadPluginModule(name, re=re) - for classname, classobj in inspect.getmembers(pluginModule, inspect.isclass): - if issubclass(classobj, mplugin.MoosePluginBase): - self._loadedPlugins[name] = classobj - # classobj.getEditorView().getCentralWidget().editObject.connect(self.objectEditSlot) - return self._loadedPlugins[name] - raise Exception('No plugin with name: %s' % (name)) - def setPlugin(self, name, root='/'): - """Set the current plugin to use. + pluginModule = self.loadPluginModule(name, _reload=_reload) + for classname, classobj in inspect.getmembers(pluginModule, inspect.isclass): + if issubclass(classobj, mplugin.MoosePluginBase): + self._loadedPlugins[name] = classobj + return self._loadedPlugins[name] - This - + errMsg = 'No plugin found with name: %s' % name + errMsg += ". Available: '{}'".format(', '.join(self._loadedPlugins.keys())) + logger_.error(errMsg) + raise IndexError(errMsg) + def setPlugin(self, name, root='/'): + """Set the current plugin to use. 1. sets the `plugin` attribute. - 2. updates menus by clearing and reinstating menus including anything provided by the plugin. - 3. sets the current view to the plugins editor view. """ @@ -530,15 +467,13 @@ def setPlugin(self, name, root='/'): if self._loadedModels[i][0]== root: c = moose.Clock('/clock') compts = moose.wildcardFind(root+'/##[ISA=ChemCompt]') - for simdt in CHEMICAL_SIMULATION_DT_CLOCKS: + for simdt in defines.CHEMICAL_SIMULATION_DT_CLOCKS: c.tickDt[simdt] = self._loadedModels[i][3] - for plotdt in CHEMICAL_PLOT_UPDATE_INTERVAL_CLOCKS: + for plotdt in defines.CHEMICAL_PLOT_UPDATE_INTERVAL_CLOCKS: c.tickDt[plotdt] = self._loadedModels[i][4] if compts: - #setCompartmentSolver(self._loadedModels[i][0],"gsl") - mooseAddChemSolver(self._loadedModels[i][0],"gsl") - #addSolver(self._loadedModels[i][0],"gsl") + moose.mooseAddChemSolver(self._loadedModels[i][0],"gsl") else: c.tickDt[7] = self._loadedModels[i][3] c.tickDt[8] = self._loadedModels[i][4] @@ -567,8 +502,10 @@ def setPlugin(self, name, root='/'): self.setCurrentView('run') if name == 'kkit': - self.objectEditDockWidget.objectNameChanged.connect(self.plugin.getEditorView().getCentralWidget().updateItemSlot) - self.objectEditDockWidget.colorChanged.connect(self.plugin.getEditorView().getCentralWidget().updateColorSlot) + self.objectEditDockWidget.objectNameChanged.connect( + self.plugin.getEditorView().getCentralWidget().updateItemSlot) + self.objectEditDockWidget.colorChanged.connect( + self.plugin.getEditorView().getCentralWidget().updateColorSlot) self.setCurrentView('editor') freeCursor() return self.plugin @@ -578,7 +515,7 @@ def updateExistingMenu(self, menu): already exists. If so, update the same and return True. Otherwise return False. """ - if not isinstance(menu, QtGui.QMenu): + if not isinstance(menu, QMenu): return False for action in self.menuBar().actions(): if menu.title() == action.text(): @@ -600,19 +537,18 @@ def updateMenus(self): """ self.menuBar().clear() self.getPluginsMenu() - menus = [self.getFileMenu(), - self.getEditMenu(), - self.getViewMenu(), - #self.getRunMenu(), - #self.getConnectMenu(), - self.getHelpMenu()] - for menu in menus: - self.menuBar().addMenu(menu) + menus = [self.getFileMenu() + , self.getEditMenu() + , self.getViewMenu(), + self.getHelpMenu() + ] + [ self.menuBar().addMenu(menu) for menu in menus ] for menu in self.plugin.getMenus(): if not self.updateExistingMenu(menu): - if not self.menuBar().isEmpty(): - action.menu().addSeparator() + # bug: action was empty here. + #if not self.menuBar().isEmpty(): + # action.menu().addSeparator() self.menuBar().addMenu(menu) menus[0].addSeparator() menus[0].addAction(self.quitAction) @@ -624,10 +560,9 @@ def updateToolbars(self): self.toolBars.extend(self.getMyToolBars()) self.toolBars.extend(self.plugin.getToolBars()) self.toolBars.extend(self.plugin.getCurrentView().getToolBars()) - if len(self.toolBars): - for toolbar in self.toolBars: - self.addToolBar(toolbar) - toolbar.setVisible(True) + for toolbar in self.toolBars: + toolbar.setVisible(True) + self.addToolBar(toolbar) def switchSubwindowSlot(self, window): """Change view based on what subwindow `window` is activated.""" @@ -660,15 +595,15 @@ def setCurrentView(self, view): title = widget.modelRoot+'/model' #subwin.setWindowTitle('%s: %s' % (view, widget.modelRoot)) subwin.setWindowTitle('%s: %s' % (view, title)) - subwin.setSizePolicy(QtGui.QSizePolicy.Minimum | - QtGui.QSizePolicy.Expanding, - QtGui.QSizePolicy.Minimum | - QtGui.QSizePolicy.Expanding) + subwin.setSizePolicy(QSizePolicy.Minimum | + QSizePolicy.Expanding, + QSizePolicy.Minimum | + QSizePolicy.Expanding) subwin.resize(600, 400) # Make dockwidgets from other views invisible and make those # from current view visible or add them if not already part of # main window. - dockWidgets = set([dockWidget for dockWidget in self.findChildren(QtGui.QDockWidget)]) + dockWidgets = set([dockWidget for dockWidget in self.findChildren(QDockWidget)]) for dockWidget in dockWidgets: if dockWidget not in self.dockWidgets: dockWidget.setVisible(False) @@ -706,98 +641,100 @@ def getMyToolBars(self): def getFileMenu(self): if self.fileMenu is None: - self.fileMenu = QtGui.QMenu('&File') + self.fileMenu = QMenu('&File') else: self.fileMenu.clear() if not hasattr(self, 'newModelAction'): - self.newModelAction = QtGui.QAction('New', self) - self.newModelAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+N", None, QtGui.QApplication.UnicodeUTF8)) - self.connect(self.newModelAction, QtCore.SIGNAL('triggered()'), self.newModelDialogSlot) + self.newModelAction = QAction('New', self) + self.newModelAction.setShortcut("Ctrl+N") + self.newModelAction.triggered.connect(self.newModelDialogSlot) + self.fileMenu.addAction(self.newModelAction) if not hasattr(self, 'loadModelAction'): - self.loadModelAction = QtGui.QAction('L&oad model', self) - self.loadModelAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+O", None, QtGui.QApplication.UnicodeUTF8)) - self.connect(self.loadModelAction, QtCore.SIGNAL('triggered()'), self.loadModelDialogSlot) + self.loadModelAction = QAction('L&oad model', self) + self.loadModelAction.setShortcut("Ctrl+O") + self.loadModelAction.triggered.connect(self.loadModelDialogSlot) + self.fileMenu.addAction(self.loadModelAction) if not hasattr(self, 'Paper_2015'): self.menuitems = OrderedDict([ - ("Fig2C (6s)" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2C.py"), - ("Fig2D (35s)", "../moose-examples/paper-2015/Fig2_elecModels/Fig2D.py"), - ("Fig2E (5s)" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2E.py"), - ("Fig3B_Gssa (2s)", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), - ("Fig3C_Gsl (2s)", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), - ("Fig3D (1s)", "../moose-examples/paper-2015/Fig3_chemModels/Fig3D.py"), - ("Fig4B (10s)", "../moose-examples/paper-2015/Fig4_ReacDiff/Fig4B.py" ), - ("Fig4K", "../moose-examples/paper-2015/Fig4_ReacDiff/rxdSpineSize.py"), - ("Fig5A (20s)", "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py"), - ("Fig5BCD (240s)" , "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py"), - ("Fig6A (60s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py" ), - ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"), - ("Squid" , "../moose-examples/squid/squid_demo.py") - ]) - self.subMenu = QtGui.QMenu('Demos') + ("Fig2C (6s)" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2C.py"), + ("Fig2D (35s)", "../moose-examples/paper-2015/Fig2_elecModels/Fig2D.py"), + ("Fig2E (5s)" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2E.py"), + ("Fig3B_Gssa (2s)", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), + ("Fig3C_Gsl (2s)", "../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g"), + ("Fig3D (1s)", "../moose-examples/paper-2015/Fig3_chemModels/Fig3D.py"), + ("Fig4B (10s)", "../moose-examples/paper-2015/Fig4_ReacDiff/Fig4B.py" ), + ("Fig4K", "../moose-examples/paper-2015/Fig4_ReacDiff/rxdSpineSize.py"), + ("Fig5A (20s)", "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py"), + ("Fig5BCD (240s)" , "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py"), + ("Fig6A (60s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py" ), + ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"), + ("Squid" , "../moose-examples/squid/squid_demo.py") + ]) + self.subMenu = QMenu('Demos') for i in range(0,len(self.menuitems)): k = self.menuitems.popitem(0) if k[0] == "Fig2C (6s)": - self.Fig2Caction = QtGui.QAction('Fig2C (6s)', self) + self.Fig2Caction = QAction('Fig2C (6s)', self) self.Fig2Caction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig2_elecModels/Fig2C.py')) self.subMenu.addAction(self.Fig2Caction) elif k[0] == "Fig2D (35s)": - self.Fig2Daction = QtGui.QAction('Fig2D (35s)', self) + self.Fig2Daction = QAction('Fig2D (35s)', self) self.Fig2Daction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig2_elecModels/Fig2D.py')) self.subMenu.addAction(self.Fig2Daction) elif k[0] == "Fig2E (5s)": - self.Fig2Eaction = QtGui.QAction('Fig2E (5s)', self) + self.Fig2Eaction = QAction('Fig2E (5s)', self) self.Fig2Eaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig2_elecModels/Fig2E.py')) self.subMenu.addAction(self.Fig2Eaction) elif k[0] == "Fig3B_Gssa (2s)": - self.Fig3B_Gssaaction = QtGui.QAction('Fig3B_Gssa (2s)', self) + self.Fig3B_Gssaaction = QAction('Fig3B_Gssa (2s)', self) self.Fig3B_Gssaaction.triggered.connect(lambda :self.run_genesis_script('../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g',"gssa")) self.subMenu.addAction(self.Fig3B_Gssaaction) elif k[0] == "Fig3C_Gsl (2s)": - self.Fig3C_Gslaction = QtGui.QAction('Fig3C_Gsl (2s)', self) + self.Fig3C_Gslaction = QAction('Fig3C_Gsl (2s)', self) self.Fig3C_Gslaction.triggered.connect(lambda :self.run_genesis_script('../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g',"gsl")) self.subMenu.addAction(self.Fig3C_Gslaction) elif k[0] == "Fig3D (1s)": - self.Fig3Daction = QtGui.QAction('Fig3D (1s)', self) + self.Fig3Daction = QAction('Fig3D (1s)', self) self.Fig3Daction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig3_chemModels/Fig3D.py')) self.subMenu.addAction(self.Fig3Daction) elif k[0] == "Fig4B (10s)": - self.Fig4Baction = QtGui.QAction('Fig4B (10s)', self) + self.Fig4Baction = QAction('Fig4B (10s)', self) self.Fig4Baction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig4_ReacDiff/Fig4B.py')) self.subMenu.addAction(self.Fig4Baction) elif k[0] == "Fig4K": - self.Fig4Kaction = QtGui.QAction('Fig4K', self) + self.Fig4Kaction = QAction('Fig4K', self) self.Fig4Kaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig4_ReacDiff/rxdSpineSize.py')) self.subMenu.addAction(self.Fig4Kaction) elif k[0] == "Fig5A (20s)": - self.Fig5Aaction = QtGui.QAction('Fig5A (20s)', self) + self.Fig5Aaction = QAction('Fig5A (20s)', self) self.Fig5Aaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py')) self.subMenu.addAction(self.Fig5Aaction) elif k[0] == "Fig5BCD (240s)": - self.Fig5BCDaction = QtGui.QAction('Fig5BCD (240s)', self) + self.Fig5BCDaction = QAction('Fig5BCD (240s)', self) self.Fig5BCDaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py')) self.subMenu.addAction(self.Fig5BCDaction) elif k[0] == "Fig6A (60s)": - self.Fig6Aaction = QtGui.QAction('Fig6A (60s)', self) + self.Fig6Aaction = QAction('Fig6A (60s)', self) self.Fig6Aaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py')) self.subMenu.addAction(self.Fig6Aaction) elif k[0] == "ReducedModel (200s)": - self.ReducedModelaction = QtGui.QAction('ReducedModel (200s)', self) + self.ReducedModelaction = QAction('ReducedModel (200s)', self) self.ReducedModelaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py')) self.subMenu.addAction(self.ReducedModelaction) else: - self.Squidaction = QtGui.QAction('Squid', self) + self.Squidaction = QAction('Squid', self) self.Squidaction.triggered.connect(lambda :self.run_python_script('../moose-examples/squid/squid_demo.py')) self.subMenu.addAction(self.Squidaction) self.fileMenu.addMenu(self.subMenu) if not hasattr(self,'loadedModels'): - self.loadedModelAction = QtGui.QAction('Recently Loaded Models',self) + self.loadedModelAction = QAction('Recently Loaded Models',self) self.loadedModelAction.setCheckable(False) - #self.fileMenu.addAction(QtGui.QAction(self.loadedModelAction,checkable=True)) + #self.fileMenu.addAction(QAction(self.loadedModelAction,checkable=True)) if bool(self._loadedModels): self.fileMenu.addSeparator() self.fileMenu.addAction(self.loadedModelAction) @@ -807,15 +744,16 @@ def getFileMenu(self): self.fileMenu.addSeparator() if not hasattr(self,'connectBioModelAction'): - self.connectBioModelAction = QtGui.QAction('&Connect BioModels', self) - self.connectBioModelAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+B", None, QtGui.QApplication.UnicodeUTF8)) - self.connect(self.connectBioModelAction, QtCore.SIGNAL('triggered()'), self.connectBioModel) + self.connectBioModelAction = QAction('&Connect BioModels', self) + self.connectBioModelAction.setShortcut("Ctrl+B") + self.connectBioModelAction.triggered.connect(self.connectBioModel) + self.fileMenu.addAction(self.connectBioModelAction) return self.fileMenu def getEditMenu(self): if self.editMenu is None: - self.editMenu = QtGui.QMenu('&Edit') + self.editMenu = QMenu('&Edit') else: self.editMenu.clear() #self.editMenu.addActions(self.getEditActions()) @@ -824,52 +762,24 @@ def getEditMenu(self): def getPluginsMenu(self): """Populate plugins menu if it does not exist already.""" if (not hasattr(self, 'pluginsMenu')) or (self.pluginsMenu is None): - self.pluginsMenu = QtGui.QMenu('&Plugins') + self.pluginsMenu = QMenu('&Plugins') mapper = QtCore.QSignalMapper(self) - pluginsGroup = QtGui.QActionGroup(self) + pluginsGroup = QActionGroup(self) pluginsGroup.setExclusive(True) for pluginName in self.getPluginNames(): - action = QtGui.QAction(pluginName, self) + action = QAction(pluginName, self) action.setObjectName(pluginName) action.setCheckable(True) - mapper.setMapping(action, QtCore.QString(pluginName)) - self.connect(action, QtCore.SIGNAL('triggered()'), mapper, QtCore.SLOT('map()')) + mapper.setMapping(action, pluginName) + action.triggered.connect(mapper.map) self.pluginsMenu.addAction(action) pluginsGroup.addAction(action) - self.connect(mapper, QtCore.SIGNAL('mapped(const QString &)'), self.setPlugin) - #self.pluginsMenu.addMenu(self.defaultPluginMenu) - #self.pluginsMenu.addMenu(self.kkitPluginMenu) - #self.pluginsMenu.addMenu(self.neurokitPluginMenu) - #openRootAction = self.defaultPluginMenu.addAction("/") - #openRootAction.triggered.connect(lambda : self.setPlugin("default", "/") ) - # if (not hasattr(self, 'loadedModelAction')) or (self.loadedModelAction is None) : - # self.loadedModelAction = QtGui.QAction("kkit",self) - # self.loadedModelAction.addMenu('test') - # self.pluginsMenu.addAction(self.loadedModelAction) - # self.pluginsMenu.addMenu(self.insertkkitMenu) - # self.insertMapperkkit = QtCore.QSignalMapper(self) - #insertMapperkkit,actions = self.getInsertkkitActions(self.loadedModels) - # ignored_bases = ['ZPool', 'Msg', 'Panel', 'SolverBase', 'none'] - # ignored_classes = ['ZPool','ZReac','ZMMenz','ZEnz','CplxEnzBase'] - # classlist = [ch[0].name for ch in moose.element('/classes').children - # if (ch[0].baseClass not in ignored_bases) - # and (ch[0].name not in (ignored_bases + ignored_classes)) - # and not ch[0].name.startswith('Zombie') - # and not ch[0].name.endswith('Base') - # ] - # insertMapper, actions = self.getInsertActions(classlist) - # for action in actions: - # self.insertMenu.addAction(action) - # self.connect(insertMapper, QtCore.SIGNAL('mapped(const QString&)'), self.tree.insertElementSlot) - # self.editAction = QtGui.QAction('Edit', self.treeMenu) - # self.editAction.triggered.connect(self.editCurrentObjectSlot) - # self.tree.elementInserted.connect(self.elementInsertedSlot) - # self.treeMenu.addAction(self.editAction) + mapper.mapped.connect(self.setPlugin) return self.pluginsMenu def getHelpMenu(self): if self.helpMenu is None: - self.helpMenu = QtGui.QMenu('&Help') + self.helpMenu = QMenu('&Help') else: self.helpMenu.clear() self.helpMenu.addActions(self.getHelpActions()) @@ -877,7 +787,7 @@ def getHelpMenu(self): ''' def getConnectMenu(self): if self.connectMenu is None: - self.connectMenu = QtGui.QMenu('&Connect') + self.connectMenu = QMenu('&Connect') else: self.connectMenu.clear() self.connectMenu.addActions(self.getConnectActions()) @@ -885,7 +795,7 @@ def getConnectMenu(self): ''' def getViewMenu(self): if (not hasattr(self, 'viewMenu')) or (self.viewMenu is None): - self.viewMenu = QtGui.QMenu('&View') + self.viewMenu = QMenu('&View') else: self.viewMenu.clear() self.viewMenu.addActions(self.getViewActions()) @@ -895,42 +805,7 @@ def getViewMenu(self): self.subWindowMenu.addActions(self.getSubWindowActions()) return self.viewMenu - # def getSubWindowVisibilityActions(self): - # if not hasattr(self, 'subwindowToToggles'): - # self.subWindowToToggle = QtGui.QSignalMapper() - # self.toggleToSubWindow = QtGui.QSignalMapper() - # for subwindow in self.mdiArea.subWindowList(): - # if self.subWindowToToggle.mapping(subwindow) is None: - # action = QtGui.QAction('Show: %s' % (subwindow.windowTitle), self) - # self.toggleToSubWindow.setMapping(action, subwindow) - # self.connect(action, QtCore.SIGNAL('triggered()'), - # self.toggleToSubWindow, - # QtCore.SLOT('mapped(QWidget*)')) - # self.subWindowToToggle.setMapping(subwindow, action) - # self.connect(subwindow, QtCore.SIGNAL('closed()') - - # self.subWindowVisibilityMenu = QtGui.Q - # for subwin in self.mdiArea.subWindowList(): - - # Removed from the menu - # def getRunMenu(self): - # if (not hasattr(self, 'runMenu')) or (self.runMenu is None): - # self.runMenu = QtGui.QMenu('&Run') - # else: - # self.runMenu.clear() - # self.runMenu.addActions(self.getRunActions()) - # return self.runMenu - def getEditActions(self): - - # self.editActions = [] - # if (not hasattr(self, 'editActions')) or (self.editActions is None): - # self.setModelRootAction = QtGui.QAction('&Set model root', self) - # self.setModelRootAction.triggered.connect(self.showSetModelRootDialog) - # self.setDataRootAction = QtGui.QAction('Set &data root', self) - # self.setDataRootAction.triggered.connect(self.showSetDataRootDialog) - # self.editActions = [self.setModelRootAction, self.setDataRootAction] - # return self.editActions return None def showSetModelRootDialog(self): @@ -944,7 +819,10 @@ def showSetModelRootDialog(self): subwin.setWindowTitle(root) def showSetDataRootDialog(self): - root, ok = QtGui.QInputDialog.getText(self, 'Data Root', 'Enter the data root path:', text=moose.element(self.plugin.dataRoot).path) + root, ok = QtGui.QInputDialog.getText( + self, 'Data Root', 'Enter the data root path:' + , text=moose.element(self.plugin.dataRoot).path + ) if not ok: return root = str(root) #convert from QString to python str @@ -952,34 +830,35 @@ def showSetDataRootDialog(self): for subwin in self.mdiArea.subWindowList(): if hasattr(subwin.widget(), 'dataRoot'): subwin.setWindowTitle(root) + return def getViewActions(self): if (not hasattr(self, 'viewActions')) or (self.viewActions is None): - self.editorViewAction = QtGui.QAction('&Editor view', self) + self.editorViewAction = QAction('&Editor view', self) self.editorViewAction.triggered.connect(self.openEditorView) - #self.plotViewAction = QtGui.QAction('&Plot view', self) + #self.plotViewAction = QAction('&Plot view', self) #self.plotViewAction.triggered.connect(self.openPlotView) - self.runViewAction = QtGui.QAction('&Run view', self) + self.runViewAction = QAction('&Run view', self) self.runViewAction.triggered.connect(self.openRunView) #self.viewActions = [self.editorViewAction, self.plotViewAction, self.runViewAction] self.viewActions = [self.editorViewAction, self.runViewAction] return self.viewActions def setTabbedView(self): - self.mdiArea.setViewMode(QtGui.QMdiArea.TabbedView) + self.mdiArea.setViewMode(QMdiArea.TabbedView) def setSubWindowView(self): - self.mdiArea.setViewMode(QtGui.QMdiArea.SubWindowView) + self.mdiArea.setViewMode(QMdiArea.SubWindowView) def getSubWindowActions(self): if not hasattr(self, 'subWindowActions') or self.subWindowActions is None: - self.tabbedViewAction = QtGui.QAction('&Tabbed view', self) + self.tabbedViewAction = QAction('&Tabbed view', self) self.tabbedViewAction.triggered.connect(self.setTabbedView) - self.subWindowViewAction = QtGui.QAction('&SubWindow view', self) + self.subWindowViewAction = QAction('&SubWindow view', self) self.subWindowViewAction.triggered.connect(self.setSubWindowView) - self.tileSubWindowsAction = QtGui.QAction('Ti&le subwindows', self) + self.tileSubWindowsAction = QAction('Ti&le subwindows', self) self.tileSubWindowsAction.triggered.connect(self.mdiArea.tileSubWindows) - self.cascadeSubWindowsAction = QtGui.QAction('&Cascade subwindows', self) + self.cascadeSubWindowsAction = QAction('&Cascade subwindows', self) self.cascadeSubWindowsAction.triggered.connect(self.mdiArea.cascadeSubWindows) self.subWindowActions = [self.tabbedViewAction, self.subWindowViewAction, @@ -992,39 +871,22 @@ def getDockWidgetsToggleActions(self): widgets """ - return [widget.toggleViewAction() for widget in self.findChildren(QtGui.QDockWidget)] - # Removed form the menu item - # def getRunActions(self): - # if (not hasattr(self, 'runActions')) or \ - # (self.runActions is None): - # self.startAction = QtGui.QAction('Start', self) - # self.startAction.triggered.connect(self.resetAndStartSimulation) - # self.pauseAction = QtGui.QAction('Pause', self) - # self.pauseAction.triggered.connect(self.pauseSimulation) - # self.continueAction = QtGui.QAction('Continue', self) - # self.continueAction.triggered.connect(self.continueSimulation) - # self.runActions = [self.startAction, self.pauseAction, self.continueAction] - # return self.runActions + return [widget.toggleViewAction() for widget in self.findChildren(QDockWidget)] def getHelpActions(self): if (not hasattr(self, 'helpActions')) or (self.helpActions is None): - self.actionAbout = QtGui.QAction('About MOOSE', self) - self.connect(self.actionAbout, QtCore.SIGNAL('triggered()'), self.showAboutMoose) - self.actionBuiltInDocumentation = QtGui.QAction('Built-in documentation', self) - self.connect(self.actionBuiltInDocumentation, QtCore.SIGNAL('triggered()'), self.showBuiltInDocumentation) - self.actionGuiBug = QtGui.QAction('Report gui bug', self) - self.connect(self.actionGuiBug, QtCore.SIGNAL('triggered()'), self.reportGuiBug) - self.actionCoreBug = QtGui.QAction('Report core bug', self) - self.connect(self.actionCoreBug, QtCore.SIGNAL('triggered()'), self.reportCoreBug) - self.helpActions = [self.actionAbout, self.actionBuiltInDocumentation, self.actionCoreBug,self.actionGuiBug] + self.actionAbout = QAction('About MOOSE', self) + self.actionAbout.triggered.connect(self.showAboutMoose) + self.actionBuiltInDocumentation = QAction('Built-in documentation', self) + self.actionBuiltInDocumentation.triggered.connect(self.showBuiltInDocumentation) + self.actionGuiBug = QAction('Report gui bug', self) + self.actionGuiBug.triggered.connect(self.reportGuiBug) + self.actionCoreBug = QAction('Report pymoose bug', self) + self.actionCoreBug.triggered.connect(self.reportCoreBug) + self.helpActions = [self.actionAbout, self.actionBuiltInDocumentation + , self.actionCoreBug,self.actionGuiBug] return self.helpActions - # Removed from the main menu item replace with File menu - # def getConnectActions(self): - # if(not hasattr(self,'connectActions')) or(self.connectActions is None): - # self.actionBioModel = QtGui.QAction('BioModels',self) - # self.connect(self.actionBioModel, QtCore.SIGNAL('triggered()'), self.connectBioModel) - # self.connectActions = [self.actionBioModel] - # return self.connectActions + def connectBioModel(self): connecttoBioModel = BioModelsClientWidget() @@ -1035,7 +897,7 @@ def connectBioModel(self): head, fileName = os.path.split(filepath) modelName = os.path.splitext(fileName)[0] pwe = moose.getCwe() - ret = loadFile(str(filepath), '/model/%s' % (modelName), merge=False) + ret = mload.loadFile(str(filepath), '/model/%s' % (modelName), merge=False) self.objectEditSlot('/',False) pluginLookup = '%s/%s' % (ret['modeltype'], ret['subtype']) try: @@ -1060,40 +922,22 @@ def connectBioModel(self): def showAboutMoose(self): - with open(config.MOOSE_ABOUT_FILE, 'r') as aboutfile: - QtGui.QMessageBox.about(self, 'About MOOSE', ''.join(aboutfile.readlines())) + about = "

MOOSE simulator

" + about += 'MOOSE Website' + about += "

VERSION " + moose.__version__ + "

" + QMessageBox.about(self, 'About MOOSE', about ) - def showDocumentation(self, source): + def showDocumentation(self): QtGui.QDesktopServices.openUrl(QtCore.QUrl(config.MOOSE_DOC_URL)) - ''' - if not hasattr(self, 'documentationViewer'): - self.documentationViewer = QtGui.QTextBrowser() - self.documentationViewer.setOpenLinks(True) - self.documentationViewer.setOpenExternalLinks(True) - #print " path ",config.settings[config.KEY_DOCS_DIR], os.path.join(config.settings[config.KEY_DOCS_DIR], 'html'), os.path.join(config.settings[config.KEY_DOCS_DIR], 'images') - self.documentationViewer.setSearchPaths([config.settings[config.KEY_DOCS_DIR], - os.path.join(config.settings[config.KEY_DOCS_DIR], 'html'), - os.path.join(config.settings[config.KEY_DOCS_DIR], 'images')]) - self.documentationViewer.setMinimumSize(800, 480) - self.documentationViewer.setSource(QtCore.QUrl(source)) - result = self.documentationViewer.loadResource(QtGui.QTextDocument.HtmlResource, self.documentationViewer.source()) - if not result.isValid(): - QtGui.QMessageBox.warning(self, 'Could not access documentation', 'The link %s could not be accessed' % (source)) - return - self.documentationViewer.setWindowTitle(source) - self.documentationViewer.reload() - self.documentationViewer.setVisible(True) - ''' + def reportGuiBug(self): QtGui.QDesktopServices.openUrl(QtCore.QUrl(config.MOOSE_GUI_BUG_URL)) + def reportCoreBug(self): QtGui.QDesktopServices.openUrl(QtCore.QUrl(config.MOOSE_CORE_BUG_URL)) - ''' - def reportBug(self): - QtGui.QDesktopServices.openUrl(QtCore.QUrl(config.MOOSE_REPORT_BUG_URL)) - ''' + def showBuiltInDocumentation(self): - self.showDocumentation('moose_builtins.html') + self.showDocumentation( ) # openEditorView, openPlotView and openRunView are identical # except the view they ask from the plugin. Consider using a @@ -1149,6 +993,7 @@ def resetAndStartSimulation(self): def pauseSimulation(self): moose.stop() + ''' def continueSimulation(self): """TODO implement this somewhere else""" @@ -1158,10 +1003,10 @@ def continueSimulation(self): simtime = 1.0 moose.start(simtime) ''' - #Harsha: added visible=True so that loadModelDialogSlot and NewModelDialogSlot call this function - # to clear out object path + def objectEditSlot(self, mobj, visible=True): """Slot for switching the current object in object editor.""" + logger_.debug("objectEditSlot is called: dropped event") self.objectEditDockWidget.setObject(mobj) self.objectEditDockWidget.setVisible(visible) @@ -1171,8 +1016,6 @@ def objectEditSlot(self, mobj, visible=True): def loadedModelsAction(self,modelPath,pluginName): - #Harsha: added under file Menu, Recently Loaded Models - #All the previously loaded chemical models, solver's and table's ticks are made -1 for model in self._loadedModels: self.disableModel(model[0]) @@ -1185,16 +1028,12 @@ def loadedModelsAction(self,modelPath,pluginName): if compt: self.simulationdt = c.tickDt[11] self.plotdt = c.tickDt[16] - #index = [(ind, self._loadedModels[ind].index(modelPath)) for ind in xrange(len(self.loadedModels)) if item in self._loadedModels[ind]] - # for i,j in enumerate(self._loadedModels): - # if j[0] == modelPath: - # #del(self._loadedModels[i]) - # pass - # break - self._loadedModels.append([modelPath,pluginName,action,self.simulationdt,self.plotdt]) - if len(self._loadedModels)>5: - self._loadedModels.pop(0) + self._loadedModels.append( + [ modelPath,pluginName,action,self.simulationdt,self.plotdt ] + ) + if len(self._loadedModels) > 5: + self._loadedModels.pop( 0 ) def disableModel(self, modelPath): compt = moose.wildcardFind(modelPath + '/##[ISA=ChemCompt]') @@ -1289,9 +1128,9 @@ def displaymodelInfo(self,ret): noOfEnz = len(moose.wildcardFind(ret['model'].path+'/##[ISA=EnzBase]')) noOfStimtab = len(moose.wildcardFind(ret['model'].path+'/##[ISA=StimulusTable]')) - reply = QtGui.QMessageBox.information(self,"Model Info","Model has : \n %s Compartment \t \n %s Group \t \n %s Pool \t \n %s Function \t \n %s reaction \t \n %s Enzyme \t \n %s StimulusTable" %(noOfCompt, grp, noOfPool, noOfFunc, noOfReac, noOfEnz, noOfStimtab)) - if reply == QtGui.QMessageBox.Ok: - QtGui.QApplication.restoreOverrideCursor() + reply = QMessageBox.information(self,"Model Info","Model has : \n %s Compartment \t \n %s Group \t \n %s Pool \t \n %s Function \t \n %s reaction \t \n %s Enzyme \t \n %s StimulusTable" %(noOfCompt, grp, noOfPool, noOfFunc, noOfReac, noOfEnz, noOfStimtab)) + if reply == QMessageBox.Ok: + QApplication.restoreOverrideCursor() return def checkPlugin(self,dialog): @@ -1300,8 +1139,8 @@ def checkPlugin(self,dialog): modelName = dialog.getTargetPath() if '/' in modelName: raise mexception.ElementNameError('Model name cannot contain `/`') - ret = loadFile(str(fileName),'%s' %(modelName),merge=False) - #ret = loadFile(str(fileName), '/model/%s' % (modelName), merge=False) + ret = mload.loadFile(str(fileName),'%s' %(modelName),merge=False) + #ret = mload.loadFile(str(fileName), '/model/%s' % (modelName), merge=False) #This will clear out object editor's objectpath and make it invisible self.objectEditSlot('/',False) #if subtype is None, in case of cspace then pluginLookup = /cspace/None @@ -1325,23 +1164,23 @@ def dialog_check(self,ret): if pluginName == 'kkit': if (ret['subtype'] == 'sbml' and ret['foundlib'] == False): - reply = QtGui.QMessageBox.question(self, "python-libsbml is not found.","\n Read SBML is not possible.\n This can be installed using \n \n pip python-libsbml or \n apt-get install python-libsbml", - QtGui.QMessageBox.Ok) - if reply == QtGui.QMessageBox.Ok: - QtGui.QApplication.restoreOverrideCursor() + reply = QMessageBox.question(self, "python-libsbml is not found.","\n Read SBML is not possible.\n This can be installed using \n \n pip python-libsbml or \n apt-get install python-libsbml", + QMessageBox.Ok) + if reply == QMessageBox.Ok: + QApplication.restoreOverrideCursor() return valid, ret else: if ret['loaderror'] != "": - reply = QtGui.QMessageBox.question(self, "Model can't be loaded", ret['loaderror']+" \n \n Do you want another file", - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if reply == QtGui.QMessageBox.Yes: + reply = QMessageBox.question(self, "Model can't be loaded", ret['loaderror']+" \n \n Do you want another file", + QMessageBox.Yes | QMessageBox.No) + if reply == QMessageBox.Yes: dialog = LoaderDialog(self,self.tr('Load model from file')) if dialog.exec_(): pluginName = None ret,pluginName = self.checkPlugin(dialog) valid,ret = self.dialog_check(ret) else: - QtGui.QApplication.restoreOverrideCursor() + QApplication.restoreOverrideCursor() return valid,ret else: valid = True @@ -1358,14 +1197,7 @@ def newModelDialogSlot(self): raise mexception.ElementNameError('Model path cannot be empty') if re.search('[ /]',modelPath) is not None: raise mexception.ElementNameError('Model path should not containe / or whitespace') - #plugin = str(newModelDialog.submenu.currentText()) plugin = str(newModelDialog.getcurrentRadioButton()) - #Harsha: All model will be forced to load/build under /model, - #2014 sep 10: All the model will be forced to load/build model under /modelName/model - ''' - modelContainer = moose.Neutral('/model') - modelRoot = moose.Neutral('%s/%s' % (modelContainer.path, modelPath)) - ''' if moose.exists(modelPath+'/model'): moose.delete(modelPath) @@ -1379,34 +1211,4 @@ def newModelDialogSlot(self): modelAnno.dirpath = " " self.loadedModelsAction(modelRoot.path,plugin) self.setPlugin(plugin, modelRoot.path) - #Harsha: This will clear out object editor's objectpath and make it invisible self.objectEditSlot('/', False) - -def main(): - # create the GUI application - app = QtGui.QApplication(sys.argv) - QtGui.qApp = app - #icon = QtGui.QIcon(os.path.join(config.KEY_ICON_DIR,'moose_icon.png')) - #app.setWindowIcon(icon) - # instantiate the main window - #moose.loadModel('../Demos/Genesis_files/Kholodenko.g','/kho') - mWindow = MWindow() - mWindow.setWindowState(QtCore.Qt.WindowMaximized) - sys.excepthook = mWindow.handleException - # show it - mWindow.show() - # start the Qt main loop execution, exiting from this script - #http://code.google.com/p/subplot/source/browse/branches/mzViewer/PyMZViewer/mpl_custom_widget.py - #http://eli.thegreenplace.net/files/prog_code/qt_mpl_bars.py.txt - #http://lionel.textmalaysia.com/a-simple-tutorial-on-gui-programming-using-qt-designer-with-pyqt4.html - #http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg13241.html - # with the same return code of Qt application - config.settings[config.KEY_FIRSTTIME] = 'False' # string not boolean - sys.exit(app.exec_()) - - -if __name__ == '__main__': - main() - -# -# mgui.py ends here diff --git a/MdiArea.py b/moosegui/MdiArea.py similarity index 76% rename from MdiArea.py rename to moosegui/MdiArea.py index 005bf7c..d13cbf6 100644 --- a/MdiArea.py +++ b/moosegui/MdiArea.py @@ -1,10 +1,12 @@ -from PyQt4 import Qt, QtCore, QtGui -from PyQt4.QtGui import * +from PyQt5.QtGui import QImage, QPainter, QColor, QBrush +from PyQt5.QtWidgets import QMdiArea +from PyQt5 import QtCore import os -APPLICATION_BACKGROUND_PATH = os.path.join( os.path.dirname(os.path.realpath(__file__)) - , "icons/moose_icon_large.png" - ) +APPLICATION_BACKGROUND_PATH = os.path.join( + os.path.dirname(os.path.realpath(__file__)) + , "icons/moose_icon_large.png" + ) class MdiArea(QMdiArea): diff --git a/moosegui/PlotWidgetContainer.py b/moosegui/PlotWidgetContainer.py new file mode 100644 index 0000000..c534469 --- /dev/null +++ b/moosegui/PlotWidgetContainer.py @@ -0,0 +1,133 @@ +# -*- coding: utf-8 -*- + +__author__ = "Aviral Goel" +__credits__ = ["Upi Lab"] +__license__ = "GPL3" +__maintainer__ = "Aviral Goel", "HarshaRani" +__email__ = "goel.aviral@gmail.com" + +from PyQt5 import QtCore +from PyQt5.QtWidgets import QWidget, QSizePolicy +from PyQt5.QtWidgets import QVBoxLayout +from PyQt5.QtWidgets import QScrollArea +from PyQt5.QtWidgets import QSplitter + +# MOOSE gui +from moosegui import sidebar + +# MOOSE +import moose + +ELECTRICAL = 0 +CHEMICAL = 1 + +class PlotWidgetContainer(QWidget): + + def __init__(self, modelRoot, *args, **kwargs): + super(PlotWidgetContainer, self).__init__(*args) + self.modelRoot = modelRoot + if len(moose.wildcardFind(modelRoot + "/##[ISA=ChemCompt]")) == 0: + self.modelType = ELECTRICAL + else: + self.modelType = CHEMICAL + + self.model = moose.element(self.modelRoot) + if self.modelRoot != "/": + self.modelRoot = self.findModelPath(self.modelRoot) + if moose.exists(modelRoot + "/data"): + self.data = moose.element(self.modelRoot + "/data") + else: + self.data = moose.Neutral(self.modelRoot + "/data") + else: + self.data = moose.element("/data") + + self._layout = QVBoxLayout() + self.graphs = QSplitter() + self.graphs.setOrientation(QtCore.Qt.Vertical) + self.graphsArea = QScrollArea() + self.rowIndex = 0 + self.graphs.setSizePolicy( QSizePolicy.Expanding, QSizePolicy.Expanding) + self.setAcceptDrops(True) + self.graphsArea.setWidget(self.graphs) + self.graphsArea.setWidgetResizable(True) + self.graphWidgets = [] + self._layout.addWidget(self.graphsArea) + self.setLayout(self._layout) + + for graph in self.data.children: + self.addPlotWidget(graph = graph) + + if len(self.data.children) == 0: + self.addPlotWidget() + + def mooseIsInstance(self,element, classNames): + return moose.element(element).__class__.__name__ in classNames + + + def findModelPath(self,element): + child = element + while not self.mooseIsInstance(element, "Shell"): + child = moose.element(element).path + element = moose.element(element).parent + return child + + def deleteWidget(self, graphWidget): + # print("Deleted => ", graphWidget) + self.graphWidgets.remove(graphWidget) + graphWidget.setParent(None) + graphWidget.close() + + def createMenuBar(self): + bar = sidebar.sidebar() + bar.addAction(sidebar.add_graph_action(bar, lambda event: self.addPlotWidget() )) + return bar + + def addPlotWidget(self, row = None, col = 0, graph = None): + if graph == None: + graph = moose.Neutral(self.data.path + "/graph_" + str(self.rowIndex)) + + + if row == None: + row = self.rowIndex + + #if self.modelType == ELECTRICAL: + # for axes in list(widget.canvas.axes.values()): + # axes.set_ylim(bottom = -0.07, top= 0.03) + + # FIXME: + # Has been removed? See #23 + # widget = default.PlotWidget(self.model, graph, self.rowIndex, self) + ## self.graphs.addWidget(widget) + ## self.rowIndex += 1 + ## self.graphWidgets.append(widget) + ## widget.widgetClosedSignal.connect(self.deleteWidget) + ## widget.addGraph.connect(lambda event : self.addPlotWidget()) + ## return widget + + def showPlotView(self): + pass + + def setModelRoot(self, *args): + pass + + def getMenus(self, *args): + return [] + + def setDataRoot(self, *args): + pass + + def updatePlots(self): + for graphWidget in self.graphWidgets: + graphWidget.updatePlots() + + def rescalePlots(self): + for graphWidget in self.graphWidgets: + graphWidget.rescalePlots() + + def extendXAxes(self, xlim): + for graphWidget in self.graphWidgets: + graphWidget.extendXAxes(xlim) + + def plotAllData(self): + for graphWidget in self.graphWidgets: + graphWidget.plotAllData() diff --git a/RunWidget.py b/moosegui/RunWidget.py similarity index 81% rename from RunWidget.py rename to moosegui/RunWidget.py index dd78a2f..e9ce380 100644 --- a/RunWidget.py +++ b/moosegui/RunWidget.py @@ -1,13 +1,12 @@ - # -*- coding: utf-8 -*- -from __future__ import print_function -"""Sidebar for plugins. The sidebar comprises of actions. +""" +Sidebar for plugins. The sidebar comprises of actions. Currently mode, connect and settings are defined. + """ __author__ = "Aviral Goel" -__credits__ = ["Upi Lab"] __license__ = "GPL3" __version__ = "1.0.0" __maintainer__ = "Aviral Goel" @@ -17,21 +16,25 @@ import sys import os -import SettingsDialog -from PyQt4 import QtGui, Qt -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QScrollArea -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QSplitter + +from PyQt5.QtWidgets import QScrollArea +from PyQt5.QtWidgets import QGridLayout +from PyQt5.QtWidgets import QSplitter +from PyQt5.QtWidgets import QWidget + +from moosegui import SettingsDialog class RunWidget(QSplitter): + """ Run view """ def __init__(self, modelRoot, *args, **kwargs): super(RunWidget, self).__init__(None) self.modelRoot = modelRoot + self.topWidget = QWidget() layout = QGridLayout() - self.setLayout(layout) + self.topWidget.setLayout(layout) self.plotWidgetContainer = None + def setChildWidget(self, widget, wrap, row, col, rowspan = 1, colspan = 1): if wrap: scrollArea = QScrollArea() diff --git a/SettingsDialog.py b/moosegui/SettingsDialog.py similarity index 52% rename from SettingsDialog.py rename to moosegui/SettingsDialog.py index bd6ce56..f565e0a 100644 --- a/SettingsDialog.py +++ b/moosegui/SettingsDialog.py @@ -1,8 +1,7 @@ - # -*- coding: utf-8 -*- -from __future__ import print_function -"""Dialog for settings. Currently only plot settings are supported +""" +Dialog for settings. Currently only plot settings are supported """ __author__ = "Aviral Goel" @@ -15,13 +14,12 @@ import sys -import os -from PyQt4 import QtGui, Qt -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QLabel -from PyQt4.QtGui import QComboBox -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QTabWidget +from PyQt5 import Qt +from PyQt5.QtWidgets import QWidget +from PyQt5.QtWidgets import QLabel +from PyQt5.QtWidgets import QComboBox +from PyQt5.QtWidgets import QGridLayout +from PyQt5.QtWidgets import QTabWidget class SettingsWidget(QTabWidget): def __init__( self @@ -40,7 +38,7 @@ def plotSettingsPage(self): layout = QGridLayout() page.setLayout(layout) index = 0 - for key, values in self.plotFieldMap.iteritems() : + for key, values in list(self.plotFieldMap.items()) : label = QLabel(key, page) combo = QComboBox(page) for value in values: @@ -50,32 +48,21 @@ def plotSettingsPage(self): index += 1 return page - # combo.move(50, 50) - # self.lbl.move(50, 150) - - # combo.activated[str].connect(self.onActivated) - - # self.setGeometry(300, 300, 300, 200) - # self.setWindowTitle('QtGui.QComboBox') - # self.show() - - def main(): - app = QtGui.QApplication(sys.argv) - window = QtGui.QMainWindow() + from PyQt5.QtWidgets import QApplication + app = QApplication(sys.argv) dialog = SettingsWidget({ - 'LeakyIaF':['Vm'], - 'Compartment':['Vm','Im'], - 'HHChannel':['Ik','Gk'], - 'ZombiePool':['n','conc'], - 'ZombieBufPool':['n','conc'], - 'HHChannel2D':['Ik','Gk'], - 'CaConc':['Ca'] - } - ) + 'LeakyIaF':['Vm'], + 'Compartment':['Vm','Im'], + 'HHChannel':['Ik','Gk'], + 'ZombiePool':['n','conc'], + 'ZombieBufPool':['n','conc'], + 'HHChannel2D':['Ik','Gk'], + 'CaConc':['Ca'] + } + ) dialog.show() sys.exit(app.exec_()) - if __name__ == "__main__": main() diff --git a/moosegui/TooltipInfo.py b/moosegui/TooltipInfo.py new file mode 100644 index 0000000..538e06d --- /dev/null +++ b/moosegui/TooltipInfo.py @@ -0,0 +1,29 @@ +"""TooltipInfo.py: + +Keeps all TooltipInfo here. + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import sys +import os + +tooltip_info_dict_ = { + "CubeMesh": "Cubical compartment", + "CylMesh": "Cylinderical compartment", + "Pool": "A Pool is a collection of molecules of a given species in a given cellular compartment.\n It can undergo reactions that convert it into other pool(s). \nParameters: initConc (Initial concentration), diffConst (diffusion constant). Variable: conc (Concentration)", + "BufPool": "A BufPool is a buffered pool. \nIt is a collection of molecules of a given species in a given cellular compartment, that are always present at the same concentration.\n This is set by the initConc parameter. \nIt can undergo reactions in the same way as a pool.", + "Function": "A Func computes an arbitrary mathematical expression of one or more input concentrations of Pools. The output can be used to control the concentration of another Pool, or as an input to another Func", + "StimulusTable": "A StimulusTable stores an array of values that are read out during a simulation, and typically control the concentration of one of the pools in the model. \nParameters: size of table, values of entries, start and stop times, and an optional loopTime that defines the period over which the StimulusTable should loop around to repeat its values", + "Reac": "A Reac is a chemical reaction that converts substrates into products, and back. \nThe rates of these conversions are specified by the rate constants Kf and Kb respectively.", + "MMenz": "An MMenz is the Michaelis-Menten version of an enzyme activity of a given Pool.\n The MMenz must be created on a pool and can only catalyze a single reaction with a specified substrate(s). \nIf a given enzyme species can have multiple substrates, then multiple MMenz activites must be created on the parent Pool. \nThe rate of an MMenz is V [S].[E].kcat/(Km + [S]). There is no enzyme-substrate complex. Parameters: Km and kcat.", + "Enz": "An Enz is an enzyme activity of a given Pool. The Enz must be created on a pool and can only catalyze a single reaction with a specified substrate(s). \nIf a given enzyme species can have multiple substrates, then multiple Enz activities must be created on the parent Pool. \nThe reaction for an Enz is E + S <===> E.S ---> E + P. \nThis means that a new Pool, the enzyme-substrate complex E.S, is always formed when you create an Enz. \nParameters: Km and kcat, or alternatively, K1, K2 and K3. Km = (K2+K3)/K1" +} diff --git a/moosegui/__init__.py b/moosegui/__init__.py new file mode 100644 index 0000000..04710fb --- /dev/null +++ b/moosegui/__init__.py @@ -0,0 +1,3 @@ +from __future__ import print_function, division, absolute_import +import matplotlib +# matplotlib.use('Qt5Agg') diff --git a/moosegui/__main__.py b/moosegui/__main__.py new file mode 100644 index 0000000..24031be --- /dev/null +++ b/moosegui/__main__.py @@ -0,0 +1,8 @@ +# -*- coding: utf-8 -*- + +def main(): + import moosegui.mgui + moosegui.mgui.main() + +if __name__ == '__main__': + main() diff --git a/biomodelsclient.py b/moosegui/biomodelsclient.py similarity index 79% rename from biomodelsclient.py rename to moosegui/biomodelsclient.py index 6a24ba2..a7c2bf8 100644 --- a/biomodelsclient.py +++ b/moosegui/biomodelsclient.py @@ -1,6 +1,4 @@ -# biomodelsclient.py --- -# -# Filename: biomodelsclient.py +# -*- coding: utf-8 -*- # Description: # Author: Subhasis Ray # Maintainer: @@ -9,83 +7,45 @@ # Last-Updated: Wed Dec 11 15:47:32 2010 (+0530) # By: # Update #: -# URL: -# Keywords: -# Compatibility: -# -# -# Commentary: -# -# This is a client for Biomodels database SOAP service. -# It imitates the SOAP client written in JAVA -# availabele at biomodels website. +import os +import pickle +import moose -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# -# Code: +from PyQt5.Qt import Qt +from PyQt5 import QtCore, QtGui +from PyQt5.QtWidgets import QDialog, QWidget +from moosegui import config from suds.client import Client from suds.transport.http import HttpTransport as SudsHttpTransport -import os -import config -import pickle -import moose BIOMODELS_WSDL_URI = 'http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl' proxyOpts = dict() -for k,v in {'http':'http_proxy','https':'https_proxy'}.items(): - if os.environ.has_key(v): +for k,v in list({'http':'http_proxy','https':'https_proxy'}.items()): + if v in os.environ: httpProxy = os.environ[v].replace('http://', '') proxyOpts[k] = httpProxy[0:httpProxy.rfind('/',0,len(httpProxy))] - elif os.environ.has_key(v.upper()): + elif v.upper() in os.environ: HttpProxy = os.environ[v.upper()].replace('http://', '') proxyOpts[k] = HttpProxy[0:HttpProxy.rfind('/',0,len(HttpProxy))] -''' -class HttpTransport(SudsHttpTransport): - """HttpTransport which properly obeys the ``*_proxy`` environment variables.""" - def u2handlers(self): - return [] -''' class BioModelsClient(Client): def __init__(self, WSDL_URI=BIOMODELS_WSDL_URI): - """Initialize the client with the available queries listed in - the WSDL file. All the queries can be executed using the following syntax: - - client.service.queryToBeExecuted() - """ - try: - Client.__init__(self, WSDL_URI,proxy=proxyOpts) - #Client.__init__(self, WSDL_URI,transport=HttpTransport()) - except Exception, e: - print e + """Initialize the client with the available queries listed in + the WSDL file. All the queries can be executed using the following syntax: + + client.service.queryToBeExecuted() + """ + try: + Client.__init__(self, WSDL_URI,proxy=proxyOpts) + except Exception as e: + print(e) -from PyQt4.Qt import Qt -from PyQt4 import QtCore, QtGui -class BioModelsClientWidget(QtGui.QDialog): +class BioModelsClientWidget(QDialog): """This is a widget with a Biomodels Client. It provides simple access to the biomodel queries and gives the user a view of the results""" @@ -102,10 +62,10 @@ class BioModelsClientWidget(QtGui.QDialog): ('Model Ids by Publication', 'getModelsIdByPublication'), ('Model Ids by Taxonomy', 'getModelsIdByTaxonomy'),] def __init__(self, parent=None): - QtGui.QWidget.__init__(self, parent) + QWidget.__init__(self, parent) self.setWindowTitle('Connect to BioModels') - self.client = BioModelsClient() - self.queryPanel = QtGui.QWidget(self) + self.client = BioModelsClient() + self.queryPanel = QWidget(self) self.queryModelLabel = QtGui.QLabel('Get ', self.queryPanel) self.queryModelCombo = QtGui.QComboBox(self.queryPanel) self.queryLineEdit = QtGui.QLineEdit(self.queryPanel) @@ -125,7 +85,7 @@ def __init__(self, parent=None): layout.addWidget(self.queryPanel) layout.addWidget(self.resultsPanel) - self.queryPanel1 = QtGui.QWidget(self) + self.queryPanel1 = QWidget(self) self.importButton = QtGui.QPushButton('Import',self.queryPanel1) self.importButton.setEnabled(False) self.closeButton = QtGui.QPushButton('Close',self.queryPanel1) @@ -139,8 +99,8 @@ def __init__(self, parent=None): self.setupActions() self.client.set_options(proxy=proxyOpts) - # TODO: - # proxy = [ can be set using set_option(proxy={'http':'proxyhost:port', ...}) function + # TODO: + # proxy = [ can be set using set_option(proxy={'http':'proxyhost:port', ...}) function def setupActions(self): self.connect(self.queryLineEdit, QtCore.SIGNAL('returnPressed()'), self.runQuery) @@ -156,7 +116,7 @@ def downloadModel(self): """ If user select multi row, only data from currentRow is downloaded and loaded into moose """ selectedRow = self.resultsPanel.currentRow() modelId = self.resultsPanel.item(selectedRow, 0).text() - modelSBML = unicode(self.client.service.getModelSBMLById(modelId)).encode("utf-8") + modelSBML = str(self.client.service.getModelSBMLById(modelId)).encode("utf-8") self.filePath = os.path.join(config.settings[config.KEY_LOCAL_DEMOS_DIR], str(modelId)+'.xml') f = open(str(self.filePath), 'w') f.write(modelSBML) @@ -181,7 +141,7 @@ def getTargetPath(self): return str(self.filePath) def runQuery(self): - print 'Running query .....' + print('Running query .....') #self.resultsPanel.cellClicked.connect(self.enableDownload) progressDialog = QtGui.QProgressDialog() progressDialog.setLabelText('Retrieving data from BioModels Database') @@ -237,7 +197,7 @@ def runQuery(self): progressDialog.setValue(r) if progressDialog.wasCanceled(): return 0 - name = unicode(self.client.service.getModelNameById(item)).encode("utf-8") + name = str(self.client.service.getModelNameById(item)).encode("utf-8") r = r+1 pickleResult.update({item:name}) updatepickleFile = True @@ -253,12 +213,12 @@ def runQuery(self): pickleResult = {} pickleResult[argument] = name; - except KeyError, e: - print 'A KeyError - "%s"' % str(e) ,' not found in ',filename + except KeyError as e: + print(('A KeyError - "%s"' % str(e) ,' not found in ',filename)) QtGui.QMessageBox.critical(None, "BioModels Database"," The Id "+ str(e) +" not found in "+ filename,QtGui.QMessageBox.Ok | QtGui.QMessageBox.Default,QtGui.QMessageBox.NoButton) display = False if display: - for value,name in pickleResult.items(): + for value,name in list(pickleResult.items()): self.resultsPanel.insertRow(row) item = QtGui.QTableWidgetItem(self.tr(value)) item.setFlags(item.flags() & ~Qt.ItemIsEditable) @@ -273,7 +233,7 @@ def runQuery(self): if progressDialog: progressDialog.close() #self.importButton.setEnabled(True) - print 'Finished running query' + print('Finished running query') def enableimportButton(self): self.importButton.setEnabled(True) diff --git a/checkcombobox.py b/moosegui/checkcombobox.py similarity index 69% rename from checkcombobox.py rename to moosegui/checkcombobox.py index 70d3c07..8f111b0 100644 --- a/checkcombobox.py +++ b/moosegui/checkcombobox.py @@ -1,54 +1,13 @@ -# checkcombobox.py --- -# -# Filename: checkcombobox.py # Description: # Author: # Maintainer: # Created: Wed Jun 5 15:06:21 2013 (+0530) # Version: -# Last-Updated: Wed Jun 5 18:42:50 2013 (+0530) -# By: subha -# Update #: 188 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# ComboBox with checkable items. Inspired by the same in libqxt. -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: import sys - -from PyQt4 import QtCore, QtGui -from PyQt4.Qt import Qt +from PyQt5 import QtCore, QtGui +from PyQt5.Qt import Qt +from PyQt5.QtWidgets import QComboBox, QApplication, QMainWindow from collections import defaultdict class CheckComboBoxModel(QtGui.QStandardItemModel): @@ -62,13 +21,13 @@ def flags(self, index): return Qt.ItemIsUserCheckable | Qt.ItemIsSelectable | Qt.ItemIsEnabled def data(self, index, role): - if index.isValid() and role == Qt.CheckStateRole: + if index and role == Qt.CheckStateRole: return QtCore.QVariant(self.checked_dict[index]) else: return QtGui.QStandardItemModel.data(self, index, role) def setData(self, index, value, role=Qt.EditRole): - if not index.isValid(): + if not index: return False ok = QtGui.QStandardItemModel.setData(self, index, value, role) if ok and role == Qt.CheckStateRole: @@ -85,15 +44,13 @@ def __init__(self, parent): def eventFilter(self, obj, event): etype = event.type() if etype == event.KeyPress or etype == event.KeyRelease: - if obj == self and \ - (event.key() == Qt.Key_UP or - event.key() == Qt.Key_Down): + if obj == self and event.key() == Qt.Key_UP or event.key() == Qt.Key_Down: self.parent().showPopup() return True elif event.key() == Qt.Key_Enter or \ - event.key() == Qt.Key_Return or \ - event.key() == Qt.Key_Escape: - QtGui.QComboBox.hidePopup(self.parent()) + event.key() == Qt.Key_Return or \ + event.key() == Qt.Key_Escape: + QComboBox.hidePopup(self.parent()) if event.key() != Qt.Key_Escape: return True elif etype == event.MouseButtonPress: @@ -102,11 +59,11 @@ def eventFilter(self, obj, event): self.parent()._containerMousePress = False return False -class CheckComboBox(QtGui.QComboBox): +class CheckComboBox(QComboBox): """Specialization of QComboBox to allow checkable items. This is inspired by the same class in Qxt""" def __init__(self, *args): - QtGui.QComboBox.__init__(self, *args) + QComboBox.__init__(self, *args) self._containerMousePress = False self.setModel(CheckComboBoxModel()) self.activated.connect(self.toggleCheckState) @@ -119,7 +76,7 @@ def __init__(self, *args): def hidePopup(self): """This is to disable hiding of the popup when an item is clicked.""" if self._containerMousePress: - QtGui.QComboBox.hidePopup(self) + QComboBox.hidePopup(self) def itemCheckState(self, index): return self.itemData(index, Qt.CheckStateRole).toInt()[0] @@ -135,14 +92,14 @@ def checkedItems(self): def setCheckedItems(self, textItemList): for text in textItemList: index = self.findText(text) - if index.isValid(): + if index: self.setItemCheckState(index, Qt.Checked) else: self.setItemCheckState(index, Qt.Unchecked) def toggleCheckState(self, index): value = self.itemData(index, Qt.CheckStateRole) - if value.isValid(): + if value: state = value.toInt()[0] if state == Qt.Checked: self.setItemData(index, Qt.Unchecked, Qt.CheckStateRole) @@ -151,8 +108,8 @@ def toggleCheckState(self, index): def main(): """Test main: load a model and display the tree for it""" - app = QtGui.QApplication([]) - mainwin = QtGui.QMainWindow() + app = QApplication([]) + mainwin = QMainWindow() mainwin.setWindowTitle('CheckComboBox test') box = CheckComboBox() for ii in range(5): @@ -161,9 +118,6 @@ def main(): mainwin.show() sys.exit(app.exec_()) + if __name__ == '__main__': main() - - -# -# checkcombobox.py ends here diff --git a/colormaps/fire b/moosegui/colormaps/fire similarity index 100% rename from colormaps/fire rename to moosegui/colormaps/fire diff --git a/colormaps/greenfire b/moosegui/colormaps/greenfire similarity index 100% rename from colormaps/greenfire rename to moosegui/colormaps/greenfire diff --git a/colormaps/grey b/moosegui/colormaps/grey similarity index 100% rename from colormaps/grey rename to moosegui/colormaps/grey diff --git a/colormaps/heat b/moosegui/colormaps/heat similarity index 100% rename from colormaps/heat rename to moosegui/colormaps/heat diff --git a/colormaps/jet b/moosegui/colormaps/jet similarity index 100% rename from colormaps/jet rename to moosegui/colormaps/jet diff --git a/colormaps/rainbow2.pkl b/moosegui/colormaps/rainbow2.pkl similarity index 100% rename from colormaps/rainbow2.pkl rename to moosegui/colormaps/rainbow2.pkl diff --git a/colormaps/redhot b/moosegui/colormaps/redhot similarity index 100% rename from colormaps/redhot rename to moosegui/colormaps/redhot diff --git a/moosegui/config.py b/moosegui/config.py new file mode 100644 index 0000000..241dd50 --- /dev/null +++ b/moosegui/config.py @@ -0,0 +1,133 @@ +# -*- coding: utf-8 -*- + +# Filename: config.py +# Description: +# Author: Subhasis Ray +# Maintainer: +# Created: Sat Feb 13 16:07:56 2010 (+0530) +# Version: + +import os +import sys +from PyQt5 import QtCore + +# Logger +import logging +logging.basicConfig(level=logging.DEBUG) + +KEY_UNDO_LENGTH = 'main/undolength' +KEY_WINDOW_GEOMETRY = 'main/geometry' +KEY_WINDOW_LAYOUT = 'main/layout' +KEY_RUNTIME_AUTOHIDE = 'main/rtautohide' +KEY_DEMOS_DIR = 'main/demosdir' +KEY_DOCS_DIR = 'main/docsdir' +KEY_HOME_DIR = 'main/homedir' +KEY_ICON_DIR = 'main/icondir' +KEY_COLORMAP_DIR = 'main/colormapdir' +KEY_BIOMODEL_DIR = 'main/biomodelsdir' +KEY_LOCAL_DEMOS_DIR = 'main/localdemosdir' +KEY_MOOSE_LOCAL_DIR = 'main/localdir' +KEY_NUMPTHREADS = 'main/numpthreads' +KEY_LOCAL_BUILD = 'main/localbuild' +KEY_LAST_PLUGIN = 'main/lastplugin' + +# These are the keys for mode specific configuration. +# Ideally the default values should be provided by the plugin. +# We use the QSettings to remember the last values +KEY_KINETICS_SIMDT = 'kinetics/simdt' +KEY_KINETICS_PLOTDT = 'kinetics/plotdt' +KEY_ELECTRICAL_SIMDT = 'electrical/simdt' +KEY_ELECTRICAL_PLOTDT = 'electrical/plotdt' +KEY_SIMTIME = 'main/simtime' + +QT_VERSION = ('%s' % QtCore.QT_VERSION_STR).split('.') +QT_MAJOR_VERSION = int(QT_VERSION[0]) +QT_MINOR_VERSION = int(QT_VERSION[1]) + +MOOSE_DOC_URL = 'http://moose.ncbs.res.in/builtins_classes/moose_builtins.html' +MOOSE_REPORT_BUG_URL = 'http://github.com/BhallaLab/moose/issues' +MOOSE_GUI_BUG_URL = 'https://github.com/BhallaLab/moose-gui/issues' +MOOSE_CORE_BUG_URL = 'https://github.com/BhallaLab/moose-core/issues' +MOOSE_DOCS_DIR = '/usr/share/doc/moose' + +MOOSE_GUI_DIR = os.path.dirname(os.path.abspath(__file__)) +assert os.path.exists(MOOSE_GUI_DIR) +MOOSE_PLUGIN_DIR = os.path.join(MOOSE_GUI_DIR, 'plugins') +assert os.path.exists(MOOSE_PLUGIN_DIR) +MOOSE_ICON_DIR = os.path.join(MOOSE_GUI_DIR, 'icons' ) +assert os.path.exists(MOOSE_ICON_DIR) +NEUROKIT_PLUGIN_DIR = os.path.join(MOOSE_GUI_DIR, 'plugins/NeuroKit') +MOOSE_NUMPTHREADS = '1' + +MOOSE_UNDO_LENGTH = 128 # Arbitrary undo length + +# It is important that MOOSE_PLUGIN_DIR is added to system path. This is ued to +# search multiple plugins. +sys.path.append( MOOSE_PLUGIN_DIR ) + + +def qvalue( qsetting, key ): + """ Return value as unicode from QSetting object. + Calling toString is not compatible with python3. + """ + return qsetting.value( key ) + + +class MooseSetting(dict): + """ + dict-like access to QSettings. + + This subclass of dict wraps a QSettings object and lets one set + and get values as Python strings rather than QVariant. + + This is supposed to be a singleton in the whole application (all + QSettings are with same parameters). + """ + _instance = None + def __new__(cls, *args, **kwargs): + # This is designed to check if the class has been + # instantiated, if so, returns the single instance, otherwise + # creates it. + if cls._instance is None: + cls._instance = super(MooseSetting, cls).__new__(cls, *args, **kwargs) + QtCore.QCoreApplication.setOrganizationName('NCBS Bangalore') + QtCore.QCoreApplication.setOrganizationDomain('ncbs.res.in') + QtCore.QCoreApplication.setApplicationName('MOOSE') + cls._instance.qsettings = QtCore.QSettings() + # If this is the first time, then set some defaults + cls._instance.qsettings.setValue(KEY_COLORMAP_DIR, os.path.join(MOOSE_GUI_DIR, 'colormaps')) + cls._instance.qsettings.setValue(KEY_BIOMODEL_DIR, os.path.join(MOOSE_GUI_DIR, 'bioModels')) + cls._instance.qsettings.setValue(KEY_ICON_DIR, os.path.join(MOOSE_GUI_DIR, 'icons')) + cls._instance.qsettings.setValue(KEY_NUMPTHREADS, '1') + cls._instance.qsettings.setValue(KEY_UNDO_LENGTH, ('%s' % MOOSE_UNDO_LENGTH)) + # These are to be checked at every run + cls._instance.qsettings.setValue(KEY_HOME_DIR, os.environ['HOME']) + cls._instance.qsettings.setValue(KEY_DOCS_DIR, MOOSE_DOCS_DIR) + return cls._instance + + def __init__(self, *args, **kwargs): + super(MooseSetting, self).__init__(self, *args, **kwargs) + + def __iter__(self): + return ('%s' % key for key in self.qsettings.allKeys()) + + def __setitem__(self, key, value): + if isinstance(key, type("")): + self.qsettings.setValue(key, value) + else: + raise TypeError('Expect only strings as keys') + + def __getitem__(self, key): + val = qvalue( self.qsettings, key ) + return val + + def keys(self): + return ['%s' % key for key in self.qsettings.allKeys()] + + def values(self): + return [ qvalue(self.qsettings, key) for key in self.qsettings.allKeys()] + + def itervalues(self): + return ( qvalue(self.qsettings, key) for key in self.qsettings.allKeys()) + +settings = MooseSetting() diff --git a/configwidget.py b/moosegui/configwidget.py similarity index 74% rename from configwidget.py rename to moosegui/configwidget.py index 87d10c3..3051910 100644 --- a/configwidget.py +++ b/moosegui/configwidget.py @@ -1,57 +1,19 @@ -# firsttime.py --- -# -# Filename: firsttime.py +# -*- coding: utf-8 -*- + # Description: # Author: Subhasis Ray # Maintainer: # Created: Sun Jul 11 15:31:00 2010 (+0530) -# Version: -# Last-Updated: Sat Sep 22 15:30:15 2012 (+0530) -# By: subha -# Update #: 505 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# Wizard to take the user through selection of some basic -# configurations for MOOSE gui. -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: import shutil import os -import config -from PyQt4 import QtGui, QtCore -import config -from utils import * + +from PyQt5 import QtGui, QtCore +from PyQt5.QtWidgets import QWidget + +from moosegui import config +from moosegui import config +from moosegui.utils import * class ConfigWidget(QtGui.QDialog): """Widget to configure MOOSE.""" @@ -76,7 +38,7 @@ def __init__(self, *args, **kwargs): def _createGeneralPanel(self): if hasattr(self, 'generalPanel'): return self.generalPanel - self.generalPanel = QtGui.QWidget(self) + self.generalPanel = QWidget(self) self.generalPanelLabel = QtGui.QLabel(self.generalPanel) self.generalPanelLabel.setText('
General configuration for MOOSE
') self.colormapDirLabel = QtGui.QLabel('Colormap directory', diff --git a/defaults.py b/moosegui/defaults.py similarity index 93% rename from defaults.py rename to moosegui/defaults.py index f7a5138..992e515 100644 --- a/defaults.py +++ b/moosegui/defaults.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- + __credits__ = ["Upi Lab"] __author__ = "Subhasis" __license__ = "GPL3" @@ -12,10 +14,11 @@ 'Compartment':['Vm','Im'], 'HHChannel':['Ik','Gk'], 'ZombiePool':['n','conc'], - 'ZombieBufPool':['n','conc'], + 'ZombieBufPool':['n','conc'], 'HHChannel2D':['Ik','Gk'], 'CaConc':['Ca'] } + FIELD_UNITS={ 'volume':'m3', 'Kd' : 'mM', diff --git a/moosegui/examples.py b/moosegui/examples.py new file mode 100644 index 0000000..f2c80df --- /dev/null +++ b/moosegui/examples.py @@ -0,0 +1,65 @@ +"""examples.py: + +Here is dictionary of demos. + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Dev,opment" + +import sys +import os + +from collections import OrderedDict + +examples_ = [ + ("Fig2C" , "demos/Fig2_elecModels/Fig2C.py") + , ("Fig2D (35s)","demos/Fig2_elecModels/Fig2D.py") + , ("Fig2E","demos/Fig2_elecModels/Fig2E.py") + , ("Fig3B_Gssa","demos/Fig3_chemModels/Fig3ABC.g") + , ("Fig3C_Gsl","demos/Fig3_chemModels/Fig3ABC.g") + , ("Fig3D","demos/Fig3_chemModels/Fig3D.py") + , ("Fig4B","demos/Fig4_ReacDiff/Fig4B.py" ) + , ("Fig4K", "demos/Fig4_ReacDiff/rxdSpineSize.py") + , ("Fig5A (20s)","demos/Fig5_CellMultiscale/Fig5A.py") + , ("Fig5BCD (240s)","demos/Fig5_CellMultiscale/Fig5BCD.py") + , ("Fig6A (60s)","demos/Fig6_NetMultiscale/Fig6A.py" ) + , ("Reduced6 (200s)","demos/Fig6_NetMultiscale/ReducedModel.py") + , ("Squid" , "demos/squid/squid_demo.py") + ] + +description_ = { + "Fig2E": + ("Illustrates loading a mod, from an SWC file, inserting chann,s, and running it") + , "Fig2D (35s)": + ("Illustrates loading a mod, from an SWC file, inserting spines, and running it") + , "Fig2C": + ("Illustrates building a pan, of multiscale mod,s to test neuronal plasticity in different contexts") + , "Fig3B_Gssa": + ("Loades Repressilator mod, into Gui with Gssa solver and runs the mod,") + , "Fig3C_Gsl": + ("Loades Repressilator mod, into Gui with Gsl solver and runs the mod,") + , "Fig3D": + ("This example implements a reaction-diffusion like system which is bistable and propagates losslessly") + , "Fig4B": + ("This program builds a multiscale mod, with a few spines inserted into a simplified c,lular morphology. Each spine has a signaling mod, in it too. The program doesn't run the mod,, it just displays it in 3D") + , "Fig4K": + ("Builds a c,l with spines and a propagating reaction wave") + , "Fig5A (20s)": + ("Illustrates building a pan, of multiscale mod,s to test neuronal plasticity in different contexts") + , "Fig5BCD (240s)": + ("Illustrates building a pan, of multiscale mod,s to test neuronal plasticity in different contexts") + , "Fig6A (60s)": + ("This LIF network with Ca plasticity is based on: Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity PLOS Computational Biology, 2014") + , "Reduced6 (200s)": + ("This is the Reduced version of LIF network with Ca plasticity mod, based on: Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity PLOS Computational Biology, 2014") + , "Squid": + ("squid Demo") + } + diff --git a/moosegui/global_constants.py b/moosegui/global_constants.py new file mode 100644 index 0000000..3a5724c --- /dev/null +++ b/moosegui/global_constants.py @@ -0,0 +1,4 @@ +# -*- coding: utf-8 -*- + +from moosegui.plugins.PreferencesPresenter import PreferencesPresenter +preferences = PreferencesPresenter() diff --git a/icons/classIcon/BufPool.png b/moosegui/icons/BufPool.png similarity index 100% rename from icons/classIcon/BufPool.png rename to moosegui/icons/BufPool.png diff --git a/icons/classIcon/CubeMesh.png b/moosegui/icons/CubeMesh.png similarity index 100% rename from icons/classIcon/CubeMesh.png rename to moosegui/icons/CubeMesh.png diff --git a/icons/classIcon/CylMesh.png b/moosegui/icons/CylMesh.png similarity index 100% rename from icons/classIcon/CylMesh.png rename to moosegui/icons/CylMesh.png diff --git a/icons/classIcon/Enz.png b/moosegui/icons/Enz.png similarity index 100% rename from icons/classIcon/Enz.png rename to moosegui/icons/Enz.png diff --git a/icons/classIcon/FuncPool.png b/moosegui/icons/FuncPool.png similarity index 100% rename from icons/classIcon/FuncPool.png rename to moosegui/icons/FuncPool.png diff --git a/icons/classIcon/Function.png b/moosegui/icons/Function.png similarity index 100% rename from icons/classIcon/Function.png rename to moosegui/icons/Function.png diff --git a/icons/classIcon/MMenz.png b/moosegui/icons/MMenz.png similarity index 100% rename from icons/classIcon/MMenz.png rename to moosegui/icons/MMenz.png diff --git a/icons/classIcon/Pool.png b/moosegui/icons/Pool.png similarity index 100% rename from icons/classIcon/Pool.png rename to moosegui/icons/Pool.png diff --git a/icons/QMdiBackground.png b/moosegui/icons/QMdiBackground.png similarity index 100% rename from icons/QMdiBackground.png rename to moosegui/icons/QMdiBackground.png diff --git a/icons/classIcon/Reac.png b/moosegui/icons/Reac.png similarity index 100% rename from icons/classIcon/Reac.png rename to moosegui/icons/Reac.png diff --git a/icons/classIcon/StimulusTable.png b/moosegui/icons/StimulusTable.png similarity index 100% rename from icons/classIcon/StimulusTable.png rename to moosegui/icons/StimulusTable.png diff --git a/icons/classIcon/SumFunc.png b/moosegui/icons/SumFunc.png similarity index 100% rename from icons/classIcon/SumFunc.png rename to moosegui/icons/SumFunc.png diff --git a/icons/add.png b/moosegui/icons/add.png similarity index 100% rename from icons/add.png rename to moosegui/icons/add.png diff --git a/icons/add_graph.png b/moosegui/icons/add_graph.png similarity index 100% rename from icons/add_graph.png rename to moosegui/icons/add_graph.png diff --git a/icons/arrow.png b/moosegui/icons/arrow.png similarity index 100% rename from icons/arrow.png rename to moosegui/icons/arrow.png diff --git a/icons/arrow_undo.png b/moosegui/icons/arrow_undo.png similarity index 100% rename from icons/arrow_undo.png rename to moosegui/icons/arrow_undo.png diff --git a/icons/clone.svg b/moosegui/icons/clone.svg similarity index 98% rename from icons/clone.svg rename to moosegui/icons/clone.svg index bb18fd9..7d7e374 100644 --- a/icons/clone.svg +++ b/moosegui/icons/clone.svg @@ -1,8 +1,8 @@ - - - - - - + + + + + + diff --git a/icons/connection.png b/moosegui/icons/connection.png similarity index 100% rename from icons/connection.png rename to moosegui/icons/connection.png diff --git a/icons/continue.png b/moosegui/icons/continue.png similarity index 100% rename from icons/continue.png rename to moosegui/icons/continue.png diff --git a/icons/delete.svg b/moosegui/icons/delete.svg similarity index 100% rename from icons/delete.svg rename to moosegui/icons/delete.svg diff --git a/icons/delete_graph.png b/moosegui/icons/delete_graph.png similarity index 100% rename from icons/delete_graph.png rename to moosegui/icons/delete_graph.png diff --git a/icons/grid.png b/moosegui/icons/grid.png similarity index 100% rename from icons/grid.png rename to moosegui/icons/grid.png diff --git a/icons/hand.png b/moosegui/icons/hand.png similarity index 100% rename from icons/hand.png rename to moosegui/icons/hand.png diff --git a/icons/help.png b/moosegui/icons/help.png similarity index 100% rename from icons/help.png rename to moosegui/icons/help.png diff --git a/icons/hopfield.png b/moosegui/icons/hopfield.png similarity index 100% rename from icons/hopfield.png rename to moosegui/icons/hopfield.png diff --git a/icons/list.png b/moosegui/icons/list.png similarity index 100% rename from icons/list.png rename to moosegui/icons/list.png diff --git a/icons/moose_icon.png b/moosegui/icons/moose_icon.png similarity index 100% rename from icons/moose_icon.png rename to moosegui/icons/moose_icon.png diff --git a/icons/moose_icon_64x64.png b/moosegui/icons/moose_icon_64x64.png similarity index 100% rename from icons/moose_icon_64x64.png rename to moosegui/icons/moose_icon_64x64.png diff --git a/icons/moose_icon_large.png b/moosegui/icons/moose_icon_large.png similarity index 100% rename from icons/moose_icon_large.png rename to moosegui/icons/moose_icon_large.png diff --git a/icons/move.svg b/moosegui/icons/move.svg similarity index 96% rename from icons/move.svg rename to moosegui/icons/move.svg index 5dd4d9a..25d2706 100644 --- a/icons/move.svg +++ b/moosegui/icons/move.svg @@ -1,39 +1,39 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/icons/plot.svg b/moosegui/icons/plot.svg similarity index 100% rename from icons/plot.svg rename to moosegui/icons/plot.svg diff --git a/icons/reset.png b/moosegui/icons/reset.png similarity index 100% rename from icons/reset.png rename to moosegui/icons/reset.png diff --git a/icons/run.png b/moosegui/icons/run.png similarity index 100% rename from icons/run.png rename to moosegui/icons/run.png diff --git a/icons/runtime.png b/moosegui/icons/runtime.png similarity index 100% rename from icons/runtime.png rename to moosegui/icons/runtime.png diff --git a/icons/squid.png b/moosegui/icons/squid.png similarity index 100% rename from icons/squid.png rename to moosegui/icons/squid.png diff --git a/icons/stop.png b/moosegui/icons/stop.png similarity index 100% rename from icons/stop.png rename to moosegui/icons/stop.png diff --git a/icons/straight_connector_with_filled_circles.png b/moosegui/icons/straight_connector_with_filled_circles.png similarity index 100% rename from icons/straight_connector_with_filled_circles.png rename to moosegui/icons/straight_connector_with_filled_circles.png diff --git a/icons/wrench.png b/moosegui/icons/wrench.png similarity index 100% rename from icons/wrench.png rename to moosegui/icons/wrench.png diff --git a/moosegui/loaderdialog.py b/moosegui/loaderdialog.py new file mode 100644 index 0000000..15fa1ea --- /dev/null +++ b/moosegui/loaderdialog.py @@ -0,0 +1,54 @@ +# -*- coding: utf-8 -*- +# Description: +# Author: +# Maintainer: +# Created: Mon Feb 25 15:59:54 2013 (+0530) + +import sys +import moose +import os +import posixpath +from PyQt5 import QtGui, QtCore +from PyQt5.QtWidgets import QFileDialog, QApplication + +class LoaderDialog(QFileDialog): + # Update ftypes to include new file types + ftypes='All Supported Files (*.cspace *.g *.xml *.p);; CSPACE (*.cspace);; GENESIS (*.g);; GENESIS Prototype (*.p);; NeuroML/SBML (*.xml)' + target_default = '' # The default target when loading a model + def __init__(self, *args): + self.modelpath = None + super(LoaderDialog, self).__init__(*args) + self.setNameFilter(self.tr(self.ftypes)) + self.setFileMode(self.ExistingFile) + self.fileSelected.connect(self.fileSelectedSlot) + + def fileSelectedSlot(self, fpath): + """On selecting a file, this function will cause the target location to change to: + + /model/filename_minus_extension + + """ + self.modelpath = os.path.splitext(os.path.basename(str(fpath)))[0] + + # def isReplace(self): + # return self.replaceExistingButton.isChecked() + + # def isMerge(self): + # return self.mergeExistingButton.isChecked() + + def getTargetPath(self): + return self.modelpath + + +if __name__ == '__main__': + app = QApplication(sys.argv) + QtGui.qApp = app + mw = LoaderDialog() + mw.show() + # mw.exec_() + sys.exit(app.exec_()) + + + +# +# fileloader.py ends here diff --git a/mexception.py b/moosegui/mexception.py similarity index 90% rename from mexception.py rename to moosegui/mexception.py index 53a728b..c2836b8 100644 --- a/mexception.py +++ b/moosegui/mexception.py @@ -57,17 +57,17 @@ class MooseWarning(Warning): def __init__(self, *args, **kwargs): Warning.__init__(self, *args, **kwargs) -class MooseError(StandardError): +class MooseError(Exception): def __init__(self, *args, **kwargs): - StandardError.__init__(self, *args, **kwargs) + Exception.__init__(self, *args, **kwargs) class FileLoadError(MooseError): def __init__(self, *args, **kwargs): - StandardError.__init__(self, *args, **kwargs) + Exception.__init__(self, *args, **kwargs) class ElementNameError(MooseError): def __init__(self, *args, **kwargs): - StandardError.__init__(self, *args, **kwargs) + Exception.__init__(self, *args, **kwargs) # # mexception.py ends here diff --git a/moosegui/mgui.py b/moosegui/mgui.py new file mode 100644 index 0000000..71cb6a1 --- /dev/null +++ b/moosegui/mgui.py @@ -0,0 +1,30 @@ +# Filename: moosegui.py +# Description: Graphical user interface of MOOSE simulator. +# Author: Subhasis Ray, Harsha Rani, Dilawar Singh +# Maintainer: +# Created: Mon Nov 12 09:38:09 2012 (+0530) + +__author__ = 'Subhasis Ray , HarshaRani, Aviral Goel, NCBS Bangalore' + +import sys +from PyQt5.QtWidgets import QApplication +from PyQt5 import QtGui, QtCore +from moosegui import config +from moosegui import MWindow as MWindow + +app_ = None + +def main(): + # create the GUI application + global app_ + app_ = QApplication(sys.argv) + QtGui.qApp = app_ + mWindow = MWindow.MWindow() + mWindow.setWindowState(QtCore.Qt.WindowMaximized) + sys.excepthook = mWindow.handleException + mWindow.show() + sys.exit( app_.exec_() ) + +if __name__ == '__main__': + main() + diff --git a/mload.py b/moosegui/mload.py similarity index 86% rename from mload.py rename to moosegui/mload.py index 3b97832..4bb8dab 100644 --- a/mload.py +++ b/moosegui/mload.py @@ -1,68 +1,28 @@ -# mload.py --- -# -# Filename: mload.py +# -*- coding: utf-8 -*- + # Description: # Author: Subhasis # Maintainer:HarshaRani # Created: Fri Feb 8 09:38:40 2013 (+0530) -# Version: -# Last-Updated: Wed Oct 5 15:16:35 2017 (+0530) -# By: HarshaRani -# Update #: 213 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# Utility to load models and detect filetype. -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# -# Code: -''' -Oct 5 : check is made for kkit model - -- Atleast one compartment should exists - -- Atleast 2 pool should exists -Oct 4 : clean up for python3 -''' -import moose -from moose import neuroml -import mtypes -from mexception import FileLoadError import posixpath +from PyQt5 import QtGui, QtCore, Qt from os.path import basename from os.path import splitext -from PyQt4 import QtGui, QtCore, Qt -from plugins.setsolver import * -from moose.SBML import * -from plugins.kkitOrdinateUtil import * + +# moosegui +from moosegui.plugins.kkitOrdinateUtil import * +from moosegui import mtypes +from moosegui.mexception import FileLoadError +from moosegui.plugins.setsolver import * + +# moose import moose._moose as moose import moose.utils as mutils +import moose +from moose import neuroml +from moose.SBML import * + def loadGenCsp(target,filename,solver="gsl"): target = target.replace(" ", "") path = '/'+target @@ -205,8 +165,8 @@ def loadFile(filename, target, solver="gsl", merge=True): if subtype == 'neuroml': popdict, projdict = neuroml.loadNeuroML_L123(filename) # Circus to get the container of populations from loaded neuroml - for popinfo in popdict.values(): - for cell in popinfo[1].values(): + for popinfo in list(popdict.values()): + for cell in list(popinfo[1].values()): solver = moose.HSolve(cell.path + "/hsolve") solver.target = cell.path # model = cell.parent diff --git a/mplot.py b/moosegui/mplot.py similarity index 69% rename from mplot.py rename to moosegui/mplot.py index 7d75392..411e99c 100644 --- a/mplot.py +++ b/moosegui/mplot.py @@ -1,94 +1,22 @@ -# mplot.py --- -# # Filename: mplot.py # Description: # Author: # Maintainer: # Created: Mon Mar 11 20:24:26 2013 (+0530) -# Version: -# Last-Updated: Wed Apr 11 15:32:35 2018 (+0530) -# By: Harsha -# Update #: -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# Moose plot widget default implementation. This should be rich enough -# to suffice for most purposes. -# -# - -# Change log: -# 2018 April 11: In chemical model, now pool can be ploted as number or concentration. -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: -""" - *TODO* - - 1) Option for default colors, markers, etc. - - 2) Option for configuring number of rows and columns of - subplots. (I think matplotlib grids will be a bit too much to - implement). Problem is this has to be done before actual axes are - created (as far as I know). Idea: can we do something like movable - widgets example in Qt? - - 3) Option for selecting any line or set of lines and change its - configuration (as in dataviz). - - 4) Association between plots and the data source. - - 5) Lots and lots of scipy/numpy/scikits/statsmodels utilities can be added. To - start with, we should have - a)digital filters - b) fft - c) curve fitting - - 6) For (5), think of another layer of plugins. Think of this as a - standalone program. All these facilities should again be - pluggable. We do not want to overwhelm novice users with fancy - machine-learning stuff. They should be made available only on - request. - - There is a proposal for data analysis library by Andrew Davison ... - -""" - __author__ = "Subhasis Ray" + import sys import numpy as np -from PyQt4 import QtGui, QtCore -from PyQt4.Qt import Qt -from matplotlib import mlab + +from PyQt5 import QtGui, QtCore +from PyQt5.Qt import Qt + from matplotlib.figure import Figure -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas -from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar -#from moose import utils +from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas +from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar + import moose -from PyQt4.QtCore import * class CanvasWidget(FigureCanvas): """Widget to draw plots on. @@ -102,8 +30,7 @@ class CanvasWidget(FigureCanvas): this). """ - updateSignal = pyqtSignal() - + updateSignal = QtCore.pyqtSignal() def __init__(self, model, graph, index, *args, **kwargs): self.model = model self.graph = graph @@ -201,7 +128,7 @@ def callAxesFn(self, fname, *args, **kwargs): return fn(*args, **kwargs) def resize_event(self, event): - print("Resize event called ", event) + print(("Resize event called ", event)) def toggleGrid(self): self.gridMode = not self.gridMode @@ -215,12 +142,11 @@ def setXLimit(self, minX, maxX): self.draw() -import sys import os -import config import unittest +from moosegui import config -from PyQt4.QtTest import QTest +from PyQt5.QtTest import QTest class CanvasWidgetTests(unittest.TestCase): def setUp(self): diff --git a/mplugin.py b/moosegui/mplugin.py similarity index 87% rename from mplugin.py rename to moosegui/mplugin.py index c4ea6d0..4e037ce 100644 --- a/mplugin.py +++ b/moosegui/mplugin.py @@ -1,51 +1,13 @@ -# mplugin.py --- -# +# -*- coding: utf-8 -*- + # Filename: mplugin.py # Description: # Author: # Maintainer: # Created: Tue Oct 2 17:25:41 2012 (+0530) -# Version: -# Last-Updated: Thu Jul 18 10:51:48 2013 (+0530) -# By: subha -# Update #: 297 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# This is to be the base class for all MOOSE GUI plugins. -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: - -from PyQt4 import QtGui,QtCore,Qt + +from PyQt5 import QtCore +from PyQt5.QtWidgets import QWidget, QAction import moose class MoosePluginBase(QtCore.QObject): @@ -63,8 +25,10 @@ class MoosePluginBase(QtCore.QObject): and getViews() functions. """ + modelRootChanged = QtCore.pyqtSignal(object, name='modelRootChanged') dataRootChanged = QtCore.pyqtSignal(object, name='dataRootChanged') + def __init__(self, root='/', mainwindow=None): """Create a plugin object whose model is the tree rooted at `root` and whose widgets will be displayed in `mainwindow`. @@ -250,7 +214,7 @@ def __init__(self, plugin, *args): super(RunBase, self).__init__(plugin) -class EditorWidgetBase(QtGui.QWidget): +class EditorWidgetBase(QWidget): """Base class for central widget displayed in editor view. The widget should display the model components in the tree rooted @@ -268,7 +232,7 @@ class EditorWidgetBase(QtGui.QWidget): """ editObject = QtCore.pyqtSignal('PyQt_PyObject') def __init__(self, *args): - QtGui.QWidget.__init__(self, *args) + QWidget.__init__(self, *args) self.modelRoot = '/' self._menus = [] self._toolBars = [] @@ -293,12 +257,9 @@ def getInsertActions(self, classlist): if len(self._insertActions) == 0: self._insertMapper = QtCore.QSignalMapper(self) for classname in classlist: - action = QtGui.QAction(classname, self) - self._insertMapper.setMapping(action, QtCore.QString(classname)) - self.connect(action, - QtCore.SIGNAL('triggered()'), - self._insertMapper, - QtCore.SLOT('map()')) + action = QAction(classname, self) + self._insertMapper.setMapping(action, classname) + action.triggered.connect(self._insertMapper.map) doc = moose.element('/classes/%s' % (classname)).docs doc = doc.split('Description:')[-1].split('Name:')[0].strip() action.setToolTip(doc) @@ -347,8 +308,3 @@ def sizeHint(self): def getCurrentMobj(self): raise NotImplementedError('should be reimplemented in subclass') - - - -# -# mplugin.py ends here diff --git a/msearch.py b/moosegui/msearch.py similarity index 96% rename from msearch.py rename to moosegui/msearch.py index 63fa809..9c580e6 100644 --- a/msearch.py +++ b/moosegui/msearch.py @@ -50,12 +50,13 @@ """ import sys -from PyQt4 import QtGui, QtCore -from PyQt4.Qt import Qt +from PyQt5 import QtGui, QtCore +from PyQt5.QtWidgets import QWidget +from PyQt5.Qt import Qt import moose -class SearchWidget(QtGui.QWidget): +class SearchWidget(QWidget): """Widget to search MOOSE model tree using wildcards. SIGNALS: @@ -66,7 +67,7 @@ class SearchWidget(QtGui.QWidget): executed = QtCore.pyqtSignal(list, name='executed') def __init__(self, *args): - QtGui.QWidget.__init__(self, *args) + QWidget.__init__(self, *args) layout = QtGui.QVBoxLayout() self.modeCombo = QtGui.QComboBox() self.modeCombo.addItem('Basic', QtCore.QVariant(QtCore.QString('basic'))) @@ -91,7 +92,7 @@ def switchModeSlot(self, text): def getBasicPanel(self): """Create a widget for basic level usage.""" if not hasattr(self, '_basicPanel'): - self._basicPanel = QtGui.QWidget() + self._basicPanel = QWidget() self.searchRootEdit = QtGui.QLineEdit() self.searchRootEdit.returnPressed.connect(self.searchSlot) self.searchRootLabel = QtGui.QLabel('Search under') @@ -131,7 +132,7 @@ def getAdvancedPanel(self): """Create a panel for advanced users who can enter the search string directly.""" if not hasattr(self, '_advancedPanel'): - self._advancedPanel = QtGui.QWidget(self) + self._advancedPanel = QWidget(self) self._searchEdit = QtGui.QLineEdit() self._searchEdit.returnPressed.connect(self.searchSlot) self._searchLabel = QtGui.QLabel('Search string:') diff --git a/mtoolbutton.py b/moosegui/mtoolbutton.py similarity index 52% rename from mtoolbutton.py rename to moosegui/mtoolbutton.py index c4d72ed..cbf04b5 100644 --- a/mtoolbutton.py +++ b/moosegui/mtoolbutton.py @@ -1,60 +1,27 @@ -# mtoolbutton.py --- -# -# Filename: mtoolbutton.py +# -*- coding: utf-8 -*- + # Description: Subclass of QToolButton to allow drag and drop # Author: # Maintainer: # Created: Fri Jun 14 14:24:11 2013 (+0530) -# Version: -# Last-Updated: Fri Jun 14 16:28:51 2013 (+0530) -# By: subha -# Update #: 89 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# -# Code: import sys -from PyQt4 import QtGui, QtCore -from PyQt4.Qt import Qt +from PyQt5 import QtGui, QtCore +from PyQt5.QtWidgets import QToolButton, QToolBar, QMainWindow +from PyQt5.QtWidgets import QApplication, QTextBrowser +from PyQt5.Qt import Qt -class MToolButton(QtGui.QToolButton): - """QToolButton subclass with dragEvent reimplemented. It sends the +import logging +logger_ = logging.getLogger('mtoolbutton') + +class MToolButton(QToolButton): + """ + QToolButton subclass with dragEvent reimplemented. It sends the text of the ToolButton as the mimedata. """ def __init__(self, *args): - QtGui.QToolButton.__init__(self, *args) + QToolButton.__init__(self, *args) self.dragStartPosition = QtCore.QPoint(0,0) def mousePressEvent(self, event): @@ -64,56 +31,55 @@ def mousePressEvent(self, event): def mouseMoveEvent(self, event): if not (event.buttons() & Qt.LeftButton): return - if (event.pos() - self.dragStartPosition).manhattanLength() < QtGui.QApplication.startDragDistance(): + if (event.pos() - self.dragStartPosition).manhattanLength() < QApplication.startDragDistance(): return drag = QtGui.QDrag(self) mimeData = QtCore.QMimeData() mimeData.setText(self.text()) drag.setMimeData(mimeData) - # print '1111', mimeData.text() - dropAction = drag.exec_(Qt.CopyAction) + drag.exec_(Qt.CopyAction) -class MyWidget(QtGui.QTextBrowser): +class MyWidget(QTextBrowser): """Class for testing the drag and drop ability of MToolButton""" def __init__(self, *args): - QtGui.QTextBrowser.__init__(self, *args) + QTextBrowser.__init__(self, *args) self.dropCount = 0 self.setPlainText('Drops: %d' % (self.dropCount)) self.setAcceptDrops(True) def dragEnterEvent(self, event): - print '2222', event.mimeData().text() + print(('2222', event.mimeData().text())) if event.mimeData().hasFormat('text/plain'): event.acceptProposedAction() - print '3333 accepted ' + print('3333 accepted ') def dragMoveEvent(self, event): """This must be reimplemented to accept the event in case of QTextBrowser. Not needed in QWidgets in general.""" - print '4444' + print('4444') event.acceptProposedAction() def dropEvent(self, event): - print '5555', event.mimeData().text() + print(('5555', event.mimeData().text())) self.dropCount += 1 self.setPlainText('`%s` dropped: %d times' % (event.mimeData().text(), self.dropCount)) event.acceptProposedAction() - QtGui.QTextBrowser.dropEvent(self, event) + QTextBrowser.dropEvent(self, event) def test_main(): """Test main: see if drag and drop is working""" - app = QtGui.QApplication(sys.argv) - mainwin = QtGui.QMainWindow() + app = QApplication(sys.argv) + mainwin = QMainWindow() mainwin.setWindowTitle('MTooButton') - toolbar = QtGui.QToolBar() + toolbar = QToolBar() mainwin.addToolBar(toolbar) button = MToolButton() button.setText('test') toolbar.addWidget(button) browser = MyWidget(mainwin) - print browser.acceptDrops() + print((browser.acceptDrops())) mainwin.setCentralWidget(browser) mainwin.show() sys.exit(app.exec_()) diff --git a/mtree.py b/moosegui/mtree.py similarity index 72% rename from mtree.py rename to moosegui/mtree.py index a95a776..f6480ac 100644 --- a/mtree.py +++ b/moosegui/mtree.py @@ -1,56 +1,15 @@ -# mtree.py --- -# -# Filename: mtree.py +# -*- coding: utf-8 -*- + # Description: # Author: Subhasis Ray # Maintainer: # Created: Tue May 14 11:51:35 2013 (+0530) -# Version: -# Last-Updated: Fri Jun 14 16:13:08 2013 (+0530) -# By: subha -# Update #: 154 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# Implementation of moose tree widget. This can be used by multiple -# components in the moose gui. -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: - -import sys -from PyQt4 import QtGui, QtCore -from PyQt4.Qt import Qt -import moose +from PyQt5 import QtCore +from PyQt5.Qt import Qt +from PyQt5.QtWidgets import QTreeWidgetItem, QTreeWidget + +import moose class MooseTreeModel(QtCore.QAbstractItemModel): """Tree model for the MOOSE element tree. @@ -117,22 +76,21 @@ def flags(self, index): return QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable -class MooseTreeItem(QtGui.QTreeWidgetItem): +class MooseTreeItem(QTreeWidgetItem): def __init__(self, *args): - QtGui.QTreeWidgetItem.__init__(self, *args) - self.mobj = None + QTreeWidgetItem.__init__(self, *args) + self.mobj = None def setObject(self, element): self.mobj = moose.element(element) - self.setText(0, QtCore.QString(self.mobj.path.rpartition('/')[-1])) - self.setText(1, QtCore.QString(self.mobj.className)) - #self.setToolTip(0, QtCore.QString('class:' + self.mooseObj_.className)) + self.setText(0, self.mobj.path.rpartition('/')[-1]) + self.setText(1, self.mobj.className) def updateSlot(self): - self.setText(0, QtCore.QString(self.mobj.name)) + self.setText(0, self.mobj.name) -class MooseTreeWidget(QtGui.QTreeWidget): +class MooseTreeWidget(QTreeWidget): """Widget for displaying MOOSE model tree. """ @@ -159,10 +117,10 @@ def __init__(self, *args): elementInserted(melement) emitted when a new element is inserted. """ - QtGui.QTreeWidget.__init__(self, *args) + QTreeWidget.__init__(self, *args) self.header().hide() - self.rootElement = moose.element('/') - self.odict = {} + self.rootElement = moose.element('/') + self.odict = {} self.recreateTree() def setupTree(self, obj, parent, odict): @@ -183,19 +141,19 @@ def setupTree(self, obj, parent, odict): for ii in MooseTreeWidget.ignored: if obj.path.startswith(ii): return None - item = MooseTreeItem(parent) - item.setObject(obj) - odict[obj] = item + item = MooseTreeItem(parent) + item.setObject(obj) + odict[obj] = item # TODO: check and verify that this still works with synapses - # there have been change in API. - Subha, Fri Sep 19 19:04:35 IST 2014 - for child in obj.children: + for child in obj.children: ch = child if child.name in obj.getFieldNames('fieldElementFinfo'): ch = obj.getField(child.name) for elm in ch: self.setupTree(moose.element(elm), item, odict) - return item + return item def recreateTree(self, root=None): """Clears the current tree and recreates the tree. If root is not @@ -220,7 +178,7 @@ def insertElementSlot(self, class_name): under currently selected element in the model tree.""" # print 'Inserting element ...', class_name current = self.currentItem() - print 'CLASS NAME:', class_name + print(('CLASS NAME:', class_name)) self.insertChildElement(current, class_name) def insertChildElement(self, item, class_name, name=''): @@ -242,25 +200,28 @@ def setCurrentItem(self, item): - adds ability to set item by corresponding moose object. """ - if isinstance(item, QtGui.QTreeWidgetItem): - QtGui.QTreeWidget.setCurrentItem(self, item) + if isinstance(item, QTreeWidgetItem): + QTreeWidget.setCurrentItem(self, item) return mobj = moose.element(item) - QtGui.QTreeWidget.setCurrentItem(self, self.odict[mobj]) + QTreeWidget.setCurrentItem(self, self.odict[mobj]) def updateItemSlot(self, element): self.odict[element].updateSlot() def main(): - """Test main: load a model and display the tree for it""" - model = moose.Neutral('/model') - moose.loadModel('../Demos/Genesis_files/Kholodenko.g', '/model/Kholodenko') - # tab = moose.element('/model/Kholodenko/graphs/conc1/MAPK_PP.Co') - # print tab - # for t in tab.children: - # print t - app = QtGui.QApplication(sys.argv) - mainwin = QtGui.QMainWindow() + """ + Test main: load a model and display the tree for it + """ + import sys + import os + sdir = os.path.dirname(__file__) + from PyQt5.QtWidgets import QApplication, QMainWindow + # model = moose.Neutral('/model') + modelfile = os.path.join(sdir, '../data/Kholodenko.g') + moose.loadModel(modelfile, '/model') + app = QApplication(sys.argv) + mainwin = QMainWindow() mainwin.setWindowTitle('Model tree test') tree = MooseTreeWidget() tree.recreateTree(root='/model/') @@ -268,10 +229,6 @@ def main(): mainwin.show() sys.exit(app.exec_()) - if __name__ == "__main__": main() - -# -# mtree.py ends here diff --git a/mtypes.py b/moosegui/mtypes.py similarity index 98% rename from mtypes.py rename to moosegui/mtypes.py index 9d04c5a..69a9a88 100644 --- a/mtypes.py +++ b/moosegui/mtypes.py @@ -45,7 +45,7 @@ # Code: -from __future__ import print_function + import re import moose @@ -143,7 +143,7 @@ def isNeuroML(filename): """ doc = md.parse(filename) for child in doc.childNodes: - print(child.nodeName, child.nodeType == child.ELEMENT_NODE) + print((child.nodeName, child.nodeType == child.ELEMENT_NODE)) if child.nodeType == child.ELEMENT_NODE and \ (child.nodeName == 'networkml' or \ child.nodeName == 'morphml' or \ diff --git a/neuroextractor.py b/moosegui/neuroextractor.py similarity index 100% rename from neuroextractor.py rename to moosegui/neuroextractor.py diff --git a/moosegui/newmodeldialog.py b/moosegui/newmodeldialog.py new file mode 100644 index 0000000..ebbdb9d --- /dev/null +++ b/moosegui/newmodeldialog.py @@ -0,0 +1,62 @@ +# -*- coding: utf-8 -*- + +import re + +from PyQt5 import QtGui, QtCore +from PyQt5.QtWidgets import QWidget, QDialogButtonBox, QDialog +from PyQt5.QtWidgets import QGridLayout, QLabel, QLineEdit +from PyQt5.QtWidgets import QHBoxLayout + +class DialogWidget(QDialog): + def __init__(self,parent=None): + QWidget.__init__(self, parent) + self.warning = None + self._currentRadioButton ="kkit" + self.layout = QGridLayout() + self.modelPathLabel = QLabel('Model Name') + self.modelPathEdit = QLineEdit('') + self.layout.addWidget(self.modelPathLabel, 0, 0) + self.layout.addWidget(self.modelPathEdit, 0, 1,1,1) + self.hbox = QHBoxLayout() + self.buttonBox = QDialogButtonBox(QDialogButtonBox.Ok) + self.buttonBox.accepted.connect(self.validateAccept) + self.hbox.addWidget(self.buttonBox,1) + self.buttonBox1 = QDialogButtonBox(QDialogButtonBox.Cancel) + self.buttonBox1.rejected.connect(self.Cancel) + self.hbox.addWidget(self.buttonBox1,0) + self.layout.addLayout(self.hbox,1,1) + self.setLayout(self.layout) + + def Cancel (self): + self.close() + + def validateAccept(self): + text = str(self.modelPathEdit.text()) + self.layout.removeWidget(self.warning) + #replace / to _ + text = text.replace('/','_') + + #print(self.layout.widgets()) + if len(text) == 0: + self.warning = QtGui.QLabel("Model name cannot be empty!") + self.layout.addWidget(self.warning, 1, 0, 1, -1) + elif not re.match("^[a-zA-Z]+.*",text): + self.warning = QtGui.QLabel("Start special characters not allowed!") + self.layout.addWidget(self.warning, 1, 0, 1, -1) + else: + self.accept() + return False + + def getcurrentRadioButton(self): + return self._currentRadioButton + +if __name__ == '__main__': + from PyQt5.QtWidgets import QApplication + app = QApplication([]) + widget = DialogWidget() + widget.setWindowTitle('New Model') + widget.setMinimumSize(400, 200) + widget.show() + app.exec_() + + diff --git a/moosegui/objectedit.py b/moosegui/objectedit.py new file mode 100644 index 0000000..320cfcd --- /dev/null +++ b/moosegui/objectedit.py @@ -0,0 +1,422 @@ +# -*- coding: utf-8 -*- +# Description: +# Author: Subhasis Ray +# Maintainer: +# Created: Wed Jun 30 11:18:34 2010 (+0530) + +import sys +from collections import deque +import numpy as np + +from PyQt5 import QtCore +from PyQt5.QtWidgets import QTextEdit, QWidget, QLineEdit +from PyQt5.QtWidgets import QVBoxLayout, QSizePolicy, QSplitter +from PyQt5.QtWidgets import QTableView, QDockWidget, QPushButton +from PyQt5.QtWidgets import QColorDialog, QMessageBox + +import moose +from moosegui import defaults +from moose.chemUtil.chemConnectUtil import getColor + +#these fields will be ignored +extra_fields = [ + 'this', + 'me', + 'parent', + 'path', + 'children', + 'linearSize', + 'objectDimensions', + 'lastDimension', + 'localNumField', + 'pathIndices', + 'msgOut', + 'msgIn', + 'diffConst', + 'speciesId', + 'Coordinates', + 'neighbors', + 'DiffusionArea', + 'DiffusionScaling', + 'x', + 'x0', + 'x1', + 'dx', + 'nx', + 'y', + 'y0', + 'y1', + 'dy', + 'ny', + 'z', + 'z0', + 'z1', + 'dz', + 'nz', + 'coords', + 'isToroid', + 'preserveNumEntries', + # 'numKm', + 'numSubstrates', + 'concK1', + 'meshToSpace', + 'spaceToMesh', + 'surface', + 'method', + 'alwaysDiffuse', + 'numData', + 'numField', + 'valueFields', + 'sourceFields', + 'motorConst', + 'destFields', + 'dt', + 'tick', + 'idValue', + 'index', + 'fieldIndex' +] + + +class ObjectEditModel(QtCore.QAbstractTableModel): + """Model class for editing MOOSE elements. This is not to be used + directly, except that its undo and redo slots should be connected + to by the GUI actions for the same. + + SIGNALS: + + objectNameChanged(PyQt_PyObject): when a moose object's name is + changed, this signal is emitted with the object as argument. This + can be captured by widgets that display the object name. + + dataChanged: emitted when any data is changed in the moose object + + """ + + objectNameChanged = QtCore.pyqtSignal('PyQt_PyObject') + dataChanged = QtCore.pyqtSignal(QtCore.QModelIndex, QtCore.QModelIndex) + + def __init__(self, + datain, + headerdata=['Field', 'Value'], + undolen=100, + parent=None, + *args): + QtCore.QAbstractTableModel.__init__(self, parent, *args) + self.fieldFlags = {} + self.fields = [] + self.mooseObject = datain + self.headerdata = headerdata + self.undoStack = deque(maxlen=undolen) + self.redoStack = deque(maxlen=undolen) + self.checkState_ = False + + for fieldName in self.mooseObject.getFieldNames('valueFinfo'): + if fieldName in extra_fields: + continue + self.fields.append(fieldName) + if (isinstance (self.mooseObject,moose.ChemCompt) or \ + isinstance(self.mooseObject,moose.ReacBase) or \ + isinstance(moose.element(moose.element(self.mooseObject).parent),moose.EnzBase) \ + ): + pass + else: + self.fields.append("Color") + + flag = QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable + self.fieldFlags[fieldName] = flag + + if (isinstance(self.mooseObject, moose.ReacBase)): + self.fields.append("Kd") + flag = QtCore.Qt.ItemIsEnabled + self.fieldFlags[fieldName] = flag + + def rowCount(self, parent): + return len(self.fields) + + def columnCount(self, parent): + return len(self.headerdata) + + def setData(self, index, value, role=QtCore.Qt.EditRole): + if not index.isValid() or index.row() >= len( + self.fields) or index.column() != 1: + return False + field = self.fields[index.row()] + if (role == QtCore.Qt.CheckStateRole): + if (index.column() == 1): + self.checkState_ = value + return True + + else: + # convert Qt datastructure to Python string + value = value.strip() + if len(value) == 0: + return False + if field == "Notes": + field = "notes" + ann = moose.Annotator(self.mooseObject.path + '/info') + oldValue = ann.getField(field) + value = type(oldValue)(value) + ann.setField(field, value) + self.undoStack.append((index, oldValue)) + elif field == "vector": + for ch in ['[', ']']: + if ch in value: + value = value.replace(ch, " ") + value = value.replace(",", " ") + valuelist = [] + if value.find(',') != -1: + valuelist = value.split(",") + elif value.find(' ') != -1: + valuelist = value.split(" ") + else: + valuelist = value + self.mooseObject.setField(field, np.array(valuelist, dtype=np.float)) + else: + oldValue = self.mooseObject.getField(field) + if field != "isBuffered": + value = type(oldValue)(value) + self.mooseObject.setField(field, value) + else: + if self.mooseObject.className == "ZombiePool" or self.mooseObject.className == "ZombieBufPool": + QMessageBox.warning( + None, 'Solver is set, Could not set the value', + '\n Unset the solver by clicking \n run widget -> Preferences -> Exponential Euler->Apply' + ) + else: + if value.lower() in ("yes", "true", "t", "1"): + self.mooseObject.setField(field, True) + else: + self.mooseObject.setField(field, False) + self.undoStack.append((index, oldValue)) + if field == 'name': + self.emit(QtCore.SIGNAL('objectNameChanged(PyQt_PyObject)'), + self.mooseObject) + return True + + self.dataChanged.emit(index, index) + return True + + def data(self, index, role): + ret = None + field = self.fields[index.row()] + if index.column() == 0 and role == QtCore.Qt.DisplayRole: + try: + ret = '%s (%s)' % (field, defaults.FIELD_UNITS[field]) + except KeyError: + ret = field + return ret + + if index.column() == 1: + if role == QtCore.Qt.CheckStateRole: + if (str(field) == "plot Conc") or (str(field) == "plot n"): + return self.checkState_ + elif (role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole): + try: + if (str(field) == "Color"): + return QPushButton("Press Me!") + if (str(field) == "Kd"): + Kd = 0 + if self.mooseObject.className == "ZombieReac" or self.mooseObject.className == "Reac": + if self.mooseObject.numSubstrates > 1 or self.mooseObject.numProducts > 1: + if self.mooseObject.Kf != 0: + Kd = self.mooseObject.Kb / self.mooseObject.Kf + ret = QtCore.QVariant(QtCore.QString(str(Kd))) + if ((str(field) != "Notes") and (str(field) != "className") + and (str(field) != "Kd")): + ret = self.mooseObject.getField(str(field)) + ret = QtCore.QString(str(ret)) + elif (str(field) == "className"): + ret = self.mooseObject.getField(str(field)) + if 'Zombie' in ret: + ret = ret.split('Zombie')[1] + ret = QtCore.QString(str(ret)) + elif (str(field) == "Notes"): + astr = self.mooseObject.path + '/info' + mastr = moose.Annotator(astr) + ret = (mastr).getField(str('notes')) + ret = (QtCore.QString(str(ret))) + except ValueError: + ret = None + return ret + + def headerData(self, col, orientation, role): + if orientation == QtCore.Qt.Horizontal and role == QtCore.Qt.DisplayRole: + return (self.headerdata[col]) + return "" + + +class ObjectEditView(QTableView): + """View class for object editor. + + This class creates an instance of ObjectEditModel using the moose + element passed as its first argument. + + undolen - specifies the size of the undo stack. By default set to + OBJECT_EDIT_UNDO_LENGTH constant in defaults.py. Specify something smaller if + large number of objects are likely to be edited. + + To enable undo/redo conect the corresponding actions from the gui + to view.model().undo and view.model().redo slots. + """ + + def __init__(self, + mobject, + undolen=defaults.OBJECT_EDIT_UNDO_LENGTH, + parent=None): + QTableView.__init__(self, parent) + vh = self.verticalHeader() + vh.setVisible(False) + hh = self.horizontalHeader() + hh.setStretchLastSection(True) + self.setAlternatingRowColors(True) + self.resizeColumnsToContents() + self.setModel(ObjectEditModel(mobject, undolen=undolen)) + self.colorButton = QPushButton() + self.colorDialog = QColorDialog() + self.textEdit = QTextEdit() + try: + notesIndex = self.model().fields.index("Notes") + self.setIndexWidget(self.model().index(notesIndex, 1), + self.textEdit) + info = moose.Annotator(self.model().mooseObject.path + '/info') + self.textEdit.setText(QtCore.QString(info.getField('notes'))) + self.setRowHeight(notesIndex, self.rowHeight(notesIndex) * 3) + + # self.colorDialog.colorSelected.connect( + # lambda color: + # + # self.setColor(getColor(self.model().mooseObject.path+'/info')[1]) + except: + pass + + try: + self.colorButton.clicked.connect(self.colorDialog.show) + self.colorButton.setFocusPolicy(QtCore.Qt.NoFocus) + self.colorDialog.colorSelected.connect( + lambda color: self.colorButton.setStyleSheet( + "QPushButton {" + "background-color: {0}; color: {0};". + format(color.name()) + "}")) + # FIXME: + # colorIndex = self.model().fields.index("Color") + # self.setIndexWidget(self.model().index(colorIndex, 1), self.colorButton) + self.setColor(getColor(self.model().mooseObject.path + '/info')[1]) + except: + pass + print('Created view with %s' % (mobject)) + + def setColor(self, color): + self.colorButton.setStyleSheet( + "QPushButton {" + + "background-color: {0}; color: {0};".format(color) + "}") + self.colorDialog.setCurrentColor(color) + + def dataChanged(self, tl, br): + QTableView.dataChanged.emit(tl, br) + self.viewport().update() + + +class ObjectEditDockWidget(QDockWidget): + """A dock widget whose title is set by the current moose + object. Allows switching the moose object. It stores the created + view in a dict for future use. + + TODO possible performance issue: storing the views (along with + their models) ensures the undo history for each object is + retained. But without a limit on the number of views stored, it + will be wasteful on memory. + + """ + objectNameChanged = QtCore.pyqtSignal('PyQt_PyObject') + colorChanged = QtCore.pyqtSignal(object, object) + + def __init__(self, mobj='/', parent=None, flags=None): + QDockWidget.__init__(self, parent=parent) + mobj = moose.element(mobj) + #self.view = view = ObjectEditView(mobj) + self.view = view = ObjectEditView(mobj) + self.view_dict = {mobj: view} + base = QWidget() + layout = QVBoxLayout() + base.setLayout(layout) + layout.addWidget(self.view) + layout.addWidget(QTextEdit()) + self.setWidget(base) + self.setWindowTitle('Edit: %s' % (mobj.path)) + # self.view.colorDialog.colorSelected.connect(self.colorChangedEmit) + + # def clearDict(self): + # self.view_dict.clear() + + def setObject(self, mobj): + element = moose.element(mobj) + try: + view = self.view_dict[element] + except KeyError: + view = ObjectEditView(element) + self.view_dict[element] = view + view.model().objectNameChanged.connect(self.emitObjectNameChanged) + view.colorDialog.colorSelected.connect(lambda color: self.colorChanged. + emit(element, color)) + textEdit = QTextEdit() + view.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Ignored) + textEdit.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Maximum) + base = QSplitter() + base.setOrientation(QtCore.Qt.Vertical) + layout = QVBoxLayout() + layout.addWidget(view) #, 0, 0) + lineedit = QLineEdit("Notes:") + lineedit.setReadOnly(True) + layout.addWidget(lineedit) + + if (isinstance(mobj, moose.PoolBase) + or isinstance(mobj, moose.ReacBase) + or isinstance(mobj, moose.EnzBase)): + info = moose.Annotator(mobj.path + '/info') + textEdit.setText(QtCore.QString(info.getField('notes'))) + textEdit.textChanged.connect(lambda: info.setField( + 'notes', str(textEdit.toPlainText()))) + layout.addWidget(textEdit) #,1,0) + base.setLayout(layout) + self.setWidget(base) + self.setWindowTitle('Edit: %s' % (element.path)) + view.update() + + def emitObjectNameChanged(self, mobj): + self.objectNameChanged.emit(mobj) + self.setWindowTitle('Edit:%s' % (mobj.path)) + + def undo(self): + if len(self.undoStack) == 0: + raise RuntimeWarning('No more undo information') + index, oldvalue, = self.undoStack.pop() + field = self.fields[index.row()] + currentvalue = self.mooseObject.getField(field) + oldvalue = type(currentvalue)(oldvalue) + self.redoStack.append((index, str(currentvalue))) + self.mooseObject.setField(field, oldvalue) + if field == 'name': + self.objectNameChanged.emit(self.mooseObject) + self.dataChanged.emit(index, index) + +def main(): + from PyQt5.QtWidgets import QApplication, QMainWindow, QAction + app = QApplication(sys.argv) + mainwin = QMainWindow() + c = moose.Compartment("test") + view = ObjectEditView(c, undolen=3) + mainwin.setCentralWidget(view) + action = QAction('Undo', mainwin) + action.setShortcut('Ctrl+z') + action.triggered.connect(view.model().undo) + mainwin.menuBar().addAction(action) + action = QAction('Redo', mainwin) + action.setShortcut('Ctrl+y') + action.triggered.connect(view.model().redo) + mainwin.menuBar().addAction(action) + mainwin.show() + sys.exit(app.exec_()) + + +if __name__ == "__main__": + main() diff --git a/plugins/NeuroKit.py b/moosegui/plugins/NeuroKit.py similarity index 91% rename from plugins/NeuroKit.py rename to moosegui/plugins/NeuroKit.py index 00785c7..290da77 100644 --- a/plugins/NeuroKit.py +++ b/moosegui/plugins/NeuroKit.py @@ -20,8 +20,8 @@ # from collections import defaultdict # import numpy as np # import re -# from PyQt4 import QtGui, QtCore -# from PyQt4.Qt import Qt +# from PyQt5 import QtGui, QtCore +# from PyQt5.Qt import Qt # from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar # import moose @@ -31,12 +31,12 @@ # from msearch import SearchWidget # from checkcombobox import CheckComboBox import sys -import default -import NeuroKitEditor -import NeuroKitRunner +from . import default +from . import NeuroKitEditor +from . import NeuroKitRunner import mplugin import moose -from PyQt4.QtGui import QWidget +from PyQt5.QtGui import QWidget # import NeuroKitPlotter # import NeuroKitRunner diff --git a/plugins/NeuroKitEditor.py b/moosegui/plugins/NeuroKitEditor.py similarity index 95% rename from plugins/NeuroKitEditor.py rename to moosegui/plugins/NeuroKitEditor.py index e0f9c81..9d538ef 100644 --- a/plugins/NeuroKitEditor.py +++ b/moosegui/plugins/NeuroKitEditor.py @@ -17,29 +17,29 @@ import moose import pprint # import NeuroKitEditorWidget -import default - -from PyQt4 import QtGui -from PyQt4 import QtCore -from PyQt4 import Qt -from PyQt4.QtGui import QPushButton -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QHBoxLayout -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QDialog -from PyQt4.QtGui import QTableWidget -from PyQt4.QtGui import QTableWidgetItem -from PyQt4.QtGui import QCheckBox -from PyQt4.QtGui import QComboBox - -from default import * +from . import default + +from PyQt5 import QtGui +from PyQt5 import QtCore +from PyQt5 import Qt +from PyQt5.QtGui import QPushButton +from PyQt5.QtGui import QWidget +from PyQt5.QtGui import QHBoxLayout +from PyQt5.QtGui import QGridLayout +from PyQt5.QtGui import QDialog +from PyQt5.QtGui import QTableWidget +from PyQt5.QtGui import QTableWidgetItem +from PyQt5.QtGui import QCheckBox +from PyQt5.QtGui import QComboBox + +from .default import * from mplugin import * import moose import neuroextractor import moogli import numpy as np from global_constants import preferences -from NeuroKitVisualizer import MorphologyEditor +from .NeuroKitVisualizer import MorphologyEditor class NeuroKitEditor(mplugin.EditorBase): @@ -142,7 +142,7 @@ def createCentralWidget(self): self.morphology = self.createMorphology(self.geometry) self.morphology.set_compartment_order( - map(lambda x : x.path, self.compartmentOrder) + [x.path for x in self.compartmentOrder] ) self.vms = np.empty(len(self.compartmentOrder), dtype=np.float, order='C') diff --git a/plugins/NeuroKitRunner.py b/moosegui/plugins/NeuroKitRunner.py similarity index 95% rename from plugins/NeuroKitRunner.py rename to moosegui/plugins/NeuroKitRunner.py index 9e7f57c..5cfe2b8 100644 --- a/plugins/NeuroKitRunner.py +++ b/moosegui/plugins/NeuroKitRunner.py @@ -9,17 +9,17 @@ from mplot import CanvasWidget import RunWidget from PlotWidgetContainer import PlotWidgetContainer -from NeuroKitVisualizer import MorphologySimulator -from PyQt4 import QtGui, Qt -from PyQt4.QtGui import QLabel -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QToolBar -from PyQt4.QtGui import QPushButton -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QTextEdit +from .NeuroKitVisualizer import MorphologySimulator +from PyQt5 import QtGui, Qt +from PyQt5.QtGui import QLabel +from PyQt5.QtGui import QWidget +from PyQt5.QtGui import QToolBar +from PyQt5.QtGui import QPushButton +from PyQt5.QtGui import QGridLayout +from PyQt5.QtGui import QTextEdit import pprint -# from PyQt4.QtGui import QToolBa -from default import * +# from PyQt5.QtGui import QToolBa +from .default import * import moose import neuroextractor import moogli @@ -74,7 +74,7 @@ def createCentralWidget(self): self.morphology = self.createMorphology(self.geometry) self.morphology.set_compartment_order( - map(lambda x : x.path, self.compartmentOrder) + [x.path for x in self.compartmentOrder] ) self.vms = np.empty(len(self.compartmentOrder), dtype=np.float, order='C') diff --git a/plugins/NeuroKitVisualizer.py b/moosegui/plugins/NeuroKitVisualizer.py similarity index 83% rename from plugins/NeuroKitVisualizer.py rename to moosegui/plugins/NeuroKitVisualizer.py index 046df19..932d3f3 100644 --- a/plugins/NeuroKitVisualizer.py +++ b/moosegui/plugins/NeuroKitVisualizer.py @@ -1,20 +1,23 @@ -from PyQt4 import QtGui, Qt, QtCore -from PyQt4.QtGui import QLabel -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QToolBar -from PyQt4.QtGui import QPushButton -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QTextEdit -from PyQt4.QtCore import QMimeData -from PyQt4.QtGui import QDrag -from PyQt4.QtGui import QPixmap -from PyQt4.QtGui import QPainter -from PyQt4.QtGui import QFont -from PyQt4.QtCore import QPoint +from PyQt5 import QtGui, Qt, QtCore +from PyQt5.QtGui import QLabel +from PyQt5.QtGui import QWidget +from PyQt5.QtGui import QToolBar +from PyQt5.QtGui import QPushButton +from PyQt5.QtGui import QGridLayout +from PyQt5.QtGui import QTextEdit +from PyQt5.QtCore import QMimeData +from PyQt5.QtGui import QDrag +from PyQt5.QtGui import QPixmap +from PyQt5.QtGui import QPainter +from PyQt5.QtGui import QFont +from PyQt5.QtCore import QPoint + import moose -import default import moogli +from moosegui.config import _logger +from moosegui.plugins import default + class MorphologyEditor(moogli.MorphologyViewer): def __init__(self, morphology, width, height, plugin): @@ -26,12 +29,12 @@ def __init__(self, morphology, width, height, plugin): self.plugin = plugin def start(self): - self._timer.timeout.connect(self.next) + self._timer.timeout.connect(self.__next__) self._timer.start(0) @QtCore.pyqtSlot() def show(self): - self._timer.timeout.connect(self.next) + self._timer.timeout.connect(self.__next__) super(MorphologyEditor, self).show() self._timer.start(0) @@ -40,7 +43,7 @@ def hide(self): self._timer.stop() super(MorphologyEditor, self).hide() - def next(self): + def __next__(self): self.frame() info_id = self.select_info.get_id() info_event = self.select_info.get_event_type() @@ -59,12 +62,12 @@ def __init__(self, morphology, width, height, plugin): self.plugin = plugin def start(self): - self._timer.timeout.connect(self.next) + self._timer.timeout.connect(self.__next__) self._timer.start(0) @QtCore.pyqtSlot() def show(self): - self._timer.timeout.connect(self.next) + self._timer.timeout.connect(self.__next__) super(MorphologySimulator, self).show() self._timer.start(0) @@ -74,10 +77,7 @@ def hide(self): super(MorphologySimulator, self).hide() def start_drag(self, info_id): - # pixmap = QPixmap() - # painter = QPainter( pixmap ) - # painter.setFont( QFont("Arial") ); - # painter.drawText( QPoint(100, 100), info_id ); + _logger.info( "started dragging" ) mimeData = QMimeData() mimeData.data =("/" + info_id.partition("/")[2].partition("/")[0], moose.element(info_id)) mimeData.setText(info_id) @@ -88,12 +88,12 @@ def start_drag(self, info_id): drag.setPixmap(pixmap) # drag.setHotSpot(e.pos() - self.rect().topLeft()) dropAction = drag.start(QtCore.Qt.MoveAction) - print(" => ", dropAction) + print((" => ", dropAction)) self.select_info.set_event_type(0) self._timer.start(0) return - def next(self): + def __next__(self): self.frame() info_id = self.select_info.get_id() info_event = self.select_info.get_event_type() diff --git a/plugins/PreferencesPresenter.py b/moosegui/plugins/PreferencesPresenter.py similarity index 97% rename from plugins/PreferencesPresenter.py rename to moosegui/plugins/PreferencesPresenter.py index 7b4a368..b8487fe 100644 --- a/plugins/PreferencesPresenter.py +++ b/moosegui/plugins/PreferencesPresenter.py @@ -1,22 +1,25 @@ -from __future__ import print_function +# -*- coding: utf-8 -*- + import sys -from PyQt4 import Qt, QtGui, QtCore -from PyQt4.QtCore import QObject -from PyQt4.QtCore import pyqtSignal -from PyQt4.QtGui import QColor -from PyQt4.QtGui import QGroupBox -from PreferencesView import PreferencesView -import moose -from defines import * import json import os -PREFERENCES_FILEPATH = os.path.join( os.path.dirname(os.path.abspath(__file__)) - , "datastore/preferences.json" - ) +from PyQt5 import Qt +from PyQt5.QtCore import QObject +from PyQt5.QtCore import pyqtSignal +from PyQt5.QtGui import QColor -class PreferencesPresenter(QObject): +import moose +from moosegui.plugins.PreferencesView import PreferencesView +from moosegui.plugins.defines import * + +PREFERENCES_FILEPATH = os.path.join( + os.path.dirname(os.path.abspath(__file__)) + , "datastore/preferences.json" + ) + +class PreferencesPresenter(QObject): electricalSimulationIntervalChanged = pyqtSignal(float) electricalPlotUpdateIntervalChanged = pyqtSignal(float) electricalDefaultSimulationRuntimeChanged = pyqtSignal(float) @@ -439,7 +442,8 @@ def cancelElectricalVisualizationSettings(self): def main(): - app = QtGui.QApplication(sys.argv) + from PyQt5.QtWidgets import QApplication + app = QApplication(sys.argv) preferences = PreferencesPresenter() preferences.view.show() sys.exit(app.exec_()) diff --git a/plugins/PreferencesView.py b/moosegui/plugins/PreferencesView.py similarity index 79% rename from plugins/PreferencesView.py rename to moosegui/plugins/PreferencesView.py index 1699c9a..94ecef8 100644 --- a/plugins/PreferencesView.py +++ b/moosegui/plugins/PreferencesView.py @@ -1,46 +1,41 @@ -from __future__ import print_function -import PyQt4 -from PyQt4 import Qt, QtGui, QtCore -from PyQt4.QtCore import pyqtSignal -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QButtonGroup -from PyQt4.QtGui import QRadioButton -from PyQt4.QtGui import QVBoxLayout -from PyQt4.QtGui import QLabel -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QLineEdit -from PyQt4.QtGui import QDoubleValidator -from PyQt4.QtGui import QComboBox -from PyQt4.QtGui import QTabWidget -from PyQt4.QtGui import QPushButton -from PyQt4.QtGui import QColorDialog -from PyQt4.QtGui import QColor -from PyQt4.QtGui import QSizePolicy +# -*- coding: utf-8 -*- + import sys +import logging + +from PyQt5 import Qt, QtCore +from PyQt5.QtCore import pyqtSignal +from PyQt5.QtWidgets import QWidget, QButtonGroup, QRadioButton, QApplication +from PyQt5.QtWidgets import QLineEdit, QGridLayout +from PyQt5.QtWidgets import QLabel +from PyQt5.QtWidgets import QTabWidget, QPushButton, QColorDialog +# from PyQt5.QtWidgets import QSizePolicy +from PyQt5.QtWidgets import QApplication +from PyQt5.QtGui import QDoubleValidator class PreferencesView(QTabWidget): - - closed = pyqtSignal() + closed = pyqtSignal() def __init__(self, parent = None): super(PreferencesView, self).__init__(parent) - self.setWindowTitle("Preferences") - # self.setFixedSize(self.maximumSize()) - # self.setMinimumSize(self.maximumSize()) - # self.setMaximumSize(self.maximumSize()) + # If QApplication does not exists then don't do anything. + if QApplication.instance() is None: + logging.warn("No QApplication exists. Won't do anything.") + return -1 - # self.setSizePolicy(QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)) + self.setWindowTitle("Preferences") self.chemicalSimulationDt = self.createFloatingPointEditor() self.chemicalDiffusionDt = self.createFloatingPointEditor() self.chemicalPlotUpdateInterval = self.createFloatingPointEditor() self.chemicalDefaultSimulationRuntime = self.createFloatingPointEditor() self.chemicalGuiUpdateInterval = self.createFloatingPointEditor() self.chemicalSolver = QButtonGroup() - self.chemicalSolvers = { "Exponential Euler" : QRadioButton("Exponential Euler") - , "Gillespie" : QRadioButton("Gillespie") - , "Runge Kutta" : QRadioButton("Runge Kutta") - } + self.chemicalSolvers = { + "Exponential Euler" : QRadioButton("Exponential Euler") + , "Gillespie" : QRadioButton("Gillespie") + , "Runge Kutta" : QRadioButton("Runge Kutta") + } self.chemicalSimulationApply = QPushButton("Apply") self.chemicalSimulationCancel = QPushButton("Cancel") self.electricalSimulationDt = self.createFloatingPointEditor() @@ -48,9 +43,10 @@ def __init__(self, parent = None): self.electricalDefaultSimulationRuntime = self.createFloatingPointEditor() self.electricalGuiUpdateInterval = self.createFloatingPointEditor() self.electricalSolver = QButtonGroup() - self.electricalSolvers = { "Gillespie" : QRadioButton("Gillespie") - , "Runge Kutta" : QRadioButton("Runge Kutta") - } + self.electricalSolvers = { + "Gillespie" : QRadioButton("Gillespie") + , "Runge Kutta" : QRadioButton("Runge Kutta") + } self.electricalSimulationApply = QPushButton("Apply") self.electricalSimulationCancel = QPushButton("Cancel") self.electricalVisualizationApply = QPushButton("Apply") @@ -72,13 +68,13 @@ def closeEvent(self, event): def create(self): # Set up the column titles self.setUsesScrollButtons(True) - self.setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) - self.addTab( self.createChemicalSettingsTab(),"Chemical") - self.addTab( self.createElectricalSettingsTab(),"Electrical") + self.setFocusPolicy(QtCore.Qt.NoFocus) + self.addTab( self.createChemicalSettingsTab(), "Chemical") + self.addTab( self.createElectricalSettingsTab(), "Electrical") def createChemicalSettingsTab(self): chemicalSettingsTab = QWidget() - layout = QtGui.QGridLayout() + layout = QGridLayout() chemicalSettingsTab.setLayout(layout) layout.addWidget(QLabel('Simulation dt'), 0, 0) @@ -102,7 +98,7 @@ def createChemicalSettingsTab(self): for solver in self.chemicalSolvers: layout.addWidget(self.chemicalSolvers[solver], 5 + index, 1) self.chemicalSolver.addButton(self.chemicalSolvers[solver], index) - self.chemicalSolvers[solver].setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) + self.chemicalSolvers[solver].setFocusPolicy(QtCore.Qt.NoFocus) index += 1 self.chemicalSolver.setExclusive(True) @@ -128,13 +124,12 @@ def createElectricalSettingsTab(self): electricalSettingsTab.setTabShape(QTabWidget.Triangular) electricalSettingsTab.setDocumentMode(True) electricalSettingsTab.setUsesScrollButtons(True) - electricalSettingsTab.setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) + electricalSettingsTab.setFocusPolicy(QtCore.Qt.NoFocus) return electricalSettingsTab def createElectricalSimulationSettingsTab(self): - widget = QWidget() - layout = QtGui.QGridLayout() + layout = QGridLayout() widget.setLayout(layout) layout.addWidget(QLabel('Simulation dt'), 0, 0) @@ -155,7 +150,7 @@ def createElectricalSimulationSettingsTab(self): for solver in self.electricalSolvers: # layout.addWidget(self.electricalSolvers[solver], 5 + index, 1) self.electricalSolver.addButton(self.electricalSolvers[solver], index) - self.electricalSolvers[solver].setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) + self.electricalSolvers[solver].setFocusPolicy(QtCore.Qt.NoFocus) index += 1 self.electricalSolver.setExclusive(True) @@ -169,7 +164,7 @@ def createElectricalSimulationSettingsTab(self): def createElectricalSimulationVisualizationTab(self): widget = QWidget() - layout = QtGui.QGridLayout() + layout = QGridLayout() widget.setLayout(layout) layout.addWidget(QLabel('Base Membrane Voltage'), 1, 0) @@ -179,7 +174,7 @@ def createElectricalSimulationVisualizationTab(self): self.electricalBaseColorDialog.setOption(QColorDialog.ShowAlphaChannel, True) layout.addWidget(self.electricalBaseColorButton, 2, 1) self.electricalBaseColorButton.clicked.connect(self.electricalBaseColorDialog.show) - self.electricalBaseColorButton.setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) + self.electricalBaseColorButton.setFocusPolicy(QtCore.Qt.NoFocus) self.electricalBaseColorDialog.colorSelected.connect( lambda color: self.electricalBaseColorButton.setStyleSheet( "QPushButton {" @@ -195,7 +190,7 @@ def createElectricalSimulationVisualizationTab(self): self.electricalPeakColorDialog.setOption(QColorDialog.ShowAlphaChannel, True) layout.addWidget(self.electricalPeakColorButton, 4, 1) self.electricalPeakColorButton.clicked.connect(self.electricalPeakColorDialog.show) - self.electricalPeakColorButton.setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) + self.electricalPeakColorButton.setFocusPolicy(QtCore.Qt.NoFocus) self.electricalPeakColorDialog.colorSelected.connect( lambda color: self.electricalPeakColorButton.setStyleSheet( "QPushButton {" @@ -208,7 +203,7 @@ def createElectricalSimulationVisualizationTab(self): self.electricalBackgroundColorDialog.setOption(QColorDialog.ShowAlphaChannel, True) layout.addWidget(self.electricalBackgroundColorButton, 5, 1) self.electricalBackgroundColorButton.clicked.connect(self.electricalBackgroundColorDialog.show) - self.electricalBackgroundColorButton.setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) + self.electricalBackgroundColorButton.setFocusPolicy(QtCore.Qt.NoFocus) self.electricalBackgroundColorDialog.colorSelected.connect( lambda color: self.electricalBackgroundColorButton.setStyleSheet( "QPushButton {" @@ -229,7 +224,7 @@ def createFloatingPointEditor(self, value = 0.0, minValue = float("-inf"), maxVa return floatingPointEditor def main(): - app = QtGui.QApplication(sys.argv) + app = QApplication(sys.argv) widget = PreferencesView() widget.show() sys.exit(app.exec_()) diff --git a/plugins/README b/moosegui/plugins/README similarity index 100% rename from plugins/README rename to moosegui/plugins/README diff --git a/plugins/Runner.py b/moosegui/plugins/Runner.py similarity index 91% rename from plugins/Runner.py rename to moosegui/plugins/Runner.py index e2dd0aa..c541e41 100644 --- a/plugins/Runner.py +++ b/moosegui/plugins/Runner.py @@ -1,9 +1,9 @@ import math import moose -from PyQt4 import Qt, QtGui, QtCore -from PyQt4.QtCore import QTimer -from PyQt4.QtCore import QObject -from PyQt4.QtCore import pyqtSignal +from PyQt5 import Qt, QtGui, QtCore +from PyQt5.QtCore import QTimer +from PyQt5.QtCore import QObject +from PyQt5.QtCore import pyqtSignal class Runner(QObject): """Helper class to control simulation execution @@ -59,9 +59,9 @@ def runSimulation(self, runTime): # print(self.simulationInterval) # print(self.runSequence) self.simulationStarted.emit(self.clock.currentTime + self.runTime) - QTimer.singleShot(0, self.next) + QTimer.singleShot(0, self.__next__) - def next(self): + def __next__(self): if self.pause: return if len(self.runSequence) == 0: @@ -69,19 +69,19 @@ def next(self): return moose.start(self.runSequence.pop(0)) self.simulationProgressed.emit(self.clock.currentTime) - QTimer.singleShot(0, self.next) + QTimer.singleShot(0, self.__next__) def pauseSimulation(self): self.pause = True def unpauseSimulation(self): self.pause = False - self.next() + next(self) def togglePauseSimulation(self): if self.pause : self.pause = False - self.next() + next(self) else: self.pause = True diff --git a/plugins/__init__.py b/moosegui/plugins/__init__.py similarity index 100% rename from plugins/__init__.py rename to moosegui/plugins/__init__.py diff --git a/plugins/buildkkit.py b/moosegui/plugins/buildkkit.py similarity index 83% rename from plugins/buildkkit.py rename to moosegui/plugins/buildkkit.py index 6e85d60..291d5a0 100644 --- a/plugins/buildkkit.py +++ b/moosegui/plugins/buildkkit.py @@ -1,25 +1,31 @@ +# -*- coding: utf-8 -*- + import sys import os import math import re -from PyQt4 import QtGui, QtCore, Qt -#import pygraphviz as pgv -import networkx as nx -#sys.path.insert(0, '/home/harsha/BuildQ/gui') -import numpy as np -import config import pickle -from default import * -from moose import * -sys.path.append('plugins') -from mplugin import * -from kkitUtil import * -from kkitQGraphics import PoolItem, ReacItem,EnzItem,CplxItem,ComptItem -from kkitViewcontrol import * -from kkitCalcArrow import * -from kkitOrdinateUtil import * import posixpath -from mtoolbutton import MToolButton + +from PyQt5 import QtGui, QtCore, Qt +from PyQt5.QtWidgets import QFileDialog, QWidget +from PyQt5.QtWidgets import QGraphicsScene, QMenu, QMessageBox + +if __name__ == "__main__": + from PyQt5.QtWidgets import QApplication + app = QApplication(sys.argv) + +import networkx as nx +import numpy as np + +from moosegui import config +from moosegui.plugins.default import * +from moosegui.plugins.kkitUtil import * +from moosegui.plugins.kkitQGraphics import * +from moosegui.plugins.kkitViewcontrol import * +from moosegui.plugins.kkitCalcArrow import * +from moosegui.plugins import kkitOrdinateUtil +from moosegui.mtoolbutton import MToolButton class KkitPlugin(MoosePlugin): """Default plugin for MOOSE GUI""" @@ -66,25 +72,25 @@ class KkitEditorView(MooseEditorView): def __init__(self, plugin): MooseEditorView.__init__(self, plugin) ''' - self.insertMenu = QtGui.QMenu('Insert') + self.insertMenu = QMenu('Insert') sortList = ['CubeMesh','CylMesh','Pool','FuncPool','SumFunc','Reac','Enz','MMenz','StimulusTable','Table'] for slist in sortList: action = QtGui.QAction(moose.element('/classes/'+slist).name, self.insertMenu) self._toolBars.append(action) ''' - self.fileinsertMenu = QtGui.QMenu('&File') + self.fileinsertMenu = QMenu('&File') if not hasattr(self,'SaveModelAction'): self.saveModelAction = QtGui.QAction('SaveToSBMLFile', self) - self.saveModelAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+S", None, QtGui.QApplication.UnicodeUTF8)) - self.connect(self.saveModelAction, QtCore.SIGNAL('triggered()'), self.SaveModelDialogSlot) + self.saveModelAction.setShortcut( "Ctrl+S" ) + self.saveModelAction.triggered.connect(self.SaveModelDialogSlot) self.fileinsertMenu.addAction(self.saveModelAction) + self._menus.append(self.fileinsertMenu) def SaveModelDialogSlot(self): type_sbml = 'SBML' - print " here in saveModelDialog" filters = {'SBML(*.xml)': type_sbml} - filename,filter_ = QtGui.QFileDialog.getSaveFileNameAndFilter(None,'Save File','',';;'.join(filters)) + filename,filter_ = QFileDialog.getSaveFileNameAndFilter(None,'Save File','',';;'.join(filters)) extension = "" if str(filename).rfind('.') != -1: filename = filename[:str(filename).rfind('.')] @@ -93,7 +99,6 @@ def SaveModelDialogSlot(self): if filename: filename = filename+extension if filters[str(filter_)] == 'SBML': - print "here",filename," ",self.plugin.modelRoot moose.writeSBML(str(filename),self.plugin.modelRoot) def getToolPanes(self): return super(KkitEditorView, self).getToolPanes() @@ -117,18 +122,18 @@ def getCentralWidget(self): class KineticsWidget(EditorWidgetBase): def __init__(self, *args): - EditorWidgetBase.__init__(self, *args) + EditorWidgetBase.__init__(self, *args) self.setAcceptDrops(True) self.border = 10 - self.sceneContainer = QtGui.QGraphicsScene(self) + self.sceneContainer = QGraphicsScene(self) self.sceneContainer.setSceneRect(self.sceneContainer.itemsBoundingRect()) self.sceneContainer.setBackgroundBrush(QtGui.QColor(230,220,219,120)) - self.insertMenu = QtGui.QMenu('&Insert') + self.insertMenu = QMenu('&Insert') self._menus.append(self.insertMenu) self.insertMapper = QtCore.QSignalMapper(self) - classlist = ['CubeMesh','CylMesh','Pool','FuncPool','SumFunc','Reac','Enz','MMenz','StimulusTable','Table'] + classlist = ['CubeMesh','CylMesh','Pool', 'Reac','Enz','MMenz','StimulusTable','Table'] insertMapper, actions = self.getInsertActions(classlist) for action in actions: @@ -150,14 +155,14 @@ def sizeHint(self): def updateModelView(self): #print "update model view",self.modelRoot if self.modelRoot == '/': - m = wildcardFind('/##[ISA=ChemCompt]') + m = moose.wildcardFind('/##[ISA=ChemCompt]') else: - m = wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]') + m = moose.wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]') #print "111",self.modelRoot,m if not m: # when we want an empty GraphicView while creating new model, # then remove all the view and add an empty view - if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget): + if hasattr(self, 'view') and isinstance(self.view, QWidget): self.layout().removeWidget(self.view) self.view = GraphicalView(self.sceneContainer,self.border,self) self.layout().addWidget(self.view) @@ -180,20 +185,17 @@ def updateModelView(self): colormap_file.close() # Compartment and its members are setup """ - self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot) - # srcdesConnection dictonary will have connection information between src and des """ + o, self.meshEntry, self.xmin, self.xmax, self.ymin, \ + self.ymax, self.noPositionInfo = kkitOrdinateUtil.setupMeshObj(self.modelRoot) self.srcdesConnection = {} - setupItem(self.modelRoot,self.srcdesConnection) + kkitOrdinateUtil.setupItem(self.modelRoot,self.srcdesConnection) if self.noPositionInfo: self.autocoordinates = True - QtGui.QMessageBox.warning(self, - 'No coordinates found for the model', - '\n Automatic layouting will be done') - #raise Exception('Unsupported kkit version') - - - self.xmin,self.xmax,self.ymin,self.ymax,self.autoCordinatepos = autoCoordinates(self.meshEntry,self.srcdesConnection) + QMessageBox.warning(self, + 'No coordinates found for the model', + '\n Automatic layouting will be done') + kkitOrdinateUtil.autoCoordinates(self.meshEntry,self.srcdesConnection) # Scale factor to translate the x -y position to fit the Qt graphicalScene, scene width. """ if self.xmax-self.xmin != 0: @@ -223,28 +225,23 @@ def updateModelView(self): # All the moose Object are connected for visualization self.drawLine_arrow(itemignoreZooming=False) - if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget): + if hasattr(self, 'view') and isinstance(self.view,QWidget): self.layout().removeWidget(self.view) self.view = GraphicalView(self.sceneContainer,self.border,self) hLayout = QtGui.QGridLayout(self) - self.setLayout(hLayout) + self.setLayout(hLayout) hLayout.addWidget(self.view) #self.layout().addWidget(self.view) def mooseObjOntoscene(self): # All the compartments are put first on to the scene \ # Need to do: Check With upi if empty compartments exist - for cmpt in sorted(self.meshEntry.iterkeys()): + for cmpt in sorted(self.meshEntry.keys()): self.createCompt(cmpt) self.qGraCompt[cmpt] - #comptRef = self.qGraCompt[cmpt] - #Enzymes of all the compartments are placed first, \ - # so that when cplx (which is pool object) queries for its parent, it gets its \ - # parent enz co-ordinates with respect to QGraphicsscene """ - - for cmpt,memb in self.meshEntry.items(): - for enzObj in find_index(memb,'enzyme'): + for cmpt,memb in list(self.meshEntry.items()): + for enzObj in memb.get('enzyme', []): enzinfo = enzObj.path+'/info' if enzObj.className == 'ZEnz': enzItem = EnzItem(enzObj,self.qGraCompt[cmpt]) @@ -253,32 +250,32 @@ def mooseObjOntoscene(self): self.setupDisplay(enzinfo,enzItem,"enzyme") self.setupSlot(enzObj,enzItem) - for cmpt,memb in self.meshEntry.items(): - for poolObj in find_index(memb,'pool'): + for cmpt,memb in list(self.meshEntry.items()): + for poolObj in kkitOrdinateUtil.find_index(memb,'pool'): poolinfo = poolObj.path+'/info' poolItem = PoolItem(poolObj,self.qGraCompt[cmpt]) self.setupDisplay(poolinfo,poolItem,"pool") self.setupSlot(poolObj,poolItem) - for cplxObj in find_index(memb,'cplx'): + for cplxObj in kkitOrdinateUtil.find_index(memb,'cplx'): cplxinfo = (cplxObj[0].parent).path+'/info' cplxItem = CplxItem(cplxObj,self.mooseId_GObj[element(cplxObj[0]).parent.getId()]) self.setupDisplay(cplxinfo,cplxItem,"cplx") self.setupSlot(cplxObj,cplxItem) - for reaObj in find_index(memb,'reaction'): + for reaObj in kkitOrdinateUtil.find_index(memb,'reaction'): reainfo = reaObj.path+'/info' reaItem = ReacItem(reaObj,self.qGraCompt[cmpt]) self.setupDisplay(reainfo,reaItem,"reaction") self.setupSlot(reaObj,reaItem) - for tabObj in find_index(memb,'table'): + for tabObj in kkitOrdinateUtil.find_index(memb,'table'): tabinfo = tabObj.path+'/info' tabItem = PoolItem(tabObj,self.qGraCompt[cmpt]) self.setupDisplay(tabinfo,tabItem,"tab") self.setupSlot(tabObj,tabItem) # compartment's rectangle size is calculated depending on children - for k, v in self.qGraCompt.items(): + for k, v in list(self.qGraCompt.items()): rectcompt = v.childrenBoundingRect() v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) v.setPen(QtGui.QPen(Qt.QColor(66,66,66,100), 5, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) @@ -339,7 +336,7 @@ def updateItemSlot(self, mooseObject): #slot for updating the display item. #In this case if the name is updated from the keyboard both in mooseobj and gui gets updation changedItem = '' - for item in self.sceneContainer.items(): + for item in list(self.sceneContainer.items()): if isinstance(item,PoolItem): if mooseObject.getId() == element(item.mobj).getId(): item.updateSlot() @@ -349,7 +346,7 @@ def updateItemSlot(self, mooseObject): def positionChange(self,mooseObject): #If the item position changes, the corresponding arrow's are calculated if isinstance(element(mooseObject),CubeMesh): - for k, v in self.qGraCompt.items(): + for k, v in list(self.qGraCompt.items()): mesh = mooseObject.path+'/mesh[0]' if k.path == mesh: for rectChilditem in v.childItems(): @@ -357,7 +354,7 @@ def positionChange(self,mooseObject): else: mobj = self.mooseId_GObj[mooseObject.getId()] self.updateArrow(mobj) - for k, v in self.qGraCompt.items(): + for k, v in list(self.qGraCompt.items()): rectcompt = v.childrenBoundingRect() v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) @@ -366,7 +363,7 @@ def emitItemtoEditor(self,mooseObject): self.editObject.emit(mooseObject.path) def drawLine_arrow(self, itemignoreZooming=False): - for inn,out in self.srcdesConnection.items(): + for inn,out in list(self.srcdesConnection.items()): # self.srcdesConnection is dictionary which contains key,value \ # key is Enzyme or Reaction and value [[list of substrate],[list of product]] (tuple) # key is FuncBase and value is [list of pool] (list) @@ -374,7 +371,7 @@ def drawLine_arrow(self, itemignoreZooming=False): #src = self.mooseId_GObj[inn] if isinstance(out,tuple): if len(out[0])== 0: - print inn.className + ':' +inn[0].name+ " doesn't output message" + print(inn.className + ':' +inn[0].name+ " doesn't output message") else: src = self.mooseId_GObj[inn] for items in (items for items in out[0] ): @@ -382,7 +379,7 @@ def drawLine_arrow(self, itemignoreZooming=False): self.lineCord(src,des,items,itemignoreZooming) if len(out[1]) == 0: - print inn.className + ':' +inn[0].name+ " doesn't output message" + print(inn.className + ':' +inn[0].name+ " doesn't output message") else: for items in (items for items in out[1] ): des = self.mooseId_GObj[element(items[0]).getId()] @@ -390,7 +387,7 @@ def drawLine_arrow(self, itemignoreZooming=False): elif isinstance(out,list): if len(out) == 0: - print "Func pool doesn't have sumtotal" + print("Func pool doesn't have sumtotal") else: src = self.mooseId_GObj[element(inn).getId()] for items in (items for items in out ): @@ -401,7 +398,7 @@ def lineCord(self,src,des,type_no,itemignoreZooming): endtype = type_no[1] line = 0 if (src == "") and (des == ""): - print "Source or destination is missing or incorrect" + print("Source or destination is missing or incorrect") return srcdes_list = [src,des,endtype,line] arrow = calcArrow(srcdes_list,itemignoreZooming,self.iconScale) @@ -414,14 +411,14 @@ def lineCord(self,src,des,type_no,itemignoreZooming): line = line +1 if type_no[2] > 5: - print "Higher order reaction will not be displayed" + print("Higher order reaction will not be displayed") def drawLine(self,srcdes_list,arrow): src = srcdes_list[0] des = srcdes_list[1] endtype = srcdes_list[2] line = srcdes_list[3] - source = element(next((k for k,v in self.mooseId_GObj.items() if v == src), None)) + source = element(next((k for k,v in list(self.mooseId_GObj.items()) if v == src), None)) for l,v,o in self.object2line[src]: if v == des and o ==line: l.setPolygon(arrow) @@ -441,7 +438,7 @@ def drawLine(self,srcdes_list,arrow): if ( (endtype == 's') or (endtype == 'p')): pen.setColor(QtCore.Qt.red) elif(endtype != 'cplx'): - p1 = (next((k for k,v in self.mooseId_GObj.items() if v == src), None)) + p1 = (next((k for k,v in list(self.mooseId_GObj.items()) if v == src), None)) pinfo = p1.path+'/info' color,bgcolor = getColor(pinfo,self.colorMap) pen.setColor(color) @@ -478,7 +475,7 @@ def cplxUpdatearrow(self,srcdes): # srcdes which is 'EnzItem' from this,get ChildItems are retrived (b'cos cplx is child of zombieEnz) #And cplxItem is passed for updatearrow - #Note: Here at this point enzItem has just one child which is cplxItem and childItems returns, PyQt4.QtGui.QGraphicsEllipseItem,CplxItem + #Note: Here at this point enzItem has just one child which is cplxItem and childItems returns, PyQt5.QtGui.QGraphicsEllipseItem,CplxItem #Assuming CplxItem is always[1], but still check if not[0], if something changes in structure one need to keep an eye. if (srcdes.childItems()[1],CplxItem): self.updateArrow(srcdes.childItems()[1]) @@ -514,14 +511,14 @@ def keyPressEvent(self,event): self.view.fitInView(self.sceneContainer.itemsBoundingRect().x()-10,self.sceneContainer.itemsBoundingRect().y()-10,self.sceneContainer.itemsBoundingRect().width()+20,self.sceneContainer.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio) def updateItemTransformationMode(self, on): - for v in self.sceneContainer.items(): + for v in list(self.sceneContainer.items()): if( not isinstance(v,ComptItem)): #if ( isinstance(v, PoolItem) or isinstance(v, ReacItem) or isinstance(v, EnzItem) or isinstance(v, CplxItem) ): if isinstance(v,KineticsDisplayItem): v.setFlag(QtGui.QGraphicsItem.ItemIgnoresTransformations, on) def updateScale( self, scale ): - for item in self.sceneContainer.items(): + for item in list(self.sceneContainer.items()): if isinstance(item,KineticsDisplayItem): item.refresh(scale) #iteminfo = item.mobj.path+'/info' @@ -544,7 +541,7 @@ def updateScale( self, scale ): item.bg.setRect(0, 0, item.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '), item.gobj.boundingRect().height()) self.drawLine_arrow(itemignoreZooming=False) - for k, v in self.qGraCompt.items(): + for k, v in list(self.qGraCompt.items()): rectcompt = v.childrenBoundingRect() comptPen = v.pen() comptWidth = self.defaultComptsize*self.iconScale @@ -553,7 +550,6 @@ def updateScale( self, scale ): v.setRect(rectcompt.x()-comptWidth,rectcompt.y()-comptWidth,(rectcompt.width()+2*comptWidth),(rectcompt.height()+2*comptWidth)) if __name__ == "__main__": - app = QtGui.QApplication(sys.argv) size = QtCore.QSize(1024 ,768) modelPath = 'Kholodenko' #modelPath = 'acc61' @@ -563,24 +559,18 @@ def updateScale( self, scale ): modelPath = '5AreacB' itemignoreZooming = False try: - filepath = '../../Demos/Genesis_files/'+modelPath+'.g' - #filepath = '/home/harsha/genesis_files/gfile/'+modelPath+'.g' - print filepath - f = open(filepath, "r") - loadModel(filepath,'/'+modelPath) - + sdir = os.path.dirname(__file__) + filepath = os.path.join(sdir, '../../data/Kholodenko.g') + print(filepath) + moose.loadModel(filepath, '/'+modelPath) moose.le('/'+modelPath+'/kinetics') dt = KineticsWidget() dt.modelRoot ='/'+modelPath - ''' Loading moose signalling model in python ''' - #execfile('/home/harsha/BuildQ/Demos/Genesis_files/scriptKineticModel.py') - #dt.modelRoot = '/model' - dt.updateModelView() dt.show() - except IOError, what: + except IOError as what: (errno, strerror) = what - print "Error number",errno,"(%s)" %strerror + print("Error number",errno,"(%s)" %strerror) sys.exit(0) sys.exit(app.exec_()) diff --git a/moosegui/plugins/constants.py b/moosegui/plugins/constants.py new file mode 100644 index 0000000..e8eeaf0 --- /dev/null +++ b/moosegui/plugins/constants.py @@ -0,0 +1,24 @@ +INVALID = 6 + +INTERIOR = 7 +BOUNDARY = 8 + +SAME_OBJECT = 9 +OTHER_OBJECT = 10 +NO_OBJECT = 11 + +RUBBERBAND_SELECTION = 12 +VALID = 13 + +ITEM = 0 +CONNECTOR = 1 +CONNECTION = 2 +EMPTY = 3 + +COMPARTMENT = 14 +COMPARTMENT_BOUNDARY = 4 +COMPARTMENT_INTERIOR = 5 + +GROUP = 15 +GROUP_BOUNDARY = 16 +GROUP_INTERIOR = 17 diff --git a/plugins/datastore/preferences.json b/moosegui/plugins/datastore/preferences.json similarity index 100% rename from plugins/datastore/preferences.json rename to moosegui/plugins/datastore/preferences.json diff --git a/plugins/default.py b/moosegui/plugins/default.py similarity index 63% rename from plugins/default.py rename to moosegui/plugins/default.py index 3cb2840..0475a0e 100644 --- a/plugins/default.py +++ b/moosegui/plugins/default.py @@ -1,104 +1,45 @@ -# default.py --- -# -# Filename: default.py +# -*- coding: utf-8 -*- + # Description: # Author: Subhasis Ray # Maintainer: # Created: Tue Nov 13 15:58:31 2012 (+0530) -# Version: -# Last-Updated: Mon Sep 10 23:35:00 2018 (+0530) -# By: Harsha -# Update #: -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# The default placeholder plugin for MOOSE -# -# -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: -''' -2018 -Sep 10: replace addSolver to mooseAddChemSolver from moose.chemUtil's -2013 -Oct 5: could not recreate if object already exist in moose which was allowed earlier - now if object exist need to use element which is cleaned here - -''' import sys -import config import pickle import os from collections import defaultdict import numpy as np -from PyQt4 import QtGui, QtCore -from PyQt4.Qt import Qt -import moose -from moose import utils -import mtree -from mtoolbutton import MToolButton -from msearch import SearchWidget -from checkcombobox import CheckComboBox - -from mplugin import MoosePluginBase, EditorBase, EditorWidgetBase, PlotBase, RunBase -#from defaultToolPanel import DefaultToolPanel -#from DataTable import DataTable from matplotlib import rcParams +from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar rcParams.update({'figure.autolayout': True}) -from matplotlib.lines import Line2D -from PlotWidgetContainer import PlotWidgetContainer - -from PyQt4 import QtCore, QtGui -from PyQt4.QtGui import QDoubleValidator -from kkitUtil import getColor -from Runner import Runner -# from Runner import Runner -# from __future__ import print_function -from PyQt4 import QtGui, QtCore -from PyQt4.QtGui import QToolBar -from PyQt4.QtGui import QToolButton -from PyQt4.QtGui import QLabel -from PyQt4.QtGui import QIcon -from PyQt4.QtGui import QLineEdit -from PyQt4.QtGui import QErrorMessage -from PyQt4.QtGui import QSizeGrip -from PyQt4.QtGui import QIcon -from PyQt4.QtGui import QPixmap -from PyQt4.QtGui import QAction -from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar -#from EventBlocker import EventBlocker -# from PlotNavigationToolbar import PlotNavigationToolbar -from global_constants import preferences -#from setsolver import * -from moose.chemUtil.add_Delete_ChemicalSolver import * + +from PyQt5 import QtCore, QtGui +from PyQt5.QtCore import Qt +from PyQt5.QtCore import pyqtSlot, pyqtSignal + +from PyQt5.QtWidgets import QToolBar, QToolButton +from PyQt5.QtWidgets import QLabel, QLineEdit +from PyQt5.QtWidgets import QAction, QSizePolicy +from PyQt5.QtWidgets import QWidget, QHBoxLayout +from PyQt5.QtWidgets import QScrollArea, QGridLayout, QMessageBox +from PyQt5.QtWidgets import QMenu, QApplication, QDockWidget +from PyQt5.QtWidgets import QFrame, QFileDialog, QVBoxLayout + +# moose +import moose + +# moosegui +from moosegui.global_constants import preferences +from moosegui.mtoolbutton import MToolButton +from moosegui.checkcombobox import CheckComboBox +from moosegui.mplugin import MoosePluginBase, EditorBase, EditorWidgetBase, RunBase +from moosegui.plugins.kkitUtil import getColor +from moosegui.plugins.Runner import Runner +from moosegui import config +from moosegui import mtree +from moosegui.PlotWidgetContainer import PlotWidgetContainer ELECTRICAL_MODEL = 0 CHEMICAL_MODEL = 1 @@ -107,8 +48,7 @@ class MoosePlugin(MoosePluginBase): """Default plugin for MOOSE GUI""" def __init__(self, root, mainwindow): MoosePluginBase.__init__(self, root, mainwindow) - #print "mplugin ",self.getRunView() - #self.connect(self, QtCore.SIGNAL("tableCreated"),self.getRunView().getCentralWidget().plotAllData) + def getPreviousPlugin(self): return None @@ -132,13 +72,7 @@ def getEditorView(self): self.currentView = self.editorView return self.editorView - def getPlotView(self): - if not hasattr(self, 'plotView'): - self.plotView = PlotView(self) - return self.plotView - def getRunView(self): - if not hasattr(self, 'runView') or self.runView is None: self.runView = RunView(self.modelRoot, self) return self.runView @@ -158,7 +92,7 @@ def __init__(self, plugin): self.__initToolBars() def __initMenus(self): - editMenu = QtGui.QMenu('&Edit') + editMenu = QMenu('&Edit') for menu in self.getCentralWidget().getMenus(): editMenu.addMenu(menu) self._menus.append(editMenu) @@ -243,7 +177,7 @@ class DefaultEditorWidget(EditorWidgetBase): """ def __init__(self, *args): EditorWidgetBase.__init__(self, *args) - layout = QtGui.QHBoxLayout() + layout = QHBoxLayout() self.setLayout(layout) self.tree = MooseTreeEditor() self.tree.setAcceptDrops(True) @@ -254,11 +188,12 @@ def getTreeMenu(self): try: return self.treeMenu except AttributeError: - self.treeMenu = QtGui.QMenu() + self.treeMenu = QMenu() + self.tree.setContextMenuPolicy(Qt.CustomContextMenu) self.tree.customContextMenuRequested.connect(lambda : self.treeMenu.exec_(QtGui.QCursor.pos()) ) # Inserting a child element - self.insertMenu = QtGui.QMenu('Insert') + self.insertMenu = QMenu('Insert') self._menus.append(self.insertMenu) self.treeMenu.addMenu(self.insertMenu) self.insertMapper = QtCore.QSignalMapper(self) @@ -273,8 +208,8 @@ def getTreeMenu(self): insertMapper, actions = self.getInsertActions(classlist) for action in actions: self.insertMenu.addAction(action) - self.connect(insertMapper, QtCore.SIGNAL('mapped(const QString&)'), self.tree.insertElementSlot) - self.editAction = QtGui.QAction('Edit', self.treeMenu) + insertMapper.mapped.connect(self.tree.insertElementSlot) + self.editAction = QAction('Edit', self.treeMenu) self.editAction.triggered.connect(self.editCurrentObjectSlot) self.tree.elementInserted.connect(self.elementInsertedSlot) self.treeMenu.addAction(self.editAction) @@ -305,7 +240,7 @@ def sizeHint(self): def getToolBars(self): if not hasattr(self, '_insertToolBar'): - self._insertToolBar = QtGui.QToolBar('Insert') + self._insertToolBar = QToolBar('Insert') return self._toolBars for action in self.insertMenu.actions(): button = MToolButton() @@ -320,9 +255,7 @@ def getToolBars(self): # View for running a simulation and runtime visualization # ############################################################ - - -from mplot import CanvasWidget +from moosegui.mplot import CanvasWidget class RunView(RunBase): """A default runtime view implementation. This should be @@ -331,8 +264,8 @@ class RunView(RunBase): canvas: widget for plotting dataRoot: location of data tables - """ + def __init__(self, modelRoot, *args, **kwargs): RunBase.__init__(self, *args, **kwargs) self.modelRoot = modelRoot @@ -386,10 +319,10 @@ def getSchedulingDockWidget(self): """Create and/or return a widget for schduling""" if hasattr(self, 'schedulingDockWidget') and self.schedulingDockWidget is not None: return self.schedulingDockWidget - self.schedulingDockWidget = QtGui.QDockWidget('Scheduling') - self.schedulingDockWidget.setFeatures( QtGui.QDockWidget.NoDockWidgetFeatures); + self.schedulingDockWidget = QDockWidget('Scheduling') + self.schedulingDockWidget.setFeatures( QDockWidget.NoDockWidgetFeatures); self.schedulingDockWidget.setWindowFlags(Qt.CustomizeWindowHint) - titleWidget = QtGui.QWidget(); + titleWidget = QWidget(); self.schedulingDockWidget.setTitleBarWidget(titleWidget) widget = SchedulingWidget() widget.setDataRoot(self.dataRoot) @@ -398,83 +331,12 @@ def getSchedulingDockWidget(self): widget.runner.simulationStarted.connect(self._centralWidget.extendXAxes) widget.runner.simulationProgressed.connect(self._centralWidget.updatePlots) widget.runner.simulationFinished.connect(self._centralWidget.rescalePlots) - # widget.runner.simulationContinued.connect(self._centralWidget.extendXAxes) widget.runner.simulationReset.connect(self._centralWidget.plotAllData) self._toolBars += widget.getToolBars() return self.schedulingDockWidget -''' -class MooseRunner(QtCore.QObject): - """Helper class to control simulation execution - See: http://doc.qt.digia.com/qq/qq27-responsive-guis.html : - 'Solving a Problem Step by Step' for design details. - """ - resetAndRun = QtCore.pyqtSignal(name='resetAndRun') - update = QtCore.pyqtSignal(name='update') - currentTime = QtCore.pyqtSignal(float, name='currentTime') - finished = QtCore.pyqtSignal(name='finished') - - def __init__( self - , runTime - , updateInterval - ): - QtCore.QObject.__init__(self) - # if (MooseRunner.inited): - # return - self.runTime = runTime - self.updateInterval = updateInterval - self._updateInterval = 100e-3 - self._simtime = 0.0 - self._clock = moose.Clock('/clock') - self._pause = False - self.dataRoot = '/data' - self.modelRoot = '/model' - #MooseRunner.inited = True - - def doResetAndRun(self, tickDtMap, tickTargetMap, simtime, updateInterval): - self._pause = False - self._updateInterval = 0.1 #updateInterval - self._simtime = simtime - utils.updateTicks(tickDtMap) - utils.assignTicks(tickTargetMap) - self.resetAndRun.emit() - moose.reinit() - QtCore.QTimer.singleShot(0, self.run) - - def run(self): - """Run simulation for a small interval.""" - print("simtime => ", self._simtime) - print("update interval => ", self._updateInterval) - print("current time => ", self._clock.currentTime) - print("Base dt => ", self._clock.baseDt) - if self._clock.currentTime >= self._simtime: - self.finished.emit() - return - if self._pause: - return - toRun = self._simtime - self._clock.currentTime - if toRun > self._updateInterval: - toRun = self._updateInterval - if toRun < self._clock.baseDt: - return - moose.start(toRun) - self.update.emit() - self.currentTime.emit(self._clock.currentTime) - QtCore.QTimer.singleShot(0, self.run) - - def continueRun(self, simtime, updateInterval): - """Continue running without reset for `simtime`.""" - self._simtime = simtime - self._updateInterval = updateInterval - self._pause = False - QtCore.QTimer.singleShot(0, self.run) - - def stop(self): - """Pause simulation""" - self._pause = True -''' -class SchedulingWidget(QtGui.QWidget): +class SchedulingWidget(QWidget): """Widget for scheduling. Important member fields: @@ -502,20 +364,11 @@ class SchedulingWidget(QtGui.QWidget): continueRun = QtCore.pyqtSignal(float, float, name='continueRun') def __init__(self, *args, **kwargs): - QtGui.QWidget.__init__(self, *args, **kwargs) + QWidget.__init__(self, *args, **kwargs) self.simulationInterval = None self.updateInterval = None self.runTime = None - # if not self.advanceOptiondisplayed: - # self.advancedOptionsWidget.hide() - - # self.__getUpdateIntervalWidget() - #layout.addWidget(self.__getUpdateIntervalWidget()) - # spacerItem = QtGui.QSpacerItem(450, 40, QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Expanding) - # layout.addItem(spacerItem) - # self.setLayout(layout) - # self._toolBars.append( self.modelRoot = None self.dataRoot = None self.runner = Runner() @@ -530,10 +383,6 @@ def __init__(self, *args, **kwargs): self.runner.simulationProgressed.connect(self.updateCurrentSimulationRuntime) self.continueFlag = False self.preferences.applyChemicalSettings.connect(self.resetSimulation) - # self.resetAndRunButton.clicked.connect(self.resetAndRunSlot) - # self.continueButton.clicked.connect(self.doContinueRun) - # self.continueRun.connect(self.runner.continueRun) - # self.stopButton.clicked.connect(self.runner.stop) def updateCurrentSimulationRuntime(self, time): self.currentSimulationRuntime.setText(str(time)) @@ -545,30 +394,33 @@ def getSchedulerToolBar(self): bar = QToolBar("Run", self) - self.resetAction = bar.addAction( QIcon('icons/arrow_undo.png') - , 'Reset' - , self.resetSimulation - ) + self.resetAction = bar.addAction( + QtGui.QIcon( os.path.join( config.MOOSE_ICON_DIR, 'reset.png' ) ) + , 'Reset' + , self.resetSimulation + ) self.resetAction.setToolTip('Reset simulation.') - self.runAction = bar.addAction( QIcon('icons/run.png') - , 'Run' - , self.runSimulation - ) + self.runAction = bar.addAction( + QtGui.QIcon( os.path.join( config.MOOSE_ICON_DIR, 'run.png') ) + , 'Run' + , self.runSimulation + ) self.runAction.setToolTip('Run simulation.') - self.stopAction = bar.addAction( QIcon('icons/stop.png') - , 'Stop' - , self.runner.togglePauseSimulation - ) + self.stopAction = bar.addAction( + QtGui.QIcon( os.path.join( config.MOOSE_ICON_DIR, 'stop.png') ) + , 'Stop' + , self.runner.togglePauseSimulation + ) self.stopAction.setToolTip('Stop simulation.') bar.addSeparator() runtimeLabel = QLabel('Run for') self.simulationRuntime = QLineEdit() - self.simulationRuntime.setValidator(QDoubleValidator()) + self.simulationRuntime.setValidator(QtGui.QDoubleValidator()) self.simulationRuntime.setFixedWidth(75) bar.addWidget(runtimeLabel) bar.addWidget(self.simulationRuntime) @@ -576,13 +428,10 @@ def getSchedulerToolBar(self): bar.addSeparator() #: current time - # spacer.setSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Preferred) - # self._runToolBar.addWidget(spacer) - # self._runToolBar.addWidget(QtGui.QLabel('Current time')) self.currentSimulationRuntime = QLineEdit() # 6 digits self.currentSimulationRuntime.setToolTip('Current simulation runtime.') self.currentSimulationRuntime.setFixedWidth(75) - self.currentSimulationRuntime.setValidator(QDoubleValidator()) + self.currentSimulationRuntime.setValidator(QtGui.QDoubleValidator()) self.currentSimulationRuntime.setText("0.0") self.currentSimulationRuntime.setReadOnly(True) @@ -590,7 +439,6 @@ def getSchedulerToolBar(self): bar.addWidget(QLabel("Current Time : ")) bar.addWidget(self.currentSimulationRuntime) bar.addWidget(QLabel(" (s)")) - # self._runToolBar.addWidget(self.()) bar.addSeparator() @@ -601,13 +449,6 @@ def getSchedulerToolBar(self): bar.addWidget(self.preferencesButton) return bar - # def updateTickswidget(self): - # if self.advanceOptiondisplayed: - # self.advancedOptionsWidget.hide() - # self.advanceOptiondisplayed = False - # else: - # self.advancedOptionsWidget.show() - # self.advanceOptiondisplayed = True def continueSimulation(self): self.runner.continueSimulation( self.runTime @@ -661,12 +502,6 @@ def runSimulation(self): self.checkConsistency() self.continueSimulation = True self.runner.runSimulation(self.runtime) - # return - # if self.continueFlag: - # self.continueSimulation() - # else: - # self.runner.runSimulation() - # self.continueFlag = True def setParameters(self): if self.modelType == ELECTRICAL_MODEL: @@ -683,7 +518,6 @@ def setChemicalParameters(self): self.simulationRuntime.setText(str(chemicalPreferences["simulation"]["default-runtime"])) self.runTime = float(self.simulationRuntime.text()) self.solver = chemicalPreferences["simulation"]["solver"] - #print(self.solver) def setElectricalParameters(self): electricalPreferences = self.preferences.getElectricalPreferences() @@ -694,27 +528,12 @@ def setElectricalParameters(self): self.simulationRuntime.setText(str(electricalPreferences["simulation"]["default-runtime"])) self.runTime = float(self.simulationRuntime.text()) self.solver = electricalPreferences["simulation"]["solver"] - #print(self.solver) def checkConsistency(self): if self.updateInterval < self.simulationInterval : self.updateInterval = self.simulationInterval - - # print("Hello") - # dialog = QErrorMessage() - # dialog.showMessage( - # """GUI Update interval should be greater than Simulation Interval. - # Please update these values in Edit > Preferences.""" - # ) - # return False if self.runTime < self.updateInterval : self.runTime = self.updateInterval - # dialog = QErrorMessage() - # dialog.showMessage( - # """Simulation runtime should greater than GUI Update interval. - # Please update the runtime in the Scheduling Toolbar""" - # ) - # return False return True def solverStatus(self): @@ -742,45 +561,29 @@ def solverStatus(self): nameRE = nameRE+"\n "+res.className + " --> "+res.parent.name+ " --> "+res.name if status == -1: - QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Reaction path not yet assigned.\n ") + QMessageBox.warning(None,"Could not Run the model","Warning: Reaction path not yet assigned.\n ") return -1 if status == 1: - #QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in a Reac or Enz.\n ") - QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in %s " %(nameRE)) + #QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in a Reac or Enz.\n ") + QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in %s " %(nameRE)) return 1 elif status == 2: - QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz %s " %(nameRE)) - #QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz.\n ") + QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz %s " %(nameRE)) + #QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz.\n ") return 2 elif status == 4: - QtGui.QMessageBox.warning(None,"Could not Run the model"," Warning: Compartment not defined.\n ") + QMessageBox.warning(None,"Could not Run the model"," Warning: Compartment not defined.\n ") return 4 elif status == 8: - QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Neither Ksolve nor Dsolve defined.\n ") + QMessageBox.warning(None,"Could not Run the model","Warning: Neither Ksolve nor Dsolve defined.\n ") return 8 elif status == 16: - QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: No objects found on path.\n ") + QMessageBox.warning(None,"Could not Run the model","Warning: No objects found on path.\n ") return 16 elif status == 0: - print "Successfully built stoichiometry matrix.\n " + print("Successfully built stoichiometry matrix.\n ") # moose.reinit() return 0 - # def setElectricalParameters(self): - # chemicalPreferences = self.preferences.getChemicalPreferences() - # self.updateInterval = chemicalPreferences["guiUpdateInterval"] - # self.simulationInterval = chemicalPreferences["simulationInterval"] - # chemicalPreferences["diffusionInterval"] - # chemicalPreferences - # self. chemicalPreferences - # self. chemicalPreferences - # self. chemicalPreferences - # self. runTime = float(self.simulationRuntime.text()) - - def __getAdvanceOptionsButton(self): - icon = QtGui.QIcon(os.path.join(config.settings[config.KEY_ICON_DIR],'arrow.png')) - # self.advancedOptionsButton.setIcon(QtGui.QIcon(icon)) - # self.advancedOptionsButton.setToolButtonStyle( Qt.ToolButtonTextBesideIcon ); - return self.advancedOptionsButton def preferencesToggler(self): visibility = not self.preferences.getView().isVisible() @@ -796,7 +599,7 @@ def updateCurrentTime(self): def updateTextFromTick(self, tickNo): tick = moose.vector('/clock/tick')[tickNo] widget = self.tickListWidget.layout().itemAtPosition(tickNo + 1, 1).widget() - if widget is not None and isinstance(widget, QtGui.QLineEdit): + if widget is not None and isinstance(widget, QLineEdit): widget.setText(str(tick.dt)) def updateFromMoose(self): @@ -811,10 +614,9 @@ def getSimTime(self): try: time = float(str(self.simtimeEdit.text())) return time - except ValueError, e: - QtGui.QMessageBox.warning(self, 'Invalid value', 'Specified runtime was meaningless.') - return 0 - + except ValueError: + QMessageBox.warning(self, 'Invalid value', 'Specified runtime was meaningless.') + return 0.0 def setDataRoot(self, root='/data'): self.dataRoot = moose.element(root).path @@ -844,13 +646,6 @@ def setModelType(self): legend = None canvas = None -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QSizeGrip -from PyQt4.QtGui import QLayout -from PyQt4.QtGui import QScrollArea -from PyQt4.QtGui import QMenu -from PyQt4.QtCore import pyqtSlot,SIGNAL,SLOT, Signal, pyqtSignal - class PlotWidget(QWidget): """A wrapper over CanvasWidget to handle additional MOOSE-specific stuff. @@ -859,9 +654,6 @@ class PlotWidget(QWidget): dataRoot - path to the container of data tables. - TODO: do we really need this separation or should we go for - standardizing location of data with respect to model root. - pathToLine - map from moose path to Line2D objects in plot. Can one moose table be plotted multiple times? Maybe yes (e.g., when you want multiple other tables to be compared with the same data). @@ -872,6 +664,7 @@ class PlotWidget(QWidget): widgetClosedSignal = pyqtSignal(object) addGraph = pyqtSignal(object) + def __init__(self, model, graph, index, parentWidget, *args, **kwargs): super(PlotWidget, self).__init__() self.model = model @@ -880,81 +673,56 @@ def __init__(self, model, graph, index, parentWidget, *args, **kwargs): self.menu = self.getContextMenu() self.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) - self.connect( self - , SIGNAL("customContextMenuRequested(QPoint)") - , self - , SLOT("contextMenuRequested(QPoint)") - ) + self.customContextMenuRequested.connect(self.contextMenuRequested) + # self.connect( self + # , SIGNAL("customContextMenuRequested(QPoint)") + # , self + # , SLOT("contextMenuRequested(QPoint)") + # ) self.canvas = CanvasWidget(self.model, self.graph, self.index) self.canvas.setParent(self) self.navToolbar = NavigationToolbar(self.canvas, self) self.hackNavigationToolbar() self.canvas.mpl_connect('pick_event',self.togglePlot) - # self.canvas. - # self.navToolbar.addSeparator() - layout = QtGui.QGridLayout() - # canvasScrollArea = QScrollArea() - # canvasScrollArea.setWidget(self.canvas) + layout = QGridLayout() layout.addWidget(self.navToolbar, 0, 0) layout.addWidget(self.canvas, 1, 0) self.setLayout(layout) - # self.setAcceptDrops(True) - #self.modelRoot = '/' self.pathToLine = defaultdict(set) self.lineToDataSource = {} self.axesRef = self.canvas.addSubplot(1, 1) - # box = self.axesRef.get_position() - # self.axesRef.set_position([box.x0, box.y0, box.width * 0.8, box.height]) - self.legend = None - # layout.setSizeConstraint( QLayout.SetNoConstraint ) - # self.setSizePolicy( QtGui.QSizePolicy.Expanding - # , QtGui.QSizePolicy.Expanding - # ) - - desktop = QtGui.QApplication.desktop() - # print("**********************") - # print(desktop.screenGeometry()) - # print("***********************") - self.setMinimumSize(desktop.screenGeometry().width() / 4, desktop.screenGeometry().height() / 3) - # self.setMaximumSize(desktop.screenGeometry().width() / 2, desktop.screenGeometry().height() / 2) - # self.setMinimumSize(self.width(), self.height()) - # self.setMaximumSize(2 * self.width(), 2* self.height()) - # QtCore.QObject.connect(utils.tableEmitter,QtCore.SIGNAL("tableCreated()"),self.plotAllData) + desktop = QApplication.desktop() + self.setMinimumSize(desktop.screenGeometry().width()//4, desktop.screenGeometry().height()//3) self.canvas.updateSignal.connect(self.plotAllData) self.plotAllData() - # self.plotView = PlotView(model, graph, index, self) - #self.dataTable = DataTable() - #utils.tableCreated.connect(plotAllData) - # self.plotAllData() - # self.setSizePolicy(QtGui.QSizePolicy.Fixed, - # QtGui.QSizePolicy.Expanding) def hackNavigationToolbar(self): # ADD Graph Action - pixmap = QPixmap("icons/add_graph.png") - icon = QIcon(pixmap) + pixmap = QtGui.QPixmap( + os.path.join( config.MOOSE_ICON_DIR, 'add_graph.png' ) + ) + icon = QtGui.QIcon(pixmap) action = QAction(icon, "Add a graph", self.navToolbar) # self.navToolbar.addAction(action) - action.triggered.connect(self.addGraph.emit) + action.triggered.connect( self.addGraph.emit ) self.navToolbar.insertAction(self.navToolbar.actions()[0], action) # Delete Graph Action - pixmap = QPixmap("icons/delete_graph.png") - icon = QIcon(pixmap) + pixmap = QtGui.QPixmap( os.path.join( config.MOOSE_ICON_DIR, + "delete_graph.png") ) + icon = QtGui.QIcon(pixmap) action = QAction(icon, "Delete this graph", self.navToolbar) - # self.navToolbar.addAction(action) action.triggered.connect(self.delete) - self.navToolbar.insertAction(self.navToolbar.actions()[1], action) #Toggle Grid Action - - pixmap = QPixmap("icons/grid.png") - icon = QIcon(pixmap) + pixmap = QtGui.QPixmap( + os.path.join( config.MOOSE_ICON_DIR, "grid.png" ) + ) + icon = QtGui.QIcon(pixmap) action = QAction(icon, "Toggle Grid", self.navToolbar) - # self.navToolbar.addAction(action) action.triggered.connect(self.canvas.toggleGrid) self.navToolbar.insertAction(self.navToolbar.actions()[2], action) self.navToolbar.insertSeparator(self.navToolbar.actions()[3]) @@ -970,7 +738,7 @@ def toggleLegend(self): self.canvas.draw() def getContextMenu(self): - menu = QMenu() + menu = QMenu() # closeAction = menu.addAction("Delete") exportCsvAction = menu.addAction("Export to CSV") exportCsvAction.triggered.connect(self.saveAllCsv) @@ -986,11 +754,13 @@ def getContextMenu(self): return menu def deleteGraph(self): - print("Deleting " + self.graph.path) + """ If there is only one graph in the view, please don't delete it """ + print( "Deleting %s " % self.graph.path) moose.delete(self.graph.path) def delete(self, event): - print("Deleting PlotWidget") + """FIXME: The last element should not be deleted """ + _logger.info("Deleting PlotWidget " ) self.deleteGraph() self.close() self.widgetClosedSignal.emit(self) @@ -1001,16 +771,6 @@ def configure(self, event): @pyqtSlot(QtCore.QPoint) def contextMenuRequested(self,point): - # menu = QtGui.QMenu() - - # # action1 = menu.addAction("Set Size 100x100") - # # action2 = menu.addAction("Set Size 500x500") - - - # # self.connect(action2,SIGNAL("triggered()"), - # # self,SLOT("slotShow500x500()")) - # # self.connect(action1,SIGNAL("triggered()"), - # # self,SLOT("slotShow100x100()")) self.menu.exec_(self.mapToGlobal(point)) def setModelRoot(self, path): @@ -1021,7 +781,6 @@ def setDataRoot(self, path): #plotAllData() def genColorMap(self,tableObject): - #print "tableObject in colorMap ",tableObject species = tableObject+'/info' colormap_file = open(os.path.join(config.settings[config.KEY_COLORMAP_DIR], 'rainbow2.pkl'),'rb') self.colorMap = pickle.load(colormap_file) @@ -1042,9 +801,8 @@ def genColorMap(self,tableObject): color = 'white' return color - def removePlot(self, table): - print("removePlot =>", table) + print(("removePlot =>", table)) moose.delete(table) self.plotAllData() @@ -1193,7 +951,7 @@ def addRasterPlot(self, eventtable, yoffset=0, *args, **kwargs): return self.canvas.plot(eventtable.vector, y, '|') def updatePlots(self): - for path, lines in self.pathToLine.items(): + for path, lines in list(self.pathToLine.items()): element = moose.element(path) if isinstance(element, moose.Table2): tab = moose.Table2(path) @@ -1206,7 +964,7 @@ def updatePlots(self): self.canvas.draw() def extendXAxes(self, xlim): - for axes in self.canvas.axes.values(): + for axes in list(self.canvas.axes.values()): # axes.autoscale(False, axis='x', tight=True) axes.set_xlim(right=xlim) axes.autoscale_view(tight=True, scalex=True, scaley=True) @@ -1217,7 +975,7 @@ def rescalePlots(self): ideally we should set xlim from simtime. """ - for axes in self.canvas.axes.values(): + for axes in list(self.canvas.axes.values()): axes.autoscale(True, tight=True) axes.relim() axes.autoscale_view(tight=True,scalex=True,scaley=True) @@ -1238,35 +996,35 @@ def saveCsv(self, line, directory): name = moose.element(nameVec[0]).name filename = str(directory)+'/'+'%s.csv' %(name) np.savetxt(filename, np.vstack((x, y)).transpose()) - print 'Saved data from %s and %s in %s' % (xSrc.path, ySrc.path, filename) + print('Saved data from %s and %s in %s' % (xSrc.path, ySrc.path, filename)) def saveAllCsv(self): """Save data for all currently plotted lines""" #Harsha: Plots were saved in GUI folder instead provided QFileDialog box to save to #user choose - fileDialog2 = QtGui.QFileDialog(self) - fileDialog2.setFileMode(QtGui.QFileDialog.Directory) + fileDialog2 = QFileDialog(self) + fileDialog2.setFileMode(QFileDialog.Directory) fileDialog2.setWindowTitle('Select Directory to save plots') - fileDialog2.setOptions(QtGui.QFileDialog.ShowDirsOnly) - fileDialog2.setLabelText(QtGui.QFileDialog.Accept, self.tr("Save")) - targetPanel = QtGui.QFrame(fileDialog2) - targetPanel.setLayout(QtGui.QVBoxLayout()) + fileDialog2.setOptions(QFileDialog.ShowDirsOnly) + fileDialog2.setLabelText(QFileDialog.Accept, self.tr("Save")) + targetPanel = QFrame(fileDialog2) + targetPanel.setLayout(QVBoxLayout()) layout = fileDialog2.layout() layout.addWidget(targetPanel) if fileDialog2.exec_(): directory = fileDialog2.directory().path() - for line in self.lineToDataSource.keys(): - self.saveCsv(line,directory) + for line in list(self.lineToDataSource.keys()): + self.saveCsv(line,directory) def getMenus(self): if not hasattr(self, '_menus'): self._menus = [] - self.plotAllAction = QtGui.QAction('Plot all data', self) + self.plotAllAction = QAction('Plot all data', self) self.plotAllAction.triggered.connect(self.plotAllData) - self.plotMenu = QtGui.QMenu('Plot') + self.plotMenu = QMenu('Plot') self.plotMenu.addAction(self.plotAllAction) - self.saveAllCsvAction = QtGui.QAction('Save all data in CSV files', self) + self.saveAllCsvAction = QAction('Save all data in CSV files', self) self.saveAllCsvAction.triggered.connect(self.saveAllCsv) self.plotMenu.addAction(self.saveAllCsvAction) self._menus.append(self.plotMenu) @@ -1281,156 +1039,7 @@ def getMenus(self): # Plot view - select fields to record # ################################################### -''' -class PlotView(PlotBase): - """View for selecting fields on elements to plot.""" - def __init__(self, model, graph, index, *args): - PlotBase.__init__(self, *args) - self.model = model - self.graph = graph - self.index = index - # self.plugin.modelRootChanged.connect(self.getSelectionPane().setSearchRoot) - # self.plugin.dataRootChanged.connect(self.setDataRoot) - # self.dataRoot = self.plugin.dataRoot - - def setDataRoot(self, root): - self.dataRoot = moose.element(root).path - - def getToolPanes(self): - return (self.getFieldSelectionDock(), ) - - def getSelectionPane(self): - """Creates a widget to select elements and fields for plotting. - search-root, field-name, comparison operator , value - """ - if not hasattr(self, '_selectionPane'): - self._searchWidget = SearchWidget() - self._searchWidget.setSearchRoot(self.model.path) - self._fieldLabel = QtGui.QLabel('Field to plot') - self._fieldEdit = QtGui.QLineEdit() - self._fieldEdit.returnPressed.connect(self._searchWidget.searchSlot) - self._selectionPane = QtGui.QWidget() - layout = QtGui.QHBoxLayout() - layout.addWidget(self._fieldLabel) - layout.addWidget(self._fieldEdit) - self._searchWidget.layout().addLayout(layout) - self._selectionPane = self._searchWidget - self._selectionPane.layout().addStretch(1) - return self._selectionPane - - def getOperationsPane(self): - """TODO: complete this""" - if hasattr(self, 'operationsPane'): - return self.operationsPane - self.operationsPane = QtGui.QWidget() - self._createTablesButton = QtGui.QPushButton('Create tables for recording selected fields', self.operationsPane) - self._createTablesButton.clicked.connect(self.setupRecording) - layout = QtGui.QVBoxLayout() - self.operationsPane.setLayout(layout) - layout.addWidget(self._createTablesButton) - return self.operationsPane - - def getFieldSelectionDock(self): - if not hasattr(self, '_fieldSelectionDock'): - self._fieldSelectionDock = QtGui.QDockWidget('Search and select elements') - self._fieldSelectionWidget = QtGui.QWidget() - layout = QtGui.QVBoxLayout() - self._fieldSelectionWidget.setLayout(layout) - layout.addWidget(self.getSelectionPane()) - layout.addWidget(self.getOperationsPane()) - self._fieldSelectionDock.setWidget(self._fieldSelectionWidget) - return self._fieldSelectionDock - - def getCentralWidget(self): - if not hasattr(self, '_centralWidget') or self._centralWidget is None: - self._centralWidget = PlotSelectionWidget(self.model, self.graph) - self.getSelectionPane().executed.connect(self.selectElements) - return self._centralWidget - - def selectElements(self, elements): - """Refines the selection. - - Currently checks if _fieldEdit has an entry and if so, selects - only elements which have that field, and ticks the same in the - PlotSelectionWidget. - - """ - field = str(self._fieldEdit.text()).strip() - if len(field) == 0: - self.getCentralWidget().setSelectedElements(elements) - return - classElementDict = defaultdict(list) - for epath in elements: - el = moose.element(epath) - classElementDict[el.className].append(el) - refinedList = [] - elementFieldList = [] - for className, elist in classElementDict.items(): - if field in elist[0].getFieldNames('valueFinfo'): - refinedList +=elist - elementFieldList += [(el, field) for el in elist] - self.getCentralWidget().setSelectedElements(refinedList) - self.getCentralWidget().setSelectedFields(elementFieldList) - - - def setupRecording(self): - """Create the tables for recording selected data and connect them.""" - for element, field in self.getCentralWidget().getSelectedFields(): - #createRecordingTable(element, field, self._recordingDict, self._reverseDict, self.dataRoot) - #harsha:CreateRecordingTable function is moved to python/moose/utils.py file as create function - #as this is required when I drop table on to the plot - utils.create(self.plugin.modelRoot,moose.element(element),field,"Table2") - #self.dataTable.create(self.plugin.modelRoot, moose.element(element), field) - #self.updateCallback() - - def createRecordingTable(self, element, field): - """Create table to record `field` from element `element` - - Tables are created under `dataRoot`, the names are generally - created by removing `/model` in the beginning of `elementPath` - and replacing `/` with `_`. If this conflicts with an existing - table, the id value of the target element (elementPath) is - appended to the name. - - """ - if len(field) == 0 or ((element, field) in self._recordingDict): - return - # The table path is not foolproof - conflict is - # possible: e.g. /model/test_object and - # /model/test/object will map to same table. So we - # check for existing table without element field - # path in recording dict. - relativePath = element.path.partition('/model[0]/')[-1] - if relativePath.startswith('/'): - relativePath = relativePath[1:] - #Convert to camelcase - if field == "concInit": - field = "ConcInit" - elif field == "conc": - field = "Conc" - elif field == "nInit": - field = "NInit" - elif field == "n": - field = "N" - elif field == "volume": - field = "Volume" - elif field == "diffConst": - field ="DiffConst" - - tablePath = relativePath.replace('/', '_') + '.' + field - tablePath = re.sub('.', lambda m: {'[':'_', ']':'_'}.get(m.group(), m.group()),tablePath) - tablePath = self.dataRoot + '/' +tablePath - if moose.exists(tablePath): - tablePath = '%s_%d' % (tablePath, element.getId().value) - if not moose.exists(tablePath): - table = moose.Table(tablePath) - print 'Created', table.path, 'for plotting', '%s.%s' % (element.path, field) - target = element - moose.connect(table, 'requestOut', target, 'get%s' % (field)) - self._recordingDict[(target, field)] = table - self._reverseDict[table] = (target, field) -''' -class PlotSelectionWidget(QtGui.QScrollArea): +class PlotSelectionWidget(QScrollArea): """Widget showing the fields of specified elements and their plottable fields. User can select any number of fields for plotting and click a button to generate the tables for recording data. @@ -1440,10 +1049,10 @@ class PlotSelectionWidget(QtGui.QScrollArea): """ def __init__(self, model, graph, *args): - QtGui.QScrollArea.__init__(self, *args) + QScrollArea.__init__(self, *args) self.model = moose.element(model.path + "/model") self.modelRoot = self.model.path - self.setLayout(QtGui.QVBoxLayout(self)) + self.setLayout(QVBoxLayout(self)) self.layout().addWidget(self.getPlotListWidget()) self.setDataRoot(self.model.path) self._elementWidgetsDict = {} # element path to corresponding qlabel and fields combo @@ -1452,10 +1061,10 @@ def getPlotListWidget(self): """An internal widget to display the list of elements and their plottable fields in comboboxes.""" if not hasattr(self, '_plotListWidget'): - self._plotListWidget = QtGui.QWidget(self) - layout = QtGui.QGridLayout(self._plotListWidget) + self._plotListWidget = QWidget(self) + layout = QGridLayout(self._plotListWidget) self._plotListWidget.setLayout(layout) - layout.addWidget(QtGui.QLabel('

Elements matching search criterion will be listed here

'), 0, 0) + layout.addWidget(QLabel('

Elements matching search criterion will be listed here

'), 0, 0) return self._plotListWidget def setSelectedElements(self, elementlist): @@ -1476,19 +1085,19 @@ def setSelectedElements(self, elementlist): del w del item self._elementWidgetsDict.clear() - label = QtGui.QLabel('Element') - label.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed) + label = QLabel('Element') + label.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) self.getPlotListWidget().layout().addWidget(label, 0, 0, 1, 2) - self.getPlotListWidget().layout().addWidget(QtGui.QLabel('Fields to plot'), 0, 2, 1, 1) + self.getPlotListWidget().layout().addWidget(QLabel('Fields to plot'), 0, 2, 1, 1) for ii, entry in enumerate(elementlist): el = moose.element(entry) plottableFields = [] - for field, dtype in moose.getFieldDict(el.className, 'valueFinfo').items(): + for field, dtype in list(moose.getFieldDict(el.className, 'valueFinfo').items()): if dtype == 'double': plottableFields.append(field) if len(plottableFields) == 0: continue - elementLabel = QtGui.QLabel(el.path) + elementLabel = QLabel(el.path) fieldsCombo = CheckComboBox(self) fieldsCombo.addItem('') for item in plottableFields: @@ -1508,7 +1117,7 @@ def setDataRoot(self, path): def getSelectedFields(self): """Returns a list containing (element, field) for all selected fields""" ret = [] - for el, widgets in self._elementWidgetsDict.items(): + for el, widgets in list(self._elementWidgetsDict.items()): combo = widgets[1] for ii in range(combo.count()): field = str(combo.itemText(ii)).strip() @@ -1531,5 +1140,3 @@ def setSelectedFields(self, elementFieldList): if idx >= 0: combo.setItemData(idx, QtCore.QVariant(Qt.Checked), Qt.CheckStateRole) combo.setCurrentIndex(idx) -# -# default.py ends here diff --git a/plugins/defines.py b/moosegui/plugins/defines.py similarity index 86% rename from plugins/defines.py rename to moosegui/plugins/defines.py index 0f550e4..e08598b 100644 --- a/plugins/defines.py +++ b/moosegui/plugins/defines.py @@ -1,7 +1,10 @@ +"""defines.py: +Various clocks used in moose. +""" + ELECTRICAL_SIMULATION_DT_CLOCKS = [1,2,3,4,5,6,7] ELECTRICAL_PLOT_UPDATE_INTERVAL_CLOCKS = [8] ELECTRICAL_DIFFUSION_INTERVAL_CLOCKS = [10] - CHEMICAL_SIMULATION_DT_CLOCKS = [11, 12, 13, 14, 15, 16, 17] CHEMICAL_PLOT_UPDATE_INTERVAL_CLOCKS = [18] CHEMICAL_DIFFUSION_DT_CLOCKS = [10] diff --git a/moosegui/plugins/kkit.py b/moosegui/plugins/kkit.py new file mode 100644 index 0000000..f755ef0 --- /dev/null +++ b/moosegui/plugins/kkit.py @@ -0,0 +1,1107 @@ +# -*- coding: utf-8 -*- + +__author__ = "HarshaRani" +__credits__ = ["Upi Lab"] +__license__ = "GPL3" +__version__ = "1.0.0" +__maintainer__ = "HarshaRani" +__email__ = "hrani@ncbs.res.in" +__status__ = "Development" +__updated__ = "Feb 22 2019" + +import os +import sys +import re +import math + +from PyQt5.QtWidgets import QApplication + +# For testing: QApplication must be created before any other widget. +if __name__ == "__main__": + app = QApplication(sys.argv) + +from PyQt5 import QtGui, QtCore, Qt +from PyQt5.QtWidgets import QWidget, QGridLayout, QFileDialog +from PyQt5.QtWidgets import QMenu, QAction, QGraphicsScene +from PyQt5.QtWidgets import QToolBar +from PyQt5.QtGui import QColor + +# moosegui +from moosegui import RunWidget +from moosegui import mplugin, config +from moosegui.mtoolbutton import MToolButton +from moosegui.plugins.default import MoosePlugin, MooseEditorView, RunView +from moosegui.plugins import kkitUtil, kkitOrdinateUtil +from moosegui.plugins import kkitQGraphics +from moosegui.plugins import kkitViewcontrol +from moosegui.PlotWidgetContainer import PlotWidgetContainer + +# moose +import moose + +# Logging +import logging +logger_ = logging.getLogger('gui.plugins.kkit') + +class KkitPlugin(MoosePlugin): + """ + Default plugin for MOOSE GUI + """ + + def __init__(self, *args): + MoosePlugin.__init__(self, *args) + self.view = None + self.fileinsertMenu = QMenu('&File') + + if not hasattr(self, 'SaveModelAction'): + #self.fileinsertMenu.addSeparator() + self.saveModelAction = QAction('Save', self) + self.saveModelAction.setShortcut("Ctrl+S") + self.saveModelAction.triggered.connect(self.SaveModelDialogSlot) + self.fileinsertMenu.addAction(self.saveModelAction) + + self._menus.append(self.fileinsertMenu) + self.getEditorView() + + def SaveModelDialogSlot(self): + + dirpath = "" + if not dirpath: + dirpath = os.path.expanduser("~") + filters = {'SBML(*.xml)': 'SBML', 'Genesis(*.g)': 'Genesis'} + filename, filter_ = QFileDialog.getSaveFileNameAndFilter( + None, 'Save File', dirpath, "SBML(*.xml);;Genesis(*.g)") + if str(filename).rfind('.') != -1: + filename = filename[:str(filename).rfind('.')] + + if filename: + filename = filename + if filters[str(filter_)] == 'SBML': + self.coOrdinates = {} + self.plugin = KkitEditorView(self).getCentralWidget().plugin + self.coOrdinates = KkitEditorView( + self).getCentralWidget().getsceneCord() + #writeerror = moose.writeSBML(self.modelRoot,str(filename),self.coOrdinates) + writeerror = -2 + writtentofile = "/test.xml" + writeerror, consistencyMessages, writtentofile = moose.SBML.mooseWriteSBML( + self.modelRoot, str(filename), self.coOrdinates) + if writeerror == -2: + QtGui.QMessageBox.warning(None, 'Could not save the Model', + consistencyMessages) + elif writeerror == -1: + QtGui.QMessageBox.warning( + None, 'Could not save the Model', + '\n This model is not valid SBML Model, failed in the consistency check' + ) + elif writeerror == 1: + QtGui.QMessageBox.information( + None, 'Saved the Model', + '\n File saved to \'{filename}\''.format( + filename=filename + '.xml'), QtGui.QMessageBox.Ok) + elif writeerror == 0: + QtGui.QMessageBox.information( + None, 'Could not save the Model', + '\nThe filename could not be opened for writing') + + elif filters[str(filter_)] == 'Genesis': + moose.Annotator(self.modelRoot + '/info') + self.coOrdinates = {} + ss = KkitEditorView(self).getCentralWidget().mooseId_GObj + for k, v in ss.items(): + if moose.exists(moose.element(k).path + '/info'): + annoInfo = moose.Annotator(k.path + '/info') + x = annoInfo.x * 10 + y = -annoInfo.y * 10 + self.coOrdinates[k] = {'x': x, 'y': y} + + error, written = moose.mooseWriteKkit(self.modelRoot, + str(filename), + self.coOrdinates) + if written == False: + QtGui.QMessageBox.information(None, + 'Could not save the Model', + '\nCheck the file') + else: + if error == "": + QtGui.QMessageBox.information( + None, 'Saved the Model', + '\n File saved to \'{filename}\''.format( + filename=filename + '.g'), + QtGui.QMessageBox.Ok) + else: + QtGui.QMessageBox.information( + None, 'Saved the Model but ...', + '{error}'.format(error=error), + QtGui.QMessageBox.Ok) + + def getPreviousPlugin(self): + return None + + def getNextPlugin(self): + return None + + def getAdjacentPlugins(self): + return [] + + def getViews(self): + return self._views + + def getCurrentView(self): + return self.currentView + + def getEditorView(self): + if not hasattr(self, 'editorView'): + self.editorView = KkitEditorView(self) + self.editorView.getCentralWidget().editObject.connect( + self.mainWindow.objectEditSlot) + self.currentView = self.editorView + return self.editorView + + def getRunView(self): + if self.view is None: + self.view = AnotherKkitRunView(self.modelRoot, self) + return self.view + + if self.view is not None: + return AnotherKkitRunView(self.modelRoot, self) + if self.view is not None: + return self.view + self.view = RunView(self.modelRoot, self) + graphView = self.view._centralWidget + graphView.setDataRoot(self.modelRoot) + graphView.plotAllData() + self._kkitWidget = self.view.plugin.getEditorView().getCentralWidget() + self.runView = KkitRunView(self, self._kkitWidget) + self.currentRunView = self.ruAnotherKkitRunViewnView.getCentralWidget() + graphView.layout().addWidget(self.currentRunView, 0, 0, 2, 1) + return self.view + + +class AnotherKkitRunView(RunView): + def __init__(self, modelRoot, plugin, *args): + RunView.__init__(self, modelRoot, plugin, *args) + self.modelRoot = modelRoot + self.plugin = plugin + self.schedular = None + + def setSolverFromSettings(self, chemicalSettings): + self.setSolver(self.modelRoot, + chemicalSettings["simulation"]["solver"]) + + def createCentralWidget(self): + self._centralWidget = RunWidget.RunWidget(self.modelRoot) + self.kkitRunView = KkitRunView(self.plugin) + self.plotWidgetContainer = PlotWidgetContainer(self.modelRoot) + self._centralWidget.setChildWidget(self.kkitRunView.getCentralWidget(), + False, 0, 0, 1, 1) + self._centralWidget.setChildWidget(self.plotWidgetContainer, False, 0, + 1, 1, 2) + self._centralWidget.setPlotWidgetContainer(self.plotWidgetContainer) + self.schedular = self.getSchedulingDockWidget().widget() + self.schedular.runner.simulationProgressed.connect( + self.kkitRunView.getCentralWidget().updateValue) + self.schedular.runner.simulationProgressed.connect( + self.kkitRunView.getCentralWidget().changeBgSize) + self.schedular.runner.simulationReset.connect( + self.kkitRunView.getCentralWidget().resetColor) + self.schedular.preferences.applyChemicalSettings.connect( + self.setSolverFromSettings) + compt = moose.wildcardFind(self.modelRoot + '/##[ISA=ChemCompt]') + ann = moose.Annotator(self.modelRoot + '/info') + if compt: + self.runTime = moose.element(ann).runtime + solver = moose.element(ann).solver + else: + self.runTime = 100 + solver = "gsl" + self.schedular.simulationRuntime.setText(str(self.runTime)) + chemprefs = self.schedular.preferences.getChemicalPreferences() + c = moose.Clock('/clock') + self.simulationdt = c.tickDt[11] + self.plotdt = c.tickDt[18] + chemprefs["simulation"]["simulation-dt"] = self.simulationdt + chemprefs["simulation"]["plot-update-interval"] = self.plotdt + chemprefs["simulation"]["gui-update-interval"] = 2 * self.plotdt + chemprefs["simulation"]["solver"] = "Runge Kutta" + if solver == "gsl": + chemprefs["simulation"]["solver"] = "Runge Kutta" + elif solver == "gssa": + chemprefs["simulation"]["solver"] = "Gillespie" + elif solver == "ee" or solver == " ": + chemprefs["simulation"]["solver"] = "Exponential Euler" + else: + chemprefs["simulation"]["solver"] = "Runge Kutta" + self.schedular.preferences.setChemicalPreferences() + return self._centralWidget + + def setSolver(self, modelRoot, solver=None): + if solver == None: + reinit = moose.mooseAddChemSolver( + modelRoot, + self.getSchedulingDockWidget().widget().solver) + if reinit: + self.getSchedulingDockWidget().widget().resetSimulation() + else: + reinit = moose.mooseAddChemSolver(modelRoot, solver) + if reinit: + self.getSchedulingDockWidget().widget().resetSimulation() + + #self.kkitRunView.getCentralWidget().addSolver(solver) + + def getCentralWidget(self): + if self._centralWidget is None: + self.createCentralWidget() + return self._centralWidget + + +class KkitRunView(MooseEditorView): + def __init__(self, plugin): + MooseEditorView.__init__(self, plugin) + self.plugin = plugin + + def getCentralWidget(self): + if self._centralWidget is None: + self._centralWidget = KineticRunWidget(self.plugin) + self._centralWidget.editor = self.plugin.editorView + self._centralWidget.setModelRoot(self.plugin.modelRoot) + return self._centralWidget + + +class KkitEditorView(MooseEditorView): + def __init__(self, plugin): + MooseEditorView.__init__(self, plugin) + + def getCentralWidget(self): + if self._centralWidget is None: + self._centralWidget = kineticEditorWidget(self.plugin) + self._centralWidget.setModelRoot(self.plugin.modelRoot) + return self._centralWidget + + +class KineticsWidget(mplugin.EditorWidgetBase): + def __init__(self, plugin, *args): + mplugin.EditorWidgetBase.__init__(self, *args) + self.plugin = plugin + self.border = 5 + self.comptPen = 5 + self.iconScale = 1 + self.arrowsize = 2 + self.reset() + + self.defaultSceneheight = 1 #800#1000 + self.defaultScenewidth = 1 #000#2400 + self.positionInfoExist = True + self.defaultComptsize = 5 + self.srcdesConnection = {} + self.meshEntry = {} + self.mooseId_GObj = {} + self.qGraCompt = {} + self.qGraGrp = {} + self.xyCord = {} + self.editor = None + + def reset(self): + self.createdItem = {} + #This are created at drawLine + self.lineItem_dict = {} + self.itemignoreZooming = False + if hasattr(self, 'sceneContainer'): + self.sceneContainer.clear() + self.sceneContainer = QGraphicsScene(self) + self.sceneContainer.setItemIndexMethod(QGraphicsScene.NoIndex) + self.sceneContainer.setBackgroundBrush(QColor(230, 220, 219, 120)) + + def getsceneCord(self): + self.cord = {} + self.view.setRefWidget("runView") + for item in self.sceneContainer.items(): + if isinstance(item, kkitQGraphics.KineticsDisplayItem): + self.cord[item.mobj] = { + 'x': item.scenePos().x(), + 'y': item.scenePos().y() + } + return self.cord + + def updateModelView(self): + self.initMooseObject() + logger_.info( "updateModelView called ... %s" % str(self.m) ) + if not self.m: + if hasattr(self, 'view') and isinstance(self.view, QWidget): + self.layout().removeWidget(self.view) + + self.view = kkitViewcontrol.GraphicalView(self.modelRoot, + self.sceneContainer, + self.border, self, + self.createdItem) + + if isinstance(self, kineticEditorWidget): + self.view.setRefWidget("editorView") + self.view.setAcceptDrops(True) + elif isinstance(self, KineticRunWidget): + self.view.setRefWidget("runView") + + self.view.dropped.connect(self.objectEditSlot) + hLayout = QGridLayout(self) + self.setLayout(hLayout) + hLayout.addWidget(self.view, 0, 0) + return + + if hasattr(self, 'view') and isinstance(self.view, QWidget): + self.layout().removeWidget(self.view) + + self.view = kkitViewcontrol.GraphicalView(self.modelRoot, + self.sceneContainer, self.border, self, self.createdItem) + + if isinstance(self, kineticEditorWidget): + self.mooseObjOntoscene() + self.drawLine_arrow() + self.view.setRefWidget("editorView") + self.view.setAcceptDrops(True) + self.view.dropped.connect(self.objectEditSlot) + hLayout = QGridLayout(self) + self.setLayout(hLayout) + hLayout.addWidget(self.view) + elif isinstance(self, KineticRunWidget): + self.view.setRefWidget("runView") + hLayout = QGridLayout(self) + self.setLayout(hLayout) + hLayout.addWidget(self.view) + self.view.fitInView( + self.sceneContainer.itemsBoundingRect().x() - 10, + self.sceneContainer.itemsBoundingRect().y() - 10, + self.sceneContainer.itemsBoundingRect().width() + 20, + self.sceneContainer.itemsBoundingRect().height() + 20, + Qt.Qt.IgnoreAspectRatio) + else: + logger_.warning("Unhandled type: %s:%s" % (type(self),self)) + + def initMooseObject(self): + self.m = moose.wildcardFind(self.modelRoot + '/##[ISA=ChemCompt]') + if self.m: + self.srcdesConnection = {} + if self.meshEntry: + self.meshEntry.clear() + else: + self.meshEntry = {} + self.objPar, self.meshEntry, self.xmin, self.xmax, self.ymin\ + , self.ymax, self.noPositionInfo = kkitOrdinateUtil.setupMeshObj(self.modelRoot) + self.autocoordinates = False + if self.srcdesConnection: + self.srcdesConnection.clear() + else: + self.srcdesConnection = {} + + kkitOrdinateUtil.setupItem(self.modelRoot, self.srcdesConnection) + if not self.noPositionInfo: + self.autocoordinates = True + kkitOrdinateUtil.autoCoordinates(self.meshEntry, + self.srcdesConnection) + + self.size = QtCore.QSize(1000, 550) + + def sizeHint(self): + return QtCore.QSize(800, 400) + + def updateItemSlot(self, mooseObject): + for item in self.sceneContainer.items(): + if isinstance(item, kkitQGraphics.PoolItem): + if mooseObject.getId() == moose.element(item.mobj).getId(): + item.updateSlot() + # once the text is edited in editor, laydisplay gets updated + # in turn resize the length, positionChanged signal shd be + # emitted. + self.positionChange(mooseObject) + self.view.removeConnector() + self.view.showConnector(item) + + def updateColorSlot(self, mooseObject, colour): + #Color slot for changing background color for Pool,Enz and group from objecteditor + anninfo = moose.Annotator(mooseObject.path + '/info') + textcolor, bgcolor = kkitUtil.getColor(anninfo) + anninfo.color = str(colour.name()) + + if mooseObject.className == "Neutral": + item = self.qGraGrp[mooseObject] + item.setPen( + QtGui.QPen(QtGui.QColor(colour), + item.pen().width(), + item.pen().style(), + item.pen().capStyle(), + item.pen().joinStyle())) + + elif (isinstance(mooseObject, moose.PoolBase) \ + or isinstance(mooseObject, moose.EnzBase) ): + item = self.mooseId_GObj[mooseObject] + item.updateColor(colour) + + def mooseObjOntoscene(self): + # All the compartments are put first on to the scene \ + # Need to do: Check With upi if empty compartments exist + self.qGraCompt = {} + self.qGraGrp = {} + self.mooseId_GObj = {} + if self.qGraCompt: + self.qGraCompt.clear() + else: + self.qGraCompt = {} + + if self.qGraGrp: + self.qGraGrp.clear() + else: + self.qGraGrp = {} + + if self.qGraGrp: + self.qGraGrp.clear() + else: + self.qGraGrp = {} + + if self.mooseId_GObj: + self.mooseId_GObj.clear() + else: + self.mooseId_GObj = {} + + logger_.debug( "self.objPar: " + str(self.objPar) ) + for k, v in self.objPar.items(): + if isinstance(moose.element(k), moose.ChemCompt): + self.createCompt(k) + self.qGraCompt[k] + + elif isinstance(moose.element(k), moose.Neutral): + if len(self.meshEntry[k]): + if isinstance(moose.element(v), moose.ChemCompt): + group_parent = self.qGraCompt[v] + elif isinstance(moose.element(v), moose.Neutral): + group_parent = self.qGraGrp[v] + self.createGroup(k, group_parent) + + for cmpt_grp, memb in self.meshEntry.items(): + if len(memb): + if isinstance(moose.element(cmpt_grp), moose.ChemCompt): + qtGrpparent = self.qGraCompt[cmpt_grp] + elif isinstance(moose.element(cmpt_grp), moose.Neutral): + qtGrpparent = self.qGraGrp[cmpt_grp] + for mclass in [ + "enzyme", "pool", "reaction", "cplx", "function", + "stimTab" + ]: + self.mObjontoscene(memb, mclass, qtGrpparent) + + self.groupChildrenBoundingRect() + # compartment's rectangle size is calculated depending on children + self.comptChildrenBoundingRect() + + def mObjontoscene(self, memb, mclass, qtGrpparent): + try: + memb[mclass] + except KeyError: + pass + else: + for mObj in memb[mclass]: + minfo = mObj.path + '/info' + if mObj.className in ['Enz', "ZombieEnz"]: + mItem = kkitQGraphics.EnzItem(mObj, qtGrpparent) + + elif mObj.className in ['MMenz', "ZombieMMenz"]: + mItem = kkitQGraphics.MMEnzItem(mObj, qtGrpparent) + + elif isinstance(moose.element(mObj), + moose.PoolBase) and mclass != "cplx": + # depending on Editor Widget or Run widget pool will be + # created a PoolItem or PoolItemCircle + mItem = self.makePoolItem(mObj, qtGrpparent) + + elif isinstance(moose.element(mObj), moose.ReacBase): + mItem = kkitQGraphics.ReacItem(mObj, qtGrpparent) + + elif mclass == "cplx": + minfo = (mObj.parent).path + '/info' + mItem = kkitQGraphics.CplxItem( + mObj, self.mooseId_GObj[moose.element(mObj).parent]) + self.mooseId_GObj[moose.element(mObj.getId())] = mItem + + elif mclass == "function": + if isinstance(moose.element(mObj.parent), moose.PoolBase): + minfo = moose.element(mObj).path + '/info' + moose.Annotator(minfo) + qtGrpparent = self.mooseId_GObj[moose.element( + mObj.parent)] + mItem = kkitQGraphics.FuncItem(mObj, qtGrpparent) + + elif mclass == "stimTab": + minfo = mObj.path + '/info' + mItem = kkitQGraphics.TableItem(mObj, qtGrpparent) + self.mooseId_GObj[moose.element(mObj.getId())] = mItem + self.setupDisplay(minfo, mItem, mclass) + + def createGroup(self, key, parent): + self.new_GRP = kkitQGraphics.GRPItem(parent, 0, 0, 0, 0, key) + self.qGraGrp[key] = self.new_GRP + self.new_GRP.setRect(20, 20, 20, 20) + + def groupChildrenBoundingRect(self): + for k, v in self.qGraGrp.items(): + grpcolor = moose.Annotator(moose.element(k.path + '/info')).color + # TODO: One may need to calculate explicitly the boundary for Group + # also if there is a cross-group connection, then + # childrenBoundrect() will take the QPolygonItem position + rectcompt = v.childrenBoundingRect() + v.setRect(rectcompt.x() - 10, + rectcompt.y() - 10, + rectcompt.width() + 20, + rectcompt.height() + 20) + v.setPen( + QtGui.QPen(Qt.QColor(grpcolor), self.comptPen, Qt.Qt.SolidLine, + Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) + + def comptChildrenBoundingRect(self): + for k, v in self.qGraCompt.items(): + # compartment's rectangle size is calculated depending on children + rectcompt = kkitUtil.calculateChildBoundingRect(v) + v.setRect(rectcompt.x() - 10, + rectcompt.y() - 10, (rectcompt.width() + 20), + (rectcompt.height() + 20)) + v.setPen( + QtGui.QPen(Qt.QColor(66, 66, 66, 100), self.comptPen, + Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) + + def createCompt(self, key): + logger_.debug( "Creating new compartment %s" % key) + self.new_Compt = kkitQGraphics.ComptItem(self, 0, 0, 0, 0, key) + self.qGraCompt[key] = self.new_Compt + self.new_Compt.setRect(10, 10, 10, 10) + self.sceneContainer.addItem(self.new_Compt) + + def setupDisplay(self, info, graphicalObj, objClass): + Annoinfo = moose.Annotator(info) + # For Reaction and Complex object I have skipped the process to get the + # facecolor and background color. + # we are not using these colors for displaying the object so just + # passing dummy color white + if (objClass == "reaction" or objClass == "cplx" + or objClass == "Function" or objClass == "StimulusTable"): + textcolor, bgcolor = QColor("white"), QColor("white") + elif (objClass == "enzyme"): + textcolor, bgcolor = kkitUtil.getColor(info) + if bgcolor.name() == "#ffffff" or bgcolor == "white": + bgcolor = kkitUtil.getRandColor() + Annoinfo.color = str(bgcolor.name()) + else: + textcolor, bgcolor = kkitUtil.getColor(info) + if bgcolor.name() == "#ffffff" or bgcolor == "white": + bgcolor = kkitUtil.getRandColor() + Annoinfo.color = str(bgcolor.name()) + if isinstance(self, kineticEditorWidget): + funct = ["Function", "ZombieFunction"] + comptt = ["CubeMesh", "CylMesh"] + + if objClass in funct: + poolt = ["ZombieBufPool", "BufPool"] + if graphicalObj.mobj.parent.className in poolt: + xpos = 0 + ypos = 30 + if graphicalObj.mobj.parent.className in comptt: + xpos, ypos = self.positioninfo(info) + else: + xpos, ypos = self.positioninfo(info) + + elif isinstance(self, KineticRunWidget): + self.editormooseId_GObj = self.editor.getCentralWidget( + ).mooseId_GObj + editorItem = self.editormooseId_GObj[moose.element(info).parent] + xpos = editorItem.scenePos().x() + ypos = editorItem.scenePos().y() + graphicalObj.setDisplayProperties(xpos, ypos, textcolor, bgcolor) + + def positioninfo(self, iteminfo): + ''' + By this time, model loaded from kkit,cspace,SBML would have info + field created and co-ordinates are added either by autocoordinates (for + cspace,SBML(unless it is not saved from moose)) or from kkit. + ''' + x = float(moose.element(iteminfo).getField('x')) + y = float(moose.element(iteminfo).getField('y')) + return x, y + + def drawLine_arrow(self, itemignoreZooming=False): + for inn, out in self.srcdesConnection.items(): + #print "inn ",inn, " out ",out + # self.srcdesConnection is dictionary which contains key,value \ + # key is Enzyme or Reaction and value [[list of substrate],[list of product]] (tuple) + # key is Function and value is [list of pool] (list) + + #src = self.mooseId_GObj[inn] + linetype = "regular" + if isinstance(out, tuple): + src = self.mooseId_GObj[inn] + if len(out[0]) == 0: + print(inn.className + ' : ' + inn.name + + " doesn't output message") + else: + for items in (items for items in out[0]): + if re.search("xfer", moose.element(items[0]).name): + xrefPool = items[0].name[:items[0].name. + index("_xfer_")] + xrefCompt = items[0].name[items[0].name. + index("_xfer_") + + len("_xfer_"):] + orgCompt = moose.wildcardFind(self.modelRoot + + '/##[FIELD(name)=' + + xrefCompt + ']')[0] + orgPool = moose.wildcardFind(orgCompt.path + + '/##[FIELD(name)=' + + xrefPool + ']')[0] + itemslist = list(items) + itemslist[0] = orgPool + items = tuple(itemslist) + linetype = "crosscompt" + des = self.mooseId_GObj[moose.element(items[0])] + self.lineCord(src, des, items, itemignoreZooming, + linetype) + if len(out[1]) == 0: + print(inn.className + ' : ' + inn.name + + " doesn't output message") + else: + for items in (items for items in out[1]): + if re.search("xfer", moose.element(items[0]).name): + xrefPool = items[0].name[:items[0].name. + index("_xfer_")] + xrefCompt = items[0].name[items[0].name. + index("_xfer_") + + len("_xfer_"):] + orgCompt = moose.wildcardFind(self.modelRoot + + '/##[FIELD(name)=' + + xrefCompt + ']')[0] + orgPool = moose.wildcardFind(orgCompt.path + + '/##[FIELD(name)=' + + xrefPool + ']')[0] + itemslist = list(items) + itemslist[0] = orgPool + items = tuple(itemslist) + linetype = "crosscompt" + des = self.mooseId_GObj[moose.element(items[0])] + self.lineCord(src, des, items, itemignoreZooming, + linetype) + elif isinstance(out, list): + if len(out) == 0: + if inn.className == "StimulusTable": + print(inn.name + " doesn't have output") + elif inn.className == "ZombieFunction" or inn.className == "Function": + print(inn.name + " doesn't have sumtotal ") + else: + src = self.mooseId_GObj[inn] + for items in (items for items in out): + if re.search("xfer", moose.element(items[0]).name): + xrefPool = items[0].name[:items[0].name. + index("_xfer_")] + xrefCompt = items[0].name[items[0].name. + index("_xfer_") + + len("_xfer_"):] + orgCompt = moose.wildcardFind(self.modelRoot + + '/##[FIELD(name)=' + + xrefCompt + ']')[0] + orgPool = moose.wildcardFind(orgCompt.path + + '/##[FIELD(name)=' + + xrefPool + ']')[0] + itemslist = list(items) + itemslist[0] = orgPool + items = tuple(itemslist) + linetype = "crosscompt" + des = self.mooseId_GObj[moose.element(items[0])] + self.lineCord(src, des, items, itemignoreZooming, + linetype) + + def lineCord(self, src, des, type_no, itemignoreZooming, linetype): + srcdes_list = [] + endtype = type_no[1] + line = 0 + if (src == "") and (des == ""): + print("Source or destination is missing or incorrect") + return + srcdes_list = [src, des, endtype, line] + arrow = kkitUtil.calcArrow(srcdes_list, itemignoreZooming, + self.iconScale) + self.drawLine(srcdes_list, arrow, linetype) + + while (type_no[2] > 1 and line <= (type_no[2] - 1)): + srcdes_list = [src, des, endtype, line] + arrow = kkitUtil.calcArrow(srcdes_list, itemignoreZooming, + self.iconScale) + self.drawLine(srcdes_list, arrow, linetype) + line = line + 1 + + if type_no[2] > 5: + print("Higher order reaction will not be displayed") + + def drawLine(self, srcdes_list, arrow, linetype="solid"): + src = srcdes_list[0] + des = srcdes_list[1] + endtype = srcdes_list[2] + line = srcdes_list[3] + source = moose.element( + next((k for k, v in self.mooseId_GObj.items() if v == src), None)) + for l, v, et, o in self.object2line[src]: + if v == des and o == line: + l.setPolygon(arrow) + arrowPen = l.pen() + arrowPenWidth = self.arrowsize * self.iconScale + arrowPen.setColor(l.pen().color()) + arrowPen.setWidth(arrowPenWidth) + l.setPen(arrowPen) + return + qgLineitem = self.sceneContainer.addPolygon(arrow) + qgLineitem.setParentItem(src.parentItem()) + pen = QtGui.QPen(QtCore.Qt.green, 0, Qt.Qt.SolidLine, Qt.Qt.RoundCap, + Qt.Qt.RoundJoin) + if linetype == "crosscompt": + pen.setStyle(Qt.Qt.CustomDashLine) + pen.setDashPattern([1, 5, 1, 5]) + + pen.setWidth(self.arrowsize) + + # Green is default color moose.ReacBase and derivatives - already set above + if isinstance(source, moose.EnzBase): + if ((endtype == 's') or (endtype == 'p')): + pen.setColor(QtCore.Qt.red) + elif (endtype != 'cplx'): + p1 = (next( + (k for k, v in self.mooseId_GObj.items() if v == src), + None)) + pinfo = p1.parent.path + '/info' + color, bgcolor = kkitUtil.getColor(pinfo) + #color = QColor(color[0],color[1],color[2]) + pen.setColor(bgcolor) + + elif isinstance(source, moose.PoolBase) or isinstance( + source, moose.Function): + pen.setColor(QtCore.Qt.blue) + elif isinstance(source, moose.StimulusTable): + pen.setColor(QtCore.Qt.yellow) + self.lineItem_dict[qgLineitem] = srcdes_list + self.object2line[src].append((qgLineitem, des, endtype, line)) + self.object2line[des].append((qgLineitem, src, endtype, line)) + qgLineitem.setPen(pen) + + def positionChange(self, mooseObject): + #If the item position changes, the corresponding arrow's are calculated + for k, v in self.qGraCompt.items(): + for rectChilditem in v.childItems(): + self.updateArrow(rectChilditem) + if isinstance(rectChilditem, kkitQGraphics.GRPItem): + for grpChilditem in rectChilditem.childItems(): + self.updateArrow(grpChilditem) + if isinstance(grpChilditem, + kkitQGraphics.KineticsDisplayItem): + if moose.exists(grpChilditem.mobj.path + '/info'): + #print grpChilditem.mobj.name, grpChilditem.scenePos() + moose.element( + grpChilditem.mobj.path + + '/info').x = grpChilditem.scenePos().x() + moose.element( + grpChilditem.mobj.path + + '/info').y = grpChilditem.scenePos().y() + if isinstance(rectChilditem, kkitUtil.KineticsDisplayItem): + if moose.exists(rectChilditem.mobj.path + '/info'): + moose.element( + rectChilditem.mobj.path + + '/info').x = rectChilditem.scenePos().x() + moose.element( + rectChilditem.mobj.path + + '/info').y = rectChilditem.scenePos().y() + + rectcompt = kkitUtil.calculateChildBoundingRect(v) + comptBoundingRect = v.boundingRect() + if not comptBoundingRect.contains(rectcompt): + self.updateCompartmentSize(v) + else: + rectcompt = kkitUtil.calculateChildBoundingRect(v) + v.setRect(rectcompt.x() - 10, + rectcompt.y() - 10, (rectcompt.width() + 20), + (rectcompt.height() + 20)) + + def positionChange_old(self, mooseObject): + # If the item position changes, the corresponding arrow's are calculated + if isinstance(moose.element(mooseObject), kkitQGraphics.ChemCompt): + for k, v in self.qGraCompt.items(): + mesh = moose.element(mooseObject).path + if k.path == mesh: + for rectChilditem in v.childItems(): + if isinstance(rectChilditem, + kkitQGraphics.KineticsDisplayItem): + if moose.exists(rectChilditem.mobj.path): + iInfo = rectChilditem.mobj.path + '/info' + moose.Annotator(iInfo) + if isinstance( + moose.element(rectChilditem.mobj.path), + moose.PoolBase): + t = moose.element(rectChilditem.mobj.path) + moose.element(t).children + for items in moose.element(t).children: + if isinstance(moose.element(items), + moose.Function): + test = moose.element(items.path + + '/x') + for i in moose.element( + test).neighbors['input']: + j = self.mooseId_GObj[ + moose.element(i)] + self.updateArrow(j) + self.updateArrow(rectChilditem) + elif moose.element(mooseObject).className == 'Neutral': + for k, v in self.qGraGrp.items(): + for grpChilditem in v.childItems(): + if isinstance(grpChilditem, + kkitQGraphics.KineticsDisplayItem): + if moose.exists(grpChilditem.mobj.path): + iInfo = grpChilditem.mobj.path + '/info' + moose.Annotator(iInfo) + + if isinstance(moose.element(grpChilditem.mobj.path), + moose.PoolBase): + t = moose.element(grpChilditem.mobj.path) + moose.element(t).children + for items in moose.element(t).children: + if isinstance(moose.element(items), + moose.Function): + test = moose.element(items.path + '/x') + for i in moose.element( + test).neighbors['input']: + j = self.mooseId_GObj[moose.element(i)] + self.updateArrow(j) + self.updateArrow(grpChilditem) + rectgrp = kkitUtil.calculateChildBoundingRect(v) + v.setRect(rectgrp.x() - 10, + rectgrp.y() - 10, (rectgrp.width() + 20), + (rectgrp.height() + 20)) + for k, v in self.qGraCompt.items(): + rectcompt = kkitUtil.calculateChildBoundingRect(v) + comptBoundingRect = v.boundingRect() + if not comptBoundingRect.contains(rectcompt): + self.updateCompartmentSize(v) + + else: + rectcompt = kkitUtil.calculateChildBoundingRect(v) + v.setRect(rectcompt.x() - 10, + rectcompt.y() - 10, + rectcompt.width() + 20, + rectcompt.height() + 20) + else: + mobj = self.mooseId_GObj[moose.element(mooseObject)] + self.updateArrow(mobj) + for k, v in self.qGraCompt.items(): + rectcompt = kkitUtil.calculateChildBoundingRect(v) + comptBoundingRect = v.boundingRect() + if not comptBoundingRect.contains(rectcompt): + self.updateCompartmentSize(v) + + else: + rectcompt = kkitUtil.calculateChildBoundingRect(v) + v.setRect(rectcompt.x() - 10, + rectcompt.y() - 10, + rectcompt.width() + 20, + rectcompt.height() + 20) + + def updateGrpSize(self, grp): + childrenBoundary = kkitUtil.calculateChildBoundingRect(grp) + x = childrenBoundary.x() + y = childrenBoundary.y() + height = childrenBoundary.height() + width = childrenBoundary.width() + grp.setRect(x - 10, y - 10, width + 20, height + 20) + + def updateCompartmentSize(self, compartment): + compartmentBoundary = compartment.rect() + childrenBoundary = kkitUtil.calculateChildBoundingRect(compartment) + x = min(compartmentBoundary.x(), childrenBoundary.x()) + y = min(compartmentBoundary.y(), childrenBoundary.y()) + width = max(compartmentBoundary.width(), childrenBoundary.width()) + height = max(compartmentBoundary.height(), childrenBoundary.height()) + compartment.setRect(x - 10, y - 10, width + 20, height + 20) + + def updateArrow(self, qGTextitem): + #if there is no arrow to update then return + listItem = self.object2line[qGTextitem] + for ql, va, endtype, order in listItem: + srcdes = [] + srcdes = self.lineItem_dict[ql] + # Checking if src (srcdes[0]) or des (srcdes[1]) is ZombieEnz, + # if yes then need to check if cplx is connected to any mooseObject, + # so that when Enzyme is moved, cplx connected arrow to other + # mooseObject(poolItem) should also be updated + if( type(srcdes[0]) == kkitQGraphics.EnzItem \ + or type(srcdes[0] == kkitQGraphics.MMEnzItem)): + self.cplxUpdatearrow(srcdes[0]) + elif( type(srcdes[1]) == kkitQGraphics.EnzItem \ + or type(srcdes[1] == kkitQGraphics.MMEnzItem)): + self.cplxUpdatearrow(srcdes[1]) + arrow = kkitUtil.calcArrow(srcdes, self.itemignoreZooming, + self.iconScale) + ql.setPolygon(arrow) + + def cplxUpdatearrow(self, srcdes): + # srcdes which is 'EnzItem' from this,get ChildItems are retrived (b'cos cplx is child of zombieEnz) + #And cplxItem is passed for updatearrow + for item in srcdes.childItems(): + if isinstance(item, kkitQGraphics.CplxItem): + self.updateArrow(item) + + def positionChange1(self, mooseObject): + #If the item position changes, the corresponding arrow's are calculated + if ( (isinstance(moose.element(mooseObject), moose.CubeMesh)) \ + or (isinstance(moose.element(mooseObject), moose.CylMesh))): + v = self.qGraCompt[mooseObject] + for rectChilditem in v.childItems(): + self.updateArrow(rectChilditem) + else: + mobj = self.mooseId_GObj[mooseObject.getId()] + self.updateArrow(mobj) + mooseObjcompt = self.findparent(mooseObject) + v = self.qGraCompt[mooseObjcompt] + #childBoundingRect = v.childrenBoundingRect() + childBoundingRect = kkitUtil.calculateChildBoundingRect(v) + comptBoundingRect = v.boundingRect() + rectcompt = comptBoundingRect.united(childBoundingRect) + comptPen = v.pen() + comptWidth = 5 + comptPen.setWidth(comptWidth) + v.setPen(comptPen) + if not comptBoundingRect.contains(childBoundingRect): + v.setRect(rectcompt.x() - comptWidth, + rectcompt.y() - comptWidth, + rectcompt.width() + (comptWidth * 2), + rectcompt.height() + (comptWidth * 2)) + + +class kineticEditorWidget(KineticsWidget): + def __init__(self, plugin, *args): + + KineticsWidget.__init__(self, plugin, *args) + self.plugin = plugin + self.insertMenu = QMenu('&Insert') + self._menus.append(self.insertMenu) + self.insertMapper = QtCore.QSignalMapper(self) + classlist = [ + 'CubeMesh', 'CylMesh', 'Pool', 'BufPool', 'Function', 'Reac', + 'Enz', 'MMenz', 'StimulusTable' + ] + self.toolTipinfo = { + "CubeMesh": + "", + "CylMesh": + "", + "Pool": + "A Pool is a collection of molecules of a given species in a given cellular compartment.\n It can undergo reactions that convert it into other pool(s). \nParameters: initConc (Initial concentration), diffConst (diffusion constant). Variable: conc (Concentration)", + "BufPool": + "A BufPool is a buffered pool. \nIt is a collection of molecules of a given species in a given cellular compartment, that are always present at the same concentration.\n This is set by the initConc parameter. \nIt can undergo reactions in the same way as a pool.", + "Function": + "A Func computes an arbitrary mathematical expression of one or more input concentrations of Pools. The output can be used to control the concentration of another Pool, or as an input to another Func", + "StimulusTable": + "A StimulusTable stores an array of values that are read out during a simulation, and typically control the concentration of one of the pools in the model. \nParameters: size of table, values of entries, start and stop times, and an optional loopTime that defines the period over which the StimulusTable should loop around to repeat its values", + "Reac": + "A Reac is a chemical reaction that converts substrates into products, and back. \nThe rates of these conversions are specified by the rate constants Kf and Kb respectively.", + "MMenz": + "An MMenz is the Michaelis-Menten version of an enzyme activity of a given Pool.\n The MMenz must be created on a pool and can only catalyze a single reaction with a specified substrate(s). \nIf a given enzyme species can have multiple substrates, then multiple MMenz activites must be created on the parent Pool. \nThe rate of an MMenz is V [S].[E].kcat/(Km + [S]). There is no enzyme-substrate complex. Parameters: Km and kcat.", + "Enz": + "An Enz is an enzyme activity of a given Pool. The Enz must be created on a pool and can only catalyze a single reaction with a specified substrate(s). \nIf a given enzyme species can have multiple substrates, then multiple Enz activities must be created on the parent Pool. \nThe reaction for an Enz is E + S <===> E.S ---> E + P. \nThis means that a new Pool, the enzyme-substrate complex E.S, is always formed when you create an Enz. \nParameters: Km and kcat, or alternatively, K1, K2 and K3. Km = (K2+K3)/K1" + } + insertMapper, actions = self.getInsertActions(classlist) + for action in actions: + self.insertMenu.addAction(action) + doc = self.toolTipinfo[str(action.text())] + if doc == "": + classname = str(action.text()) + doc = moose.element('/classes/%s' % (classname)).docs + doc = doc.split('Description:')[-1].split('Name:')[0].strip() + action.setToolTip(doc) + + def GrViewresize(self, event): + #when Gui resize and event is sent which inturn call resizeEvent of qgraphicsview + pass + #self.view.resizeEvent1(event) + + def makePoolItem(self, poolObj, qGraCompt): + return kkitQGraphics.PoolItem(poolObj, qGraCompt) + + def getToolBars(self): + #Add specific tool items with respect to kkit + if not hasattr(self, '_insertToolBar'): + self._insertToolBar = QToolBar('Insert') + self._toolBars.append(self._insertToolBar) + for action in self.insertMenu.actions(): + button = MToolButton() + button.setDefaultAction(action) + iconPath = os.path.join(config.MOOSE_ICON_DIR, action.text() + '.png') + assert os.path.exists(iconPath), "Does not exists %s" % iconPath + button.setIcon(QtGui.QIcon(iconPath)) + self._insertToolBar.addWidget(button) + return self._toolBars + +class KineticRunWidget(KineticsWidget): + def __init__(self, plugin, *args): + KineticsWidget.__init__(self, plugin, *args) + + def showEvent(self, event): + self.refresh() + # pass + def refresh(self): + self.sceneContainer.clear() + self.Comptexist = moose.wildcardFind(self.modelRoot + + '/##[ISA=ChemCompt]') + if self.Comptexist: + # pass + self.initMooseObject() + self.mooseObjOntoscene() + self.drawLine_arrow(itemignoreZooming=False) + + def makePoolItem(self, poolObj, qGraCompt): + return kkitQGraphics.PoolItemCircle(poolObj, qGraCompt) + + def getToolBars(self): + return self._toolBars + + def updateValue(self): + for item in self.sceneContainer.items(): + if isinstance(item, kkitQGraphics.ReacItem) \ + or isinstance(item, kkitQGraphics.MMEnzItem) \ + or isinstance(item, kkitQGraphics.EnzItem) \ + or isinstance(item, kkitQGraphics.PoolItemCircle) \ + or isinstance(item, kkitQGraphics.CplxItem): + item.updateValue(item.mobj) + + def changeBgSize(self): + for item in self.sceneContainer.items(): + if isinstance(item, kkitQGraphics.PoolItemCircle): + initialConc = moose.element(item.mobj).concInit + presentConc = moose.element(item.mobj).conc + if initialConc != 0: + ratio = presentConc / initialConc + else: + ratio = presentConc + if ratio > '10': + ratio = 9 + if ratio < '0.0': + ratio = 0.1 + item.updateRect(math.sqrt(abs(ratio))) + + def resetColor(self): + for item in self.sceneContainer.items(): + if isinstance(item, kkitQGraphics.PoolItemCircle): + item.returnEllispeSize() + + +if __name__ == "__main__": + size = QtCore.QSize(1024, 768) + sdir = os.path.dirname(__file__) + modelPath = 'Kholodenko' + itemignoreZooming = False + try: + filepath = os.path.join(sdir, '../../data/' + modelPath + '.g') + print("%s" % (filepath)) + moose.loadModel(filepath, '/' + modelPath) + dt = KineticsWidget( "kkit" ) + dt.modelRoot = '/' + modelPath + dt.updateModelView() + dt.show() + except IOError as e: + print(e) + sys.exit(app.exec_()) diff --git a/plugins/kkitCalcArrow.py b/moosegui/plugins/kkitCalcArrow.py similarity index 95% rename from plugins/kkitCalcArrow.py rename to moosegui/plugins/kkitCalcArrow.py index 4a3128f..83764ba 100644 --- a/plugins/kkitCalcArrow.py +++ b/moosegui/plugins/kkitCalcArrow.py @@ -7,8 +7,8 @@ __status__ = "Development" __updated__ = "Jul 27 2017" -from PyQt4.QtGui import QPolygonF -from PyQt4.QtCore import QLineF,QPointF +from PyQt5.QtGui import QPolygonF +from PyQt5.QtCore import QLineF,QPointF from math import sin,cos,atan2,radians from kkitQGraphics import PoolItem #, ReacItem,EnzItem,CplxItem,ComptItem @@ -80,9 +80,9 @@ def calcArrow(srcdes_list,itemignoreZooming,iconScale): destIntersects, lineDestPoint = calcLineRectIntersection(desRect, tmpLine) if not srcIntersects: - print 'Source does not intersect line. Arrow points:',lineSrcPoint,src.mobj.name, src.mobj.className + print('Source does not intersect line. Arrow points:',lineSrcPoint,src.mobj.name, src.mobj.className) if not destIntersects: - print 'Dest does not intersect line. Arrow points:', lineDestPoint, des.mobj.name, des.mobj.className + print('Dest does not intersect line. Arrow points:', lineDestPoint, des.mobj.name, des.mobj.className) '''src and des are connected with line co-ordinates Arrow head is drawned if the distance between src and des line is >8 just for clean appeareance diff --git a/moosegui/plugins/kkitOrdinateUtil.py b/moosegui/plugins/kkitOrdinateUtil.py new file mode 100644 index 0000000..51685a7 --- /dev/null +++ b/moosegui/plugins/kkitOrdinateUtil.py @@ -0,0 +1,418 @@ +# -*- coding: utf-8 -*- + +__author__ = "HarshaRani" +__credits__ = ["Upi Lab"] +__license__ = "GPL3" +__version__ = "1.0.0" +__maintainer__ = "HarshaRani" +__email__ = "hrani@ncbs.res.in" +__status__ = "Development" +__updated__ = "Oct 26 2018" + +import collections +import numpy as np +from networkx.drawing.nx_agraph import graphviz_layout +import networkx as nx +import re + +from PyQt5.QtGui import QColor + +import moose + +from moosegui.plugins.kkitUtil import colorCheck, findGroup_compt + + +def getxyCord(xcord, ycord, list1): + for item in list1: + if not isinstance(item, moose.Function): + objInfo = item.path + '/info' + xcord.append(xyPosition(objInfo, 'x')) + ycord.append(xyPosition(objInfo, 'y')) + + +def xyPosition(objInfo, xory): + try: + return moose.element(objInfo).getField(xory) + except ValueError: + return 0.0, 0.0 + + +def populateMeshEntry(meshEntry, parent, types, obj): + try: + meshEntry[moose.element(parent.path)][types] + except KeyError: + # Key is not present + meshEntry[moose.element(parent.path)].update( + {types: [moose.element(obj)]}) + else: + mlist = meshEntry[moose.element(parent.path)][types] + mlist.append(moose.element(obj)) + + +def updateMeshObj(modelRoot): + meshEntry = {} + if meshEntry: + meshEntry.clear() + else: + meshEntry = {} + + objPar = collections.OrderedDict() + for compt in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'): + try: + meshEntry[moose.element(compt)] + except KeyError: + # Compt is not present + meshEntry[moose.element(compt)] = {} + objPar[moose.element(compt)] = moose.element('/') + + for grp in moose.wildcardFind(compt.path + '/##[TYPE=Neutral]'): + try: + meshEntry[moose.element(grp)] + except KeyError: + # Grp is not present + grp_cmpt = findGroup_compt(grp.parent) + meshEntry[moose.element(grp)] = {} + objPar[moose.element(grp)] = moose.element(grp_cmpt) + + for compt in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'): + for m in moose.wildcardFind(compt.path + '/##[ISA=PoolBase]'): + grp_cmpt = findGroup_compt(m) + if isinstance(moose.element(grp_cmpt), moose.Neutral): + if isinstance(moose.element(m.parent), moose.EnzBase): + populateMeshEntry(meshEntry, grp_cmpt, "cplx", m) + else: + populateMeshEntry(meshEntry, grp_cmpt, "pool", m) + else: + if isinstance(moose.element(m.parent), moose.EnzBase): + populateMeshEntry(meshEntry, compt, "cplx", m) + else: + populateMeshEntry(meshEntry, compt, "pool", m) + + for r in moose.wildcardFind(compt.path + '/##[ISA=ReacBase]'): + rgrp_cmpt = findGroup_compt(r) + if isinstance(moose.element(rgrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, rgrp_cmpt, "reaction", r) + else: + populateMeshEntry(meshEntry, compt, "reaction", r) + + for e in moose.wildcardFind(compt.path + '/##[ISA=EnzBase]'): + egrp_cmpt = findGroup_compt(e) + if isinstance(moose.element(egrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, egrp_cmpt, "enzyme", e) + else: + populateMeshEntry(meshEntry, compt, "enzyme", e) + + for f in moose.wildcardFind(compt.path + '/##[ISA=Function]'): + fgrp_cmpt = findGroup_compt(f) + if isinstance(moose.element(fgrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, fgrp_cmpt, "function", f) + else: + populateMeshEntry(meshEntry, compt, "function", f) + + for t in moose.wildcardFind(compt.path + '/##[ISA=StimulusTable]'): + tgrp_cmpt = findGroup_compt(t) + if isinstance(moose.element(tgrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, tgrp_cmpt, "stimTab", t) + else: + populateMeshEntry(meshEntry, compt, "stimTab", t) + return (objPar, meshEntry) + + +def setupMeshObj(modelRoot): + ''' + Setup compartment and its members pool,reaction,enz cplx under + self.meshEntry dictionaries, self.meshEntry with "key" as compartment, + value is key2:list where key2 represents moose object type,list of objects + of a perticular type e.g self.meshEntry[meshEnt] = { 'reaction': + reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist} + ''' + + xmin = 0.0 + xmax = 1.0 + ymin = 0.0 + ymax = 1.0 + positionInfoExist = True + meshEntry = {} + if meshEntry: + meshEntry.clear() + else: + meshEntry = {} + xcord = [] + ycord = [] + objPar = collections.OrderedDict() + + for compt in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'): + groupColor = [] + try: + meshEntry[moose.element(compt)] + except KeyError: + # Compt is not present + meshEntry[moose.element(compt)] = {} + objPar[moose.element(compt)] = moose.element('/') + + for grp in moose.wildcardFind(compt.path + '/##[TYPE=Neutral]'): + grpinfo = moose.Annotator(moose.element(grp).path + '/info') + validatecolor = colorCheck(grpinfo.color, "bg") + validatedgrpcolor = str(QColor(validatecolor).name()) + + groupColor.append(validatedgrpcolor) + grp_cmpt = findGroup_compt(grp.parent) + + try: + meshEntry[moose.element(grp)] + except KeyError: + # Grp is not present + meshEntry[moose.element(grp)] = {} + objPar[moose.element(grp)] = moose.element(grp_cmpt) + + for compt in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'): + for m in moose.wildcardFind(compt.path + '/##[ISA=PoolBase]'): + if not re.search("xfer", m.name): + grp_cmpt = findGroup_compt(m) + xcord.append(xyPosition(m.path + '/info', 'x')) + ycord.append(xyPosition(m.path + '/info', 'y')) + if isinstance(moose.element(grp_cmpt), moose.Neutral): + if isinstance(moose.element(m.parent), moose.EnzBase): + populateMeshEntry(meshEntry, grp_cmpt, "cplx", m) + else: + populateMeshEntry(meshEntry, grp_cmpt, "pool", m) + else: + if isinstance(moose.element(m.parent), moose.EnzBase): + populateMeshEntry(meshEntry, compt, "cplx", m) + else: + populateMeshEntry(meshEntry, compt, "pool", m) + + for r in moose.wildcardFind(compt.path + '/##[ISA=ReacBase]'): + rgrp_cmpt = findGroup_compt(r) + xcord.append(xyPosition(r.path + '/info', 'x')) + ycord.append(xyPosition(r.path + '/info', 'y')) + if isinstance(moose.element(rgrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, rgrp_cmpt, "reaction", r) + else: + populateMeshEntry(meshEntry, compt, "reaction", r) + + for e in moose.wildcardFind(compt.path + '/##[ISA=EnzBase]'): + egrp_cmpt = findGroup_compt(e) + xcord.append(xyPosition(e.path + '/info', 'x')) + ycord.append(xyPosition(e.path + '/info', 'y')) + if isinstance(moose.element(egrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, egrp_cmpt, "enzyme", e) + else: + populateMeshEntry(meshEntry, compt, "enzyme", e) + + for f in moose.wildcardFind(compt.path + '/##[ISA=Function]'): + fgrp_cmpt = findGroup_compt(f) + if isinstance(moose.element(fgrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, fgrp_cmpt, "function", f) + else: + populateMeshEntry(meshEntry, compt, "function", f) + + for t in moose.wildcardFind(compt.path + '/##[ISA=StimulusTable]'): + tgrp_cmpt = findGroup_compt(t) + xcord.append(xyPosition(t.path + '/info', 'x')) + ycord.append(xyPosition(t.path + '/info', 'y')) + if isinstance(moose.element(tgrp_cmpt), moose.Neutral): + populateMeshEntry(meshEntry, tgrp_cmpt, "stimTab", t) + else: + populateMeshEntry(meshEntry, compt, "stimTab", t) + + xmin = min(xcord) + xmax = max(xcord) + ymin = min(ycord) + ymax = max(ycord) + positionInfoExist = not (len(np.nonzero(xcord)[0]) == 0 + and len(np.nonzero(ycord)[0]) == 0) + return (objPar, meshEntry, xmin, xmax, ymin, ymax, positionInfoExist) + + +def setupItem(modelPath, cntDict): + # This function collects information of what is connected to what. \ + # eg. substrate and product connectivity to reaction's and enzyme's \ + # sumtotal connectivity to its pool are collected + #print " setupItem" + sublist = [] + prdlist = [] + zombieType = ['ReacBase', 'EnzBase', 'Function', 'StimulusTable'] + for baseObj in zombieType: + path = '/##[ISA=' + baseObj + ']' + if modelPath != '/': + path = modelPath + path + if ((baseObj == 'ReacBase') or (baseObj == 'EnzBase')): + for items in moose.wildcardFind(path): + sublist = [] + prdlist = [] + uniqItem, countuniqItem = countitems(items, 'subOut') + subNo = uniqItem + for sub in uniqItem: + sublist.append( + (moose.element(sub), 's', countuniqItem[sub])) + + uniqItem, countuniqItem = countitems(items, 'prd') + prdNo = uniqItem + if (len(subNo) == 0 or len(prdNo) == 0): + print("Substrate Product is empty ", path, " ", items) + + for prd in uniqItem: + prdlist.append( + (moose.element(prd), 'p', countuniqItem[prd])) + + if (baseObj == 'CplxEnzBase'): + uniqItem, countuniqItem = countitems(items, 'toEnz') + for enzpar in uniqItem: + sublist.append((moose.element(enzpar), 't', + countuniqItem[enzpar])) + + uniqItem, countuniqItem = countitems(items, 'cplxDest') + for cplx in uniqItem: + prdlist.append( + (moose.element(cplx), 'cplx', countuniqItem[cplx])) + + if (baseObj == 'EnzBase'): + uniqItem, countuniqItem = countitems(items, 'enzDest') + for enzpar in uniqItem: + sublist.append((moose.element(enzpar), 't', + countuniqItem[enzpar])) + cntDict[items] = sublist, prdlist + elif baseObj == 'Function': + for items in moose.wildcardFind(path): + sublist = [] + prdlist = [] + item = items.path + '/x[0]' + uniqItem, countuniqItem = countitems(item, 'input') + for funcpar in uniqItem: + sublist.append((moose.element(funcpar), 'sts', + countuniqItem[funcpar])) + + uniqItem, countuniqItem = countitems(items, 'valueOut') + for funcpar in uniqItem: + prdlist.append((moose.element(funcpar), 'stp', + countuniqItem[funcpar])) + cntDict[items] = sublist, prdlist + + else: + for tab in moose.wildcardFind(path): + tablist = [] + uniqItem, countuniqItem = countitems(tab, 'output') + for tabconnect in uniqItem: + tablist.append((moose.element(tabconnect), 'tab', + countuniqItem[tabconnect])) + cntDict[tab] = tablist + + +def countitems(mitems, objtype): + items = [] + items = moose.element(mitems).neighbors[objtype] + uniqItems = set(items) + #countuniqItemsauto = Counter(items) + countuniqItems = dict((i, items.count(i)) for i in items) + return (uniqItems, countuniqItems) + + +def recalculatecoordinatesforKkit(mObjlist, xcord, ycord): + positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \ + and len(np.nonzero(ycord)[0]) == 0) + + if positionInfoExist: + # Here all the object has been taken now recalculate and reassign back x + # and y co-ordinates + xmin = min(xcord) + xmax = max(xcord) + ymin = min(ycord) + ymax = max(ycord) + for merts in mObjlist: + objInfo = merts.path + '/info' + if moose.exists(objInfo): + Ix = (xyPosition(objInfo, 'x') - xmin) / (xmax - xmin) + Iy = (ymin - xyPosition(objInfo, 'y')) / (ymax - ymin) + moose.element(objInfo).x = Ix * 1000 + moose.element(objInfo).y = Iy * 800 + + +def autoCoordinates(meshEntry, srcdesConnection): + G = nx.Graph() + for cmpt, memb in meshEntry.items(): + if memb in ["enzyme"]: + for enzObj in find_index(memb, 'enzyme'): + #G.add_node(enzObj.path) + G.add_node(enzObj.path, + label='', + shape='ellipse', + color='', + style='filled', + fontname='Helvetica', + fontsize=12, + fontcolor='blue') + for cmpt, memb in meshEntry.items(): + #if memb.has_key + if memb in ["pool", "cplx", "reaction"]: + for poolObj in find_index(memb, 'pool'): + #G.add_node(poolObj.path) + G.add_node(poolObj.path, + label=poolObj.name, + shape='box', + color='', + style='filled', + fontname='Helvetica', + fontsize=9, + fontcolor='blue') + for cplxObj in find_index(memb, 'cplx'): + G.add_node(cplxObj.path) + G.add_node(cplxObj.path, + label=cplxObj.name, + shape='box', + color='', + style='filled', + fontname='Helvetica', + fontsize=12, + fontcolor='blue') + #G.add_edge((cplxObj.parent).path,cplxObj.path) + for reaObj in find_index(memb, 'reaction'): + #G.add_node(reaObj.path) + G.add_node(reaObj.path, label='', shape='circle', color='') + + for inn, out in list(srcdesConnection.items()): + if isinstance(out, tuple): + if len(out[0]) == 0: + print(inn.className + ':' + inn.name + + " doesn't have input message") + else: + for items in (items for items in out[0]): + G.add_edge(moose.element(items[0]).path, inn.path) + if len(out[1]) == 0: + print(inn.className + ':' + inn.name + + "doesn't have output mssg") + else: + for items in (items for items in out[1]): + G.add_edge(inn.path, moose.element(items[0]).path) + elif isinstance(out, list): + if len(out) == 0: + print("Func pool doesn't have sumtotal") + else: + for items in (items for items in out): + G.add_edge(moose.element(items[0]).path, inn.path) + + position = graphviz_layout(G) + xcord, ycord = [], [] + for item in position.items(): + xy = item[1] + xroundoff = round(xy[0], 0) + yroundoff = round(xy[1], 0) + xcord.append(xroundoff) + ycord.append(yroundoff) + + for item in position.items(): + xy = item[1] + anno = moose.Annotator(item[0] + '/info') + anno.x = xy[0] + anno.y = xy[1] + + +def find_index(value, key): + """ + Value.get(key) to avoid expection which would raise if empty value in + dictionary for a given key. + """ + if key in value: + return value[key] + else: + raise ValueError("key '%s' not found" % key) diff --git a/moosegui/plugins/kkitQGraphics.py b/moosegui/plugins/kkitQGraphics.py new file mode 100644 index 0000000..8d8823d --- /dev/null +++ b/moosegui/plugins/kkitQGraphics.py @@ -0,0 +1,740 @@ +# -*- coding: utf-8 -*- + +__author__ = "HarshaRani" +__credits__ = ["Upi Lab"] +__license__ = "GPL3" +__version__ = "1.0.0" +__maintainer__ = "HarshaRani" +__email__ = "hrani@ncbs.res.in" +__status__ = "Development" +__updated__ = "Sep 19 2017" + +import os + +from PyQt5 import QtGui, QtCore, Qt +from PyQt5.QtWidgets import QGraphicsPixmapItem, QGraphicsWidget +from PyQt5.QtWidgets import QGraphicsRectItem, QGraphicsItem +from PyQt5.QtWidgets import QGraphicsObject, QGraphicsPathItem +from PyQt5.QtWidgets import QGraphicsEllipseItem + +from moosegui.plugins import constants +from moosegui import config + +import moose + + +class KineticsDisplayItem(QGraphicsWidget): + """Base class for display elemenets in kinetics layout""" + + name = constants.ITEM + defaultFontName = "Helvetica" + defaultFontSize = 10 + qgtextItemSelectedChange = QtCore.pyqtSignal('PyQt_PyObject') + + def __init__(self, mooseObject, parent=None): + QGraphicsObject.__init__(self, parent) + self.mobj = mooseObject + self.gobj = None + self.pressed = False + self.setFlag(QGraphicsItem.ItemIsSelectable, True) + self.setFlag(QGraphicsItem.ItemIsMovable, True) + self.setAcceptHoverEvents(True) + self.setFocusPolicy(QtCore.Qt.StrongFocus) + if QtCore.QT_VERSION >= 0x040600: + self.setFlag(QGraphicsItem.ItemSendsGeometryChanges, 1) + self.setFlag(QGraphicsItem.ItemIgnoresTransformations, False) + + def getParentMooseObject(self): + return moose.element(self.mobj).parent + + def getParentGraphicsObject(self): + return self.parentItem() + + def setDisplayProperties(self, dinfo): + self.setGeometry(dinfo.x, dinfo.y) + + def paint(self, painter=None, option=None, widget=None): + #If item is selected + if self.hasFocus() or self.isSelected(): + painter.setPen( + QtGui.QPen(QtCore.Qt.black, 1.8, Qt.Qt.DashLine, + Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) + painter.drawRect(self.boundingRect()) + + # def mouseDoubleClickEvent(self, event): + # self.emit(QtCore.SIGNAL("qgtextDoubleClick(PyQt_PyObject)"),moose.element(self.mobj)) + + def itemChange(self, change, value): + #pass + #if change == QGraphicsItem.ItemPositionChange: + #print "itemChange ---->",self.mobj + # self.emit(QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.mobj) + if change == QGraphicsItem.ItemSelectedChange and value == True: + self.qgtextPositionChange.emit( moose.element(self.mobj) ) + # self.emit(QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"), + # moose.element(self.mobj)) + return QGraphicsItem.itemChange(self, change, value) + + +class FuncItem(KineticsDisplayItem): + name = constants.ITEM + """Class for displaying Functions""" + #fontMetrics = None + font = QtGui.QFont(KineticsDisplayItem.defaultFontName) + font.setPointSize(KineticsDisplayItem.defaultFontSize) + fontMetrics = QtGui.QFontMetrics(font) + + def __init__(self, mobj, parent): + super(FuncItem, self).__init__(mobj, parent) + self.setFlag(QGraphicsItem.ItemIsMovable, True) + iconmap_file = (os.path.join(config.settings[config.KEY_ICON_DIR], + 'classIcon/Function.png')) + self.funcImage = QtGui.QImage(iconmap_file).scaled(15, 33) + self.bg = QGraphicsRectItem(self) + self.bg.setAcceptHoverEvents(True) + self.gobj = QGraphicsPixmapItem( + QtGui.QPixmap.fromImage(self.funcImage), self.bg) + self.gobj.setAcceptHoverEvents(True) + self.gobj.mobj = self.mobj + funcdoc = (moose.element(self.mobj.path)).expr + self.gobj.setToolTip(funcdoc) + + def setDisplayProperties(self, x, y, textcolor, bgcolor): + """Set the display properties of this item.""" + poolt = ["ZombieBufPool", "BufPool", "ZombiePool", "Pool"] + if self.gobj.mobj.parent.className in poolt: + self.setGeometry(0, 30, + self.gobj.boundingRect().width(), + self.gobj.boundingRect().height()) + else: + self.setGeometry(x, y, + self.gobj.boundingRect().width(), + self.gobj.boundingRect().height()) + self.bg.setBrush(QtGui.QBrush(bgcolor)) + self.setFlag(QGraphicsItem.ItemIsMovable, False) + + def refresh(self, scale): + pass + + def boundingRect(self): + ''' reimplimenting boundingRect for redrawning ''' + return QtCore.QRectF(0, 0, + self.gobj.boundingRect().width(), + self.gobj.boundingRect().height()) + + def updateSlot(self): + return None + + def updateColor(self, bgcolor): + return None + + def updateRect(self, ratio): + return None + + def returnColor(self): + return (self.bg.brush().color()) + + def updateValue(self, gobj, funcdoc='Not Available'): + self.gobj.setToolTip(funcdoc) + + +class PoolItem(KineticsDisplayItem): + name = constants.ITEM + """Class for displaying pools. Uses a QGraphicsSimpleTextItem to + display the name.""" + #fontMetrics = None + font = QtGui.QFont(KineticsDisplayItem.defaultFontName) + font.setPointSize(KineticsDisplayItem.defaultFontSize) + fontMetrics = QtGui.QFontMetrics(font) + + def __init__(self, mobj, parent): + KineticsDisplayItem.__init__(self, mobj, parent) + self.bg = QGraphicsRectItem(self) + self.bg.setAcceptHoverEvents(True) + self.gobj = QtGui.QGraphicsSimpleTextItem(self.mobj.name, self.bg) + self.gobj.mobj = self.mobj + self._conc = self.mobj.conc + self._n = self.mobj.n + doc = "Conc\t: " + str(self._conc) + "\nn\t: " + str(self._n) + self.gobj.setToolTip(doc) + self.gobj.setFont(PoolItem.font) + if not PoolItem.fontMetrics: + PoolItem.fontMetrics = QtGui.QFontMetrics(self.gobj.font()) + self.bg.setRect( + 0, 0, + self.gobj.boundingRect().width() + + PoolItem.fontMetrics.width(' '), + self.gobj.boundingRect().height()) + self.bg.setPen(Qt.QColor(0, 0, 0, 0)) + self.gobj.setPos(PoolItem.fontMetrics.width(' '), 0) + + def setDisplayProperties(self, x, y, textcolor, bgcolor): + """Set the display properties of this item.""" + self.setGeometry( + x, y, + self.gobj.boundingRect().width() + PoolItem.fontMetrics.width(''), + self.gobj.boundingRect().height()) + self.bg.setBrush(QtGui.QBrush(bgcolor)) + + def refresh(self, scale): + fontsize = KineticsDisplayItem.defaultFontSize * scale + font = QtGui.QFont(KineticsDisplayItem.defaultFontName) + if (fontsize < 1): + fontsize = self.gobj.font().pointSize() + font.setPointSize(fontsize) + #self.gobj.setFont(PoolItem.font) + self.gobj.setFont(font) + + def boundingRect(self): + ''' reimplimenting boundingRect for redrawning ''' + return QtCore.QRectF( + 0, 0, + self.gobj.boundingRect().width() + + PoolItem.fontMetrics.width(' '), + self.gobj.boundingRect().height()) + + def updateSlot(self): + #This func will adjust the background color with respect to text size + self.gobj.setText(self.mobj.name) + self.bg.setRect( + 0, 0, + self.gobj.boundingRect().width() + + PoolItem.fontMetrics.width(' '), + self.gobj.boundingRect().height()) + self.setGeometry( + self.pos().x(), + self.pos().y(), + self.gobj.boundingRect().width() + PoolItem.fontMetrics.width(''), + self.gobj.boundingRect().height()) + + def updateColor(self, bgcolor): + self.bg.setBrush(QtGui.QBrush(QtGui.QColor(bgcolor))) + + def updateRect(self, ratio=1.0): + width = self.gobj.boundingRect().width() + PoolItem.fontMetrics.width( + ' ') + height = self.gobj.boundingRect().height() + adjustw = width * ratio + adjusth = height * ratio + self.bg.setRect(width / 2 - abs(adjustw / 2), + height / 2 - abs(adjusth / 2), adjustw, adjusth) + + def returnColor(self): + return (self.bg.brush().color()) + + def updateValue(self, gobj): + self._gobj = gobj + if (isinstance(self._gobj, moose.PoolBase)): + self._conc = self.mobj.conc + self._n = self.mobj.n + doc = "Conc\t: " + str(self._conc) + "\nn\t: " + str(self._n) + self.gobj.setToolTip(doc) + + +class PoolItemCircle(PoolItem): + name = constants.ITEM + + def __init__(self, *args, **kwargs): + PoolItem.__init__(self, *args, **kwargs) + self.setFlag(QGraphicsItem.ItemIsMovable, True) + self.bgColor = QGraphicsEllipseItem(self) + self.bgColor.setFlag(QGraphicsItem.ItemStacksBehindParent, True) + self.bgColor.setRect(((self.gobj.boundingRect().width() + + PoolItem.fontMetrics.width(' ')) / 2) - 5, + self.gobj.boundingRect().height() / 2 - 5, 10, 10) + + def setDisplayProperties(self, x, y, textcolor, bgcolor): + self.setGeometry( + x, y, + self.gobj.boundingRect().width() + + PoolItem.fontMetrics.width(' '), + self.gobj.boundingRect().height()) + self.bgColor.setBrush( + QtGui.QBrush( + QtGui.QColor(bgcolor.red(), bgcolor.green(), bgcolor.blue(), + 255))) + + def updateRect(self, ratio): + width = self.gobj.boundingRect().width() + PoolItem.fontMetrics.width( + ' ') + height = self.gobj.boundingRect().height() + adjustw = width * ratio + adjusth = height * ratio + self.bgColor.setRect(width / 2 - abs(adjustw / 2), + height / 2 - abs(adjusth / 2), adjustw, adjusth) + self.updateValue(self.gobj) + + def returnEllispeSize(self): + self.bgColor.setRect(((self.gobj.boundingRect().width() + + PoolItem.fontMetrics.width(' ')) / 2) - 5, + self.gobj.boundingRect().height() / 2 - 5, 10, 10) + + def refresh(self, scale): + fontsize = KineticsDisplayItem.defaultFontSize * scale + font = QtGui.QFont(KineticsDisplayItem.defaultFontName) + if (fontsize < 1): + fontsize = self.gobj.font().pointSize() + font.setPointSize(fontsize) + self.gobj.setFont(font) + + def MooseRef(self): + return self.gobj.mobj + + +class TableItem(KineticsDisplayItem): + defaultWidth = 30 + defaultHeight = 30 + defaultPenWidth = 2 + name = constants.ITEM + + def __init__(self, *args, **kwargs): + KineticsDisplayItem.__init__(self, *args, **kwargs) + + points = [ + QtCore.QPointF(0, TableItem.defaultWidth / 2), + QtCore.QPointF(TableItem.defaultHeight / 2 - 2, 0), + QtCore.QPointF(TableItem.defaultWidth / 2 + 2, 0), + QtCore.QPointF(TableItem.defaultWidth, + TableItem.defaultHeight / 2), + ] + + path = QtGui.QPainterPath() + path.moveTo(points[0]) + for p in points[1:]: + path.lineTo(p) + path.moveTo(p) + path.moveTo(0, 0) + path.lineTo(TableItem.defaultWidth, 0) + path.moveTo(-(TableItem.defaultWidth / 3), TableItem.defaultHeight / 4) + path.lineTo((TableItem.defaultWidth + 10), TableItem.defaultHeight / 4) + + self.gobj = QGraphicsPathItem(path, self) + #self.gobj.setToolTip("Need to see what to show unlike conc/nint for pool") + tabledoc = (moose.element(self.mobj.path)).outputValue + self.gobj.setToolTip(str(tabledoc)) + self.gobj.setPen( + QtGui.QPen(QtCore.Qt.black, 2, Qt.Qt.SolidLine, Qt.Qt.RoundCap, + Qt.Qt.RoundJoin)) + self.gobj.mobj = self.mobj + + def refresh(self, scale): + defaultWidth = TableItem.defaultWidth * scale + defaultHeight = TableItem.defaultHeight * scale + points = [ + QtCore.QPointF(0, defaultWidth / 2), + QtCore.QPointF(defaultHeight / 2 - 2, 0), + QtCore.QPointF(defaultWidth / 2 + 2, 0), + QtCore.QPointF(defaultWidth, defaultHeight / 2) + ] + path = QtGui.QPainterPath() + path.moveTo(points[0]) + for p in points[1:]: + path.lineTo(p) + path.moveTo(p) + path.moveTo(0, 0) + path.lineTo(defaultWidth, 0) + path.moveTo(-(defaultWidth / 3), defaultHeight / 4) + path.lineTo((defaultWidth + 10), defaultHeight / 4) + self.gobj.setPath(path) + TablePen = self.gobj.pen() + tableWidth = TableItem.defaultPenWidth * scale + TablePen.setWidth(tableWidth) + self.gobj.setPen(TablePen) + + def setDisplayProperties(self, x, y, textcolor, bgcolor): + """Set the display properties of this item.""" + # TODO: check the table bounding reactangle b'cos selection looks ugly + self.setGeometry(x, y, + self.gobj.boundingRect().width(), + self.gobj.boundingRect().height()) + + +class ReacItem(KineticsDisplayItem): + defaultWidth = 30 + defaultHeight = 30 + defaultPenWidth = 2 + name = constants.ITEM + + def __init__(self, *args, **kwargs): + KineticsDisplayItem.__init__(self, *args, **kwargs) + points = [ + QtCore.QPointF(ReacItem.defaultWidth / 4, 0), + QtCore.QPointF(0, ReacItem.defaultHeight / 4), + QtCore.QPointF(ReacItem.defaultWidth, ReacItem.defaultHeight / 4), + QtCore.QPointF(3 * ReacItem.defaultWidth / 4, + ReacItem.defaultHeight / 2) + ] + path = QtGui.QPainterPath() + path.moveTo(points[0]) + for p in points[1:]: + path.lineTo(p) + path.moveTo(p) + self.gobj = QGraphicsPathItem(path, self) + self.gobj.setPen( + QtGui.QPen(QtCore.Qt.black, 2, Qt.Qt.SolidLine, Qt.Qt.RoundCap, + Qt.Qt.RoundJoin)) + self.gobj.mobj = self.mobj + self._Kf = self.gobj.mobj.Kf + self._Kb = self.gobj.mobj.Kb + doc = "Kf\t: " + str(self._Kf) + "\nKb\t: " + str(self._Kb) + self.gobj.setToolTip(doc) + + def updateValue(self, gobj): + self._gobj = gobj + if (isinstance(self._gobj, moose.ReacBase)): + self._Kf = self._gobj.Kf + self._Kb = self._gobj.Kb + doc = "Kf\t: " + str(self._Kf) + "\nKb\t: " + str(self._Kb) + self.gobj.setToolTip(doc) + + def refresh(self, scale): + defaultWidth = ReacItem.defaultWidth * scale + defaultHeight = ReacItem.defaultHeight * scale + points = [ + QtCore.QPointF(defaultWidth / 4, 0), + QtCore.QPointF(0, defaultHeight / 4), + QtCore.QPointF(defaultWidth, defaultHeight / 4), + QtCore.QPointF(3 * defaultWidth / 4, defaultHeight / 2) + ] + path = QtGui.QPainterPath() + path.moveTo(points[0]) + for p in points[1:]: + path.lineTo(p) + path.moveTo(p) + + self.gobj.setPath(path) + ReacPen = self.gobj.pen() + defaultpenwidth = ReacItem.defaultPenWidth + reacWidth = defaultpenwidth * scale + ReacPen.setWidth(reacWidth) + self.gobj.setPen(ReacPen) + + def setDisplayProperties(self, x, y, textcolor, bgcolor): + """Set the display properties of this item.""" + self.setGeometry(x, y, + self.gobj.boundingRect().width(), + self.gobj.boundingRect().height()) + + +class EnzItem(KineticsDisplayItem): + defaultWidth = 20 + defaultHeight = 10 + name = constants.ITEM + + def __init__(self, *args, **kwargs): + KineticsDisplayItem.__init__(self, *args, **kwargs) + self.gobj = QGraphicsEllipseItem(0, 0, EnzItem.defaultWidth, + EnzItem.defaultHeight, self) + self.gobj.mobj = self.mobj + self._Km = self.gobj.mobj.Km + self._Kcat = self.gobj.mobj.kcat + doc = "Km\t: " + str(self._Km) + "\nKcat\t: " + str(self._Kcat) + self.gobj.setToolTip(doc) + + def updateValue(self, gobj): + self._gobj = gobj + if (isinstance(self.gobj, moose.EnzBase)): + self._Km = self._gobj.Km + self._Kcat = self._gobj.kcat + doc = "Km\t: " + str(self._Km) + "\nKcat\t: " + str(self._Kcat) + self.gobj.setToolTip(doc) + + def updateColor(self, bgcolor): + self.gobj.setBrush(QtGui.QBrush(QtGui.QColor(bgcolor))) + + def setDisplayProperties(self, x, y, textcolor, bgcolor): + """Set the display properties of this item.""" + self.setGeometry(x, y, + self.gobj.boundingRect().width(), + self.gobj.boundingRect().height()) + self.gobj.setBrush(QtGui.QBrush(bgcolor)) + + def refresh(self, scale): + defaultWidth = EnzItem.defaultWidth * scale + defaultHeight = EnzItem.defaultHeight * scale + self.gobj.setRect(0, 0, defaultWidth, defaultHeight) + + +class MMEnzItem(EnzItem): + name = constants.ITEM + + def __init__(self, *args, **kwargs): + EnzItem.__init__(self, *args, **kwargs) + + +class CplxItem(KineticsDisplayItem): + defaultWidth = 10 + defaultHeight = 10 + name = constants.ITEM + + def __init__(self, *args, **kwargs): + KineticsDisplayItem.__init__(self, *args, **kwargs) + self.gobj = QGraphicsRectItem(0, 0, CplxItem.defaultWidth, + CplxItem.defaultHeight, self) + self.gobj.mobj = self.mobj + self._conc = self.mobj.conc + self._n = self.mobj.n + doc = "Conc\t: " + str(self._conc) + "\nn\t: " + str(self._n) + self.gobj.setToolTip(doc) + + def updateValue(self, gobj): + self._gobj = gobj + if (isinstance(self._gobj, moose.PoolBase)): + self._conc = self.mobj.conc + self._n = self.mobj.n + doc = "Conc\t: " + str(self._conc) + "\nn\t: " + str(self._n) + self.gobj.setToolTip(doc) + + def setDisplayProperties(self, x, y, textcolor, bgcolor): + """Set the display properties of this item.""" + self.setGeometry(self.gobj.boundingRect().width() / 2, + self.gobj.boundingRect().height(), + self.gobj.boundingRect().width(), + self.gobj.boundingRect().height()) + self.setFlag(QGraphicsItem.ItemIsMovable, False) + + def refresh(self, scale): + defaultWidth = CplxItem.defaultWidth * scale + defaultHeight = CplxItem.defaultHeight * scale + + self.gobj.setRect(0, 0, defaultWidth, defaultHeight) + + +class GRPItem(QGraphicsRectItem): + #This is used for displaying Grp Item + name = constants.GROUP + + def __init__(self, parent, x, y, w, h, item): + QGraphicsRectItem.__init__(self, x, y, w, h, parent) + self.mobj = item + self.setFlag(QGraphicsItem.ItemIsMovable, True) + self.setFlag(QGraphicsItem.ItemIsSelectable) + self.setAcceptHoverEvents(True) + self.setToolTip(self.mobj.name) + if config.QT_MINOR_VERSION >= 6: + self.setFlag(QGraphicsItem.ItemSendsGeometryChanges, 1) + + def itemChange(self, change, value): + if change == QGraphicsItem.ItemPositionChange: + self.qgtextItemSelectedChange.emit(self.mobj) + # self.grpEmitter.emit( + # QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"), + # self.mobj) + if change == QGraphicsItem.ItemSelectedChange and value == True: + self.qgtextItemSelectedChange.emit(self.mobj) + # self.grpEmitter.emit( + # QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"), + # self.mobj) + + return QGraphicsItem.itemChange(self, change, value) + + +class ComptItem(QGraphicsRectItem): + name = constants.COMPARTMENT + + def __init__(self, parent, x, y, w, h, item): + self.cmptEmitter = QtCore.QObject() + iParent = item + ''' + self._rect = QtCore.QRectF(x,y,w,h) + self._scene = parent + print "self comptItem",self._scene.sceneContainer ," and",self._scene.sceneContainer.graphicsView + self.mouseOver = False + self.resizeHandleSize = 4.0 + self.mousePressPos = None + self.mouseMovePos = None + self.mouseIsPressed = False + #self.setAcceptsHoverEvents(True) + self.updateResizeHandles() + ''' + if hasattr(iParent, "__iter__"): + self.mobj = iParent[0] + else: + self.mobj = iParent + self.layoutWidgetPt = parent + QGraphicsRectItem.__init__(self, x, y, w, h) + + self.setFlag(QGraphicsItem.ItemIsMovable, True) + self.setFlag(QGraphicsItem.ItemIsSelectable) + #self.setFlag(QGraphicsItem.ItemSendsGeometryChanges, 1) + QT_VERSION = str(QtCore.QT_VERSION_STR).split('.') + QT_MINOR_VERSION = int(QT_VERSION[1]) + if QT_MINOR_VERSION >= 6: + #if config.QT_MINOR_VERSION >= 6: + self.setFlag(QGraphicsItem.ItemSendsGeometryChanges, 1) + self.setAcceptHoverEvents(True) + self.setToolTip(iParent.name) + + ''' + def hoverEnterEvent(self, event): + self.updateResizeHandles() + self.mouseOver = True + self.prepareGeometryChange() + + def hoverLeaveEvent(self, event): + self.mouseOver = False + self.prepareGeometryChange() + + def hoverMoveEvent(self, event): + + if self.topLeft.contains(event.scenePos()) or self.bottomRight.contains(event.scenePos()): + self.setCursor(QtCore.Qt.SizeFDiagCursor) + elif self.topRight.contains(event.scenePos()) or self.bottomLeft.contains(event.scenePos()): + self.setCursor(QtCore.Qt.SizeBDiagCursor) + else: + self.setCursor(QtCore.Qt.SizeAllCursor) + + QGraphicsRectItem.hoverMoveEvent(self, event) + + def mousePressEvent(self, event): + """ + Capture mouse press events and find where the mosue was pressed on the object + """ + self.mousePressPos = event.scenePos() + self.mouseIsPressed = True + self.rectPress = copy.deepcopy(self._rect) + + # Top left corner + if self.topLeft.contains(event.scenePos()): + self.mousePressArea = 'topleft' + # top right corner + elif self.topRight.contains(event.scenePos()): + self.mousePressArea = 'topright' + # bottom left corner + elif self.bottomLeft.contains(event.scenePos()): + self.mousePressArea = 'bottomleft' + # bottom right corner + elif self.bottomRight.contains(event.scenePos()): + self.mousePressArea = 'bottomright' + # entire rectangle + else: + self.mousePressArea = None + + QGraphicsRectItem.mousePressEvent(self, event) + + def mouseReleaseEvent(self, event): + """ + Capture nmouse press events. + """ + self.mouseIsPressed = False + + self.updateResizeHandles() + self.prepareGeometryChange() + + QGraphicsRectItem.mouseReleaseEvent(self, event) + + def mouseMoveEvent(self, event): + """ + Handle mouse move events. + """ + self.mouseMovePos = event.scenePos() + + if self.mouseIsPressed: + # Move top left corner + if self.mousePressArea=='topleft': + self._rect.setTopLeft(self.rectPress.topLeft()-(self.mousePressPos-self.mouseMovePos)) + # Move top right corner + elif self.mousePressArea=='topright': + self._rect.setTopRight(self.rectPress.topRight()-(self.mousePressPos-self.mouseMovePos)) + # Move bottom left corner + elif self.mousePressArea=='bottomleft': + self._rect.setBottomLeft(self.rectPress.bottomLeft()-(self.mousePressPos-self.mouseMovePos)) + # Move bottom right corner + elif self.mousePressArea=='bottomright': + self._rect.setBottomRight(self.rectPress.bottomRight()-(self.mousePressPos-self.mouseMovePos)) + # Move entire rectangle, don't resize + else: + self._rect.moveCenter(self.rectPress.center()-(self.mousePressPos-self.mouseMovePos)) + + self.updateResizeHandles() + self.prepareGeometryChange() + + QGraphicsRectItem.mousePressEvent(self, event) + + def boundingRect(self): + """ + Return bounding rectangle + """ + return self._boundingRect + + def updateResizeHandles(self): + """ + Update bounding rectangle and resize handles + """ + self.offset = self.resizeHandleSize*(self._scene.sceneContainer.graphicsView.mapToScene(1,0)-self._scene.sceneContainer.graphicsView.mapToScene(0,1)).x() + + self._boundingRect = self._rect.adjusted(-self.offset, self.offset, self.offset, -self.offset) + + # Note: this draws correctly on a view with an inverted y axes. i.e. QGraphicsView.scale(1,-1) + self.topLeft = QtCore.QRectF(self._boundingRect.topLeft().x(), self._boundingRect.topLeft().y() - 2*self.offset, + 2*self.offset, 2*self.offset) + self.topRight = QtCore.QRectF(self._boundingRect.topRight().x() - 2*self.offset, self._boundingRect.topRight().y() - 2*self.offset, + 2*self.offset, 2*self.offset) + self.bottomLeft = QtCore.QRectF(self._boundingRect.bottomLeft().x(), self._boundingRect.bottomLeft().y(), + 2*self.offset, 2*self.offset) + self.bottomRight = QtCore.QRectF(self._boundingRect.bottomRight().x() - 2*self.offset, self._boundingRect.bottomRight().y(), + 2*self.offset, 2*self.offset) + + def paint(self, painter, option, widget): + """ + Paint Widget + """ + + # show boundingRect for debug purposes + painter.setPen(QtGui.QPen(QtCore.Qt.red, 0, QtCore.Qt.DashLine)) + painter.drawRect(self._boundingRect) + + # Paint rectangle + painter.setPen(QtGui.QPen(QtCore.Qt.black, 0, QtCore.Qt.SolidLine)) + painter.drawRect(self._rect) + + # If mouse is over, draw handles + if self.mouseOver: + # if rect selected, fill in handles + if self.isSelected(): + painter.setBrush(QtGui.QBrush(QtGui.QColor(0,0,0))) + painter.drawRect(self.topLeft) + painter.drawRect(self.topRight) + painter.drawRect(self.bottomLeft) + painter.drawRect(self.bottomRight) + ''' + + def pointerLayoutpt(self): + return (self.layoutWidgetPt) + + # def mouseDoubleClickEvent(self, event): + # self.cmptEmitter.emit(QtCore.SIGNAL("qgtextDoubleClick(PyQt_PyObject)"),moose.element(self.mooseObj_)) + + def itemChange(self, change, value): + if change == QGraphicsItem.ItemPositionChange: + self.cmptEmitter.emit( + QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"), + self.mobj) + if change == QGraphicsItem.ItemSelectedChange and value == True: + self.qgtextPositionChange.emit(self.mobj) + # self.cmptEmitter.emit( + # QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"), + # self.mobj) + return QGraphicsItem.itemChange(self, change, value) + + +if __name__ == '__main__': + import sys + from PyQt5.QtWidgets import QApplication, QGraphicsView, QGraphicsScene + app = QApplication(sys.argv) + a = moose.Pool('pool') + b = moose.Reac('reac') + c = moose.Enz('enzyme') + gview = QGraphicsView() + scene = QGraphicsScene(gview) + reacItem = ReacItem(b) + reacItem.setDisplayProperties(50, 5, QtGui.QColor('yellow'), + QtGui.QColor('green')) + enzItem = EnzItem(c) + enzItem.setDisplayProperties(100, 10, QtGui.QColor('blue'), + QtGui.QColor('yellow')) + scene.addItem(reacItem) + scene.addItem(enzItem) + gview.setScene(scene) + gview.show() + sys.exit(app.exec_()) diff --git a/plugins/kkitUtil.py b/moosegui/plugins/kkitUtil.py similarity index 71% rename from plugins/kkitUtil.py rename to moosegui/plugins/kkitUtil.py index 09170c2..8c431e0 100644 --- a/plugins/kkitUtil.py +++ b/moosegui/plugins/kkitUtil.py @@ -1,43 +1,47 @@ +# -*- coding: utf-8 -*- + __author__ = "HarshaRani" -__credits__ = ["Upi Lab"] -__license__ = "GPL3" -__version__ = "1.0.0" +__credits__ = ["Bhalla Lab, NCBS Bangalore"] +__license__ = "GPLv3" __maintainer__ = "HarshaRani" __email__ = "hrani@ncbs.res.in" -__status__ = "Development" -__updated__ = "Oct 11 2018" - -''' -2018 -Oct 11: when collision is handled an update of position is done -Sep 28: spell corrected cyclMesh to cylMesh -Sep 17: when vertical or horizontal layout is applied for group, compartment size is recalculated -Sep 11: group size is calculated based on sceneBoundingRect for compartment size -2017 -Oct 18 some of the function moved to this file from kkitOrdinateUtils -''' -from moose import Annotator,element,ChemCompt -from kkitQGraphics import PoolItem, ReacItem,EnzItem,CplxItem,GRPItem,ComptItem -from PyQt4 import QtCore,QtGui,QtSvg -from PyQt4.QtGui import QColor + import numpy as np import os -import config import pickle import random import matplotlib +from PyQt5 import QtCore, QtGui, QtSvg +from PyQt5.QtGui import QColor + +# MOOSE +from moose import Annotator, element, ChemCompt + +# MOOSE gui +from moosegui.plugins.kkitQGraphics import PoolItem, EnzItem, GRPItem +from moosegui import config + colormap_file = open(os.path.join(config.settings[config.KEY_COLORMAP_DIR], 'rainbow2.pkl'),'rb') colorMap = pickle.load(colormap_file) colormap_file.close() -ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"] +ignoreColor= ["mistyrose", "antiquewhite", "aliceblue", "azure", "bisque", + "black", "blanchedalmond", "blue", "cornsilk", "darkolivegreen", + "darkslategray", "dimgray", "floralwhite", "gainsboro", "ghostwhite", + "honeydew", "ivory", "lavender", "lavenderblush", "lemonchiffon", + "lightcyan", "lightgoldenrodyellow", "lightgray", "lightyellow", + "linen", "mediumblue", "mintcream", "navy", "oldlace", "papayawhip", + "saddlebrown", "seashell", "snow", "wheat", "white", "whitesmoke", + "aquamarine", "lightsalmon", "moccasin", "limegreen", "snow", "sienna", + "beige", "dimgrey", "lightsage"] + matplotcolor = {} -for name,hexno in matplotlib.colors.cnames.iteritems(): +for name,hexno in matplotlib.colors.cnames.items(): matplotcolor[name]=hexno def getRandColor(): - k = random.choice(matplotcolor.keys()) + k = random.choice(list(matplotcolor.keys())) if k in ignoreColor: return getRandColor() else: @@ -70,12 +74,11 @@ def getColor(iteminfo): return(textcolor,bgcolor) def colorCheck(fc_bgcolor,fcbg): - """ textColor or background can be anything like string or tuple or list \ - if string its taken as colorname further down in validColorcheck checked for valid color, \ - but for tuple and list its taken as r,g,b value. + """ + textColor or background can be anything like string or tuple or list \ + if string its taken as colorname further down in validColorcheck checked for valid color, \ + but for tuple and list its taken as r,g,b value. """ - #import re - #fc_bgcolor = re.sub('[^a-zA-Z0-9-_*.]', '', fc_bgcolor) if isinstance(fc_bgcolor,str): if fc_bgcolor.startswith("#"): fc_bgcolor = QColor(fc_bgcolor) @@ -97,11 +100,6 @@ def colorCheck(fc_bgcolor,fcbg): return(fc_bgcolor) def validColorcheck(color): - ''' - Both in Qt4.7 and 4.8 if not a valid color it makes it as back but in 4.7 there will be a warning mssg which is taken here - checking if textcolor or backgroundcolor is valid color, if 'No' making white color as default - where I have not taken care for checking what will be backgroundcolor for textcolor or textcolor for backgroundcolor - ''' if QColor(color).isValid(): return (QColor(color)) else: @@ -118,10 +116,7 @@ def moveMin(reference, collider, layoutPt,margin): else: yDistance = referenceRect.y() + referenceRect.height() / 2.0 + colliderRect.height() / 2.0 + margin - colliderRect.y() - #if xDistance > yDistance: collider.moveBy(xDistance, yDistance) - #else: - # collider.moveBy(xDistance, 0.0) layoutPt.drawLine_arrow(itemignoreZooming=False) def moveX(reference, collider, layoutPt, margin): @@ -136,22 +131,20 @@ def handleCollisions(compartments, moveCallback, layoutPt,margin = 5.0): if len(compartments) is 0 : return compartments = sorted(compartments, key = lambda c: c.sceneBoundingRect().center().x()) reference = compartments.pop(0); - print (reference.name) referenceRect = reference.sceneBoundingRect() - colliders = filter( lambda compartment : referenceRect.intersects(compartment.sceneBoundingRect()) - , compartments - ) + colliders = [compartment for compartment in compartments + if referenceRect.intersects(compartment.sceneBoundingRect()) + ] for collider in colliders: moveCallback(reference, collider, layoutPt,margin) - #print (reference.mobj).parent + if isinstance(element(((reference.mobj).parent)),ChemCompt): v = layoutPt.qGraCompt[element(((reference.mobj).parent))] - #layoutPt.updateCompartmentSize(x) rectcompt = calculateChildBoundingRect(v) comptBoundingRect = v.boundingRect() if not comptBoundingRect.contains(rectcompt): layoutPt.updateCompartmentSize(v) - + else: rectcompt = calculateChildBoundingRect(v) v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) @@ -181,17 +174,14 @@ def calculateChildBoundingRect(compt): xpos.append(l.sceneBoundingRect().bottomRight().x()) ypos.append(l.sceneBoundingRect().y()) ypos.append(l.sceneBoundingRect().bottomRight().y()) - ''' - xpos.append(l.rect().x()) - xpos.append(l.boundingRect().bottomRight().x()) - ypos.append(l.rect().y()) - ypos.append(l.boundingRect().bottomRight().y()) - ''' if (isinstance(l,PoolItem) or isinstance(l,EnzItem)): ''' For Enz cplx height and for pool function height needs to be taken''' for ll in l.childItems(): - ''' eleminating polygonItem (arrow) [This is happen in cross-compartment model that arrow from one compartment will be child] - pool's outboundary RectItem and Enz's outerboundary Ellipse is eleminating since its same + ''' eleminating polygonItem (arrow) [This is happen in + cross-compartment model that arrow from one compartment will be + child] + pool's outboundary RectItem and Enz's outerboundary Ellipse + is eleminating since its samee ''' if ( (not isinstance(ll,QtGui.QGraphicsPolygonItem)) and (not isinstance(ll,QtGui.QGraphicsRectItem)) and @@ -221,4 +211,4 @@ def findGroup(melement): def findGroup_compt(melement): while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CylMesh"])): melement = melement.parent - return melement \ No newline at end of file + return melement diff --git a/plugins/kkitViewcontrol.py b/moosegui/plugins/kkitViewcontrol.py similarity index 55% rename from plugins/kkitViewcontrol.py rename to moosegui/plugins/kkitViewcontrol.py index 1f80fca..7a79f68 100644 --- a/plugins/kkitViewcontrol.py +++ b/moosegui/plugins/kkitViewcontrol.py @@ -1,68 +1,61 @@ +# -*- coding: utf-8 -*- + __author__ = "HarshaRani" __credits__ = ["Upi Lab"] __license__ = "GPL3" -__version__ = "1.0.0" __maintainer__ = "HarshaRani" __email__ = "hrani@ncbs.res.in" -__status__ = "Development" -__updated__ = "Oct 27 2018" - -''' -2018 -Oct 27 : When group is moved within another group, outer group is resize inturn compartmet is also resized -Oct 10 : Groups are handled with collision detection, - messagebox when object moved from one group to another - layout updated when object moved etc -Sep 18 : one can close the messagebox if doesn't want to plot -Sep 07 : when object qgraphicalparent is changed then connecting arrow's parent also need to be changed -Jun 08 : If object is moved from one group or compartment to another group or with in same Compartment, - then both at moose level (group or compartment path is updated ) and qt level the setParentItem is set - -If object is moved to Empty place or not allowed place in the GUI its moved back to origin position - -also some clean up when object is just clicked in QsvgItem and v/s clicked and some action done - -with Rubber selection if object are moved then group size is updated -2017 -Oct 03 : At mousePressEvent, a clean way of checking on what object mouse press Event happened is checked. - This is after group is added where Group Interior and Boundary is checked, with in groupInterior if click in - on COMPARTMENT BOUNDARY is clicked then COMPARTMENT_BOUNDARY is return, else top most group object is returned. -Sep 20 : Group related function added - -resolveGroupInteriorAndBoundary, findGraphic_groupcompt, graphicsIsInstance - -@resolveItem,editorMousePressEvent,editorMouseMoveEvent,editorMouseReleaseEvent checks made for group - -''' -import sys -from modelBuild import * -from constants import * -from PyQt4.QtGui import QPixmap, QImage, QPen, QGraphicsPixmapItem, QGraphicsLineItem -from PyQt4.QtCore import pyqtSignal -from kkitUtil import * -#from setsolver import * -from PyQt4 import QtSvg -from moose import utils -from functools import partial +import os +from functools import partial -class GraphicalView(QtGui.QGraphicsView): - - def __init__(self, modelRoot,parent,border,layoutPt,createdItem): - QtGui.QGraphicsView.__init__(self,parent) - +from PyQt5 import QtSvg, Qt, QtGui, QtCore +from PyQt5.QtWidgets import QGraphicsLineItem, QApplication +from PyQt5.QtWidgets import QGraphicsScene, QGraphicsView +from PyQt5.QtWidgets import QMenu, QMessageBox, QGraphicsPolygonItem +from PyQt5.QtWidgets import QGraphicsItem, QPushButton, QRubberBand + +# MOOSE +import moose + +# moosegui +from moosegui.plugins import kkitUtil +from moosegui.plugins import modelBuild +from moosegui.plugins import constants +from moosegui.plugins import kkitQGraphics +from moosegui.plugins import kkitOrdinateUtil + +# logger +from moosegui import config +import logging +logger_ = logging.getLogger("moosegui.kkit.viewcontrol") + +SDIR_ = os.path.dirname(__file__) + +class GraphicalView(QGraphicsView): + # NOTE: why this is not inside __init__? See + # https://stackoverflow.com/a/2971426/1805129 and cry! + dropped = QtCore.pyqtSignal('PyQt_PyObject') + + def __init__(self, modelRoot, parent, border, layoutPt, createdItem): + QGraphicsView.__init__(self, parent) + logging.debug( "Creating GraphicalView " ) self.state = None - self.move = False + self.move = False self.resetState() - self.connectionSign = None - self.connectionSource = None - self.expectedConnection = None - self.selections = [] - self.connector = None - self.connectionSignImagePath = "../gui/icons/connection.png" - self.connectionSignImage = QImage(self.connectionSignImagePath) - - # self.expectedConnectionPen = QPen() + self.connectionSign = None + self.connectionSource = None + self.expectedConnection = None + self.selections = [] + self.connector = None + self.connectionSignImagePath = os.path.join(SDIR_, "../icons/connection.png") + assert os.path.exists( self.connectionSignImagePath ) + self.connectionSignImage = QtGui.QImage(self.connectionSignImagePath) self.setScene(parent) self.modelRoot = modelRoot self.sceneContainerPt = parent - self.sceneContainerPt.setItemIndexMethod(QtGui.QGraphicsScene.NoIndex) - self.setDragMode(QtGui.QGraphicsView.RubberBandDrag) + self.sceneContainerPt.setItemIndexMethod(QGraphicsScene.NoIndex) + self.setDragMode(QGraphicsView.RubberBandDrag) self.itemSelected = False self.customrubberBand = None self.rubberbandWidth = 0 @@ -75,47 +68,57 @@ def __init__(self, modelRoot,parent,border,layoutPt,createdItem): self.layoutPt = layoutPt # All the object which are stacked on the scene are listed self.stackOrder = self.sceneContainerPt.items(Qt.Qt.DescendingOrder) - #From stackOrder selecting only compartment - self.cmptStackorder = [i for i in self.stackOrder if isinstance(i,ComptItem)] + # From stackOrder selecting only compartment + self.cmptStackorder = [ + i for i in self.stackOrder if isinstance(i, kkitQGraphics.ComptItem)] self.viewBaseType = " " self.iconScale = 1 self.arrowsize = 2 self.defaultComptsize = 5 - self.connectorlist = {"plot": None ,"clone": None,"move": None,"delete": None} - self.setHorizontalScrollBarPolicy(PyQt4.QtCore.Qt.ScrollBarAlwaysOn) - self.setVerticalScrollBarPolicy(PyQt4.QtCore.Qt.ScrollBarAlwaysOn) - - def setRefWidget(self,path): + self.connectorlist = { + "plot": None, + "clone": None, + "move": None, + "delete": None} + self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn) + self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn) + + def setRefWidget(self, path): self.viewBaseType = path - - def resizeEvent(self, event): - #print event.size().width(),event.size().height() - self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio) - #print("Called =>", event) + def resizeEvent(self, event): + self.fitInView( + self.sceneContainerPt.itemsBoundingRect().x() - 10, + self.sceneContainerPt.itemsBoundingRect().y() - 10, + self.sceneContainerPt.itemsBoundingRect().width() + 20, + self.sceneContainerPt.itemsBoundingRect().height() + 20, + Qt.Qt.IgnoreAspectRatio) return - + def resolveCompartmentInteriorAndBoundary(self, item, position): - bound = item.rect().adjusted(3,3,-3,-3) - return COMPARTMENT_INTERIOR if bound.contains(item.mapFromScene(position)) else COMPARTMENT_BOUNDARY + bound = item.rect().adjusted(3, 3, -3, -3) + return constants.COMPARTMENT_INTERIOR if bound.contains( + item.mapFromScene(position)) else constants.COMPARTMENT_BOUNDARY def resolveGroupInteriorAndBoundary(self, item, position): bound = item.rect().adjusted(3,3,-3,-3) - return GROUP_INTERIOR if bound.contains(item.mapFromScene(position)) else GROUP_BOUNDARY + return constants.GROUP_INTERIOR \ + if bound.contains(item.mapFromScene(position)) \ + else constants.GROUP_BOUNDARY def resetState(self): - self.state = { "press" : { "mode" : INVALID - , "item" : None - , "sign" : None - , "pos" : None - , "scenepos" : None - } - , "move" : { "happened": False - } - , "release" : { "mode" : INVALID - , "item" : None - , "sign" : None - } + self.state = { + "press" : { + "mode": constants.INVALID + , "item" : None + , "sign" : None + , "pos" : None + , "scenepos" : None } + , "move" : { "happened": False } + , "release" : { "mode" : constants.INVALID + , "item" : None + , "sign" : None + } } @@ -127,36 +130,35 @@ def resolveItem(self, items, position): comptInteriorfound = False comptBoundary = [] - # If clicked , moved and dropped then drop object should not take polygonItem it shd take Goup or compartment - #(this is checked is self.state["move"]), else qpolygonItem then deleting the connection b/w 2 objects - #move is True the + # If clicked , moved and dropped then drop object should not take + # polygonItem it shd take Goup or compartment + # (this is checked is self.state["move"]), else qpolygonItem then + # deleting the connection b/w 2 objects move is True. for item in items: if isinstance(item, QtSvg.QGraphicsSvgItem): - return (item, CONNECTOR) + return (item, constants.CONNECTOR) if not self.state["move"]["happened"]: for item in items: - if isinstance(item, QtGui.QGraphicsPolygonItem): - return (item, CONNECTION) + if isinstance(item, QGraphicsPolygonItem): + return (item, constants.CONNECTION) for item in items: - if hasattr(item, "name"): - if item.name == ITEM: - return (item, ITEM) - if item.name == GROUP: - gsolution = (item, self.resolveGroupInteriorAndBoundary(item, position)) - if gsolution[1] == GROUP_BOUNDARY: - return gsolution - elif gsolution[1] == GROUP_INTERIOR: - groupInteriorfound = True - groupList.append(gsolution) - if item.name == COMPARTMENT: - csolution = (item, self.resolveCompartmentInteriorAndBoundary(item, position)) - if csolution[1] == COMPARTMENT_BOUNDARY: - return csolution - # elif csolution[1] == COMPARTMENT_INTERIOR: - # comptInteriorfound = True - # comptBoundary.append(csolution) + if not hasattr(item, "name"): + continue + if item.name == constants.ITEM: + return item, constants.ITEM + if item.name == constants.GROUP: + gsolution = (item, self.resolveGroupInteriorAndBoundary(item, position)) + if gsolution[1] == constants.GROUP_BOUNDARY: + return gsolution + elif gsolution[1] == constants.GROUP_INTERIOR: + groupInteriorfound = True + groupList.append(gsolution) + if item.name == constants.COMPARTMENT: + csolution = (item, self.resolveCompartmentInteriorAndBoundary(item, position)) + if csolution[1] == constants.COMPARTMENT_BOUNDARY: + return csolution if groupInteriorfound: if comptInteriorfound: @@ -165,7 +167,7 @@ def resolveItem(self, items, position): return groupList[0] else: if csolution is None: - return (None, EMPTY) + return (None, constants.EMPTY) return csolution def findGraphic_groupcompt(self,gelement): @@ -174,70 +176,76 @@ def findGraphic_groupcompt(self,gelement): return gelement def graphicsIsInstance(self, gelement, classNames): + assert '.' not in gelement.__class__.__name__ return gelement.__class__.__name__ in classNames def editorMousePressEvent(self, event): self.clickPosition = self.mapToScene(event.pos()) (item, itemType) = self.resolveItem(self.items(event.pos()), self.clickPosition) if event.buttons() == QtCore.Qt.LeftButton: - self.state["press"]["mode"] = VALID + self.state["press"]["mode"] = constants.VALID self.state["press"]["item"] = item self.state["press"]["type"] = itemType self.state["press"]["pos"] = event.pos() if isinstance(item, QtSvg.QGraphicsSvgItem): - ##This is kept for reference, so that if object (P,R,E,Tab,Fun) is moved outside the compartment, - #then it need to be pull back to original position + # This is kept for reference, so that if object (P,R,E,Tab,Fun) + # is moved outside the compartment, then it need to be pull back + # to original position self.state["press"]["scenepos"] = item.parent().scenePos() - if itemType == COMPARTMENT_INTERIOR or itemType == GROUP_BOUNDARY or itemType == GROUP_INTERIOR: + if itemType == constants.COMPARTMENT_INTERIOR \ + or itemType == constants.GROUP_BOUNDARY \ + or itemType == constants.GROUP_INTERIOR: self.removeConnector() - - elif itemType == ITEM: + + elif itemType == constants.ITEM: if not self.move: self.showConnector(self.state["press"]["item"]) else: - #If right button clicked self.resetState() - # if itemType == GROUP_INTERIOR: - # print " self.layoutPt.qGraGrp ",item, item.childItems() - # grouplist = [] - # for i in item.childItems(): - # if isinstance(i,KineticsDisplayItem): - # grouplist.append(i) - # popupmenu = QtGui.QMenu('PopupMenu', self) - # popupmenu.addAction("LinearLayout", lambda : handleCollisions(list(grouplist), moveX, self.layoutPt)) - # popupmenu.addAction("VerticalLayout" ,lambda : handleCollisions(list(grouplist), moveMin, self.layoutPt )) - # popupmenu.exec_(self.mapToGlobal(event.pos())) - # self.layoutPt.updateGrpSize(item) - - if itemType == GROUP_BOUNDARY: - popupmenu = QtGui.QMenu('PopupMenu', self) + if itemType == constants.GROUP_BOUNDARY: + popupmenu = QMenu('PopupMenu', self) popupmenu.addAction("DeleteGroup", lambda : self.deleteGroup(item,self.layoutPt)) - popupmenu.addAction("LinearLayout", lambda : handleCollisions(list(self.layoutPt.qGraGrp.values()), moveX, self.layoutPt)) - popupmenu.addAction("VerticalLayout" ,lambda : handleCollisions(list(self.layoutPt.qGraGrp.values()), moveMin, self.layoutPt )) - - #popupmenu.addAction("CloneGroup" ,lambda : handleCollisions(comptList, moveMin, self.layoutPt )) + popupmenu.addAction("LinearLayout" + , lambda: kkitUtil.handleCollisions( + list(self.layoutPt.qGraGrp.values() ), kkitUtil.moveX, self.layoutPt) + ) + popupmenu.addAction("VerticalLayout" + , lambda : kkitUtil.handleCollisions( + list(self.layoutPt.qGraGrp.values()), kkitUtil.moveMin, self.layoutPt + ) + ) popupmenu.exec_(self.mapToGlobal(event.pos())) - - elif itemType == COMPARTMENT_BOUNDARY: + + elif itemType == constants.COMPARTMENT_BOUNDARY: if len(list(self.layoutPt.qGraCompt.values())) > 1: - popupmenu = QtGui.QMenu('PopupMenu', self) - #popupmenu.addAction("DeleteCmpt", lambda : self.deleteCmpt(item,self.layoutPt)) - popupmenu.addAction("LinearLayout", lambda : handleCollisions(list(self.layoutPt.qGraCompt.values()), moveX, self.layoutPt)) - popupmenu.addAction("VerticalLayout" ,lambda : handleCollisions(list(self.layoutPt.qGraCompt.values()), moveMin, self.layoutPt )) + popupmenu = QMenu('PopupMenu', self) + popupmenu.addAction("LinearLayout" + , lambda : kkitUtil.handleCollisions( + list(self.layoutPt.qGraCompt.values()), kkitUtil.moveX, self.layoutPt + ) + ) + popupmenu.addAction("VerticalLayout" + , lambda : kkitUtil.handleCollisions( + list(self.layoutPt.qGraCompt.values()), kkitUtil.moveMin, self.layoutPt + ) + ) popupmenu.exec_(self.mapToGlobal(event.pos())) - def editorMouseMoveEvent(self,event): - if self.state["press"]["mode"] == INVALID: + logger_.debug( "editorMouseMoveEvent %s" % str(event)) + if self.state["press"]["mode"] == constants.INVALID: self.state["move"]["happened"] = False return if self.move: - #This part of the code is when rubberband selection is done and move option is selected + # This part of the code is when rubberband selection is done and + # move option is selected initial = self.mapToScene(self.state["press"]["pos"]) final = self.mapToScene(event.pos()) displacement = final - initial for item in self.selectedItems: - if isinstance(item, KineticsDisplayItem) and not isinstance(item,ComptItem) and not isinstance(item,CplxItem): + if isinstance(item, kkitQGraphics.KineticsDisplayItem) \ + and not isinstance(item, kkitQGraphics.ComptItem) \ + and not isinstance(item, kkitQGraphics.CplxItem): item.moveBy(displacement.x(), displacement.y()) self.layoutPt.positionChange(item.mobj.path) self.state["press"]["pos"] = event.pos() @@ -246,19 +254,20 @@ def editorMouseMoveEvent(self,event): self.state["move"]["happened"] = True itemType = self.state["press"]["type"] item = self.state["press"]["item"] - if itemType == CONNECTOR: + if itemType == constants.CONNECTOR: actionType = str(item.data(0).toString()) if actionType == "move": - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(QtCore.Qt.CrossCursor)) + QApplication.setOverrideCursor( + QtGui.QCursor(QtCore.Qt.CrossCursor)) initial = self.mapToScene(self.state["press"]["pos"]) final = self.mapToScene(event.pos()) displacement = final-initial self.removeConnector() item.parent().moveBy(displacement.x(), displacement.y()) - #self.layoutPt.updateArrow(item.parent()) - if isinstance(item.parent(),PoolItem): + # self.layoutPt.updateArrow(item.parent()) + if isinstance(item.parent(), kkitQGraphics.PoolItem): for funcItem in item.parent().childItems(): - if isinstance(funcItem,FuncItem): + if isinstance(funcItem, kkitQGraphics.FuncItem): self.layoutPt.updateArrow(funcItem) self.state["press"]["pos"] = event.pos() self.layoutPt.positionChange(item.parent().mobj) @@ -271,92 +280,97 @@ def editorMouseMoveEvent(self,event): pen = QtGui.QPen(QtGui.QBrush(QtGui.QColor("black")), 1) pen.setWidthF(1.5) painter.setPen(pen) - painter.drawLine(12,7,12,17) - painter.drawLine(7,12,17,12) + painter.drawLine(12, 7, 12, 17) + painter.drawLine(7, 12, 17, 12) painter.end() - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(pixmap)) + QApplication.setOverrideCursor(QtGui.QCursor(pixmap)) - if itemType == ITEM: + if itemType == constants.ITEM: self.drawExpectedConnection(event) - if itemType == COMPARTMENT_BOUNDARY or itemType == GROUP_BOUNDARY: + if itemType == constants.COMPARTMENT_BOUNDARY or itemType == constants.GROUP_BOUNDARY: '''When Comparement or group is moved from boundary''' initial = self.mapToScene(self.state["press"]["pos"]) final = self.mapToScene(event.pos()) displacement = final - initial item.moveBy(displacement.x(), displacement.y()) - if isinstance(item.parentItem(),GRPItem): + if isinstance(item.parentItem(), kkitQGraphics.GRPItem): self.layoutPt.updateGrpSize(item.parentItem()) self.layoutPt.positionChange(item.mobj.path) self.state["press"]["pos"] = event.pos() - if itemType == COMPARTMENT_INTERIOR or itemType == GROUP_INTERIOR: + if itemType == constants.COMPARTMENT_INTERIOR or itemType == constants.GROUP_INTERIOR: if self.customrubberBand == None: - self.customrubberBand = QtGui.QRubberBand(QtGui.QRubberBand.Rectangle,self) + self.customrubberBand = QRubberBand(QRubberBand.Rectangle,self) self.customrubberBand.show() startingPosition = self.state["press"]["pos"] endingPosition = event.pos() - displacement = endingPosition - startingPosition + displacement = endingPosition - startingPosition - x0 = startingPosition.x() + x0 = startingPosition.x() x1 = endingPosition.x() - y0 = startingPosition.y() - y1 = endingPosition.y() - - if displacement.x() < 0 : - x0,x1= x1,x0 + y0 = startingPosition.y() - if displacement.y() < 0 : - y0,y1= y1,y0 + if displacement.x() < 0: + x0, x1 = x1, x0 - self.customrubberBand.setGeometry(QtCore.QRect(QtCore.QPoint(x0, y0), QtCore.QSize(abs(displacement.x()), abs(displacement.y())))) + self.customrubberBand.setGeometry( + QtCore.QRect( + QtCore.QPoint(x0, y0) + , QtCore.QSize(abs(displacement.x()), abs(displacement.y())) + ) + ) def editorMouseReleaseEvent(self,event): if self.move: self.move = False self.setCursor(Qt.Qt.ArrowCursor) - if self.state["press"]["mode"] == INVALID: - self.state["release"]["mode"] = INVALID + if self.state["press"]["mode"] == constants.INVALID: + self.state["release"]["mode"] = constants.INVALID self.resetState() return - self.clickPosition = self.mapToScene(event.pos()) - (item, itemType) = self.resolveItem(self.items(event.pos()), self.clickPosition) - self.state["release"]["mode"] = VALID + self.clickPosition = self.mapToScene(event.pos()) + (item, itemType) = self.resolveItem( + self.items(event.pos()), self.clickPosition) + self.state["release"]["mode"] = constants.VALID self.state["release"]["item"] = item self.state["release"]["type"] = itemType clickedItemType = self.state["press"]["type"] - if clickedItemType == ITEM: + if clickedItemType == constants.ITEM: if not self.state["move"]["happened"]: if not self.move: self.showConnector(self.state["press"]["item"]) - self.layoutPt.plugin.mainWindow.objectEditSlot(self.state["press"]["item"].mobj, True) + self.layoutPt.plugin.mainWindow.objectEditSlot( + self.state["press"]["item"].mobj, True) # compartment's rectangle size is calculated depending on children - #self.layoutPt.comptChilrenBoundingRect() + # self.layoutPt.comptChilrenBoundingRect() l = self.modelRoot if self.modelRoot.find('/',1) > 0: l = self.modelRoot[0:self.modelRoot.find('/',1)] linfo = moose.Annotator(l+'/info') for k,v in self.layoutPt.qGraGrp.items(): - rectgrp = calculateChildBoundingRect(v) + rectgrp = kkitUtil.calculateChildBoundingRect(v) v.setRect(rectgrp.x()-10,rectgrp.y()-10,(rectgrp.width()+20),(rectgrp.height()+20)) for k, v in self.layoutPt.qGraCompt.items(): rectcompt = v.childrenBoundingRect() if linfo.modeltype == "new_kkit": - #if newly built model then compartment is size is fixed for some size. + # if newly built model then compartment is size is + # fixed for some size. comptBoundingRect = v.boundingRect() if not comptBoundingRect.contains(rectcompt): self.layoutPt.updateCompartmentSize(v) else: - #if already built model then compartment size depends on max and min objects - rectcompt = calculateChildBoundingRect(v) + # if already built model then compartment size depends + # on max and min objects + rectcompt = kkitUtil.calculateChildBoundingRect(v) v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) else: #When group is moved then compartment need to be update which is done here - if isinstance(self.state["release"]["item"], KineticsDisplayItem): + if isinstance(self.state["release"]["item"], kkitQGraphics.KineticsDisplayItem): if not moose.element(self.state["press"]["item"].mobj) == moose.element(self.state["release"]["item"].mobj): self.populate_srcdes( self.state["press"]["item"].mobj , self.state["release"]["item"].mobj @@ -366,7 +380,7 @@ def editorMouseReleaseEvent(self,event): self.removeExpectedConnection() self.removeConnector() self.move = False - elif clickedItemType == CONNECTOR: + elif clickedItemType == constants.CONNECTOR: actionType = str(self.state["press"]["item"].data(0).toString()) pressItem = self.state["press"]["item"] initscenepos = self.state["press"]["scenepos"] @@ -376,7 +390,7 @@ def editorMouseReleaseEvent(self,event): movedGraphObj = self.state["press"]["item"].parent() if actionType == "move": - if itemType == EMPTY: + if itemType == constants.EMPTY: self.objectpullback("Empty",item,movedGraphObj,xx,yy) else: @@ -384,22 +398,22 @@ def editorMouseReleaseEvent(self,event): if movedGraphObj.parentItem() != grpCmpt: '''Not same compartment/group to which it belonged to ''' - if isinstance(movedGraphObj,FuncItem): + if isinstance(movedGraphObj, kkitQGraphics.FuncItem): funcPool = moose.element((movedGraphObj.mobj.neighbors['valueOut'])[0]) parentGrapItem = self.layoutPt.mooseId_GObj[moose.element(funcPool)] if parentGrapItem.parentItem() != grpCmpt: self.objectpullback("Functionparent",grpCmpt,movedGraphObj,xx,yy) - if isinstance(movedGraphObj,(EnzItem,MMEnzItem)): + if isinstance(movedGraphObj, (kkitQGraphics.EnzItem, moose.MMEnzItem)): parentPool = moose.element((movedGraphObj.mobj.neighbors['enzDest'])[0]) - if isinstance(parentPool,PoolBase): + if isinstance(parentPool, moose.PoolBase): if moose.exists(grpCmpt.mobj.path+'/'+parentPool.name): if moose.exists(grpCmpt.mobj.path+'/'+parentPool.name+'/'+movedGraphObj.name): self.objectpullback("Enzyme",grpCmpt,movedGraphObj,xx,yy) else: - reply = QtGui.QMessageBox.question(self, "Moving the Object",'Do want to move \'{movedGraphObj}\' \n from \'{parent}\' to \'{grpCmpt}\''.format(movedGraphObj=movedGraphObj.mobj.name,parent= movedGraphObj.parentItem().mobj.name,grpCmpt=grpCmpt.mobj.name), - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if reply == QtGui.QMessageBox.No: + reply = QMessageBox.question(self, "Moving the Object",'Do want to move \'{movedGraphObj}\' \n from \'{parent}\' to \'{grpCmpt}\''.format(movedGraphObj=movedGraphObj.mobj.name,parent= movedGraphObj.parentItem().mobj.name,grpCmpt=grpCmpt.mobj.name), + QMessageBox.Yes | QMessageBox.No) + if reply == QMessageBox.No: movedGraphObj.moveBy(-xx,-yy) self.layoutPt.updateArrow(movedGraphObj) @@ -412,37 +426,36 @@ def editorMouseReleaseEvent(self,event): if moose.exists(grpCmpt.mobj.path+'/'+movedGraphObj.mobj.name): self.objectpullback("All",grpCmpt,movedGraphObj,xx,yy) else: - reply = QtGui.QMessageBox.question(self, "Moving the Object",'Do want to move \'{movedGraphObj}\' \n from \'{parent}\' to \'{grpCmpt}\''.format(movedGraphObj=movedGraphObj.mobj.name,parent= movedGraphObj.parentItem().mobj.name,grpCmpt=grpCmpt.mobj.name), - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if reply == QtGui.QMessageBox.No: + reply = QMessageBox.question(self, "Moving the Object",'Do want to move \'{movedGraphObj}\' \n from \'{parent}\' to \'{grpCmpt}\''.format(movedGraphObj=movedGraphObj.mobj.name,parent= movedGraphObj.parentItem().mobj.name,grpCmpt=grpCmpt.mobj.name), + QMessageBox.Yes | QMessageBox.No) + if reply == QMessageBox.No: movedGraphObj.moveBy(-xx,-yy) self.layoutPt.updateArrow(movedGraphObj) else: self.moveObjSceneParent(grpCmpt,movedGraphObj,item.pos(),self.mapToScene(event.pos())) else: '''Same compt/grp to which it was belong to ''' - if isinstance(movedGraphObj,KineticsDisplayItem): + if isinstance(movedGraphObj, kkitQGraphics.KineticsDisplayItem): itemPath = movedGraphObj.mobj.path if moose.exists(itemPath): iInfo = itemPath+'/info' anno = moose.Annotator(iInfo) eventpos = self.mapToScene(event.pos()) - itempos = item.pos() - x = eventpos.x()+(15/2)#-itempos.x() - y = eventpos.y()+(2/2)#-itempos.y() + x = eventpos.x()+(15/2) + y = eventpos.y()+(2/2) anno.x = x anno.y = y self.layoutPt.updateArrow(itemPath) - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) + QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) self.layoutPt.updateGrpSize(movedGraphObj.parentItem()) self.layoutPt.positionChange(movedGraphObj.mobj) self.updateScale(self.iconScale) - if isinstance(grpCmpt,GRPItem): + if isinstance(grpCmpt, kkitQGraphics.GRPItem): self.layoutPt.updateGrpSize(movedGraphObj.parentItem()) - elif isinstance(grpCmpt,ComptItem): + elif isinstance(grpCmpt, kkitQGraphics.ComptItem): self.layoutPt.updateCompartmentSize(movedGraphObj.parentItem()) - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) + QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) if actionType == "delete": self.removeConnector() @@ -454,125 +467,138 @@ def editorMouseReleaseEvent(self,event): pen = QtGui.QPen(QtGui.QBrush(QtGui.QColor("black")), 1) pen.setWidthF(1.5) painter.setPen(pen) - painter.drawLine(8,8,16,16) - painter.drawLine(8,16,16,8) + painter.drawLine(8, 8, 16, 16) + painter.drawLine(8, 16, 16, 8) painter.end() - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(pixmap)) - reply = QtGui.QMessageBox.question(self, "Deleting Object","Do want to delete object and its connections", - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if reply == QtGui.QMessageBox.Yes: - #delete solver first as topology is changing - mooseDeleteChemSolver(self.layoutPt.modelRoot) + QApplication.setOverrideCursor(QtGui.QCursor(pixmap)) + reply = QMessageBox.question( + self, + "Deleting Object", + "Do want to delete object and its connections", + QMessageBox.Yes | QMessageBox.No) + if reply == QMessageBox.Yes: + # delete solver first as topology is changing + moose.mooseDeleteChemSolver(self.layoutPt.modelRoot) self.deleteObj([item.parent()]) - QtGui.QApplication.restoreOverrideCursor() + QApplication.restoreOverrideCursor() else: - QtGui.QApplication.restoreOverrideCursor() + QApplication.restoreOverrideCursor() elif actionType == "plot": element = moose.element(item.parent().mobj.path) if isinstance (element,moose.PoolBase): - msgBox = QtGui.QMessageBox() + msgBox = QMessageBox() msgBox.setText('What to plot?') - self.pushButtonNumber = QtGui.QPushButton(('Number'))#, QtGui.QMessageBox.YesRole) - self.pushButtonConc = QtGui.QPushButton('Concentration')#, QtGui.QMessageBox.NoRole + self.pushButtonNumber = QPushButton(('Number')) + self.pushButtonConc = QPushButton('Concentration') self.pushButtonConc.setAutoDefault(False) self.pushButtonNumber.setAutoDefault(False) - msgBox.addButton(self.pushButtonNumber,QtGui.QMessageBox.YesRole) - msgBox.addButton(self.pushButtonConc,QtGui.QMessageBox.NoRole) + msgBox.addButton(self.pushButtonNumber,QMessageBox.YesRole) + msgBox.addButton(self.pushButtonConc,QMessageBox.NoRole) msgBox.buttonClicked.connect(partial(self.onClicked, str(self.modelRoot),element)) msgBox.exec_() self.removeConnector() elif actionType == "clone": if self.state["move"]["happened"]: - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) + QApplication.setOverrideCursor( + QtGui.QCursor(Qt.Qt.ArrowCursor)) self.state["press"]["item"].parent().mobj cloneObj = self.state["press"]["item"] posWrtComp = self.mapToScene(event.pos()) - itemAtView = self.sceneContainerPt.itemAt(self.mapToScene(event.pos())) + itemAtView = self.sceneContainerPt.itemAt( + self.mapToScene(event.pos())) self.removeConnector() - if isinstance(itemAtView,ComptItem) or isinstance(itemAtView, GRPItem): - #Solver should be deleted - ## if there is change in 'Topology' of the model - ## or if copy has to made then oject should be in unZombify mode - mooseDeleteChemSolver(self.layoutPt.modelRoot) - #As name is suggesting, if item is Compartment, then search in qGraCompt and if group then qGraGrp - if isinstance(itemAtView,ComptItem): - lKey = [key for key, value in self.layoutPt.qGraCompt.iteritems() if value == itemAtView][0] - if isinstance (itemAtView, GRPItem): - lKey = [key for key, value in self.layoutPt.qGraGrp.iteritems() if value == itemAtView][0] + if isinstance(itemAtView, kkitQGraphics.ComptItem) \ + or isinstance(itemAtView, kkitQGraphics.GRPItem): + moose.mooseDeleteChemSolver(self.layoutPt.modelRoot) + + # As name is suggesting, if item is Compartment, then + # search in qGraCompt and if group then qGraGrp + if isinstance(itemAtView, kkitQGraphics.ComptItem): + lKey = [key for key, value in self.layoutPt.qGraCompt.iteritems() + if value == itemAtView][0] + if isinstance (itemAtView, kkitQGraphics.GRPItem): + lKey = [key for key, value in self.layoutPt.qGraGrp.iteritems() + if value == itemAtView][0] iR = 0 iP = 0 t = moose.element(cloneObj.parent().mobj) name = t.name - if isinstance(cloneObj.parent().mobj,PoolBase): - retValue = self.objExist(lKey.path,name,iP) - if retValue != None: + if isinstance(cloneObj.parent().mobj, moose.PoolBase): + retValue = self.objExist(lKey.path, name, iP) + if retValue is not None: name += retValue pmooseCp = moose.copy(t,lKey.path,name,1) if pmooseCp.path != '/': ct = moose.element(pmooseCp) concInit = pmooseCp.concInit[0] - #this is b'cos if pool copied across the comptartment, - #then it doesn't calculate nInit according but if one set - #concInit then it would, just a hack + # this is b'cos if pool copied across the comptartment, + # then it doesn't calculate nInit according but if one set + # concInit then it would, just a hack ct.concInit = concInit - #itemAtView = self.state["release"]["item"] poolObj = moose.element(ct) - poolinfo = moose.element(poolObj.path+'/info') - qGItem = PoolItem(poolObj,itemAtView) + poolinfo = moose.element( + poolObj.path + '/info') + qGItem = kkitQGraphics.PoolItem(poolObj, itemAtView) self.layoutPt.mooseId_GObj[poolObj] = qGItem - #bgcolor = getRandColor() - color,bgcolor = getColor(poolinfo) - qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),color,bgcolor) - self.emit(QtCore.SIGNAL("dropped"),poolObj) - - if isinstance(cloneObj.parent().mobj,ReacBase): - retValue = self.objExist(lKey.path,name,iR) - if retValue != None : + color, bgcolor = kkitUtil.getColor(poolinfo) + qGItem.setDisplayProperties( + posWrtComp.x(), posWrtComp.y(), color, bgcolor) + self.dropped.emit(poolObj) + + if isinstance(cloneObj.parent().mobj, moose.ReacBase): + retValue = self.objExist(lKey.path, name, iR) + if retValue is not None: name += retValue - rmooseCp = moose.copy(t,lKey.path,name,1) + rmooseCp = moose.copy(t, lKey.path, name, 1) if rmooseCp.path != '/': ct = moose.element(rmooseCp) reacObj = moose.element(ct) - reacinfo = moose.Annotator(reacObj.path+'/info') - qGItem = ReacItem(reacObj,itemAtView) + moose.Annotator(reacObj.path + '/info') + qGItem = kkitQGraphics.ReacItem(reacObj, itemAtView) self.layoutPt.mooseId_GObj[reacObj] = qGItem posWrtComp = self.mapToScene(event.pos()) qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),"white", "white") - self.emit(QtCore.SIGNAL("dropped"),reacObj) + self.dropped.emit(reacObj) self.updateScale(self.iconScale) else: - if itemAtView == None: - QtGui.QMessageBox.information(None,'Dropping Not possible ','Dropping not allowed outside the compartment',QtGui.QMessageBox.Ok) + if itemAtView is None: + QMessageBox.information( + None, + 'Dropping Not possible ', + 'Dropping not allowed outside the compartment', + QMessageBox.Ok) else: srcdesString = ((self.state["release"]["item"]).mobj).className - QtGui.QMessageBox.information(None,'Dropping Not possible','Dropping on \'{srcdesString}\' not allowed'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) + QMessageBox.information(None,'Dropping Not possible','Dropping on \'{srcdesString}\' not allowed'.format(srcdesString = srcdesString),QMessageBox.Ok) - if clickedItemType == CONNECTION: - popupmenu = QtGui.QMenu('PopupMenu', self) - popupmenu.addAction("Delete", lambda : self.deleteConnection(item)) + if clickedItemType == constants.CONNECTION: + popupmenu = QMenu('PopupMenu', self) + popupmenu.addAction("Delete", lambda: self.deleteConnection(item)) popupmenu.exec_(self.mapToGlobal(event.pos())) - if clickedItemType == COMPARTMENT_BOUNDARY or clickedItemType == GROUP_BOUNDARY: + if clickedItemType == constants.COMPARTMENT_BOUNDARY \ + or clickedItemType == constants.GROUP_BOUNDARY: if item != None: item.setSelected(True) if not self.state["move"]["happened"]: self.layoutPt.plugin.mainWindow.objectEditSlot(self.state["press"]["item"].mobj, True) self.resetState() - if clickedItemType == COMPARTMENT_INTERIOR or clickedItemType == GROUP_INTERIOR: + if clickedItemType == constants.COMPARTMENT_INTERIOR \ + or clickedItemType == constants.GROUP_INTERIOR: if self.state["move"]["happened"]: startingPosition = self.state["press"]["pos"] endingPosition = event.pos() - displacement = endingPosition - startingPosition - x0 = startingPosition.x() + displacement = endingPosition - startingPosition + x0 = startingPosition.x() x1 = endingPosition.x() - y0 = startingPosition.y() + y0 = startingPosition.y() y1 = endingPosition.y() - if displacement.x() < 0 : - x0,x1= x1,x0 + if displacement.x() < 0: + x0, x1 = x1, x0 if displacement.y() < 0 : y0,y1= y1,y0 @@ -580,17 +606,19 @@ def editorMouseReleaseEvent(self,event): self.selectedItems = selectedItems = self.items(x0,y0,abs(displacement.x()), abs(displacement.y())) self.selectSelections(selectedItems) for item in selectedItems: - if isinstance(item, KineticsDisplayItem) and not isinstance(item,ComptItem): + if isinstance( item, kkitQGraphics.KineticsDisplayItem) \ + and not isinstance( item, kkitQGraphics.ComptItem): item.setSelected(True) if self.customrubberBand != None: self.customrubberBand.hide() self.customrubberBand = None - popupmenu = QtGui.QMenu('PopupMenu', self) + popupmenu = QMenu('PopupMenu', self) popupmenu.addAction("Delete", lambda: self.deleteSelections(x0,y0,x1,y1)) popupmenu.addAction("Zoom", lambda: self.zoomSelections(x0,y0,x1,y1)) popupmenu.addAction("Move", lambda: self.moveSelections()) popupmenu.exec_(self.mapToGlobal(event.pos())) + self.resetState() def onClicked(self,modelRoot,element, btn): @@ -608,15 +636,11 @@ def onClicked(self,modelRoot,element, btn): else: plotType = "Conc" - tablePath = moose.utils.create_table_path(moose.element(self.modelRoot), self.graph, element, plotType) - table = moose.utils.create_table(tablePath, element, plotType,"Table2") - ''' - tablePath = utils.create_table_path(moose.element(self.modelRoot), self.graph, element, "Conc") - table = utils.create_table(tablePath, element, "Conc","Table2") - ''' + tablePath = moose.utils.create_table_path( + moose.element(self.modelRoot), self.graph, element, plotType) + moose.utils.create_table(tablePath, element, plotType,"Table2") self.layoutPt.plugin.view.getCentralWidget().plotWidgetContainer.plotAllData() - reply = QtGui.QMessageBox.information(self, "plot Object","Plot is added to Graph1", - QtGui.QMessageBox.Ok) + QMessageBox.information(self, "plot Object", "Plot is added to Graph1", QMessageBox.Ok) self.removeConnector() def objectpullback(self,messgtype,item,movedGraphObj,xx,yy): @@ -641,30 +665,30 @@ def objectpullback(self,messgtype,item,movedGraphObj,xx,yy): elif messgtype.lower() =="functionparent": messgstr = "The Function parent \'{0}\' doesn't exist in \'{2}\' {1} \n If you need to move the function to {1} first move the parent pool".format(movedGraphObj.mobj.parent.name,desObj,item.mobj.name) - QtGui.QMessageBox.warning(None,'Could not move the object', messgstr ) - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) + QMessageBox.warning(None,'Could not move the object', messgstr ) + QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) - def moveObjSceneParent(self,item,movedGraphObj,itempos,eventpos): + def moveObjSceneParent(self,item, movedGraphObj, itempos, eventpos): ''' Scene parent object needs to be updated ''' - if isinstance(movedGraphObj,FuncItem): + if isinstance(movedGraphObj, kkitQGraphics.FuncItem): return prevPar = movedGraphObj.parentItem() movedGraphObj.setParentItem(item) - if isinstance(movedGraphObj,ReacItem): + if isinstance(movedGraphObj, kkitQGraphics.ReacItem): for ll in self.layoutPt.object2line[movedGraphObj]: ll[0].setParentItem(item) moose.move(movedGraphObj.mobj, item.mobj) self.layoutPt.plugin.mainWindow.objectEditSlot(movedGraphObj.mobj, True) - if isinstance(movedGraphObj ,PoolItem): + if isinstance(movedGraphObj, moose.PoolItem): ''' if pool is moved, a check is made to see if this pool is parent of a enzyme if yes then Graphicalparent is changed, and not moose path since it will be taken care while we move pool ''' pl = (movedGraphObj.mobj).neighbors['nOut'] for es in pl: - if isinstance(moose.element(es), EnzBase): + if isinstance(moose.element(es), moose.EnzBase): if moose.element(moose.element(es).neighbors['enzDest'][0]) == movedGraphObj.mobj: enzGrapObj = self.layoutPt.mooseId_GObj[moose.element(es)] enzXpos = enzGrapObj.scenePos().x() @@ -680,74 +704,78 @@ def moveObjSceneParent(self,item,movedGraphObj,itempos,eventpos): self.setnewPostion(movedGraphObj,itempos,eventpos) self.layoutPt.updateArrow(movedGraphObj) self.layoutPt.positionChange(movedGraphObj.mobj) - if isinstance(prevPar,GRPItem): + if isinstance(prevPar, kkitQGraphics.GRPItem): if item != prevPar: self.layoutPt.updateGrpSize(prevPar) self.layoutPt.updateGrpSize(item) def setnewPostion(self,movedGraphObj,itempos,eventpos): - if isinstance(movedGraphObj,KineticsDisplayItem): + if isinstance(movedGraphObj, kkitQGraphics.KineticsDisplayItem): itemPath = movedGraphObj.mobj.path if moose.exists(itemPath): iInfo = itemPath+'/info' - anno = moose.Annotator(iInfo) + moose.Annotator(iInfo) x = eventpos.x()+(15/2)-itempos.x() y = eventpos.y()+(2/2)-itempos.y() - if isinstance(movedGraphObj,ReacItem) or isinstance(movedGraphObj,EnzItem) or isinstance(movedGraphObj,MMEnzItem): + if isinstance(movedGraphObj, kkitQGraphics.ReacItem) \ + or isinstance(movedGraphObj, kkitQGraphics.EnzItem) \ + or isinstance(movedGraphObj, kkitQGraphics.MMEnzItem): movedGraphObj.setGeometry(x,y, movedGraphObj.gobj.boundingRect().width(), movedGraphObj.gobj.boundingRect().height()) - elif isinstance(movedGraphObj,PoolItem): - movedGraphObj.setGeometry(x, y,movedGraphObj.gobj.boundingRect().width() - +PoolItem.fontMetrics.width(' '), + elif isinstance(movedGraphObj, moose.PoolItem): + movedGraphObj.setGeometry(x, y, movedGraphObj.gobj.boundingRect().width() + + moose.PoolItem.fontMetrics.width(' '), movedGraphObj.gobj.boundingRect().height()) - movedGraphObj.bg.setRect(0, 0, movedGraphObj.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '), movedGraphObj.gobj.boundingRect().height()) - QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) + movedGraphObj.bg.setRect(0, 0, + movedGraphObj.gobj.boundingRect().width() + moose.PoolItem.fontMetrics.width(' '), movedGraphObj.gobj.boundingRect().height()) + QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor)) def deleteGroup(self,item,layoutPt): - reply = QtGui.QMessageBox.question(self, "Deleting Object",'Do want to delete group \'{groupname}\' and its children and connections'.format(groupname=item.mobj.name), - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if reply == QtGui.QMessageBox.Yes: - mooseDeleteChemSolver(self.layoutPt.modelRoot) + reply = QMessageBox.question(self + , "Deleting Object" + , "Do want to delete group \ + '{}' and its children and connections".format(item.mobj.name) + , QMessageBox.Yes | QMessageBox.No + ) + if reply == QMessageBox.Yes: + moose.mooseDeleteChemSolver(self.layoutPt.modelRoot) key = [k for k,v in self.layoutPt.qGraGrp.items() if v == item] if key[0] in self.layoutPt.qGraGrp: self.layoutPt.qGraGrp.pop(key[0]) self.groupItemlist1 = item.childItems() - self.groupItemlist = [ i for i in self.groupItemlist1 if not isinstance(i,QtGui.QGraphicsPolygonItem)] + self.groupItemlist = [ i for i in self.groupItemlist1 if not isinstance(i, QGraphicsPolygonItem)] self.deleteObj(self.groupItemlist) self.deleteItem(item) def drawExpectedConnection(self, event): self.connectionSource = self.state["press"]["item"] - sourcePoint = self.connectionSource.mapToScene( + sourcePoint = self.connectionSource.mapToScene( self.connectionSource.boundingRect().center() - ) + ) destinationPoint = self.mapToScene(event.pos()) if self.expectedConnection is None: - self.expectedConnection = QGraphicsLineItem( sourcePoint.x() - , sourcePoint.y() - , destinationPoint.x() - , destinationPoint.y() - ) - self.expectedConnection.setPen(QPen(Qt.Qt.DashLine)) + self.expectedConnection = QGraphicsLineItem( + sourcePoint.x(), sourcePoint.y(), destinationPoint.x(), destinationPoint.y()) + self.expectedConnection.setPen(QtGui.QPen(Qt.Qt.DashLine)) self.sceneContainerPt.addItem(self.expectedConnection) else: - self.expectedConnection.setLine( sourcePoint.x() - , sourcePoint.y() - , destinationPoint.x() - , destinationPoint.y() - ) + self.expectedConnection.setLine( + sourcePoint.x(), + sourcePoint.y(), + destinationPoint.x(), + destinationPoint.y()) def removeExpectedConnection(self): self.sceneContainerPt.removeItem(self.expectedConnection) self.expectedConnection = None - self.connectionSource = None + self.connectionSource = None def removeConnector(self): try: - for l,k in self.connectorlist.items(): + for l, k in list(self.connectorlist.items()): if k is not None: self.sceneContainerPt.removeItem(k) self.connectorlist[l] = None @@ -760,34 +788,42 @@ def showConnector(self, item): self.connectionSource = item rectangle = item.boundingRect() - for l in self.connectorlist.keys(): + for l in list(self.connectorlist.keys()): self.xDisp = 0 self.yDisp = 0 self.connectionSign = None - if isinstance(item.mobj,PoolBase) or isinstance(item.mobj,ReacBase): + if isinstance(item.mobj, moose.PoolBase) \ + or isinstance(item.mobj, moose.ReacBase): if l == "clone": - self.connectionSign = QtSvg.QGraphicsSvgItem('icons/clone.svg') + self.connectionSign = QtSvg.QGraphicsSvgItem( + os.path.join(config.MOOSE_ICON_DIR, 'clone.svg') + ) self.connectionSign.setData(0, QtCore.QVariant("clone")) self.connectionSign.setParent(self.connectionSource) self.connectionSign.setScale( - (1.0 * rectangle.height()) / self.connectionSign.boundingRect().height() - ) + (1.0 * rectangle.height()) / + self.connectionSign.boundingRect().height() + ) position = item.mapToParent(rectangle.bottomLeft()) self.xDisp = 15 self.yDisp = 2 self.connectionSign.setZValue(1) - self.connectionSign.setToolTip("Click and drag to clone the object") - self.connectorlist["clone"] = self.connectionSign - - if isinstance(item.mobj,PoolBase): + self.connectionSign.setToolTip( + "Click and drag to clone the object") + self.connectorlist["clone"] = self.connectionSign + + if isinstance(item.mobj, moose.PoolBase): if l == "plot": - self.connectionSign = QtSvg.QGraphicsSvgItem('icons/plot.svg') + self.connectionSign = QtSvg.QGraphicsSvgItem( + os.path.join(config.MOOSE_ICON_DIR, 'plot.svg') + ) self.connectionSign.setData(0, QtCore.QVariant("plot")) self.connectionSign.setParent(self.connectionSource) self.connectionSign.setScale( - (1.0 * rectangle.height()) / self.connectionSign.boundingRect().height() - ) + (1.0 * rectangle.height()) / + self.connectionSign.boundingRect().height() + ) position = item.mapToParent(rectangle.bottomRight()) #self.xDisp = 15 #self.yDisp = 2 @@ -796,166 +832,179 @@ def showConnector(self, item): self.connectorlist["plot"] = self.connectionSign if l == "move": - if ((item.mobj.parent.className == "ZombieEnz") or (item.mobj.parent.className == "Enz")): + if ((item.mobj.parent.className == "ZombieEnz") + or (item.mobj.parent.className == "Enz")): pass else: - self.connectionSign = QtSvg.QGraphicsSvgItem('icons/move.svg') + self.connectionSign = QtSvg.QGraphicsSvgItem( + os.path.join(config.MOOSE_ICON_DIR, 'move.svg') + ) self.connectionSign.setData(0, QtCore.QVariant("move")) self.connectionSign.setParent(self.connectionSource) self.connectionSign.setToolTip("Drag to move.") - if ( item.mobj.className == "ZombieFunction" or item.mobj.className == "Function"): + if (item.mobj.className == + "ZombieFunction" or item.mobj.className == "Function"): self.connectionSign.setScale( - (0.75 * rectangle.height()) / self.connectionSign.boundingRect().height() - ) + (0.75 * rectangle.height()) / + self.connectionSign.boundingRect().height() + ) else: self.connectionSign.setScale( - (1 * rectangle.height()) / self.connectionSign.boundingRect().height() - ) + (1 * rectangle.height()) / + self.connectionSign.boundingRect().height() + ) position = item.mapToParent(rectangle.topLeft()) self.xDisp = 15 self.yDisp = 2 self.connectionSign.setZValue(1) self.connectorlist["move"] = self.connectionSign elif l == "delete": - if ((item.mobj.parent.className == "ZombieEnz") or (item.mobj.parent.className == "Enz")): + if ((item.mobj.parent.className == "ZombieEnz") + or (item.mobj.parent.className == "Enz")): pass else: - self.connectionSign = QtSvg.QGraphicsSvgItem('icons/delete.svg') + self.connectionSign = QtSvg.QGraphicsSvgItem( + os.path.join(config.MOOSE_ICON_DIR, 'delete.svg') + ) self.connectionSign.setParent(self.connectionSource) self.connectionSign.setData(0, QtCore.QVariant("delete")) - if ( item.mobj.className == "ZombieFunction" or item.mobj.className == "Function"): + if (item.mobj.className == + "ZombieFunction" or item.mobj.className == "Function"): self.connectionSign.setScale( - (0.75 * rectangle.height()) / self.connectionSign.boundingRect().height() - ) + (0.75 * rectangle.height()) / + self.connectionSign.boundingRect().height() + ) else: self.connectionSign.setScale( - (1.0 * rectangle.height()) / self.connectionSign.boundingRect().height() - ) + (1.0 * rectangle.height()) / + self.connectionSign.boundingRect().height() + ) position = item.mapToParent(rectangle.topRight()) self.connectionSign.setZValue(1) self.connectionSign.setToolTip("Delete the object") self.connectorlist["delete"] = self.connectionSign - if self.connectionSign != None: - self.connectionSign.setFlag(QtGui.QGraphicsItem.ItemIsSelectable,True) + if self.connectionSign is not None: + self.connectionSign.setFlag( + QGraphicsItem.ItemIsSelectable, True) self.connectionSign.setParentItem(item.parentItem()) - self.connectionSign.setPos(0.0,0.0) - self.connectionSign.moveBy( position.x()-self.xDisp - , position.y() +self.yDisp - rectangle.height() / 2.0 - ) + self.connectionSign.setPos(0.0, 0.0) + self.connectionSign.moveBy( + position.x() - self.xDisp, + position.y() + self.yDisp - rectangle.height() / 2.0) - def objExist(self,path,name,index): + def objExist(self, path, name, index): if index == 0: - fPath = path+'/'+name + fPath = path + '/' + name else: - fPath = path+'/'+name+'_'+str(index) + fPath = path + '/' + name + '_' + str(index) if moose.exists(fPath): index += 1 - return self.objExist(path,name,index) + return self.objExist(path, name, index) else: if index == 0: return else: - return ('_'+str(index)) + return ('_' + str(index)) def selectSelections(self, selections): - for selection in selections : - if isinstance(selection, KineticsDisplayItem): + for selection in selections: + if isinstance(selection, kkitQGraphics.KineticsDisplayItem): self.selections.append(selection) def deselectSelections(self): for selection in self.selections: selection.setSelected(False) - self.selections = [] + self.selections = [] def mousePressEvent(self, event): - selectedItem = None if self.viewBaseType == "editorView": return self.editorMousePressEvent(event) - - elif self.viewBaseType == "runView": + if self.viewBaseType == "runView": pos = event.pos() item = self.itemAt(pos) - if item: - itemClass = type(item).__name__ - if ( itemClass!='ComptItem' and itemClass != 'QGraphicsPolygonItem' and - itemClass != 'QGraphicsEllipseItem' and itemClass != 'QGraphicsRectItem'): - self.setCursor(Qt.Qt.CrossCursor) - mimeData = QtCore.QMimeData() - mimeData.setText(item.mobj.name) - mimeData.setData("text/plain", "") - mimeData.data =(self.modelRoot,item.mobj) - drag = QtGui.QDrag(self) - drag.setMimeData(mimeData) - dropAction = drag.start(QtCore.Qt.MoveAction) - self.setCursor(Qt.Qt.ArrowCursor) + if not item: + return + itemClass = type(item).__name__ + if itemClass in ['ComptItem', 'QGraphicsPolygonItem', + 'QGraphicsEllipseItem', 'QGraphicsRectItem' ]: + return + self.setCursor(Qt.Qt.CrossCursor) + mimeData = QtCore.QMimeData() + mimeData.setText(item.mobj.name) + mimeData.setData("text/plain", "") + mimeData.data = (self.modelRoot, item.mobj) + drag = QtGui.QGrag(self) + drag.setMimeData(mimeData) + drag.start(QtCore.Qt.MoveAction) + self.setCursor(Qt.Qt.ArrowCursor) - - def mouseMoveEvent(self,event): + def mouseMoveEvent(self, event): if self.viewBaseType == "editorView": return self.editorMouseMoveEvent(event) - def mouseReleaseEvent(self, event): if self.viewBaseType == "editorView": for preSelectedItem in self.sceneContainerPt.selectedItems(): preSelectedItem.setSelected(False) return self.editorMouseReleaseEvent(event) - - return - - if self.state["press"]["mode"] == CONNECTION: - desPos =self.mapToScene(event.pos()) - destination = self.items(event.pos()) - src = self.state["press"]["item"] - des = [j for j in destination if isinstance(j,KineticsDisplayItem)] - if len(des): - self.populate_srcdes(src.mobj,des[0].mobj) - self.setCursor(Qt.Qt.ArrowCursor) - QtGui.QGraphicsView.mouseReleaseEvent(self, event) + return None + # if self.state["press"]["mode"] == constants.CONNECTION: + # destination = self.items(event.pos()) + # src = self.state["press"]["item"] + # des = [ + # j for j in destination if isinstance(j, kkitQGraphics.KineticsDisplayItem)] + # if len(des): + # self.populate_srcdes(src.mobj,des[0].mobj) + # self.setCursor(Qt.Qt.ArrowCursor) + # QGraphicsView.mouseReleaseEvent(self, event) def updateItemTransformationMode(self, on): for v in self.sceneContainerPt.items(): - #v.setFlag(QtGui.QGraphicsItem.ItemIgnoresTransformations,on) - if( not isinstance(v,ComptItem)): - #if ( isinstance(v, PoolItem) or isinstance(v, ReacItem) or isinstance(v, EnzItem) or isinstance(v, CplxItem) ): - if isinstance(v,KineticsDisplayItem): - v.setFlag(QtGui.QGraphicsItem.ItemIgnoresTransformations, on) + if( not isinstance(v, kkitQGraphics.ComptItem)): + if isinstance(v, kkitQGraphics.KineticsDisplayItem): + v.setFlag(QGraphicsItem.ItemIgnoresTransformations, on) def keyPressEvent(self,event): key = event.key() self.removeConnector() - if (key == Qt.Qt.Key_A and (event.modifiers() & Qt.Qt.ShiftModifier)): # 'A' fits the view to iconScale factor + if (key == Qt.Qt.Key_A and (event.modifiers() & Qt.Qt.ShiftModifier)): itemignoreZooming = False self.updateItemTransformationMode(itemignoreZooming) - #self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio) self.layoutPt.drawLine_arrow(itemignoreZooming=False) - elif (key == Qt.Qt.Key_Less or key == Qt.Qt.Key_Minus):# and (event.modifiers() & Qt.Qt.ShiftModifier)): # '<' key. zooms-in to iconScale factor + # and (event.modifiers() & Qt.Qt.ShiftModifier)): # '<' key. zooms-in + # to iconScale factor + elif (key == Qt.Qt.Key_Less or key == Qt.Qt.Key_Minus): self.iconScale *= 0.8 - self.updateScale( self.iconScale ) + self.updateScale(self.iconScale) - elif (key == Qt.Qt.Key_Greater or key == Qt.Qt.Key_Plus):# and (event.modifiers() & Qt.Qt.ShiftModifier)): # '>' key. zooms-out to iconScale factor + # and (event.modifiers() & Qt.Qt.ShiftModifier)): # '>' key. zooms-out + # to iconScale factor + elif (key == Qt.Qt.Key_Greater or key == Qt.Qt.Key_Plus): self.iconScale *= 1.25 - self.updateScale( self.iconScale ) + self.updateScale(self.iconScale) - elif (key == Qt.Qt.Key_Period): # '.' key, lower case for '>' zooms in - self.scale(1.1,1.1) + elif (key == Qt.Qt.Key_Period): # '.' key, lower case for '>' zooms in + self.scale(1.1, 1.1) - elif (key == Qt.Qt.Key_Comma): # ',' key, lower case for '<' zooms in - self.scale(1/1.1,1/1.1) + elif (key == Qt.Qt.Key_Comma): # ',' key, lower case for '<' zooms in + self.scale(1 / 1.1, 1 / 1.1) elif (key == Qt.Qt.Key_A): # 'a' fits the view to initial value where iconscale=1 self.iconscale = 1 self.updateScale( 1 ) - self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio) + self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10 + , self.sceneContainerPt.itemsBoundingRect().y()-10 + , self.sceneContainerPt.itemsBoundingRect().width()+20 + , self.sceneContainerPt.itemsBoundingRect().height()+20 + , Qt.Qt.IgnoreAspectRatio) + def updateScale( self, scale ): for item in self.sceneContainerPt.items(): - if isinstance(item,KineticsDisplayItem): + if isinstance(item, kkitQGraphics.KineticsDisplayItem): item.refresh(scale) - xpos = item.pos().x() - ypos = item.pos().y() self.layoutPt.drawLine_arrow(itemignoreZooming=False) self.layoutPt.comptChildrenBoundingRect() @@ -963,17 +1012,20 @@ def moveSelections(self): self.setCursor(Qt.Qt.CrossCursor) self.move = True return - + def GrVfitinView(self): itemignoreZooming = False self.layoutPt.updateItemTransformationMode(itemignoreZooming) - self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio) + self.fitInView( + self.sceneContainerPt.itemsBoundingRect().x() - 10, + self.sceneContainerPt.itemsBoundingRect().y() - 10, + self.sceneContainerPt.itemsBoundingRect().width() + 20, + self.sceneContainerPt.itemsBoundingRect().height() + 20, + Qt.Qt.IgnoreAspectRatio) self.layoutPt.drawLine_arrow(itemignoreZooming=False) def deleteSelections(self,x0,y0,x1,y1): if( x1-x0 > 0 and y1-y0 >0): - # self.rubberbandlist = self.sceneContainerPt.items(self.mapToScene(QtCore.QRect(x0, y0, x1 - x0, y1 - y0)).boundingRect(), Qt.Qt.IntersectsItemShape) - # for unselectitem in self.rubberbandlist: self.rubberbandlist_qpolygon = [] for unselectitem in self.rubberbandlist_qpolygon: if unselectitem.isSelected() == True: @@ -981,7 +1033,7 @@ def deleteSelections(self,x0,y0,x1,y1): self.rubberbandlist_qpolygon = self.sceneContainerPt.items(self.mapToScene(QtCore.QRect(x0, y0, x1 - x0, y1 - y0)).boundingRect(), Qt.Qt.IntersectsItemShape) for item in self.rubberbandlist_qpolygon: ''' in RubberbandSelection if entire group object contains then group is removed,if partly selected then group is retained''' - if isinstance(item,GRPItem): + if isinstance(item, kkitQGraphics.GRPItem): if not (self.mapToScene(QtCore.QRect(x0, y0, x1 - x0, y1 - y0)).boundingRect()).contains(item.sceneBoundingRect()): self.rubberbandlist_qpolygon.remove(item) @@ -990,17 +1042,23 @@ def deleteSelections(self,x0,y0,x1,y1): def deleteObj(self,item): self.rubberbandlist = item - mooseDeleteChemSolver(self.layoutPt.modelRoot) - self.list_EnzReccplx = [ i for i in self.rubberbandlist if (isinstance(i,MMEnzItem) or isinstance(i,EnzItem) or isinstance(i,CplxItem) or isinstance(i,ReacItem) )] - self.list_PFS = [ i for i in self.rubberbandlist if (isinstance(i,PoolItem) or isinstance(i,TableItem) or isinstance(i,FuncItem) )] - self.grp = [ i for i in self.rubberbandlist if isinstance(i,GRPItem)] + moose.mooseDeleteChemSolver(self.layoutPt.modelRoot) + self.list_EnzReccplx = [ i for i in self.rubberbandlist if + (isinstance(i, moose.MMEnzItem) or isinstance(i, moose.EnzItem) + or isinstance(i, moose.CplxItem) or isinstance(i, moose.ReacItem) )] + self.list_PFS = [ i for i in self.rubberbandlist if + (isinstance(i, moose.PoolItem) or isinstance(i, + kkitQGraphics.TableItem) or isinstance(i, kkitQGraphics.FuncItem) )] + self.grp = [ i for i in self.rubberbandlist if isinstance(i, + kkitQGraphics.GRPItem) ] for item in self.list_EnzReccplx: #First Loop to remove all the enz b'cos if parent (which is a Pool) is removed, #then it will created problem at qgraphicalitem not having parent. #So first delete enz, then Reac and then delete pool self.deleteItem(item) for item in self.list_PFS: - if isinstance(item,PoolItem) or isinstance(item,BufPool): + if isinstance(item, moose.PoolItem) \ + or isinstance(item, moose.BufPool): plot = moose.wildcardFind(self.layoutPt.modelRoot+'/data/graph#/#') for p in plot: if len(p.neighbors['requestOut']): @@ -1014,43 +1072,43 @@ def deleteObj(self,item): if key[0] in self.layoutPt.qGraGrp: self.layoutPt.qGraGrp.pop(key[0]) self.groupItemlist1 = item.childItems() - self.groupItemlist = [ i for i in self.groupItemlist1 if not isinstance(i,QtGui.QGraphicsPolygonItem)] + self.groupItemlist = [ i for i in self.groupItemlist1 if not isinstance(i,QGraphicsPolygonItem)] self.deleteObj(self.groupItemlist) self.deleteItem(item) def deleteObject2line(self,qpolygonline,src,des,endt): object2lineInfo = self.layoutPt.object2line[des] if len(object2lineInfo) == 1: - for polygon,objdes,endtype,numL in object2lineInfo: + for polygon, objdes, endtype, numL in object2lineInfo: if polygon == qpolygonline and objdes == src and endtype == endt: del(self.layoutPt.object2line[des]) else: print( " check this condition when is len is single and else condition",qpolygonline, objdes,endtype) else: n = 0 - for polygon,objdes,endtype,numL in object2lineInfo: + for polygon, objdes, endtype, numL in object2lineInfo: if polygon == qpolygonline and objdes == src and endtype == endt: - tup = object2lineInfo[:n]+object2lineInfo[n+1:] + tup = object2lineInfo[:n] + object2lineInfo[n + 1:] self.layoutPt.object2line[des] = tup - #d[keyNo].append((a,b,c)) + # d[keyNo].append((a,b,c)) else: n = n+1 def deleteConnection(self,item): #Delete moose connection, i.e one can click on connection arrow and delete the connection - reply = QtGui.QMessageBox.question(self, "Deleting Object","Do want to delete object and its connections", - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if reply == QtGui.QMessageBox.Yes: - mooseDeleteChemSolver(self.layoutPt.modelRoot) + reply = QMessageBox.question(self, "Deleting Object","Do want to delete object and its connections", + QMessageBox.Yes | QMessageBox.No) + if reply == QMessageBox.Yes: + moose.mooseDeleteChemSolver(self.layoutPt.modelRoot) msgIdforDeleting = " " - if isinstance(item,QtGui.QGraphicsPolygonItem): + if isinstance(item, QGraphicsPolygonItem): src = self.layoutPt.lineItem_dict[item] lineItem_value = self.layoutPt.lineItem_dict[item] i = iter(lineItem_value) source = i.next() destination = i.next() endt = i.next() - numl = i.next() + i.next() self.deleteObject2line(item,source,destination,endt) self.deleteObject2line(item,destination,source,endt) try: @@ -1073,7 +1131,7 @@ def deleteConnection(self,item): if src[2] == "t": if msg.destFieldsOnE2[0] == "enzDest": # delete indivial msg if later adding parent is possible - # msgIdforDeleting = msg + # msgIdforDeleting = msg # moose.delete(msgIdforDeleting) # self.sceneContainerPt.removeItem(item) self.deleteItem(gItem) @@ -1082,7 +1140,7 @@ def deleteConnection(self,item): self.getMsgId(src,srcZero,srcOne,item) moose.delete(msgIdforDeleting) self.sceneContainerPt.removeItem(item) - setupItem(self.modelRoot,self.layoutPt.srcdesConnection) + modelBuild.setupItem(self.modelRoot,self.layoutPt.srcdesConnection) for msg in moose.element(srcZero[0].parent).msgIn: if moose.element(msg.e2.path) == moose.element(srcZero[0].parent.path): if src[2] == 't': @@ -1130,12 +1188,12 @@ def deleteConnection(self,item): else: pass - def deleteSceneObj(self,msgIdforDeleting,item): + def deleteSceneObj(self, msgIdforDeleting, item): moose.delete(msgIdforDeleting) self.sceneContainerPt.removeItem(item) - setupItem(self.modelRoot,self.layoutPt.srcdesConnection) + modelBuild.setupItem(self.modelRoot, self.layoutPt.srcdesConnection) - def getMsgId(self,src,srcZero,srcOne,item): + def getMsgId(self, src, srcZero, srcOne, item): for msg in srcZero[0].msgOut: msgIdforDeleting = " " if moose.element(msg.e2.path) == moose.element(srcOne[0].path): @@ -1143,69 +1201,75 @@ def getMsgId(self,src,srcZero,srcOne,item): # substrate connection for R,E if msg.srcFieldsOnE1[0] == "subOut": msgIdforDeleting = msg - self.deleteSceneObj(msgIdforDeleting,item) + self.deleteSceneObj(msgIdforDeleting, item) return elif src[2] == 'p': # product connection for R,E if msg.srcFieldsOnE1[0] == "prdOut": msgIdforDeleting = msg - self.deleteSceneObj(msgIdforDeleting,item) - return + self.deleteSceneObj(msgIdforDeleting, item) + return elif src[2] == 't': if msg.srcFieldsOnE1[0] == "enzOut": - gItem =self.layoutPt.mooseId_GObj[moose.element(srcZero[0])] + gItem = self.layoutPt.mooseId_GObj[ + moose.element(srcZero[0])] self.deleteItem(gItem) return elif src[2] == 'tab': - #stimulation Table connection + # stimulation Table connection if msg.srcFieldsOnE1[0] == "output": msgIdforDeleting = msg - self.deleteSceneObj(msgIdforDeleting,item) - return - - def deleteItem(self,item): - #delete Items + self.deleteSceneObj(msgIdforDeleting, item) + return + def deleteItem(self, item): + # delete Items self.layoutPt.plugin.mainWindow.objectEditSlot('/', False) - if isinstance(item,KineticsDisplayItem) or isinstance(item,GRPItem): + if isinstance(item, kkitQGraphics.KineticsDisplayItem) \ + or isinstance(item, kkitQGraphics.GRPItem): if moose.exists(item.mobj.path): - if isinstance(item,PoolItem) or isinstance(item,BufPool): + if isinstance(item, moose.PoolItem) or isinstance(item, moose.BufPool): # pool is item is removed, then check is made if its a parent to any # enz if 'yes', then enz and its connection are removed before # removing Pool for items in moose.element(item.mobj.path).children: - if isinstance(moose.element(items), EnzBase): - gItem = self.layoutPt.mooseId_GObj[moose.element(items)] + if isinstance(moose.element(items), moose.EnzBase): + gItem = self.layoutPt.mooseId_GObj[ + moose.element(items)] for l in self.layoutPt.object2line[gItem]: # Need to check if the connection on the scene exist # or its removed from some other means - # E.g Enz to pool and pool to Enz is connected, - # when enz is removed the connection is removed, - # but when pool tried to remove then qgraphicscene says + # E.g Enz to pool and pool to Enz is connected, + # when enz is removed the connection is removed, + # but when pool tried to remove then qgraphicscene says # "item scene is different from this scene" - sceneItems = self.sceneContainerPt.items() + sceneItems = list( + self.sceneContainerPt.items()) if l[0] in sceneItems: - #deleting the connection which is connected to Enz + # deleting the connection which is + # connected to Enz self.sceneContainerPt.removeItem(l[0]) moose.delete(items) self.sceneContainerPt.removeItem(gItem) - #If pool/bufpool is input to a function and if pool/bufpool is removed then function is also removed. + # If pool/bufpool is input to a function and if + # pool/bufpool is removed then function is also removed. for msg in moose.element(item.mobj.path).msgOut: - if (moose.element(msg.e2.path).className == "Variable" and msg.destFieldsOnE2[0]=="input"): + if (moose.element(msg.e2.path).className == + "Variable" and msg.destFieldsOnE2[0] == "input"): funcp = moose.element(msg.e2.path).parent - pool = moose.element(funcp).parent self.deleteItem(self.layoutPt.mooseId_GObj[funcp]) for l in self.layoutPt.object2line[item]: - sceneItems = self.sceneContainerPt.items() + sceneItems = list(self.sceneContainerPt.items()) if l[0] in sceneItems: self.sceneContainerPt.removeItem(l[0]) self.sceneContainerPt.removeItem(item) moose.delete(item.mobj) - for key, value in self.layoutPt.object2line.items(): - self.layoutPt.object2line[key] = filter( lambda tup: tup[1] != item ,value) + for key, value in list(self.layoutPt.object2line.items()): + self.layoutPt.object2line[key] = [ + tup for tup in value if tup[1] != item] self.layoutPt.getMooseObj() - setupItem(self.modelRoot,self.layoutPt.srcdesConnection) + kkitOrdinateUtil.setupItem(self.modelRoot, self.layoutPt.srcdesConnection) def zoomSelections(self, x0, y0, x1, y1): p0 = self.mapToScene(x0, y0) @@ -1213,13 +1277,13 @@ def zoomSelections(self, x0, y0, x1, y1): self.fitInView(QtCore.QRectF(p0, p1), Qt.Qt.KeepAspectRatio) self.deselectSelections() return - - def wheelEvent(self,event): - factor = 1.41 ** (event.delta() / 240.0) + def wheelEvent(self, event): + pD = event.angleDelta().y() + factor = 1.41 ** (pD / 240.0) + logger_.debug( "WheelEvent %s and factor: %s" % (pD, factor)) self.scale(factor, factor) - def dragEnterEvent(self, event): if self.viewBaseType == "editorView": if event.mimeData().hasFormat('text/plain'): @@ -1234,41 +1298,55 @@ def dragMoveEvent(self, event): else: pass - def eventFilter(self, source, event): - if self.viewBase == "editorView": - if (event.type() == QtCore.QEvent.Drop): - pass - else: - pass - def dropEvent(self, event): - """Insert an element of the specified class in drop location""" - """ Pool and reaction should have compartment as parent, dropping outside the compartment is not allowed """ - """ Enz should be droped on the PoolItem which inturn will be under compartment""" + """Insert an element of the specified class in drop location + + Pool and reaction should have compartment as parent, dropping outside + the compartment is not allowed. + + Enz should be droped on the PoolItem which inturn will be under compartment + + """ if self.viewBaseType == "editorView": if not event.mimeData().hasFormat('text/plain'): + logger_.warn("MIMEData is not text/plain. Doing nothing ...") return event_pos = event.pos() string = str(event.mimeData().text()) - createObj(self.viewBaseType,self,self.modelRoot,string,event_pos,self.layoutPt) + modelBuild.createObj( + self.viewBaseType, + self, + self.modelRoot, + string, + event_pos, + self.layoutPt + ) + else: + logger_.debug("Not in editorView ") + return - def populate_srcdes(self,src,des): + def populate_srcdes(self, src, des): self.modelRoot = self.layoutPt.modelRoot callsetupItem = True - #print " populate_srcdes ",src,des - srcClass = moose.element(src).className + # print " populate_srcdes ",src,des + srcClass = moose.element(src).className if 'Zombie' in srcClass: srcClass = srcClass.split('Zombie')[1] desClass = moose.element(des).className if 'Zombie' in desClass: desClass = desClass.split('Zombie')[1] - if ( isinstance(moose.element(src),PoolBase) and ( (isinstance(moose.element(des),ReacBase) ) or isinstance(moose.element(des),EnzBase) )): - #If one to tries to connect pool to Reac/Enz (substrate to Reac/Enz), check if already (product to Reac/Enz) exist. - #If exist then connection not allowed one need to delete the msg and try connecting back. - #And in moose Enzyme can't have 2nd order reaction. + if ( isinstance(moose.element(src), moose.PoolBase) + and ( + (isinstance(moose.element(des), moose.ReacBase) ) + or isinstance(moose.element(des), moose.EnzBase))): + # If one to tries to connect pool to Reac/Enz (substrate to + # Reac/Enz), check if already (product to Reac/Enz) exist. + # If exist then connection not allowed one need to delete the msg + # and try connecting back. + # And in moose Enzyme can't have 2nd order reaction. founds, foundp = False,False - if isinstance(moose.element(des),EnzBase): + if isinstance(moose.element(des), moose.EnzBase): if len(moose.element(des).neighbors["subOut"]) > 0: founds = True @@ -1282,78 +1360,101 @@ def populate_srcdes(self,src,des): moose.connect(des, 'sub', src, 'reac', 'OneToOne') elif foundp: srcdesString = srcClass+' is already connected as '+ '\'Product\''+' to '+desClass +' \n \nIf you wish to connect this object then first delete the exist connection' - QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) + QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QMessageBox.Ok) elif founds: srcdesString = desClass+' has already connected to a'+ '\'Substrate\''+' \n \nIn moose Enzyme\'s can not have second order reaction. If you wish to connect this object then first delete the exist connection' - QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) + QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QMessageBox.Ok) - elif (isinstance (moose.element(src),PoolBase) and (isinstance(moose.element(des),Function))): + elif (isinstance (moose.element(src), moose.PoolBase) and + (isinstance(moose.element(des), moose.Function))): numVariables = des.numVars expr = "" - expr = (des.expr+'+'+'x'+str(numVariables)) + expr = (des.expr + '+' + 'x' + str(numVariables)) expr = expr.lstrip("0 +") - expr = expr.replace(" ","") + expr = expr.replace(" ", "") des.expr = expr - moose.connect( src, 'nOut', des.x[numVariables], 'input' ) - - elif ( isinstance(moose.element(src),Function) and (moose.element(des).className=="Pool") or - isinstance(moose.element(src),ZombieFunction) and (moose.element(des).className=="ZombiePool") - ): - if ((element(des).parent).className != 'Enz'): - #moose.connect(src, 'valueOut', des, 'increment', 'OneToOne') - found = False - if len(moose.element(src).neighbors["valueOut"]): - for psl in moose.element(src).neighbors["valueOut"]: - if moose.element(psl) == moose.element(des): - found = True - if found == False: - moose.connect(src, 'valueOut', des, 'setN', 'OneToOne') - else: - srcdesString = '\"'+moose.element(src).name+'\" is already connected to \"'+ moose.element(des).name +'\" \n' - QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) - - + moose.connect(src, 'nOut', des.x[numVariables], 'input') + + elif (isinstance(moose.element(src), moose.Function) and + (moose.element(des).className == "Pool") + or isinstance(moose.element(src), moose.ZombieFunction) and + (moose.element(des).className == "ZombiePool") + ): + if ((moose.element(des).parent).className != 'Enz'): + found = False + if len(moose.element(src).neighbors["valueOut"]): + for psl in moose.element(src).neighbors["valueOut"]: + if moose.element(psl) == moose.element(des): + found = True + if not found: + moose.connect(src, 'valueOut', des, 'setN', 'OneToOne') else: - srcdesString = element(src).className+'-- EnzCplx' - QtGui.QMessageBox.information(None,'Connection Not possible','\'{srcdesString}\' not allowed to connect'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) + srcdesString = moose.element(src).className+'-- EnzCplx' + QMessageBox.information(None + , 'Connection Not possible','\'{}\' not allowed to connect'.format(srcdesString) + , QMessageBox.Ok + ) callsetupItem = False - elif ( isinstance(moose.element(src),Function) and (moose.element(des).className=="BufPool") or - isinstance(moose.element(src),ZombieFunction) and (moose.element(des).className=="ZombieBufPool") + elif (isinstance(moose.element(src), moose.Function) and + (moose.element(des).className=="BufPool") + or isinstance(moose.element(src), moose.ZombieFunction) and + (moose.element(des).className=="ZombieBufPool") ): moose.connect(src, 'valueOut', des, 'setN', 'OneToOne') - elif ( isinstance(moose.element(src),Function) and (isinstance(moose.element(des),ReacBase) ) or - isinstance(moose.element(src),ZombieFunction) and (moose.element(des).className=="ZombieReac") + elif ( isinstance(moose.element(src), moose.Function) and + (isinstance(moose.element(des), moose.ReacBase)) + or isinstance(moose.element(src), moose.ZombieFunction) and + (moose.element(des).className=="ZombieReac") ): moose.connect(src, 'valueOut', des, 'setNumKf', 'OneToOne') - elif (((isinstance(moose.element(src),ReacBase))or (isinstance(moose.element(src),EnzBase))) and (isinstance(moose.element(des),PoolBase))): - founds,foundp = False,False - if isinstance(moose.element(src),EnzBase): + elif ((isinstance(moose.element(src), moose.ReacBase) \ + or isinstance(moose.element(src), moose.EnzBase)) \ + and isinstance(moose.element(des), moose.PoolBase)): + founds, foundp = False, False + if isinstance(moose.element(src), moose.EnzBase): if len(moose.element(src).neighbors["prdOut"]) > 0: foundp = True - for msg in src.msgOut: if moose.element(msg.e2.path) == des: if msg.srcFieldsOnE1[0] == "subOut": founds = True if founds == False and foundp == False: - #moose.connect(src, 'prd', des, 'reac', 'OneToOne') moose.connect(src, 'prd', des, 'reac', 'OneToOne') elif foundp: - srcdesString = srcClass+' is already connected as '+ '\'Product\''+' to '+desClass +' \n \nIn moose Enzyme\'s can not have second order reaction. If you wish to connect this object then first delete the exist connection' - QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) + srcdesString = srcClass + ' is already connected as ' \ + + "'Product' + to {}\n\n'".format(desClass) + \ + 'In MOOSE, Enzyme\'s can not have second order reaction.'+\ + ' If you wish to connect this object then first delete'+\ + ' the existing connection.' + QMessageBox.information( None + , 'Connection Not possible','{}'.format(srcdesString) + , QMessageBox.Ok + ) elif founds: - srcdesString = desClass+' is already connected as '+'\'Substrate\''+' to '+srcClass +' \n \nIf you wish to connect this object then first delete the exist connection' - QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) - elif( isinstance(moose.element(src),StimulusTable) and (isinstance(moose.element(des),PoolBase) ) ): + srcdesString = desClass+' is already connected as '+\ + '\'Substrate\''+' to '+srcClass +\ + ' \n\nIf you wish to connect this object '+\ + ' then first delete the exist connection.' + QMessageBox.information(None + ,'Connection Not possible' + , srcdesString + , QMessageBox.Ok) + elif( isinstance(moose.element(src), moose.StimulusTable) \ + and (isinstance(moose.element(des), moose.PoolBase)) + ): moose.connect(src, 'output', des, 'setConcInit', 'OneToOne') else: srcString = moose.element(src).className desString = moose.element(des).className - srcdesString = srcString+'--'+desString - QtGui.QMessageBox.information(None,'Connection Not possible','\'{srcdesString}\' not allowed to connect'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok) + srcdesString = srcString + '--' + desString + QMessageBox.information( + None, + 'Connection Not possible', + '\'{}\' not allowed to connect'.format(srcdesString), + QMessageBox.Ok) callsetupItem = False - + if callsetupItem: self.layoutPt.getMooseObj() - setupItem(self.modelRoot,self.layoutPt.srcdesConnection) + kkitOrdinateUtil.setupItem(self.modelRoot,self.layoutPt.srcdesConnection) self.layoutPt.drawLine_arrow(False) diff --git a/plugins/list.txt b/moosegui/plugins/list.txt similarity index 93% rename from plugins/list.txt rename to moosegui/plugins/list.txt index c3e68ca..7eaf8f2 100644 --- a/plugins/list.txt +++ b/moosegui/plugins/list.txt @@ -1,3 +1,2 @@ kkit NeuroKit - diff --git a/moosegui/plugins/modelBuild.py b/moosegui/plugins/modelBuild.py new file mode 100644 index 0000000..3a12a9f --- /dev/null +++ b/moosegui/plugins/modelBuild.py @@ -0,0 +1,359 @@ +# -*- coding: utf-8 -*- + +__author__ = "Harsha Rani" +__credits__ = ["Upi Lab"] +__license__ = "GPLv3" +__maintainer__ = "Harsha Rani, Dilawar Singh" +__email__ = "hrani@ncbs.res.in" + +import moose +from moosegui.plugins import kkitQGraphics +from moosegui.plugins import kkitUtil +from PyQt5 import Qt, QtCore +from PyQt5 import QtGui +from PyQt5.QtWidgets import QGraphicsScene, QMessageBox + +import logging +logger_ = logging.getLogger("moosegui.plugin.kkit") + +def updateCompartmentSize(qGraCompt): + #childBoundingRect = qGraCompt.childrenBoundingRect() + childBoundingRect = kkitUtil.calculateChildBoundingRect(qGraCompt) + comptBoundingRect = qGraCompt.boundingRect() + rectcompt = comptBoundingRect.united(childBoundingRect) + comptPen = qGraCompt.pen() + comptWidth = 1 + comptPen.setWidth(comptWidth) + qGraCompt.setPen(comptPen) + if not comptBoundingRect.contains(childBoundingRect): + qGraCompt.setRect(rectcompt.x() - comptWidth, + rectcompt.y() - comptWidth, + rectcompt.width() + (comptWidth * 2), + rectcompt.height() + (comptWidth * 2)) + + +def checkCreate(scene, view, modelpath, mobj, string, ret_string, num, + event_pos, layoutPt): + # The variable 'compt' will be empty when dropping cubeMesh,cyclMesh, + # but rest it shd be compartment + logger_.debug( "checkCreate is called") + if moose.exists(modelpath + '/info'): + moose.Annotator((moose.element(modelpath + '/info'))).modeltype + itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos)) + pos = view.mapToScene(event_pos) + modelpath = moose.element(modelpath) + if num: + string_num = ret_string + str(num) + else: + string_num = ret_string + if string == "CubeMesh" or string == "CylMesh": + if string == "CylMesh": + mobj = moose.CylMesh(modelpath.path + '/' + string_num) + else: + mobj = moose.CubeMesh(modelpath.path + '/' + string_num) + + mobj.volume = 1e-15 + qGItem = kkitQGraphics.ComptItem(scene, + pos.toPoint().x(), + pos.toPoint().y(), 100, 100, mobj) + qGItem.setPen( + QtGui.QPen(Qt.QColor(66, 66, 66, 100), 1, Qt.Qt.SolidLine, + Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) + view.sceneContainerPt.addItem(qGItem) + + qGItem.cmptEmitter.connect( + qGItem.cmptEmitter, + QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"), + layoutPt.positionChange1) + + qGItem.cmptEmitter.connect( + qGItem.cmptEmitter, + QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"), + layoutPt.objectEditSlot) + layoutPt.qGraCompt[mobj] = qGItem + + # Attach a drop signal. + qGItem.dropped.emit() + + elif string == "Pool" or string == "BufPool": + #getting pos with respect to compartment otherwise if compartment is moved then pos would be wrong + posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() + if string == "Pool": + poolObj = moose.Pool(mobj.path + '/' + string_num) + else: + poolObj = moose.BufPool(mobj.path + '/' + string_num) + + poolinfo = moose.Annotator(poolObj.path + '/info') + + qGItem = kkitQGraphics.PoolItem(poolObj, itemAtView) + layoutPt.mooseId_GObj[poolObj] = qGItem + posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() + bgcolor = kkitUtil.getRandColor() + qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(), + QtGui.QColor('green'), bgcolor) + poolinfo.color = str(bgcolor.getRgb()) + qGItem.dropped.emit() + + kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection) + layoutPt.drawLine_arrow(False) + x, y = roundoff(qGItem.scenePos(), layoutPt) + poolinfo.x = x + poolinfo.y = y + #Dropping is on compartment then update Compart size + if isinstance(mobj, moose.ChemCompt): + compt = layoutPt.qGraCompt[moose.element(mobj)] + updateCompartmentSize(compt) + + elif string == "Reac": + posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() + reacObj = moose.Reac(mobj.path + '/' + string_num) + reacinfo = moose.Annotator(reacObj.path + '/info') + qGItem = kkitQGraphics.ReacItem(reacObj, itemAtView) + qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(), "white", + "white") + layoutPt.mooseId_GObj[reacObj] = qGItem + qGItem.dopped.emit() + # view.emit(QtCore.SIGNAL("dropped"), reacObj) + kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection) + layoutPt.drawLine_arrow(False) + #Dropping is on compartment then update Compart size + if isinstance(mobj, moose.ChemCompt): + compt = layoutPt.qGraCompt[moose.element(mobj)] + updateCompartmentSize(compt) + x, y = roundoff(qGItem.scenePos(), layoutPt) + reacinfo.x = x + reacinfo.y = y + + elif string == "StimulusTable": + posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() + tabObj = moose.StimulusTable(mobj.path + '/' + string_num) + tabinfo = moose.Annotator(tabObj.path + '/info') + qGItem = kkitQGraphics.TableItem(tabObj, itemAtView) + qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(), + QtGui.QColor('white'), + QtGui.QColor('white')) + layoutPt.mooseId_GObj[tabObj] = qGItem + qGItem.dropped.emit() + # view.emit(QtCore.SIGNAL("dropped"), tabObj) + kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection) + layoutPt.drawLine_arrow(False) + # Dropping is on compartment then update Compart size + if isinstance(mobj, moose.ChemCompt): + compt = layoutPt.qGraCompt[moose.element(mobj)] + updateCompartmentSize(compt) + x, y = roundoff(qGItem.scenePos(), layoutPt) + tabinfo.x = x + tabinfo.y = y + + elif string == "Function": + posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() + funcObj = moose.Function(mobj.path + '/' + string_num) + funcinfo = moose.Annotator(funcObj.path + '/info') + #moose.connect( funcObj, 'valueOut', mobj ,'setN' ) + poolclass = ["ZombieBufPool", "BufPool"] + comptclass = ["CubeMesh", "cyclMesh"] + + if mobj.className in poolclass: + funcParent = layoutPt.mooseId_GObj[moose.element(mobj.path)] + elif mobj.className in comptclass: + funcParent = layoutPt.qGraCompt[moose.element(mobj)] + posWrtComp = funcParent.mapFromScene(pos).toPoint() + elif mobj.className in "Neutral": + funcParent = layoutPt.qGraGrp[moose.element(mobj)] + + qGItem = kkitQGraphics.FuncItem(funcObj, funcParent) + qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(), + QtGui.QColor('red'), QtGui.QColor('green')) + layoutPt.mooseId_GObj[funcObj] = qGItem + qGItem.dropped.emit() + # view.emit(QtCore.SIGNAL("dropped"), funcObj) + kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection) + layoutPt.drawLine_arrow(False) + #Dropping is on compartment then update Compart size + mooseCmpt = findCompartment(mobj) + if isinstance(mooseCmpt, moose.ChemCompt): + compt = layoutPt.qGraCompt[moose.element(mooseCmpt)] + updateCompartmentSize(compt) + x, y = roundoff(qGItem.scenePos(), layoutPt) + funcinfo.x = x + funcinfo.y = y + + elif string == "Enz" or string == "MMenz": + # FIXME: If 2 enz has same pool parent, then pos of the 2nd enz shd be + # displaced by some position, need to check how to deal with it + posWrtComp = pos + if ((mobj.parent).className == "Enz"): + QMessageBox.information( + None, "Drop Not possible", + "'{}' has to have Pool as its parent and not Enzyme Complex". + format(string), QMessageBox.Ok) + return None + else: + enzparent = findCompartment(mobj) + parentcompt = layoutPt.qGraCompt[enzparent] + if string == "Enz": + enzObj = moose.Enz(moose.element(mobj).path + '/' + string_num) + enzinfo = moose.Annotator(enzObj.path + '/info') + moose.connect(enzObj, 'enz', mobj, 'reac') + qGItem = kkitQGraphics.EnzItem(enzObj, parentcompt) + layoutPt.mooseId_GObj[enzObj] = qGItem + posWrtComp = pos + bgcolor = kkitUtil.getRandColor() + qGItem.setDisplayProperties(posWrtComp.x(), + posWrtComp.y() - 40, + QtGui.QColor('green'), bgcolor) + x, y = roundoff(qGItem.scenePos(), layoutPt) + enzinfo.x = x + enzinfo.y = y + enzinfo.color = str(bgcolor.name()) + enzinfo.textColor = str(QtGui.QColor('green').name()) + moose.Annotator(enzinfo) + Enz_cplx = enzObj.path + '/' + string_num + '_cplx' + cplxItem = moose.Pool(Enz_cplx) + moose.Annotator(cplxItem.path + '/info') + qGEnz = layoutPt.mooseId_GObj[enzObj] + kkitQGraphics.CplxItem(cplxItem, qGEnz) + layoutPt.mooseId_GObj[cplxItem] = qGItem + enzboundingRect = qGEnz.boundingRect() + moose.connect(enzObj, 'cplx', cplxItem, 'reac') + qGItem.setDisplayProperties(int(enzboundingRect.height() / 2), + enzboundingRect.height() - 40, + QtGui.QColor('white'), + QtGui.QColor('white')) + qGItem.dropped.emit() + # view.emit(QtCore.SIGNAL("dropped"), enzObj) + else: + enzObj = moose.MMenz(mobj.path + '/' + string_num) + enzinfo = moose.Annotator(enzObj.path + '/info') + moose.connect(mobj, "nOut", enzObj, "enzDest") + qGItem = kkitQGraphics.MMEnzItem(enzObj, parentcompt) + posWrtComp = pos + bgcolor = kkitUtil.getRandColor() + qGItem.setDisplayProperties(posWrtComp.x(), + posWrtComp.y() - 30, + QtGui.QColor('green'), bgcolor) + enzinfo.color = str(bgcolor.name()) + layoutPt.mooseId_GObj[enzObj] = qGItem + qGItem.dropped.emit() + # view.emit(QtCore.SIGNAL("dropped"), enzObj) + x, y = roundoff(qGItem.scenePos(), layoutPt) + enzinfo.x = x + enzinfo.y = y + kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection) + layoutPt.drawLine_arrow(False) + + # Dropping is on compartment then update Compart size + if isinstance(enzparent, moose.ChemCompt): + updateCompartmentSize(parentcompt) + if view.iconScale != 1: + view.updateScale(view.iconScale) + +def createObj(scene, view, modelpath, string, pos, layoutPt): + logger_.debug( "Crating object %s, %s, %s" % (modelpath, string, str(pos))) + assert isinstance(view.sceneContainerPt, QGraphicsScene) + event_pos, num, ret_string = pos, 0, "" + pos = view.mapToScene(event_pos) + itemAt = view.sceneContainerPt.itemAt(float(pos.x()), float(pos.y()), QtGui.QTransform()) + logger_.debug( "\tItem At %s" % str(itemAt)) + moose.wildcardFind(modelpath + '/##[ISA=ChemCompt]') + moose.mooseDeleteChemSolver(modelpath) + mobj = None + + if itemAt is not None: + itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos)) + itemClass = type(itemAtView).__name__ + if (itemClass == 'QGraphicsRectItem'): + mobj = itemAtView.parentItem().mobj + elif (itemClass == 'QGraphicsSvgItem'): + mobj = itemAtView.parent().mobj + else: + mobj = itemAtView.mobj + + if string == "CubeMesh" or string == "CylMesh": + ret_string, num = findUniqId(moose.element(modelpath), "Compartment", 0) + comptexist = moose.wildcardFind(modelpath + '/##[ISA=ChemCompt]') + if not len(comptexist): + if itemAt is not None: + QMessageBox.information( + None, 'Drop Not possible', + "'{}' currently single compartment model building is allowed" + .format(string), QMessageBox.Ok) + return False + else: + # create Rect here. + logger_.info("Mesh is not available") + mobj = moose.element(modelpath) + return True + else: + QMessageBox.information( + None, 'Drop Not possible', + "'{}' currently single compartment model building is allowed" .format(string) + , QMessageBox.Ok) + return False + + elif string == "Pool" or string == "BufPool" or string == "Reac" or string == "StimulusTable": + if itemAt == None: + QMessageBox.information( + None, 'Drop Not possible', + "'{}' has to have compartment as its parent".format(string), QMessageBox.Ok) + return False + else: + mobj = findCompartment(mobj) + ret_string, num = findUniqId(mobj, string, num) + return True + + elif string == "Function": + #mobj = findCompartment(mobj) + ret_string, num = findUniqId(mobj, string, num) + return True + elif string == "Enz" or string == "MMenz": + if itemAt != None: + if ((mobj).className != "Pool" and (mobj).className != "BufPool"): + QMessageBox.information( + None, 'Drop Not possible', + "'{}' has to have Pool as its parent".format(string), + QMessageBox.Ok) + return False + else: + ret_string, num = findUniqId(mobj, string, num) + return True + else: + QMessageBox.information( + None, 'Drop Not possible', + "'{}' has to have Pool as its parent".format(string), + QMessageBox.Ok) + return False + + if ret_string.strip(): + checkCreate(scene, view, modelpath, mobj, string, ret_string, num, + event_pos, layoutPt) + + +def roundoff(scenePos, layoutPt): + xtest = scenePos.x() / layoutPt.defaultScenewidth + xroundoff = round(xtest, 1) + + ytest = scenePos.y() / layoutPt.defaultSceneheight + yroundoff = round(ytest, 1) + + return (xroundoff, yroundoff) + + +def findUniqId(mobj, string, num): + if num == 0: + path = mobj.path + '/' + string + else: + path = mobj.path + '/' + string + str(num) + if not moose.exists(path): + return (string, num) + else: + num += 1 + return findUniqId(mobj, string, num) + +def findCompartment(mooseObj): + if mooseObj.path == '/': + return None + elif isinstance(mooseObj, kkitQGraphics.ChemCompt): + return (mooseObj) + else: + return findCompartment(moose.element(mooseObj.parent)) diff --git a/plugins/setsolver.py b/moosegui/plugins/setsolver.py similarity index 96% rename from plugins/setsolver.py rename to moosegui/plugins/setsolver.py index f55b067..f365898 100644 --- a/plugins/setsolver.py +++ b/moosegui/plugins/setsolver.py @@ -1,3 +1,5 @@ +from __future__ import print_function + import moose def deleteSolver(modelRoot): @@ -61,7 +63,7 @@ def setCompartmentSolver(modelRoot,solver): compts = moose.wildcardFind(modelRoot+'/##[ISA=ChemCompt]') if ( len(compts) > 3 ): - print "Warning: setSolverOnCompt Cannot handle " , + print("Warning: setSolverOnCompt Cannot handle ", end=' ') len(compts) , " chemical compartments\n" return; @@ -94,4 +96,4 @@ def setCompartmentSolver(modelRoot,solver): stoichList[1].buildXreacs (stoichList [2]) for i in stoichList: - i.filterXreacs() \ No newline at end of file + i.filterXreacs() diff --git a/plugins/test_plotwidget.py b/moosegui/plugins/test_plotwidget.py similarity index 96% rename from plugins/test_plotwidget.py rename to moosegui/plugins/test_plotwidget.py index 72c0a33..f2fbf4b 100644 --- a/plugins/test_plotwidget.py +++ b/moosegui/plugins/test_plotwidget.py @@ -47,15 +47,15 @@ import sys import os import numpy as np -from PyQt4 import QtGui, QtCore -from PyQt4.Qt import Qt +from PyQt5 import QtGui, QtCore +from PyQt5.Qt import Qt from matplotlib import mlab from matplotlib.figure import Figure from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar import unittest sys.path.append('..') -from default import PlotWidget +from .default import PlotWidget import moose import config diff --git a/scishell.py b/moosegui/scishell.py similarity index 96% rename from scishell.py rename to moosegui/scishell.py index a9a63de..95f349e 100644 --- a/scishell.py +++ b/moosegui/scishell.py @@ -27,10 +27,10 @@ import os, sys -from PyQt4 import QtCore, QtGui -from PyQt4.QtCore import Qt +from PyQt5 import QtCore, QtGui +from PyQt5.QtCore import Qt -from PyQt4.Qsci import QsciScintilla, QsciLexerPython, QsciAPIs +from PyQt5.Qsci import QsciScintilla, QsciLexerPython, QsciAPIs class History: """ Backup and restore history between sessions @@ -234,7 +234,7 @@ def paste(self): """ Reimplemented slot to handle the paste action. """ - lines = unicode(QApplication.clipboard().text()) + lines = str(QApplication.clipboard().text()) self.__executeLines(lines) @@ -242,7 +242,7 @@ def __middleMouseButton(self): """ Private method to handle the middle mouse button press. """ - lines = unicode(QApplication.clipboard().text(QClipboard.Selection)) + lines = str(QApplication.clipboard().text(QClipboard.Selection)) self.__executeLines(lines) @@ -338,7 +338,7 @@ def keyPressEvent(self, ev): if(ctrl): QsciScintilla.keyPressEvent(self, ev) - elif(self.keymap.has_key(key)): + elif(key in self.keymap): self.keymap[key]() # See it is text to insert. @@ -362,7 +362,7 @@ def __QScintillaTab(self): self.SendScintilla(QsciScintilla.SCI_TAB) elif self.__isCursorOnLastLine(): line, index = self.getCursorPosition() - buf = unicode(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") + buf = str(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") if self.more and not buf[:index-len(sys.ps2)].strip(): self.SendScintilla(QsciScintilla.SCI_TAB) @@ -427,7 +427,7 @@ def __QScintillaNewline(self): self.incrementalSearchActive = False line, col = self.__getEndPos() self.setCursorPosition(line,col) - buf = unicode(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") + buf = str(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") self.insert('\n') self.__executeCommand(buf) @@ -500,7 +500,7 @@ def __QScintillaLineUp(self): self.SendScintilla(QsciScintilla.SCI_LINEUP) else: line, col = self.__getEndPos() - buf = unicode(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") + buf = str(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") if buf and self.incrementalSearchActive: if self.incrementalSearchString: idx = self.__rsearchHistory(self.incrementalSearchString, @@ -530,7 +530,7 @@ def __QScintillaLineDown(self): self.SendScintilla(QsciScintilla.SCI_LINEDOWN) else: line, col = self.__getEndPos() - buf = unicode(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") + buf = str(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") if buf and self.incrementalSearchActive: if self.incrementalSearchString: idx = self.__searchHistory(self.incrementalSearchString, self.histidx) @@ -627,14 +627,14 @@ def __showDynCompletion(self): # get line line, col = self.__getEndPos() self.setCursorPosition(line,col) - buf = unicode(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") + buf = str(self.text(line)).replace(sys.ps1, "").replace(sys.ps2, "") text = buf.split()[-1][:-1] try: locals = self.interpreter.locals obj = eval(text, globals(), self.interpreter.locals) l = dir(obj) - l = filter(lambda x : not x.startswith('__'), l) + l = [x for x in l if not x.startswith('__')] self.__showCompletions(l, text) except : pass @@ -672,11 +672,11 @@ def __completionListSelected(self, id, txt): # Remove already written characters line, col = self.__getEndPos() self.setCursorPosition(line,col) - buf = unicode(self.text(line)) + buf = str(self.text(line)) ind = len(buf) - buf.rfind(".") - 1 if id == 1: - txt = unicode(txt[ind:]) + txt = str(txt[ind:]) #if self.completionText != "": # txt = txt.replace(self.completionText, "") self.__insertText(txt) diff --git a/shell.py b/moosegui/shell.py similarity index 93% rename from shell.py rename to moosegui/shell.py index 2eeafb5..b63dbcd 100644 --- a/shell.py +++ b/moosegui/shell.py @@ -1,24 +1,26 @@ # -*- python -*- # -# OpenAlea.Visualea: OpenAlea graphical user interface +# OpenAlea.Visualea: OpenAlea graphical user interface # -# Copyright 2006 INRIA - CIRAD - INRA +# Copyright 2006 INRIA - CIRAD - INRA # -# File author(s): Samuel Dufour-Kowalski -# Christophe Pradal +# File author(s): Samuel Dufour-Kowalski +# Christophe Pradal # -# Distributed under the CeCILL v2 License. -# See accompanying file LICENSE.txt or copy at -# http://www.cecill.info/licences/Licence_CeCILL_V2-en.html +# Distributed under the CeCILL v2 License. +# See accompanying file LICENSE.txt or copy at +# http://www.cecill.info/licences/Licence_CeCILL_V2-en.html # -# OpenAlea WebSite : http://openalea.gforge.inria.fr +# OpenAlea WebSite : http://openalea.gforge.inria.fr # # Fri Mar 15 15:10:58 IST 2013: This file was obtained from: # http://obswww.unige.ch/~revaz/git/old.glups-4.0/glups/shell.py - +# Wednesday 12 June 2019 08:37:21 PM IST +# + Ported to Qt5 # Subhasis Ray __doc__=""" -This module implements a QT4 python interpreter widget. +This module implements a Qt5 python interpreter widget. It is inspired bu PyCute : http://gerard.vermeulen.free.fr """ @@ -26,11 +28,11 @@ __revision__=" $Id: shell.py 579 2007-06-13 10:27:57Z dufourko $" -import os, sys -from PyQt4 import QtCore, QtGui -from PyQt4.QtGui import QTextEdit, QTextCursor -from PyQt4.QtCore import Qt - +import os +import sys +from PyQt5.QtWidgets import QTextEdit +from PyQt5.QtGui import QTextCursor +from PyQt5 import QtCore, QtGui class History: """ Backup and restore history between sessions @@ -65,13 +67,10 @@ def get_shell_class(): # Test QScintilla try: - from scishell import SciShell + from .scishell import SciShell return SciShell - except ImportError: return PyCutExt - - class MultipleRedirection: """ Dummy file which redirects stream to multiple file """ @@ -123,7 +122,7 @@ def __init__(self, interpreter, message="", log='', parent=None): # to exit the main interpreter by a Ctrl-D if PyCute has no parent if parent is None: - self.eofKey = Qt.Key_D + self.eofKey = QtCore.Qt.Key_D else: self.eofKey = None @@ -134,7 +133,7 @@ def __init__(self, interpreter, message="", log='', parent=None): # last line + last incomplete lines - self.line = QtCore.QString() + self.line = "" self.lines = [] # the cursor position in the last line self.point = 0 @@ -268,7 +267,7 @@ def writelines(self, text): """ Simulate stdin, stdout, and stderr. """ - map(self.write, text) + list(map(self.write, text)) def fakeUser(self, lines): @@ -276,7 +275,7 @@ def fakeUser(self, lines): Simulate a user: lines is a sequence of strings, (Python statements). """ for line in lines: - self.line = QtCore.QString(line.rstrip()) + self.line = line.rstrip() self.write(self.line) self.write('\n') self.__run() @@ -291,12 +290,12 @@ def __run(self): (3) the interpreter fails, finds errors and writes them to sys.stderr """ self.pointer = 0 - self.history.append(QtCore.QString(self.line)) - self.H.append(QtCore.QString(self.line)) # Added by yr + self.history.append(self.line) + self.H.append(self.line) try: self.lines.append(str(self.line)) - except Exception,e: - print e + except Exception as e: + print(e) source = '\n'.join(self.lines) self.more = self.interpreter.runsource(source) diff --git a/moosegui/sidebar.py b/moosegui/sidebar.py new file mode 100644 index 0000000..cb42999 --- /dev/null +++ b/moosegui/sidebar.py @@ -0,0 +1,185 @@ +# -*- coding: utf-8 -*- + +""" +Sidebar for plugins. The sidebar comprises of actions. +Currently mode, connect and settings are defined. +""" + +__author__ = "Aviral Goel" +__email__ = "goel.aviral@gmail.com" +__credits__ = ["NCBS Bangalore"] +__license__ = "GPL3" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh " +__status__ = "Development" + + +import sys +import os +from PyQt5.QtWidgets import QDialog +from PyQt5.QtWidgets import QHBoxLayout +from PyQt5.QtWidgets import QAction, QToolBar +from PyQt5.QtGui import QPixmap, QIcon + +from moosegui import SettingsDialog +from moosegui import config + +import logging +logger_ = logging.getLogger("sidebar") + +ICON_DIRECTORY = "../icons" +HAND_ICON_FILENAME = "hand.png" +CONNECTOR_ICON_FILENAME = "straight_connector_with_filled_circles.png" +WRENCH_ICON_FILENAME = "wrench.png" +DELETE_GRAPH_ICON_FILENAME = "add_graph.png" +ADD_GRAPH_ICON_FILENAME = "delete_graph.png" +LIST_ICON_FILENAME = "list.png" + + +def create_action( parent + , callback + , text + , checkable + , checked + , icon_path + ): + pixmap = QPixmap(icon_path) + icon = QIcon(pixmap) + action = QAction(icon, text, parent) + action.triggered.connect(callback) + action.setCheckable(checkable) + action.setChecked(checked) + return action + +def do_nothing(event, msg): + logger_.debug( "do_nothing: %s" % msg ) + +def mode_action( parent + , callback = lambda ev: do_nothing(ev, "Action clicked") + , text = "Mode" + , checkable = True + , checked = True + , icon_path = os.path.join( ICON_DIRECTORY + , HAND_ICON_FILENAME + ) + ): + return create_action( parent + , callback + , text + , checkable + , checked + , icon_path + ) + +def add_graph_action( parent + , callback = lambda event: do_nothing(event, "Add Graph Clicked!") + , text = "Add Graph" + , checkable = False + , checked = False + , icon_path = os.path.join( ICON_DIRECTORY + , ADD_GRAPH_ICON_FILENAME + ) + ): + return create_action( parent + , callback + , text + , checkable + , checked + , icon_path + ) + +def delete_graph_action( parent + , callback = lambda event: do_nothing(event, "Delete Graph Clicked!") + , text = "Delete Graph" + , checkable = False + , checked = False + , icon_path = os.path.join( ICON_DIRECTORY + , DELETE_GRAPH_ICON_FILENAME + ) + ): + return create_action( parent + , callback + , text + , checkable + , checked + , icon_path + ) + +def list_action( parent + , callback = lambda event: do_nothing(event, "List Clicked!") + , text = "Show List" + , checkable = False + , checked = False + , icon_path = os.path.join( ICON_DIRECTORY + , LIST_ICON_FILENAME + ) + ): + return create_action( parent + , callback + , text + , checkable + , checked + , icon_path + ) + +def connector_action( parent + , callback = lambda event: do_nothing(event, "Connector Clicked!") + , text = "Mode" + , checkable = True + , checked = False + , icon_path = os.path.join( ICON_DIRECTORY , CONNECTOR_ICON_FILENAME) + ): + return create_action( parent + , callback + , text + , checkable + , checked + , icon_path + ) + +def settings_action( parent + , callback = (lambda event: do_nothing(event, "Settings Clicked")) + , text = "Mode" + , checkable = False + , checked = False + , icon_path = os.path.join(ICON_DIRECTORY, WRENCH_ICON_FILENAME) + ): + return create_action( parent + , callback + , text + , checkable + , checked + , icon_path + ) + +def sidebar(): + return QToolBar() + + +def main(): + from PyQt5.QtWidgets import QApplication, QMainWindow + app = QApplication(sys.argv) + window = QMainWindow() + widget = SettingsDialog.SettingsWidget({ + 'LeakyIaF':['Vm'], + 'Compartment':['Vm','Im'], + 'HHChannel':['Ik','Gk'], + 'ZombiePool':['n','conc'], + 'ZombieBufPool':['n','conc'], + 'HHChannel2D':['Ik','Gk'], + 'CaConc':['Ca'] + }) + d = QDialog() + l = QHBoxLayout() + d.setLayout(l) + l.addWidget(widget) + bar = sidebar() + bar.addAction(mode_action(bar)) + bar.addAction(connector_action(bar)) + bar.addAction(settings_action(bar, d.show)) + window.addToolBar(bar) + window.show() + sys.exit(app.exec_()) + +if __name__ == "__main__": + main() diff --git a/utils.py b/moosegui/utils.py similarity index 90% rename from utils.py rename to moosegui/utils.py index 6873a9c..3687184 100644 --- a/utils.py +++ b/moosegui/utils.py @@ -47,7 +47,7 @@ import shutil import os -from PyQt4 import QtGui, QtCore +from PyQt5 import QtGui, QtCore def resizeWidthToContents(lineEdit): """Resize a QLineEdit object to fit its content.""" @@ -82,13 +82,13 @@ def copyTree(src, dst, progressDialog=None): dst = dst.strip() errors = [] if not os.access(src, os.R_OK + os.X_OK): - print 'Failed to access directory', src + print(('Failed to access directory', src)) return - print 'Copying %s to : %s' % (src, dst) + print(('Copying %s to : %s' % (src, dst))) if not os.access(src, os.R_OK + os.X_OK): try: os.makedirs(dst) - except OSError, e: + except OSError as e: # print e errors.append(e) totalsize = 0 @@ -97,7 +97,7 @@ def copyTree(src, dst, progressDialog=None): srcname = os.path.join(dirpath, fname) try: totalsize += os.path.getsize(srcname) - except OSError, e: + except OSError as e: # print e errors.append(e) if progressDialog: @@ -108,7 +108,7 @@ def copyTree(src, dst, progressDialog=None): # print 'Destination dir', dstdir, dirpath[len(src)+1:] try: os.makedirs(dstdir) - except OSError, e: + except OSError as e: # print e errors.append(e) # print 'Copying files from %s to %s' % (dirpath, dstdir) @@ -118,7 +118,7 @@ def copyTree(src, dst, progressDialog=None): # print 'Copying:', srcname, 'to', dstname try: shutil.copy2(srcname, dstname) - except IOError, e: + except IOError as e: # print e errors.append(e) size += os.path.getsize(srcname) @@ -127,11 +127,11 @@ def copyTree(src, dst, progressDialog=None): if progressDialog.wasCanceled(): return errors else: - print 'Copied %d bytes of %d.' % (size, totalsize) + print(('Copied %d bytes of %d.' % (size, totalsize))) if progressDialog: progressDialog.close() else: - print 'Finished.' + print('Finished.') return errors diff --git a/newmodeldialog.py b/newmodeldialog.py deleted file mode 100644 index 6b5bf80..0000000 --- a/newmodeldialog.py +++ /dev/null @@ -1,71 +0,0 @@ -import os -from PyQt4 import QtGui, QtCore,Qt -import config -from mplugin import MoosePluginBase, EditorBase, EditorWidgetBase, PlotBase, RunBase -import re - -class DialogWidget(QtGui.QDialog): - def __init__(self,parent=None): - QtGui.QWidget.__init__(self, parent) - self.warning = None - self._currentRadioButton ="kkit" - self.layout = QtGui.QGridLayout() - self.modelPathLabel = QtGui.QLabel('Model Name') - self.modelPathEdit = QtGui.QLineEdit('') - self.layout.addWidget(self.modelPathLabel, 0, 0) - self.layout.addWidget(self.modelPathEdit, 0, 1,1,1) - # self.defaultRadio = QtGui.QRadioButton('default') - # #self.defaultRadio.setChecked(True); - # self.kkitRadio = QtGui.QRadioButton('kkit') - # self.kkitRadio.setChecked(True) - # self.defaultRadio.toggled.connect(lambda : self.setcurrentRadioButton('default')) - # self.kkitRadio.toggled.connect(lambda : self.setcurrentRadioButton('kkit')) - # layout.addWidget(self.defaultRadio,2,1) - # layout.addWidget(self.kkitRadio,2,0) - self.hbox = QtGui.QHBoxLayout() - self.buttonBox = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Ok) - self.connect(self.buttonBox, QtCore.SIGNAL('accepted()'), self.validateAccept) - self.hbox.addWidget(self.buttonBox,1) - - self.buttonBox1 = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Cancel) - self.connect(self.buttonBox1, QtCore.SIGNAL('rejected()'), self.Cancel) - self.hbox.addWidget(self.buttonBox1,0) - #self.hbox.setBackgroundColor(Blue) - #self.modelPathEdit.returnPressed.connect(self.validateAccept) - # self.connect(self.buttonBox, QtCore.SIGNAL('rejected()'), self.reject) - #self.hbox.addStretch(1) - self.layout.addLayout(self.hbox,1,1) - self.setLayout(self.layout) - - def Cancel (self): - self.close() - - def validateAccept(self): - text = str(self.modelPathEdit.text()) - self.layout.removeWidget(self.warning) - #replace / to _ - text = text.replace('/','_') - - #print(self.layout.widgets()) - if len(text) == 0: - self.warning = QtGui.QLabel("Model name cannot be empty!") - self.layout.addWidget(self.warning, 1, 0, 1, -1) - elif not re.match("^[a-zA-Z]+.*",text): - self.warning = QtGui.QLabel("Start special characters not allowed!") - self.layout.addWidget(self.warning, 1, 0, 1, -1) - else: - self.accept() - return False - - def getcurrentRadioButton(self): - return self._currentRadioButton - -if __name__ == '__main__': - app =QtGui.QApplication([]) - widget = DialogWidget() - widget.setWindowTitle('New Model') - widget.setMinimumSize(400, 200) - widget.show() - app.exec_() - - diff --git a/objectedit.py b/objectedit.py deleted file mode 100644 index 11a35b6..0000000 --- a/objectedit.py +++ /dev/null @@ -1,553 +0,0 @@ -# objectedit.py --- -# -# Filename: objectedit.py -# Description: -# Author: Subhasis Ray -# Maintainer: -# Created: Wed Jun 30 11:18:34 2010 (+0530) -# Version: -# Last-Updated: Fri Feb 01 11:05:59 2017 (+0530) -# By: Harsha -# Update #: -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# This code is for a widget to edit MOOSE objects. We can now track if -# a field is a Value field and make it editable accordingly. There -# seems to be no clean way of determining whether the field is worth -# plotting (without a knowledge of the model/biology there is no way -# we can tell this). But we can of course check if the field is a -# numeric one. -# -# - -# Change log: -# -# Wed Jun 30 11:18:34 2010 (+0530) - Originally created by Subhasis -# Ray, the model and the view -# -# Modified/adapted to dh_branch by Chaitanya/Harsharani -# -# Thu Apr 18 18:37:31 IST 2013 - Reintroduced into multiscale GUI by -# Subhasis -# -# Fri Apr 19 15:05:53 IST 2013 - Subhasis added undo redo -# feature. Create ObjectEditModel as part of ObjectEditView. -# Tue Mar 7 16:10:54 IST 2017 - Harsha now Pool or BufPool can be interchangable -# by setting/unsetting isbuffered field -# Fri May 17 23:45:59 2017 (+0530) - Harsha added, notes header, -# Kd is calculated for the second order reaction and value is displayed -# Tue Jun 18 12:10:54 IST 2018 - Harsha now group boundary color can be editable from the object editor -# Mon Sep 10 16:21:00 IST 2018 - When name is edited, the editorTitle gets updated -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: -import PyQt4 -from PyQt4 import QtCore -from PyQt4 import QtGui -from PyQt4.QtGui import QTextEdit -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QVBoxLayout -from PyQt4.QtGui import QSizePolicy -from PyQt4.QtCore import QMargins -from PyQt4.QtGui import QSplitter -import sys -from collections import deque -import traceback - -#sys.path.append('../python') -import moose -import defaults -import config -#from plugins.kkitUtil import getColor -from moose.chemUtil.chemConnectUtil import getColor - -#these fields will be ignored -extra_fields = ['this', - 'me', - 'parent', - 'path', - 'children', - 'linearSize', - 'objectDimensions', - 'lastDimension', - 'localNumField', - 'pathIndices', - 'msgOut', - 'msgIn', - 'diffConst', - 'speciesId', - 'Coordinates', - 'neighbors', - 'DiffusionArea', - 'DiffusionScaling', - 'x', - 'x0', - 'x1', - 'dx', - 'nx', - 'y', - 'y0', - 'y1', - 'dy', - 'ny', - 'z', - 'z0', - 'z1', - 'dz', - 'nz', - 'coords', - 'isToroid', - 'preserveNumEntries', - # 'numKm', - 'numSubstrates', - 'concK1', - 'meshToSpace', - 'spaceToMesh', - 'surface', - 'method', - 'alwaysDiffuse', - 'numData', - 'numField', - 'valueFields', - 'sourceFields', - 'motorConst', - 'destFields', - 'dt', - 'tick', - 'idValue', - 'index', - 'fieldIndex' - ] - - -class ObjectEditModel(QtCore.QAbstractTableModel): - """Model class for editing MOOSE elements. This is not to be used - directly, except that its undo and redo slots should be connected - to by the GUI actions for the same. - - SIGNALS: - - objectNameChanged(PyQt_PyObject): when a moose object's name is - changed, this signal is emitted with the object as argument. This - can be captured by widgets that display the object name. - - dataChanged: emitted when any data is changed in the moose object - - """ - objectNameChanged = QtCore.pyqtSignal('PyQt_PyObject') - # dataChanged = QtCore.pyqtSignal('PyQt_PyObject') - def __init__(self, datain, headerdata=['Field','Value'], undolen=100, parent=None, *args): - QtCore.QAbstractTableModel.__init__(self, parent, *args) - self.fieldFlags = {} - self.fields = [] - self.mooseObject = datain - self.headerdata = headerdata - self.undoStack = deque(maxlen=undolen) - self.redoStack = deque(maxlen=undolen) - self.checkState_ = False - - for fieldName in self.mooseObject.getFieldNames('valueFinfo'): - if fieldName in extra_fields : - continue - - value = self.mooseObject.getField(fieldName) - self.fields.append(fieldName) - #harsha: For signalling models will be pulling out notes field from Annotator - # can updates if exist for other types also - if (isinstance (self.mooseObject,moose.ChemCompt) or \ - isinstance(self.mooseObject,moose.ReacBase) or \ - isinstance(moose.element(moose.element(self.mooseObject).parent),moose.EnzBase) \ - ): - pass - else: - self.fields.append("Color") - - flag = QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable - self.fieldFlags[fieldName] = flag - - if ( isinstance(self.mooseObject, moose.ReacBase) ) : - self.fields.append("Kd") - flag = QtCore.Qt.ItemIsEnabled - self.fieldFlags[fieldName] = flag - - def rowCount(self, parent): - return len(self.fields) - - def columnCount(self, parent): - return len(self.headerdata) - - def setData(self, index, value, role=QtCore.Qt.EditRole): - if not index.isValid() or index.row () >= len(self.fields) or index.column() != 1: - return False - field = self.fields[index.row()] - if (role == QtCore.Qt.CheckStateRole): - if (index.column() == 1): - self.checkState_ = value - return True - - else: - value = str(value.toString()).strip() # convert Qt datastructure to Python string - if len(value) == 0: - return False - if field == "Notes": - field = "notes" - ann = moose.Annotator(self.mooseObject.path+'/info') - oldValue = ann.getField(field) - value = type(oldValue)(value) - ann.setField(field,value) - self.undoStack.append((index,oldValue)) - elif field == "vector": - for ch in ['[',']']: - if ch in value: - value = value.replace(ch," ") - value = value.replace(",", " ") - valuelist = [] - if value.find(',') != -1: - valuelist = value.split(",") - elif value.find(' ') != -1: - valuelist = value.split(" ") - else: - valuelist = value - vectorlist = [] - for d in valuelist: - try: - float(d) - vectorlist.append(float(d)) - except: - pass - from numpy import array - a = array( vectorlist ) - self.mooseObject.setField(field, a) - - else: - oldValue = self.mooseObject.getField(field) - if field != "isBuffered": - value = type(oldValue)(value) - self.mooseObject.setField(field, value) - else: - if self.mooseObject.className == "ZombiePool" or self.mooseObject.className =="ZombieBufPool": - QtGui.QMessageBox.warning(None,'Solver is set, Could not set the value','\n Unset the solver by clicking \n run widget -> Preferences -> Exponential Euler->Apply') - else: - if value.lower() in ("yes", "true", "t", "1"): - self.mooseObject.setField(field, True) - else: - self.mooseObject.setField(field, False) - self.undoStack.append((index, oldValue)) - if field == 'name': - self.emit(QtCore.SIGNAL('objectNameChanged(PyQt_PyObject)'), self.mooseObject) - return True - - self.dataChanged.emit(index, index) - return True - - def undo(self): - print ('Undo') - if len(self.undoStack) == 0: - raise Info('No more undo information') - index, oldvalue, = self.undoStack.pop() - field = self.fields[index.row()] - currentvalue = self.mooseObject.getField(field) - oldvalue = type(currentvalue)(oldvalue) - self.redoStack.append((index, str(currentvalue))) - self.mooseObject.setField(field, oldvalue) - if field == 'name': - self.objectNameChanged.emit(self.mooseObject) - self.emit(QtCore.SIGNAL('dataChanged(const QModelIndex&, const QModelIndex&)'), index, index) - - def redo(self): - if len(self.redoStack) ==0: - raise Info('No more redo information') - index, oldvalue, = self.redoStack.pop() - currentvalue = self.mooseObject.getField(self.fields[index.row()]) - self.undoStack.append((index, str(currentvalue))) - self.mooseObject.setField(self.fields[index.row()], type(currentvalue)(oldvalue)) - if field == 'name': - self.emit(QtCore.SIGNAL('objectNameChanged(PyQt_PyObject)'), self.mooseObject) - self.emit(QtCore.SIGNAL('dataChanged(const QModelIndex&, const QModelIndex&)'), index, index) - - def flags(self, index): - flag = QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable - #flag = QtCore.Qt.NoItemFlags - if not index.isValid(): - return None - # Replacing the `outrageous` up stuff with something sensible - field = self.fields[index.row()] - newstr = field[0] - newstr = newstr.upper() - field_string = newstr + field[1:] - setter = 'set%s' %(field_string) - #setter = 'set_%s' % (self.fields[index.row()]) - #print " from Object setter",setter, "object",self.mooseObject, " ",self.mooseObject.getFieldNames('destFinfo'); - if index.column() == 1: - # if field == "Color": - # flag = QtCore.Qt.ItemIsEnabled - if field == "Notes": - ann = moose.Annotator(self.mooseObject.path+'/info') - if setter in ann.getFieldNames('destFinfo'): - flag |= QtCore.Qt.ItemIsEditable - - if isinstance(self.mooseObject, moose.PoolBase) or isinstance(self.mooseObject,moose.Function): - if field == 'volume' or field == 'expr': - pass - elif setter in self.mooseObject.getFieldNames('destFinfo'): - flag |= QtCore.Qt.ItemIsEditable - else: - if setter in self.mooseObject.getFieldNames('destFinfo'): - flag |= QtCore.Qt.ItemIsEditable - - #if field == "Notes": - # flag |= QtCore.Qt.ItemIsEditable - - # !! Replaced till here - - return flag - - def data(self, index, role): - ret = None - field = self.fields[index.row()] - if index.column() == 0 and role == QtCore.Qt.DisplayRole: - try: - ret = QtCore.QVariant(QtCore.QString(field)+' ('+defaults.FIELD_UNITS[field]+')') - except KeyError: - ret = QtCore.QVariant(QtCore.QString(field)) - elif index.column() == 1: - if role==QtCore.Qt.CheckStateRole: - if ((str(field) == "plot Conc") or (str(field) == "plot n") ): - # print index.data(QtCore.Qt. ), str(field) - return self.checkState_ - elif (role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole): - try: - if (str(field) =="Color" ): - return QtGui.QPushButton("Press Me!") - if (str(field) =="Kd" ): - #ret = self.mooseObject.getField(str(field)) - Kd = 0 - - if self.mooseObject.className == "ZombieReac" or self.mooseObject.className == "Reac": - if self.mooseObject.numSubstrates > 1 or self.mooseObject.numProducts > 1: - if self.mooseObject.Kf != 0: - Kd = self.mooseObject.Kb/self.mooseObject.Kf - - #Kd = QtCore.QVariant(QtCore.QString(str(ret))) - ret = QtCore.QVariant(QtCore.QString(str(Kd))) - if ( (str(field) != "Notes") and (str(field) != "className") and (str(field) != "Kd")): - ret = self.mooseObject.getField(str(field)) - ret = QtCore.QVariant(QtCore.QString(str(ret))) - elif(str(field) == "className"): - ret = self.mooseObject.getField(str(field)) - if 'Zombie' in ret: - ret = ret.split('Zombie')[1] - ret = QtCore.QVariant(QtCore.QString(str(ret))) - elif(str(field) == "Notes"): - astr = self.mooseObject.path+'/info' - mastr = moose.Annotator(astr) - ret = (mastr).getField(str('notes')) - ret = QtCore.QVariant(QtCore.QString(str(ret))) - except ValueError: - ret = None - return ret - - def headerData(self, col, orientation, role): - if orientation == QtCore.Qt.Horizontal and role == QtCore.Qt.DisplayRole: - return QtCore.QVariant(self.headerdata[col]) - return QtCore.QVariant() - -class ObjectEditView(QtGui.QTableView): - """View class for object editor. - - This class creates an instance of ObjectEditModel using the moose - element passed as its first argument. - - undolen - specifies the size of the undo stack. By default set to - OBJECT_EDIT_UNDO_LENGTH constant in defaults.py. Specify something smaller if - large number of objects are likely to be edited. - - To enable undo/redo conect the corresponding actions from the gui - to view.model().undo and view.model().redo slots. - """ - def __init__(self, mobject, undolen=defaults.OBJECT_EDIT_UNDO_LENGTH, parent=None): - QtGui.QTableView.__init__(self, parent) - #self.setEditTriggers(self.DoubleClicked | self.SelectedClicked | self.EditKeyPressed) - vh = self.verticalHeader() - vh.setVisible(False) - hh = self.horizontalHeader() - hh.setStretchLastSection(True) - self.setAlternatingRowColors(True) - self.resizeColumnsToContents() - self.setModel(ObjectEditModel(mobject, undolen=undolen)) - self.colorButton = QtGui.QPushButton() - self.colorDialog = QtGui.QColorDialog() - self.textEdit = QTextEdit() - try: - notesIndex = self.model().fields.index("Notes") - self.setIndexWidget(self.model().index(notesIndex,1), self.textEdit) - info = moose.Annotator(self.model().mooseObject.path+'/info') - self.textEdit.setText(QtCore.QString(info.getField('notes'))) - self.setRowHeight(notesIndex, self.rowHeight(notesIndex) * 3) - - # self.colorDialog.colorSelected.connect( - # lambda color: - # - # self.setColor(getColor(self.model().mooseObject.path+'/info')[1]) - except: - pass - - - try: - colorIndex = self.model().fields.index("Color") - self.colorButton.clicked.connect(self.colorDialog.show) - self.colorButton.setFocusPolicy(PyQt4.QtCore.Qt.NoFocus) - self.colorDialog.colorSelected.connect( - lambda color: self.colorButton.setStyleSheet( - "QPushButton {" - + "background-color: {0}; color: {0};".format(color.name()) - + "}" - ) - ) - self.setIndexWidget(self.model().index(colorIndex,1), self.colorButton) - # self.colorDialog.colorSelected.connect( - # lambda color: - # - self.setColor(getColor(self.model().mooseObject.path+'/info')[1]) - except: - pass - print ('Created view with %s' %(mobject)) - - def setColor(self, color): - self.colorButton.setStyleSheet( - "QPushButton {" - + "background-color: {0}; color: {0};".format(color) - + "}" - ) - self.colorDialog.setCurrentColor(color) - - def dataChanged(self, tl, br): - QtGui.QTableView.dataChanged(self, tl, br) - self.viewport().update() - -class ObjectEditDockWidget(QtGui.QDockWidget): - """A dock widget whose title is set by the current moose - object. Allows switching the moose object. It stores the created - view in a dict for future use. - - TODO possible performance issue: storing the views (along with - their models) ensures the undo history for each object is - retained. But without a limit on the number of views stored, it - will be wasteful on memory. - - """ - objectNameChanged = QtCore.pyqtSignal('PyQt_PyObject') - colorChanged = QtCore.pyqtSignal(object, object) - def __init__(self, mobj='/', parent=None, flags=None): - QtGui.QDockWidget.__init__(self, parent=parent) - mobj = moose.element(mobj) - #self.view = view = ObjectEditView(mobj) - self.view = view = ObjectEditView(mobj) - self.view_dict = {mobj: view} - base = QWidget() - layout = QVBoxLayout() - base.setLayout(layout) - layout.addWidget(self.view) - layout.addWidget(QTextEdit()) - self.setWidget(base) - self.setWindowTitle('Edit: %s' % (mobj.path)) - # self.view.colorDialog.colorSelected.connect(self.colorChangedEmit) - - # def clearDict(self): - # self.view_dict.clear() - - def setObject(self, mobj): - element = moose.element(mobj) - try: - view = self.view_dict[element] - except KeyError: - view = ObjectEditView(element) - self.view_dict[element] = view - view.model().objectNameChanged.connect(self.emitObjectNameChanged) - view.colorDialog.colorSelected.connect(lambda color: self.colorChanged.emit(element, color)) - textEdit = QTextEdit() - view.setSizePolicy( QSizePolicy.Ignored - , QSizePolicy.Ignored - ) - textEdit.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Maximum) - base = QSplitter() - base.setOrientation(PyQt4.QtCore.Qt.Vertical) - layout = QVBoxLayout() - layout.addWidget(view)#, 0, 0) - lineedit = QtGui.QLineEdit("Notes:") - lineedit.setReadOnly(True) - layout.addWidget(lineedit) - - if ( isinstance(mobj, moose.PoolBase) - or isinstance(mobj,moose.ReacBase) - or isinstance(mobj,moose.EnzBase) - ) : - info = moose.Annotator(mobj.path +'/info') - textEdit.setText(QtCore.QString(info.getField('notes'))) - textEdit.textChanged.connect(lambda : info.setField('notes', str(textEdit.toPlainText()))) - layout.addWidget(textEdit)#,1,0) - - # self.setRowHeight(notesIndex, self.rowHeight(notesIndex) * 3) - base.setLayout(layout) - # base.setSizes( [ view.height() - # , base.height() - view.height() - # ] - # ) - # print("a =>", view.height()) - # print("b =>", base.height()) - - - # layout.setStretch(0,3) - # layout.setStretch(1,1) - # layout.setContentsMargins(QMargins(0,0,0,0)) - self.setWidget(base) - self.setWindowTitle('Edit: %s' % (element.path)) - view.update() - - def emitObjectNameChanged(self, mobj): - self.objectNameChanged.emit(mobj) - self.setWindowTitle('Edit:%s'%(mobj.path)) -def main(): - app = QtGui.QApplication(sys.argv) - mainwin = QtGui.QMainWindow() - c = moose.Compartment("test") - view = ObjectEditView(c, undolen=3) - mainwin.setCentralWidget(view) - action = QtGui.QAction('Undo', mainwin) - action.setShortcut('Ctrl+z') - action.triggered.connect(view.model().undo) - mainwin.menuBar().addAction(action) - action = QtGui.QAction('Redo', mainwin) - action.setShortcut('Ctrl+y') - action.triggered.connect(view.model().redo) - mainwin.menuBar().addAction(action) - mainwin.show() - sys.exit(app.exec_()) - - -if __name__ == "__main__": - main() -# ojectedit.py ends here diff --git a/plugins/constants.py b/plugins/constants.py deleted file mode 100644 index 3596f2c..0000000 --- a/plugins/constants.py +++ /dev/null @@ -1,24 +0,0 @@ -INVALID = 6 - -INTERIOR = 7 -BOUNDARY = 8 - -SAME_OBJECT = 9 -OTHER_OBJECT = 10 -NO_OBJECT = 11 - -RUBBERBAND_SELECTION = 12 -VALID = 13 - -ITEM = 0 -CONNECTOR = 1 -CONNECTION = 2 -EMPTY = 3 - -COMPARTMENT = 14 -COMPARTMENT_BOUNDARY = 4 -COMPARTMENT_INTERIOR = 5 - -GROUP = 15 -GROUP_BOUNDARY = 16 -GROUP_INTERIOR = 17 diff --git a/plugins/kkit.py b/plugins/kkit.py deleted file mode 100644 index c375e06..0000000 --- a/plugins/kkit.py +++ /dev/null @@ -1,1228 +0,0 @@ - -__author__ = "HarshaRani" -__credits__ = ["Upi Lab"] -__license__ = "GPL3" -__version__ = "1.0.0" -__maintainer__ = "HarshaRani" -__email__ = "hrani@ncbs.res.in" -__status__ = "Development" -__updated__ = "Feb 22 2019" - -#Change log: -#2019 -#Feb 22: cross compartment molecules are checked for destination -# 2018 -#Oct 26: xfer cross compartment molecules are hidden and for cross compartment reaction's -# connection are now dotted line -#Oct 10: filedialog default is sbml -# layout co-ordainates are updated with scenepos -#Sep 11: comparment size is calculated based on group sceneBoundingRect size -#Sep 07: in positionChange all the group's boundingRect is calculated -# and when group is moved the children's position are stored -#Jun 18: update the color of the group from objecteditor -#code - -import math -import sys -from PyQt4 import QtGui, QtCore, Qt -from default import * -from moose import * -from moose import SBML -from moose.genesis.writeKkit import mooseWriteKkit -from mplugin import * -from kkitUtil import * -from kkitQGraphics import * -from kkitViewcontrol import * -from kkitCalcArrow import * -from kkitOrdinateUtil import * -import posixpath -from mtoolbutton import MToolButton -from PyQt4.QtGui import QWidget -from PyQt4.QtGui import QGridLayout -from PyQt4.QtGui import QColor -import RunWidget -from os.path import expanduser -#from setsolver import * -from moose.chemUtil.add_Delete_ChemicalSolver import * -import re - -class KkitPlugin(MoosePlugin): - """Default plugin for MOOSE GUI""" - def __init__(self, *args): - #print args - MoosePlugin.__init__(self, *args) - self.view = None - #self.plotView = PlotView(self) - #self.getRunView() - #self.plotView.dataTable = self.view._centralWidget.dataTable - #self.plotView.updateCallback = self.view._centralWidget.legendUpdate - #self.view._centralWidget.legendUpdate() - #self.dataTable = DataTable(self.dataRoot) - self.fileinsertMenu = QtGui.QMenu('&File') - if not hasattr(self,'SaveModelAction'): - #self.fileinsertMenu.addSeparator() - self.saveModelAction = QtGui.QAction('Save', self) - self.saveModelAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+S", None, QtGui.QApplication.UnicodeUTF8)) - self.connect(self.saveModelAction, QtCore.SIGNAL('triggered()'), self.SaveModelDialogSlot) - self.fileinsertMenu.addAction(self.saveModelAction) - self._menus.append(self.fileinsertMenu) - self.getEditorView() - - def SaveModelDialogSlot(self): - - dirpath = "" - if not dirpath: - dirpath = expanduser("~") - filters = {'SBML(*.xml)': 'SBML','Genesis(*.g)':'Genesis'} - #filename,filter_ = QtGui.QFileDialog.getSaveFileNameAndFilter(None,'Save File',dirpath,';;'.join(filters)) - filename,filter_ = QtGui.QFileDialog.getSaveFileNameAndFilter(None,'Save File',dirpath,"SBML(*.xml);;Genesis(*.g)") - extension = "" - if str(filename).rfind('.') != -1: - filename = filename[:str(filename).rfind('.')] - if str(filter_).rfind('.') != -1: - extension = filter_[str(filter_).rfind('.'):len(filter_)-1] - - if filename: - filename = filename - if filters[str(filter_)] == 'SBML': - self.coOrdinates = {} - self.plugin = KkitEditorView(self).getCentralWidget().plugin - self.coOrdinates = KkitEditorView(self).getCentralWidget().getsceneCord() - #writeerror = moose.writeSBML(self.modelRoot,str(filename),self.coOrdinates) - writeerror = -2 - conisitencyMessages = "" - writtentofile = "/test.xml" - writeerror,consistencyMessages,writtentofile = moose.SBML.mooseWriteSBML(self.modelRoot,str(filename),self.coOrdinates) - if writeerror == -2: - #QtGui.QMessageBox.warning(None,'Could not save the Model','\n WriteSBML : This copy of MOOSE has not been compiled with SBML writing support.') - QtGui.QMessageBox.warning(None,'Could not save the Model',consistencyMessages) - elif writeerror == -1: - QtGui.QMessageBox.warning(None,'Could not save the Model','\n This model is not valid SBML Model, failed in the consistency check') - elif writeerror == 1: - QtGui.QMessageBox.information(None,'Saved the Model','\n File saved to \'{filename}\''.format(filename =filename+'.xml'),QtGui.QMessageBox.Ok) - elif writeerror == 0: - QtGui.QMessageBox.information(None,'Could not save the Model','\nThe filename could not be opened for writing') - - elif filters[str(filter_)] == 'Genesis': - mdtype = moose.Annotator(self.modelRoot+'/info') - self.coOrdinates = {} - ss = KkitEditorView(self).getCentralWidget().mooseId_GObj - for k,v in ss.items(): - if moose.exists(moose.element(k).path+'/info'): - annoInfo = Annotator(k.path+'/info') - #co-ordinates will be in decimals converting to int which should be b/w 0 to 10 - x = annoInfo.x * 10 - y = -annoInfo.y * 10 - self.coOrdinates[k] = {'x':x, 'y':y} - - error,written = mooseWriteKkit(self.modelRoot,str(filename),self.coOrdinates) - if written == False: - QtGui.QMessageBox.information(None,'Could not save the Model','\nCheck the file') - else: - if error == "": - QtGui.QMessageBox.information(None,'Saved the Model','\n File saved to \'{filename}\''.format(filename =filename+'.g'),QtGui.QMessageBox.Ok) - else: - status = QtCore.QString("File saved but %2").arg(error); - QtGui.QMessageBox.information(None,'Saved the Model but ...','{error}'.format(error=error),QtGui.QMessageBox.Ok) - - def getPreviousPlugin(self): - return None - - def getNextPlugin(self): - return None - - def getAdjacentPlugins(self): - return [] - - def getViews(self): - return self._views - - def getCurrentView(self): - return self.currentView - - def getEditorView(self): - if not hasattr(self, 'editorView'): - #self.editorView = KkitEditorView(self, self.dataTable) - self.editorView = KkitEditorView(self) - self.editorView.getCentralWidget().editObject.connect(self.mainWindow.objectEditSlot) - #self.editorView.GrViewresize(self) - #self.editorView.connect(self,QtCore.SIGNAL("resize(QResizeEvent)"),self.editorView.GrViewresize) - self.currentView = self.editorView - return self.editorView - - def getRunView(self): - if self.view is None: - self.view = AnotherKkitRunView(self.modelRoot, self) - return self.view - - - if self.view is not None: return AnotherKkitRunView(self.modelRoot, self) - if self.view is not None: return self.view - self.view = RunView(self.modelRoot, self) - graphView = self.view._centralWidget - graphView.setDataRoot(self.modelRoot) - graphView.plotAllData() - schedulingDockWidget = self.view.getSchedulingDockWidget().widget() - self._kkitWidget = self.view.plugin.getEditorView().getCentralWidget() - #self.runView = KkitRunView(self,self.dataTable) - self.runView = KkitRunView(self, self._kkitWidget) - self.currentRunView = self.ruAnotherKkitRunViewnView.getCentralWidget() - - #schedulingDockWidget.runner.update.connect(self.currentRunView.changeBgSize) - #schedulingDockWidget.runner.resetAndRun.connect(self.currentRunView.resetColor) - graphView.layout().addWidget(self.currentRunView,0,0,2,1) - return self.view - -class AnotherKkitRunView(RunView): - - def __init__(self, modelRoot, plugin,*args): - RunView.__init__(self, modelRoot, plugin, *args) - self.modelRoot = modelRoot - self.plugin = plugin - self.schedular = None - - def setSolverFromSettings(self, chemicalSettings): - self.setSolver(self.modelRoot, - chemicalSettings["simulation"]["solver"]) - - def createCentralWidget(self): - self._centralWidget = RunWidget.RunWidget(self.modelRoot) - self.kkitRunView = KkitRunView(self.plugin) - self.plotWidgetContainer = PlotWidgetContainer(self.modelRoot) - self._centralWidget.setChildWidget(self.kkitRunView.getCentralWidget(), False, 0, 0, 1, 1) - self._centralWidget.setChildWidget(self.plotWidgetContainer, False, 0, 1, 1, 2) - self._centralWidget.setPlotWidgetContainer(self.plotWidgetContainer) - self.schedular = self.getSchedulingDockWidget().widget() - self.schedular.runner.simulationProgressed.connect(self.kkitRunView.getCentralWidget().updateValue) - self.schedular.runner.simulationProgressed.connect(self.kkitRunView.getCentralWidget().changeBgSize) - self.schedular.runner.simulationReset.connect(self.kkitRunView.getCentralWidget().resetColor) - # self.schedular.runner.simulationReset.connect(self.setSolver) - self.schedular.preferences.applyChemicalSettings.connect(self.setSolverFromSettings) - compt = moose.wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]') - ann = moose.Annotator(self.modelRoot+'/info') - if compt: - #self.runTime = (moose.Annotator(self.modelRoot+'/info')).runtime - #solver = (moose.Annotator(self.modelRoot+'/info')).solver - self.runTime = moose.element(ann).runtime - solver = moose.element(ann).solver - else: - self.runTime = 100 - solver = "gsl" - self.schedular.simulationRuntime.setText(str(self.runTime)) - #preferences - chemprefs = self.schedular.preferences.getChemicalPreferences() - c = moose.Clock('/clock') - self.simulationdt = c.tickDt[11] - self.plotdt = c.tickDt[18] - chemprefs["simulation"]["simulation-dt"] = self.simulationdt - chemprefs["simulation"]["plot-update-interval"] = self.plotdt - chemprefs["simulation"]["gui-update-interval"] = 2 * self.plotdt - chemprefs["simulation"]["solver"] = "Runge Kutta" - if solver == "gsl": - chemprefs["simulation"]["solver"] = "Runge Kutta" - elif solver == "gssa": - chemprefs["simulation"]["solver"] = "Gillespie" - elif solver == "ee" or solver == " ": - chemprefs["simulation"]["solver"] = "Exponential Euler" - else: - chemprefs["simulation"]["solver"] = "Runge Kutta" - self.schedular.preferences.setChemicalPreferences() - return self._centralWidget - - def setSolver(self, modelRoot,solver = None): - if solver == None: - reinit = mooseAddChemSolver(modelRoot,self.getSchedulingDockWidget().widget().solver) - if reinit: - self.getSchedulingDockWidget().widget().resetSimulation() - else: - reinit = mooseAddChemSolver(modelRoot,solver) - if reinit: - self.getSchedulingDockWidget().widget().resetSimulation() - - #self.kkitRunView.getCentralWidget().addSolver(solver) - - def getCentralWidget(self): - if self._centralWidget is None: - self.createCentralWidget() - return self._centralWidget - -class KkitRunView(MooseEditorView): - - #def __init__(self, plugin,dataTable): - def __init__(self, plugin): - MooseEditorView.__init__(self, plugin) - #self.dataTable =dataTable - self.plugin = plugin - ''' - def getToolPanes(self): - return super(KkitRunView, self).getToolPanes() - - def getLibraryPane(self): - return super(KkitRunView, self).getLibraryPane() - - def getOperationsWidget(self): - return super(KkitRunView, self).getOperationsPane() - - def getToolBars(self): - return self._toolBars - ''' - def getCentralWidget(self): - if self._centralWidget is None: - self._centralWidget = kineticRunWidget(self.plugin) - self._centralWidget.editor = self.plugin.editorView - # self._centralWidget.view.objectSelected.connect(self.plugin.mainWindow.objectEditSlot) - self._centralWidget.setModelRoot(self.plugin.modelRoot) - return self._centralWidget - -class KkitEditorView(MooseEditorView): - #def __init__(self, plugin, dataTable): - def __init__(self, plugin): - MooseEditorView.__init__(self, plugin) - ''' EditorView ''' - #self.dataTable = dataTable - #self.fileinsertMenu = QtGui.QMenu('&File') - # if not hasattr(self,'SaveModelAction'): - # #self.fileinsertMenu.addSeparator() - # self.saveModelAction = QtGui.QAction('SaveToGenesisFormat', self) - # self.saveModelAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+S", None, QtGui.QApplication.UnicodeUTF8)) - # self.connect(self.saveModelAction, QtCore.SIGNAL('triggered()'), self.SaveToGenesisSlot) - # self.fileinsertMenu.addAction(self.saveModelAction) - #self._menus.append(self.fileinsertMenu) - - # def SaveModelDialogSlot(self): - # type_sbml = 'SBML' - # filters = {'SBML(*.xml)': type_sbml} - # filename,filter_ = QtGui.QFileDialog.getSaveFileNameAndFilter(None,'Save File','',';;'.join(filters)) - # extension = "" - # if str(filename).rfind('.') != -1: - # filename = filename[:str(filename).rfind('.')] - # if str(filter_).rfind('.') != -1: - # extension = filter_[str(filter_).rfind('.'):len(filter_)-1] - # if filename: - # filename = filename+extension - # if filters[str(filter_)] == 'SBML': - # writeerror = moose.writeSBML(str(filename),self.plugin.modelRoot) - # if writeerror: - # QtGui.QMessageBox.warning(None,'Could not save the Model','\n Error in the consistency check') - # else: - # QtGui.QMessageBox.information(None,'Saved the Model','\n File Saved to \'{filename}\''.format(filename =filename),QtGui.QMessageBox.Ok) - ''' - def getToolPanes(self): - return super(KkitEditorView, self).getToolPanes() - - def getLibraryPane(self): - return super(KkitEditorView, self).getLibraryPane() - - def getOperationsWidget(self): - return super(KkitEditorView, self).getOperationsPane() - - def getToolBars(self): - return self._toolBars - ''' - def getCentralWidget(self): - if self._centralWidget is None: - self._centralWidget = kineticEditorWidget(self.plugin) - self._centralWidget.setModelRoot(self.plugin.modelRoot) - return self._centralWidget - -class KineticsWidget(EditorWidgetBase): - def __init__(self, plugin, *args): - EditorWidgetBase.__init__(self, *args) - self.plugin = plugin - self.border = 5 - self.comptPen = 5 - self.iconScale = 1 - self.arrowsize = 2 - self.reset() - - self.defaultSceneheight = 1#800#1000 - self.defaultScenewidth = 1#000#2400 - self.positionInfoExist = True - self.defaultComptsize = 5 - self.srcdesConnection = {} - self.meshEntry = {} - self.mooseId_GObj = {} - self.qGraCompt = {} - self.qGraGrp = {} - self.xyCord = {} - self.editor = None - - def reset(self): - self.createdItem = {} - #This are created at drawLine - self.lineItem_dict = {} - self.object2line = defaultdict(list) - self.itemignoreZooming = False - - if hasattr(self,'sceneContainer'): - self.sceneContainer.clear() - self.sceneContainer = QtGui.QGraphicsScene(self) - self.sceneContainer.setItemIndexMethod(QtGui.QGraphicsScene.NoIndex) - sceneDim = self.sceneContainer.itemsBoundingRect() - # if (sceneDim.width() == 0 and sceneDim.height() == 0): - # self.sceneContainer.setSceneRect(0,0,30,30) - # else: - #elf.sceneContainer.setSceneRect(self.sceneContainer.itemsBoundingRect()) - self.sceneContainer.setBackgroundBrush(QColor(230,220,219,120)) - - def getsceneCord(self): - self.cord = {} - self.view.setRefWidget("runView") - for item in self.sceneContainer.items(): - if isinstance(item,KineticsDisplayItem): - self.cord[item.mobj] = {'x':item.scenePos().x(),'y':item.scenePos().y()} - return self.cord - - def updateModelView(self): - self.getMooseObj() - #minmaxratiodict = {'xmin':self.xmin,'xmax':self.xmax,'ymin':self.ymin,'ymax':self.ymax,'xratio':self.xratio,'yratio':self.yratio} - if not self.m: - #At the time of model building - # when we want an empty GraphicView while creating new model, - # then remove all the view and add an empty view - if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget): - self.layout().removeWidget(self.view) - #self.sceneContainer.setSceneRect(-self.width()/2,-self.height()/2,self.width(),self.height()) - #self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict) - self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem) - if isinstance(self,kineticEditorWidget): - self.view.setRefWidget("editorView") - self.view.setAcceptDrops(True) - elif isinstance(self,kineticRunWidget): - self.view.setRefWidget("runView") - self.connect(self.view, QtCore.SIGNAL("dropped"), self.objectEditSlot) - hLayout = QtGui.QGridLayout(self) - self.setLayout(hLayout) - hLayout.addWidget(self.view,0,0) - else: - # Already created Model - # maxmium and minimum coordinates of the objects specified in kkit file. - #self.mooseObjOntoscene() - #self.drawLine_arrow() - if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget): - self.layout().removeWidget(self.view) - # self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict) - self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem) - if isinstance(self,kineticEditorWidget): - #self.getMooseObj() - self.mooseObjOntoscene() - self.drawLine_arrow() - self.view.setRefWidget("editorView") - self.view.setAcceptDrops(True) - self.connect(self.view, QtCore.SIGNAL("dropped"), self.objectEditSlot) - hLayout = QtGui.QGridLayout(self) - self.setLayout(hLayout) - hLayout.addWidget(self.view) - elif isinstance(self,kineticRunWidget): - self.view.setRefWidget("runView") - hLayout = QtGui.QGridLayout(self) - self.setLayout(hLayout) - hLayout.addWidget(self.view) - self.view.fitInView(self.sceneContainer.itemsBoundingRect().x()-10,self.sceneContainer.itemsBoundingRect().y()-10,self.sceneContainer.itemsBoundingRect().width()+20,self.sceneContainer.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio) - - def getMooseObj(self): - #This fun call 2 more function - # -- setupMeshObj(self.modelRoot), - # ----self.meshEntry has [meshEnt] = function: {}, Pool: {} etc - # setupItem - self.m = wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]') - if self.m: - self.srcdesConnection = {} - if self.meshEntry: - self.meshEntry.clear() - else: - self.meshEntry = {} - #self.meshEntry.clear= {} - # Compartment and its members are setup - #self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot) - - #self.meshEntry,xcord,ycord = setupMeshObj(self.modelRoot) - #self.positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \ - # and len(np.nonzero(ycord)[0]) == 0) - self.objPar,self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot) - self.autocoordinates = False - if self.srcdesConnection: - self.srcdesConnection.clear() - else: - self.srcdesConnection = {} - - setupItem(self.modelRoot,self.srcdesConnection) - #self.noPositionInfo = False - if not self.noPositionInfo: - self.autocoordinates = True - #self.xmin,self.xmax,self.ymin,self.ymax,self.autoCordinatepos = autoCoordinates(self.meshEntry,self.srcdesConnection) - autoCoordinates(self.meshEntry,self.srcdesConnection) - - self.size = QtCore.QSize(1000 ,550) - - ''' - if self.xmax-self.xmin != 0: - self.xratio = (self.size.width()-10)/(self.xmax-self.xmin) - else: self.xratio = self.size.width()-10 - - if self.ymax-self.ymin: - self.yratio = (self.size.height()-10)/(self.ymax-self.ymin) - else: self.yratio = (self.size.height()-10) - - self.xratio = int(self.xratio) - self.yratio = int(self.yratio) - if self.xratio == 0: - self.xratio = 1 - if self.yratio == 0: - self.yratio = 1 - ''' - def sizeHint(self): - return QtCore.QSize(800,400) - - def updateItemSlot(self, mooseObject): - #This is overridden by derived classes to connect appropriate - #slot for updating the display item. - #In this case if the name is updated from the keyboard both in mooseobj and gui gets updation - changedItem = '' - - for item in self.sceneContainer.items(): - if isinstance(item,PoolItem): - if mooseObject.getId() == element(item.mobj).getId(): - item.updateSlot() - #once the text is edited in editor, laydisplay gets updated in turn resize the length, positionChanged signal shd be emitted - self.positionChange(mooseObject) - self.view.removeConnector() - self.view.showConnector(item) - - def updateColorSlot(self,mooseObject, colour): - #Color slot for changing background color for Pool,Enz and group from objecteditor - anninfo = moose.Annotator(mooseObject.path+'/info') - textcolor,bgcolor = getColor(anninfo) - anninfo.color = str(colour.name()) - - if mooseObject.className == "Neutral": - item = self.qGraGrp[mooseObject] - item.setPen(QtGui.QPen(QtGui.QColor(colour),item.pen().width(),item.pen().style(),item.pen().capStyle(),item.pen().joinStyle()))# self.comptPen, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) - - elif (isinstance(mooseObject,PoolBase) or isinstance(mooseObject,EnzBase) ): - item = self.mooseId_GObj[mooseObject] - item.updateColor(colour) - - ''' - def mooseObjOntoscene(self): - # All the compartments are put first on to the scene \ - # Need to do: Check With upi if empty compartments exist - self.qGraCompt = {} - self.mooseId_GObj = {} - if self.qGraCompt: - self.qGraCompt.clear() - else: - self.qGraCompt = {} - if self.mooseId_GObj: - self.mooseId_GObj.clear() - else: - self.mooseId_GObj = {} - - for cmpt in sorted(self.meshEntry.iterkeys()): - self.createCompt(cmpt) - self.qGraCompt[cmpt] - #comptRef = self.qGraCompt[cmpt] - - #Enzymes of all the compartments are placed first, \ - # so that when cplx (which is pool object) queries for its parent, it gets its \ - # parent enz co-ordinates with respect to QGraphicsscene """ - - for cmpt,memb in self.meshEntry.items(): - for enzObj in find_index(memb,'enzyme'): - enzinfo = enzObj.path+'/info' - if enzObj.className == 'Enz': - enzItem = EnzItem(enzObj,self.qGraCompt[cmpt]) - else: - enzItem = MMEnzItem(enzObj,self.qGraCompt[cmpt]) - self.mooseId_GObj[element(enzObj.getId())] = enzItem - self.setupDisplay(enzinfo,enzItem,"enzyme") - - #self.setupSlot(enzObj,enzItem) - for cmpt,memb in self.meshEntry.items(): - for poolObj in find_index(memb,'pool'): - poolinfo = poolObj.path+'/info' - #depending on Editor Widget or Run widget pool will be created a PoolItem or PoolItemCircle - poolItem = self.makePoolItem(poolObj,self.qGraCompt[cmpt]) - self.mooseId_GObj[element(poolObj.getId())] = poolItem - self.setupDisplay(poolinfo,poolItem,"pool") - - for reaObj in find_index(memb,'reaction'): - reainfo = reaObj.path+'/info' - reaItem = ReacItem(reaObj,self.qGraCompt[cmpt]) - self.setupDisplay(reainfo,reaItem,"reaction") - self.mooseId_GObj[element(reaObj.getId())] = reaItem - - for tabObj in find_index(memb,'table'): - tabinfo = tabObj.path+'/info' - tabItem = TableItem(tabObj,self.qGraCompt[cmpt]) - self.setupDisplay(tabinfo,tabItem,"tab") - self.mooseId_GObj[element(tabObj.getId())] = tabItem - - for funcObj in find_index(memb,'function'): - funcinfo = moose.element(funcObj).path+'/info' - if funcObj.parent.className == "ZombieBufPool" or funcObj.parent.className == "BufPool": - funcinfo = moose.element(funcObj).path+'/info' - Af = Annotator(funcinfo) - funcParent =self.mooseId_GObj[element(funcObj.parent)] - elif funcObj.parent.className == "CubeMesh" or funcObj.parent.className == "CylMesh": - funcParent = self.qGraCompt[cmpt] - funcItem = FuncItem(funcObj,funcParent) - self.mooseId_GObj[element(funcObj.getId())] = funcItem - self.setupDisplay(funcinfo,funcItem,"Function") - - for cplxObj in find_index(memb,'cplx'): - cplxinfo = (cplxObj.parent).path+'/info' - p = element(cplxObj).parent - cplxItem = CplxItem(cplxObj,self.mooseId_GObj[element(cplxObj).parent]) - self.mooseId_GObj[element(cplxObj.getId())] = cplxItem - self.setupDisplay(cplxinfo,cplxItem,"cplx") - - # compartment's rectangle size is calculated depending on children - self.comptChildrenBoundingRect() - ''' - def mooseObjOntoscene(self): - # All the compartments are put first on to the scene \ - # Need to do: Check With upi if empty compartments exist - self.qGraCompt = {} - self.qGraGrp = {} - self.mooseId_GObj = {} - if self.qGraCompt: - self.qGraCompt.clear() - else: - self.qGraCompt = {} - - if self.qGraGrp: - self.qGraGrp.clear() - else: - self.qGraGrp = {} - - if self.qGraGrp: - self.qGraGrp.clear() - else: - self.qGraGrp = {} - - if self.mooseId_GObj: - self.mooseId_GObj.clear() - else: - self.mooseId_GObj = {} - for k,v in self.objPar.items(): - if isinstance(moose.element(k),moose.ChemCompt): - self.createCompt(k) - self.qGraCompt[k] - - elif isinstance(moose.element(k),Neutral): - if len(self.meshEntry[k]): - if isinstance(moose.element(v), moose.ChemCompt): - group_parent = self.qGraCompt[v] - elif isinstance(moose.element(v), moose.Neutral): - group_parent = self.qGraGrp[v] - self.createGroup(k,group_parent) - - for cmpt_grp,memb in self.meshEntry.items(): - if len(memb): - if isinstance(moose.element(cmpt_grp),moose.ChemCompt): - qtGrpparent = self.qGraCompt[cmpt_grp] - elif isinstance(moose.element(cmpt_grp), moose.Neutral): - qtGrpparent = self.qGraGrp[cmpt_grp] - for mclass in ["enzyme","pool","reaction","cplx","function","stimTab"]: - self.mObjontoscene(memb,mclass,qtGrpparent) - - self.groupChildrenBoundingRect() - # compartment's rectangle size is calculated depending on children - self.comptChildrenBoundingRect() - - def mObjontoscene(self,memb,mclass,qtGrpparent): - try: - value = memb[mclass] - except KeyError: - pass - else: - for mObj in memb[mclass]: - minfo = mObj.path+'/info' - if mObj.className in['Enz',"ZombieEnz"]: - mItem = EnzItem(mObj,qtGrpparent) - - elif mObj.className in['MMenz',"ZombieMMenz"]: - mItem = MMEnzItem(mObj,qtGrpparent) - - elif isinstance (moose.element(mObj),moose.PoolBase) and mclass != "cplx": - #depending on Editor Widget or Run widget pool will be created a PoolItem or PoolItemCircle - mItem = self.makePoolItem(mObj,qtGrpparent) - - elif isinstance (moose.element(mObj),moose.ReacBase): - mItem = ReacItem(mObj,qtGrpparent) - - elif mclass == "cplx": - minfo = (mObj.parent).path+'/info' - mItem = CplxItem(mObj,self.mooseId_GObj[element(mObj).parent]) - self.mooseId_GObj[element(mObj.getId())] = mItem - - elif mclass == "function": - if isinstance(moose.element(mObj.parent),moose.PoolBase): - minfo = moose.element(mObj).path+'/info' - Af = Annotator(minfo) - qtGrpparent = self.mooseId_GObj[element(mObj.parent)] - mItem = FuncItem(mObj,qtGrpparent) - - elif mclass == "stimTab": - minfo = mObj.path+'/info' - mItem = TableItem(mObj,qtGrpparent) - self.mooseId_GObj[element(mObj.getId())] = mItem - self.setupDisplay(minfo,mItem,mclass) - - def createGroup(self,key,parent): - self.new_GRP = GRPItem(parent,0,0,0,0,key) - self.qGraGrp[key] = self.new_GRP - self.new_GRP.setRect(20,20,20,20) - - def groupChildrenBoundingRect(self): - for k, v in self.qGraGrp.items(): - grpcolor = moose.Annotator(moose.element(k.path+'/info')).color - #Todo: One may need to calculate explicitly the boundary for Group also if there is a cross-group connection, then - # childrenBoundrect() will take the QPolygonItem position - rectcompt = v.childrenBoundingRect() - v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) - v.setPen(QtGui.QPen(Qt.QColor(grpcolor), self.comptPen, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) - - def comptChildrenBoundingRect(self): - comptlist = [] - for k, v in self.qGraCompt.items(): - # compartment's rectangle size is calculated depending on children - rectcompt = calculateChildBoundingRect(v) - v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) - v.setPen(QtGui.QPen(Qt.QColor(66,66,66,100), self.comptPen, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) - - def createCompt(self,key): - self.new_Compt = ComptItem(self,0,0,0,0,key) - self.qGraCompt[key] = self.new_Compt - self.new_Compt.setRect(10,10,10,10) - self.sceneContainer.addItem(self.new_Compt) - - def setupDisplay(self,info,graphicalObj,objClass): - Annoinfo = Annotator(info) - # For Reaction and Complex object I have skipped the process to get the facecolor and background color as \ - # we are not using these colors for displaying the object so just passing dummy color white - if( objClass == "reaction" or objClass == "cplx" or objClass == "Function" or objClass == "StimulusTable"): - textcolor,bgcolor = QColor("white"),QColor("white") - elif(objClass == "enzyme"): - textcolor,bgcolor = getColor(info) - if bgcolor.name() == "#ffffff" or bgcolor == "white": - bgcolor = getRandColor() - Annoinfo.color = str(bgcolor.name()) - else: - textcolor,bgcolor = getColor(info) - if bgcolor.name() == "#ffffff" or bgcolor == "white": - bgcolor = getRandColor() - Annoinfo.color = str(bgcolor.name()) - if isinstance(self,kineticEditorWidget): - funct = ["Function","ZombieFunction"] - comptt = ["CubeMesh","CylMesh"] - - if objClass in funct: - poolt = ["ZombieBufPool","BufPool"] - if graphicalObj.mobj.parent.className in poolt: - xpos = 0 - ypos = 30 - if graphicalObj.mobj.parent.className in comptt: - xpos,ypos = self.positioninfo(info) - else: - xpos,ypos = self.positioninfo(info) - - elif isinstance(self,kineticRunWidget): - self.editormooseId_GObj = self.editor.getCentralWidget().mooseId_GObj - editorItem = self.editormooseId_GObj[moose.element(info).parent] - xpos = editorItem.scenePos().x() - ypos = editorItem.scenePos().y() - graphicalObj.setDisplayProperties(xpos,ypos,textcolor,bgcolor) - - - def positioninfo(self,iteminfo): - '''By this time, model loaded from kkit,cspace,SBML would have info field created and co-ordinates are added - either by autocoordinates (for cspace,SBML(unless it is not saved from moose)) or from kkit - ''' - - x = float(element(iteminfo).getField('x')) - y = float(element(iteminfo).getField('y')) - #print " positioninfo", iteminfo,x,y - # if moose.Annotator(self.plugin.modelRoot+'/info').modeltype == 'kkit': - # x = self.defaultScenewidth * float(element(iteminfo).getField('x')) - # y = self.defaultSceneheight * float(element(iteminfo).getField('y')) - # print " positioninfo ",iteminfo, element(iteminfo).getField('x'), element(iteminfo).getField('y'), x, y - - # #x = x /self.defaultScenewidth - # #y = y /self.defaultSceneheight - # else: - # x = float(element(iteminfo).getField('x')) - # y = float(element(iteminfo).getField('y')) - # self.defaultScenewidth = 1 - # self.defaultSceneheight = 1 - return(x,y) - - def drawLine_arrow(self, itemignoreZooming=False): - for inn,out in self.srcdesConnection.items(): - #print "inn ",inn, " out ",out - # self.srcdesConnection is dictionary which contains key,value \ - # key is Enzyme or Reaction and value [[list of substrate],[list of product]] (tuple) - # key is Function and value is [list of pool] (list) - - #src = self.mooseId_GObj[inn] - linetype = "regular" - if isinstance(out,tuple): - src = self.mooseId_GObj[inn] - if len(out[0])== 0: - print (inn.className + ' : ' +inn.name+ " doesn't output message") - else: - for items in (items for items in out[0] ): - if re.search("xfer",element(items[0]).name): - xrefPool = items[0].name[:items[0].name.index("_xfer_")] - xrefCompt = items[0].name[items[0].name.index("_xfer_") + len("_xfer_"):] - orgCompt = moose.wildcardFind(self.modelRoot+'/##[FIELD(name)='+xrefCompt+']')[0] - orgPool = moose.wildcardFind(orgCompt.path+'/##[FIELD(name)='+xrefPool+']')[0] - itemslist = list(items) - itemslist[0] = orgPool - items = tuple(itemslist) - linetype = "crosscompt" - des = self.mooseId_GObj[element(items[0])] - self.lineCord(src,des,items,itemignoreZooming,linetype) - if len(out[1]) == 0: - print (inn.className + ' : ' +inn.name+ " doesn't output message") - else: - for items in (items for items in out[1] ): - if re.search("xfer",element(items[0]).name): - xrefPool = items[0].name[:items[0].name.index("_xfer_")] - xrefCompt = items[0].name[items[0].name.index("_xfer_") + len("_xfer_"):] - orgCompt = moose.wildcardFind(self.modelRoot+'/##[FIELD(name)='+xrefCompt+']')[0] - orgPool = moose.wildcardFind(orgCompt.path+'/##[FIELD(name)='+xrefPool+']')[0] - itemslist = list(items) - itemslist[0] = orgPool - items = tuple(itemslist) - linetype = "crosscompt" - des = self.mooseId_GObj[element(items[0])] - self.lineCord(src,des,items,itemignoreZooming,linetype) - elif isinstance(out,list): - if len(out) == 0: - if inn.className == "StimulusTable": - print (inn.name +" doesn't have output") - elif inn.className == "ZombieFunction" or inn.className == "Function": - print (inn.name + " doesn't have sumtotal ") - else: - src = self.mooseId_GObj[inn] - for items in (items for items in out ): - if re.search("xfer",element(items[0]).name): - xrefPool = items[0].name[:items[0].name.index("_xfer_")] - xrefCompt = items[0].name[items[0].name.index("_xfer_") + len("_xfer_"):] - orgCompt = moose.wildcardFind(self.modelRoot+'/##[FIELD(name)='+xrefCompt+']')[0] - orgPool = moose.wildcardFind(orgCompt.path+'/##[FIELD(name)='+xrefPool+']')[0] - itemslist = list(items) - itemslist[0] = orgPool - items = tuple(itemslist) - linetype = "crosscompt" - des = self.mooseId_GObj[element(items[0])] - self.lineCord(src,des,items,itemignoreZooming,linetype) - - def lineCord(self,src,des,type_no,itemignoreZooming,linetype): - srcdes_list = [] - endtype = type_no[1] - line = 0 - if (src == "") and (des == ""): - print ("Source or destination is missing or incorrect") - return - srcdes_list = [src,des,endtype,line] - arrow = calcArrow(srcdes_list,itemignoreZooming,self.iconScale) - self.drawLine(srcdes_list,arrow,linetype) - - while(type_no[2] > 1 and line <= (type_no[2]-1)): - srcdes_list =[src,des,endtype,line] - arrow = calcArrow(srcdes_list,itemignoreZooming,self.iconScale) - self.drawLine(srcdes_list,arrow,linetype) - line = line +1 - - if type_no[2] > 5: - print ("Higher order reaction will not be displayed") - - def drawLine(self,srcdes_list,arrow,linetype="solid"): - src = srcdes_list[0] - des = srcdes_list[1] - endtype = srcdes_list[2] - line = srcdes_list[3] - source = element(next((k for k,v in self.mooseId_GObj.items() if v == src), None)) - for l,v,et,o in self.object2line[src]: - if v == des and o ==line: - l.setPolygon(arrow) - arrowPen = l.pen() - arrowPenWidth = self.arrowsize*self.iconScale - arrowPen.setColor(l.pen().color()) - arrowPen.setWidth(arrowPenWidth) - l.setPen(arrowPen) - return - qgLineitem = self.sceneContainer.addPolygon(arrow) - qgLineitem.setParentItem(src.parentItem()) - pen = QtGui.QPen(QtCore.Qt.green, 0, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin) - if linetype == "crosscompt": - pen.setStyle(Qt.Qt.CustomDashLine) - pen.setDashPattern([1, 5, 1, 5]) - - pen.setWidth(self.arrowsize) - - # Green is default color moose.ReacBase and derivatives - already set above - if isinstance(source, EnzBase): - if ( (endtype == 's') or (endtype == 'p')): - pen.setColor(QtCore.Qt.red) - elif(endtype != 'cplx'): - p1 = (next((k for k,v in self.mooseId_GObj.items() if v == src), None)) - pinfo = p1.parent.path+'/info' - color,bgcolor = getColor(pinfo) - #color = QColor(color[0],color[1],color[2]) - pen.setColor(bgcolor) - - elif isinstance(source, moose.PoolBase) or isinstance(source,moose.Function): - pen.setColor(QtCore.Qt.blue) - elif isinstance(source,moose.StimulusTable): - pen.setColor(QtCore.Qt.yellow) - self.lineItem_dict[qgLineitem] = srcdes_list - self.object2line[ src ].append( ( qgLineitem, des,endtype,line) ) - self.object2line[ des ].append( ( qgLineitem, src,endtype,line ) ) - qgLineitem.setPen(pen) - - def positionChange(self,mooseObject): - #If the item position changes, the corresponding arrow's are calculated - print mooseObject - for k, v in self.qGraCompt.items(): - for rectChilditem in v.childItems(): - self.updateArrow(rectChilditem) - if isinstance(rectChilditem,GRPItem): - for grpChilditem in rectChilditem.childItems(): - self.updateArrow(grpChilditem) - if isinstance(grpChilditem,KineticsDisplayItem): - if moose.exists(grpChilditem.mobj.path+'/info'): - #print grpChilditem.mobj.name, grpChilditem.scenePos() - moose.element(grpChilditem.mobj.path+'/info').x = grpChilditem.scenePos().x() - moose.element(grpChilditem.mobj.path+'/info').y = grpChilditem.scenePos().y() - #self.updateGrpSize(rectChilditem) - if isinstance(rectChilditem,KineticsDisplayItem): - if moose.exists(rectChilditem.mobj.path+'/info'): - #print rectChilditem.mobj.name, rectChilditem.scenePos() - moose.element(rectChilditem.mobj.path+'/info').x = rectChilditem.scenePos().x() - moose.element(rectChilditem.mobj.path+'/info').y = rectChilditem.scenePos().y() - - rectcompt = calculateChildBoundingRect(v) - comptBoundingRect = v.boundingRect() - if not comptBoundingRect.contains(rectcompt): - self.updateCompartmentSize(v) - else: - rectcompt = calculateChildBoundingRect(v) - v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) - - def positionChange_old(self,mooseObject): - #If the item position changes, the corresponding arrow's are calculated - if isinstance(element(mooseObject),ChemCompt): - for k, v in self.qGraCompt.items(): - mesh = moose.element(mooseObject).path - if k.path == mesh: - for rectChilditem in v.childItems(): - if isinstance(rectChilditem, KineticsDisplayItem): - if moose.exists(rectChilditem.mobj.path): - iInfo = rectChilditem.mobj.path+'/info' - anno = moose.Annotator(iInfo) - #storing scenePos back to annotator file for further use - x = rectChilditem.scenePos().x() - y = rectChilditem.scenePos().y() - #anno.x = x - #anno.y = y - if isinstance(moose.element(rectChilditem.mobj.path),PoolBase): - t = moose.element(rectChilditem.mobj.path) - moose.element(t).children - for items in moose.element(t).children: - if isinstance(moose.element(items),Function): - test = moose.element(items.path+'/x') - for i in moose.element(test).neighbors['input']: - j = self.mooseId_GObj[moose.element(i)] - self.updateArrow(j) - self.updateArrow(rectChilditem) - elif element(mooseObject).className == 'Neutral': - for k,v in self.qGraGrp.items(): - for grpChilditem in v.childItems(): - if isinstance(grpChilditem, KineticsDisplayItem): - if moose.exists(grpChilditem.mobj.path): - iInfo = grpChilditem.mobj.path+'/info' - anno = moose.Annotator(iInfo) - #storing scenePos back to annotator file for further use - x = grpChilditem.scenePos().x() - y = grpChilditem.scenePos().y() - #anno.x = x - #anno.y = y - - if isinstance(moose.element(grpChilditem.mobj.path),PoolBase): - t = moose.element(grpChilditem.mobj.path) - moose.element(t).children - for items in moose.element(t).children: - if isinstance(moose.element(items),Function): - test = moose.element(items.path+'/x') - for i in moose.element(test).neighbors['input']: - j = self.mooseId_GObj[moose.element(i)] - self.updateArrow(j) - self.updateArrow(grpChilditem) - # grpcompt = self.qGraCompt[self.objPar[k]] - # rectcompt = calculateChildBoundingRect(grpcompt) - rectgrp = calculateChildBoundingRect(v) - v.setRect(rectgrp.x()-10,rectgrp.y()-10,(rectgrp.width()+20),(rectgrp.height()+20)) - for k, v in self.qGraCompt.items(): - #rectcompt = v.childrenBoundingRect() - rectcompt = calculateChildBoundingRect(v) - comptBoundingRect = v.boundingRect() - if not comptBoundingRect.contains(rectcompt): - self.updateCompartmentSize(v) - - else: - rectcompt = calculateChildBoundingRect(v) - v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) - else: - mobj = self.mooseId_GObj[element(mooseObject)] - self.updateArrow(mobj) - # elePath = moose.element(mooseObject).path - # pos = elePath.find('/',1) - # l = elePath[0:pos] - # linfo = moose.Annotator(l+'/info') - # if moose.exists(l): - # #anno = moose.Annotator(linfo) - # # if moose.Annotator(self.plugin.modelRoot+'/info').modeltype == 'kkit': - # # x = mobj.scenePos().x()/self.defaultScenewidth - # # y = mobj.scenePos().y()/self.defaultSceneheight - # # else: - # # x = mobj.scenePos().x() - # # y = mobj.scenePos().y() - # x = mobj.scenePos().x() - # y = mobj.scenePos().y() - #print " x and y at 863 ",mobj.scenePos() - # for gk,gv in self.qGraGrp.items(): - # rectgrp = calculateChildBoundingRect(gv) - # grpBoundingRect = gv.boundingRect() - # if not grpBoundingRect.contains(rectgrp): - # self.updateCompartmentSize(v) - # else: - # gv.setRect(rectgrp.x()-10,rectgrp.y()-10,(rectgrp.width()+20),(rectgrp.height()+20)) - for k, v in self.qGraCompt.items(): - #rectcompt = v.childrenBoundingRect() - rectcompt = calculateChildBoundingRect(v) - comptBoundingRect = v.boundingRect() - if not comptBoundingRect.contains(rectcompt): - self.updateCompartmentSize(v) - - else: - rectcompt = calculateChildBoundingRect(v) - v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20)) - # print " position change " - # for item in self.sceneContainer.items(): - # if isinstance(item,KineticsDisplayItem): - # print item.mobj.name, moose.element(item.mobj.path+'/info').x,moose.element(item.mobj.path+'/info').y - - def updateGrpSize(self,grp): - compartmentBoundary = grp.rect() - - childrenBoundary = calculateChildBoundingRect(grp) - x = childrenBoundary.x() - y = childrenBoundary.y() - height = childrenBoundary.height() - width = childrenBoundary.width() - grp.setRect( x-10 - , y-10 - , width + 20 - , height + 20 - ) - def updateCompartmentSize(self, compartment): - compartmentBoundary = compartment.rect() - childrenBoundary = calculateChildBoundingRect(compartment) - x = min(compartmentBoundary.x(), childrenBoundary.x()) - y = min(compartmentBoundary.y(), childrenBoundary.y()) - width = max(compartmentBoundary.width(), childrenBoundary.width()) - height = max(compartmentBoundary.height(), childrenBoundary.height()) - compartment.setRect( x-10 - , y-10 - , width + 20 - , height + 20 - ) - - def updateArrow(self,qGTextitem): - #if there is no arrow to update then return - if qGTextitem not in self.object2line: - return - listItem = self.object2line[qGTextitem] - for ql, va,endtype,order in self.object2line[qGTextitem]: - srcdes = [] - srcdes = self.lineItem_dict[ql] - # Checking if src (srcdes[0]) or des (srcdes[1]) is ZombieEnz, - # if yes then need to check if cplx is connected to any mooseObject, - # so that when Enzyme is moved, cplx connected arrow to other mooseObject(poolItem) should also be updated - if( type(srcdes[0]) == EnzItem or type(srcdes[0] == MMEnzItem)): - self.cplxUpdatearrow(srcdes[0]) - elif( type(srcdes[1]) == EnzItem or type(srcdes[1] == MMEnzItem)): - self.cplxUpdatearrow(srcdes[1]) - # For calcArrow(src,des,endtype,itemignoreZooming) is to be provided - arrow = calcArrow(srcdes,self.itemignoreZooming,self.iconScale) - ql.setPolygon(arrow) - - def cplxUpdatearrow(self,srcdes): - # srcdes which is 'EnzItem' from this,get ChildItems are retrived (b'cos cplx is child of zombieEnz) - #And cplxItem is passed for updatearrow - for item in srcdes.childItems(): - if isinstance(item,CplxItem): - self.updateArrow(item) - - def positionChange1(self,mooseObject): - #If the item position changes, the corresponding arrow's are calculated - if ( (isinstance(element(mooseObject),CubeMesh)) or (isinstance(element(mooseObject),CylMesh))): - v = self.qGraCompt[mooseObject] - for rectChilditem in v.childItems(): - self.updateArrow(rectChilditem) - else: - mobj = self.mooseId_GObj[mooseObject.getId()] - self.updateArrow(mobj) - mooseObjcompt = self.findparent(mooseObject) - v = self.qGraCompt[mooseObjcompt] - #childBoundingRect = v.childrenBoundingRect() - childBoundingRect = calculateChildBoundingRect(v) - comptBoundingRect = v.boundingRect() - rectcompt = comptBoundingRect.united(childBoundingRect) - comptPen = v.pen() - comptWidth = 5 - comptPen.setWidth(comptWidth) - v.setPen(comptPen) - if not comptBoundingRect.contains(childBoundingRect): - v.setRect(rectcompt.x()-comptWidth,rectcompt.y()-comptWidth,rectcompt.width()+(comptWidth*2),rectcompt.height()+(comptWidth*2)) - -class kineticEditorWidget(KineticsWidget): - def __init__(self, plugin,*args): - - KineticsWidget.__init__(self, plugin, *args) - self.plugin = plugin - self.insertMenu = QtGui.QMenu('&Insert') - self._menus.append(self.insertMenu) - self.insertMapper = QtCore.QSignalMapper(self) - classlist = ['CubeMesh','CylMesh','Pool','BufPool','Function','Reac','Enz','MMenz','StimulusTable'] - self.toolTipinfo = { "CubeMesh":"", - "CylMesh" : "", - "Pool":"A Pool is a collection of molecules of a given species in a given cellular compartment.\n It can undergo reactions that convert it into other pool(s). \nParameters: initConc (Initial concentration), diffConst (diffusion constant). Variable: conc (Concentration)", - "BufPool":"A BufPool is a buffered pool. \nIt is a collection of molecules of a given species in a given cellular compartment, that are always present at the same concentration.\n This is set by the initConc parameter. \nIt can undergo reactions in the same way as a pool.", - "Function":"A Func computes an arbitrary mathematical expression of one or more input concentrations of Pools. The output can be used to control the concentration of another Pool, or as an input to another Func", - "StimulusTable":"A StimulusTable stores an array of values that are read out during a simulation, and typically control the concentration of one of the pools in the model. \nParameters: size of table, values of entries, start and stop times, and an optional loopTime that defines the period over which the StimulusTable should loop around to repeat its values", - "Reac":"A Reac is a chemical reaction that converts substrates into products, and back. \nThe rates of these conversions are specified by the rate constants Kf and Kb respectively.", - "MMenz":"An MMenz is the Michaelis-Menten version of an enzyme activity of a given Pool.\n The MMenz must be created on a pool and can only catalyze a single reaction with a specified substrate(s). \nIf a given enzyme species can have multiple substrates, then multiple MMenz activites must be created on the parent Pool. \nThe rate of an MMenz is V [S].[E].kcat/(Km + [S]). There is no enzyme-substrate complex. Parameters: Km and kcat.", - "Enz":"An Enz is an enzyme activity of a given Pool. The Enz must be created on a pool and can only catalyze a single reaction with a specified substrate(s). \nIf a given enzyme species can have multiple substrates, then multiple Enz activities must be created on the parent Pool. \nThe reaction for an Enz is E + S <===> E.S ---> E + P. \nThis means that a new Pool, the enzyme-substrate complex E.S, is always formed when you create an Enz. \nParameters: Km and kcat, or alternatively, K1, K2 and K3. Km = (K2+K3)/K1" - - } - insertMapper, actions = self.getInsertActions(classlist) - for action in actions: - self.insertMenu.addAction(action) - doc = self.toolTipinfo[str(action.text())] - if doc == "": - classname = str(action.text()) - doc = moose.element('/classes/%s' % (classname)).docs - doc = doc.split('Description:')[-1].split('Name:')[0].strip() - action.setToolTip(doc) - - def GrViewresize(self,event): - #when Gui resize and event is sent which inturn call resizeEvent of qgraphicsview - pass - #self.view.resizeEvent1(event) - - def makePoolItem(self, poolObj, qGraCompt): - return PoolItem(poolObj, qGraCompt) - - def getToolBars(self): - #Add specific tool items with respect to kkit - if not hasattr(self, '_insertToolBar'): - self._insertToolBar = QtGui.QToolBar('Insert') - self._toolBars.append(self._insertToolBar) - for action in self.insertMenu.actions(): - button = MToolButton() - button.setDefaultAction(action) - #set the unicode instead of image by setting - #button.setText(unicode(u'\u20de')) - Iconpath = os.path.join(config.MOOSE_GUI_DIR, 'icons/classIcon/') - button.setIcon(QtGui.QIcon(Iconpath+action.text()+".png")) - #button.setIcon(QtGui.QIcon("icons/classIcon/"+action.text()+".png")) - #button.setIconSize(QtCore.QSize(200,200)) - self._insertToolBar.addWidget(button) - return self._toolBars - -class kineticRunWidget(KineticsWidget): - def __init__(self, plugin, *args): - KineticsWidget.__init__(self, plugin,*args) - - def showEvent(self, event): - self.refresh() - # pass - def refresh(self): - self.sceneContainer.clear() - self.Comptexist = wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]') - if self.Comptexist: - # pass - self.getMooseObj() - self.mooseObjOntoscene() - self.drawLine_arrow(itemignoreZooming=False) - - def makePoolItem(self, poolObj, qGraCompt): - return PoolItemCircle(poolObj, qGraCompt) - - def getToolBars(self): - return self._toolBars - - def updateValue(self): - for item in self.sceneContainer.items(): - if isinstance(item,ReacItem) or isinstance(item,MMEnzItem) or isinstance(item,EnzItem) or isinstance(item,PoolItemCircle) or isinstance(item,CplxItem): - item.updateValue(item.mobj) - - def changeBgSize(self): - for item in self.sceneContainer.items(): - if isinstance(item,PoolItemCircle): - initialConc = moose.element(item.mobj).concInit - presentConc = moose.element(item.mobj).conc - if initialConc != 0: - ratio = presentConc/initialConc - else: - # multipying by 1000 b'cos moose concentration is in milli in moose - ratio = presentConc - #print "ratio",item.mobj,ratio - if ratio > '10': - ratio = 9 - if ratio < '0.0': - ratio =0.1 - #print "size ",ratio - item.updateRect(math.sqrt(abs(ratio))) - - def resetColor(self): - for item in self.sceneContainer.items(): - if isinstance(item,PoolItemCircle): - item.returnEllispeSize() -if __name__ == "__main__": - app = QtGui.QApplication(sys.argv) - size = QtCore.QSize(1024 ,768) - #modelPath = 'Kholodenko' - modelPath = 'acc27' - #modelPath = 'acc8' - #modelPath = '3ARECB' - #modelPath = '3AreacB' - #modelPath = '5AreacB' - itemignoreZooming = False - try: - filepath = '../../Demos/Genesis_files/'+modelPath+'.g' - filepath = '/home/harsha/genesis_files/gfile/'+modelPath+'.g' - print( "%s" %(filepath)) - f = open(filepath, "r") - loadModel(filepath,'/'+modelPath) - - #moose.le('/'+modelPath+'/kinetics') - dt = KineticsWidget() - dt.modelRoot ='/'+modelPath - ''' Loading moose signalling model in python ''' - #execfile('/home/harsha/BuildQ/Demos/Genesis_files/scriptKineticModel.py') - #dt.modelRoot = '/model' - - dt.updateModelView() - dt.show() - - except IOError, what: - (errno, strerror) = what - print ("Error number",errno,"(%s)" %(strerror)) - sys.exit(0) - sys.exit(app.exec_()) diff --git a/plugins/kkitOrdinateUtil.py b/plugins/kkitOrdinateUtil.py deleted file mode 100644 index 4d27c9a..0000000 --- a/plugins/kkitOrdinateUtil.py +++ /dev/null @@ -1,488 +0,0 @@ -__author__ = "HarshaRani" -__credits__ = ["Upi Lab"] -__license__ = "GPL3" -__version__ = "1.0.0" -__maintainer__ = "HarshaRani" -__email__ = "hrani@ncbs.res.in" -__status__ = "Development" -__updated__ = "Oct 26 2018" - -''' -2018 -Oct 26: xfer molecules are not put into screen -Sep 28: to zoom the kkit co-ordinates a factor of w=1000 and h=800 is multipled here -2017 -Oct 18: moved some function to kkitUtil -getxyCord, etc function are added -''' -import collections -from moose import * -import numpy as np -from moose import wildcardFind,element,PoolBase,CplxEnzBase,Annotator,exists -from networkx.drawing.nx_agraph import graphviz_layout -import numpy as np -import networkx as nx -from kkitUtil import getRandColor,colorCheck,findCompartment, findGroup, findGroup_compt, mooseIsInstance -from PyQt4.QtGui import QColor -import re -import moose._moose as moose - -def getxyCord(xcord,ycord,list1): - for item in list1: - # if isinstance(item,Function): - # objInfo = element(item.parent).path+'/info' - # else: - # objInfo = item.path+'/info' - if not isinstance(item,Function): - objInfo = item.path+'/info' - xcord.append(xyPosition(objInfo,'x')) - ycord.append(xyPosition(objInfo,'y')) - -def xyPosition(objInfo,xory): - try: - return(float(element(objInfo).getField(xory))) - except ValueError: - return (float(0)) -''' -def mooseIsInstance(melement, classNames): - return element(melement).__class__.__name__ in classNames - - -def findCompartment(melement): - while not mooseIsInstance(melement, ["CubeMesh", "CyclMesh"]): - melement = melement.parent - return melement - -def findGroup(melement): - while not mooseIsInstance(melement, ["Neutral"]): - melement = melement.parent - return melement - -def findGroup_compt(melement): - while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CyclMesh"])): - melement = melement.parent - return melement -''' -def populateMeshEntry(meshEntry,parent,types,obj): - #print " parent ",parent, "types ",types, " obj ",obj - try: - value = meshEntry[element(parent.path)][types] - except KeyError: - # Key is not present - meshEntry[element(parent.path)].update({types :[element(obj)]}) - else: - mlist = meshEntry[element(parent.path)][types] - mlist.append(element(obj)) -def updateMeshObj(modelRoot): - print " updateMeshObj " - meshEntry = {} - if meshEntry: - meshEntry.clear() - else: - meshEntry = {} - - objPar = collections.OrderedDict() - for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'): - groupColor = [] - try: - value = meshEntry[element(compt)] - except KeyError: - # Compt is not present - meshEntry[element(compt)] = {} - objPar[element(compt)] = element('/') - - for grp in wildcardFind(compt.path+'/##[TYPE=Neutral]'): - test = [x for x in wildcardFind(element(grp).path+'/#') if x.className in ["Pool","Reac","Enz"]] - grp_cmpt = findGroup_compt(grp.parent) - - try: - value = meshEntry[element(grp)] - except KeyError: - # Grp is not present - meshEntry[element(grp)] = {} - objPar[element(grp)] = element(grp_cmpt) - - for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'): - for m in wildcardFind(compt.path+'/##[ISA=PoolBase]'): - grp_cmpt = findGroup_compt(m) - if isinstance(element(grp_cmpt),Neutral): - if isinstance(element(m.parent),EnzBase): - populateMeshEntry(meshEntry,grp_cmpt,"cplx",m) - else: - populateMeshEntry(meshEntry,grp_cmpt,"pool",m) - else: - if isinstance(element(m.parent),EnzBase): - populateMeshEntry(meshEntry,compt,"cplx",m) - else: - populateMeshEntry(meshEntry,compt,"pool",m) - - for r in wildcardFind(compt.path+'/##[ISA=ReacBase]'): - rgrp_cmpt = findGroup_compt(r) - if isinstance(element(rgrp_cmpt),Neutral): - populateMeshEntry(meshEntry,rgrp_cmpt,"reaction",r) - else: - populateMeshEntry(meshEntry,compt,"reaction",r) - - for e in wildcardFind(compt.path+'/##[ISA=EnzBase]'): - egrp_cmpt = findGroup_compt(e) - if isinstance(element(egrp_cmpt),Neutral): - populateMeshEntry(meshEntry,egrp_cmpt,"enzyme",e) - else: - populateMeshEntry(meshEntry,compt,"enzyme",e) - - for f in wildcardFind(compt.path+'/##[ISA=Function]'): - fgrp_cmpt = findGroup_compt(f) - if isinstance(element(fgrp_cmpt),Neutral): - populateMeshEntry(meshEntry,fgrp_cmpt,"function",f) - else: - populateMeshEntry(meshEntry,compt,"function",f) - - for t in wildcardFind(compt.path+'/##[ISA=StimulusTable]'): - tgrp_cmpt = findGroup_compt(t) - if isinstance(element(tgrp_cmpt),Neutral): - populateMeshEntry(meshEntry,tgrp_cmpt,"stimTab",t) - else: - populateMeshEntry(meshEntry,compt,"stimTab",t) - return(objPar,meshEntry) - -def setupMeshObj(modelRoot): - ''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \ - self.meshEntry with "key" as compartment, - value is key2:list where key2 represents moose object type,list of objects of a perticular type - e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist } - ''' - xmin = 0.0 - xmax = 1.0 - ymin = 0.0 - ymax = 1.0 - positionInfoExist = True - meshEntry = {} - if meshEntry: - meshEntry.clear() - else: - meshEntry = {} - xcord = [] - ycord = [] - n = 1 - objPar = collections.OrderedDict() - - for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'): - groupColor = [] - try: - value = meshEntry[element(compt)] - except KeyError: - # Compt is not present - meshEntry[element(compt)] = {} - objPar[element(compt)] = element('/') - - for grp in wildcardFind(compt.path+'/##[TYPE=Neutral]'): - test = [x for x in wildcardFind(element(grp).path+'/#') if x.className in ["Pool","Reac","Enz"]] - #if len(test) >1: - grpinfo = Annotator(element(grp).path+'/info') - validatecolor = colorCheck(grpinfo.color,"bg") - validatedgrpcolor = str(QColor(validatecolor).name()) - - groupColor.append(validatedgrpcolor) - grp_cmpt = findGroup_compt(grp.parent) - - try: - value = meshEntry[element(grp)] - except KeyError: - # Grp is not present - meshEntry[element(grp)] = {} - objPar[element(grp)] = element(grp_cmpt) - # if n > 1: - # validatecolor = colorCheck(grpinfo.color,"bg") - # validatedgrpcolor = str(QColor(validatecolor).name()) - # if validatedgrpcolor in groupColor: - # print " inside " - # c = getRandColor() - # print " c ",c, c.name() - # grpinfo.color = str(c.name()) - # groupColor.append(str(c.name())) - # print " groupColor ",grpinfo,grpinfo.color, groupColor - # n =n +1 - for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'): - for m in wildcardFind(compt.path+'/##[ISA=PoolBase]'): - if not re.search("xfer",m.name): - grp_cmpt = findGroup_compt(m) - xcord.append(xyPosition(m.path+'/info','x')) - ycord.append(xyPosition(m.path+'/info','y')) - if isinstance(element(grp_cmpt),Neutral): - if isinstance(element(m.parent),EnzBase): - populateMeshEntry(meshEntry,grp_cmpt,"cplx",m) - else: - populateMeshEntry(meshEntry,grp_cmpt,"pool",m) - else: - if isinstance(element(m.parent),EnzBase): - populateMeshEntry(meshEntry,compt,"cplx",m) - else: - populateMeshEntry(meshEntry,compt,"pool",m) - - for r in wildcardFind(compt.path+'/##[ISA=ReacBase]'): - rgrp_cmpt = findGroup_compt(r) - xcord.append(xyPosition(r.path+'/info','x')) - ycord.append(xyPosition(r.path+'/info','y')) - if isinstance(element(rgrp_cmpt),Neutral): - populateMeshEntry(meshEntry,rgrp_cmpt,"reaction",r) - else: - populateMeshEntry(meshEntry,compt,"reaction",r) - - for e in wildcardFind(compt.path+'/##[ISA=EnzBase]'): - egrp_cmpt = findGroup_compt(e) - xcord.append(xyPosition(e.path+'/info','x')) - ycord.append(xyPosition(e.path+'/info','y')) - - if isinstance(element(egrp_cmpt),Neutral): - populateMeshEntry(meshEntry,egrp_cmpt,"enzyme",e) - else: - populateMeshEntry(meshEntry,compt,"enzyme",e) - - for f in wildcardFind(compt.path+'/##[ISA=Function]'): - fgrp_cmpt = findGroup_compt(f) - if isinstance(element(fgrp_cmpt),Neutral): - populateMeshEntry(meshEntry,fgrp_cmpt,"function",f) - else: - populateMeshEntry(meshEntry,compt,"function",f) - - for t in wildcardFind(compt.path+'/##[ISA=StimulusTable]'): - tgrp_cmpt = findGroup_compt(t) - xcord.append(xyPosition(t.path+'/info','x')) - ycord.append(xyPosition(t.path+'/info','y')) - if isinstance(element(tgrp_cmpt),Neutral): - populateMeshEntry(meshEntry,tgrp_cmpt,"stimTab",t) - else: - populateMeshEntry(meshEntry,compt,"stimTab",t) - - xmin = min(xcord) - xmax = max(xcord) - ymin = min(ycord) - ymax = max(ycord) - positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 and len(np.nonzero(ycord)[0]) == 0) - return(objPar,meshEntry,xmin,xmax,ymin,ymax,positionInfoExist) -''' -def setupMeshObj(modelRoot): - # Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \ - # self.meshEntry with "key" as compartment, - # value is key2:list where key2 represents moose object type,list of objects of a perticular type - # e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist } - - meshEntry = {} - if meshEntry: - meshEntry.clear() - else: - meshEntry = {} - xcord = [] - ycord = [] - meshEntryWildcard = '/##[ISA=ChemCompt]' - if modelRoot != '/': - meshEntryWildcard = modelRoot+meshEntryWildcard - for meshEnt in wildcardFind(meshEntryWildcard): - mollist = [] - realist = [] - enzlist = [] - cplxlist = [] - tablist = [] - funclist = [] - - mol_cpl = wildcardFind(meshEnt.path+'/##[ISA=PoolBase]') - funclist = wildcardFind(meshEnt.path+'/##[ISA=Function]') - enzlist = wildcardFind(meshEnt.path+'/##[ISA=EnzBase]') - realist = wildcardFind(meshEnt.path+'/##[ISA=ReacBase]') - tablist = wildcardFind(meshEnt.path+'/##[ISA=StimulusTable]') - if mol_cpl or funclist or enzlist or realist or tablist: - for m in mol_cpl: - if isinstance(element(m.parent),CplxEnzBase): - cplxlist.append(m) - elif isinstance(element(m),moose.PoolBase): - mollist.append(m) - - meshEntry[meshEnt] = {'enzyme':enzlist, - 'reaction':realist, - 'pool':mollist, - 'cplx':cplxlist, - 'table':tablist, - 'function':funclist - } - - for mert in [mollist,enzlist,realist,tablist]: - for merts in mert: - objInfo = merts.path+'/info' - if exists(objInfo): - xcord.append(element(objInfo).x) - ycord.append(element(objInfo).y) - return(meshEntry,xcord,ycord) - -def sizeHint(self): - return QtCore.QSize(800,400) -''' -def setupItem(modelPath,cntDict): - # This function collects information of what is connected to what. \ - # eg. substrate and product connectivity to reaction's and enzyme's \ - # sumtotal connectivity to its pool are collected - #print " setupItem" - sublist = [] - prdlist = [] - zombieType = ['ReacBase','EnzBase','Function','StimulusTable'] - for baseObj in zombieType: - path = '/##[ISA='+baseObj+']' - if modelPath != '/': - path = modelPath+path - if ( (baseObj == 'ReacBase') or (baseObj == 'EnzBase')): - for items in wildcardFind(path): - sublist = [] - prdlist = [] - uniqItem,countuniqItem = countitems(items,'subOut') - subNo = uniqItem - for sub in uniqItem: - sublist.append((element(sub),'s',countuniqItem[sub])) - - uniqItem,countuniqItem = countitems(items,'prd') - prdNo = uniqItem - if (len(subNo) == 0 or len(prdNo) == 0): - print ("Substrate Product is empty ",path, " ",items) - - for prd in uniqItem: - prdlist.append((element(prd),'p',countuniqItem[prd])) - - if (baseObj == 'CplxEnzBase') : - uniqItem,countuniqItem = countitems(items,'toEnz') - for enzpar in uniqItem: - sublist.append((element(enzpar),'t',countuniqItem[enzpar])) - - uniqItem,countuniqItem = countitems(items,'cplxDest') - for cplx in uniqItem: - prdlist.append((element(cplx),'cplx',countuniqItem[cplx])) - - if (baseObj == 'EnzBase'): - uniqItem,countuniqItem = countitems(items,'enzDest') - for enzpar in uniqItem: - sublist.append((element(enzpar),'t',countuniqItem[enzpar])) - cntDict[items] = sublist,prdlist - elif baseObj == 'Function': - for items in wildcardFind(path): - sublist = [] - prdlist = [] - item = items.path+'/x[0]' - uniqItem,countuniqItem = countitems(item,'input') - for funcpar in uniqItem: - sublist.append((element(funcpar),'sts',countuniqItem[funcpar])) - - uniqItem,countuniqItem = countitems(items,'valueOut') - for funcpar in uniqItem: - prdlist.append((element(funcpar),'stp',countuniqItem[funcpar])) - cntDict[items] = sublist,prdlist - - else: - for tab in wildcardFind(path): - tablist = [] - uniqItem,countuniqItem = countitems(tab,'output') - for tabconnect in uniqItem: - tablist.append((element(tabconnect),'tab',countuniqItem[tabconnect])) - cntDict[tab] = tablist - -def countitems(mitems,objtype): - items = [] - items = element(mitems).neighbors[objtype] - uniqItems = set(items) - #countuniqItemsauto = Counter(items) - countuniqItems = dict((i, items.count(i)) for i in items) - return(uniqItems,countuniqItems) - -def recalculatecoordinatesforKkit(mObjlist,xcord,ycord): - positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \ - and len(np.nonzero(ycord)[0]) == 0) - - if positionInfoExist: - #Here all the object has been taken now recalculate and reassign back x and y co-ordinates - xmin = min(xcord) - xmax = max(xcord) - ymin = min(ycord) - ymax = max(ycord) - for merts in mObjlist: - objInfo = merts.path+'/info' - if moose.exists(objInfo): - Ix = (xyPosition(objInfo,'x')-xmin)/(xmax-xmin) - Iy = (ymin-xyPosition(objInfo,'y'))/(ymax-ymin) - element(objInfo).x = Ix*1000 - element(objInfo).y = Iy*800 - -def xyPosition(objInfo,xory): - try: - return(float(element(objInfo).getField(xory))) - except ValueError: - return (float(0)) - - -def autoCoordinates(meshEntry,srcdesConnection): - - G = nx.Graph() - for cmpt,memb in meshEntry.items(): - if memb in ["enzyme"]: - for enzObj in find_index(memb,'enzyme'): - #G.add_node(enzObj.path) - G.add_node(enzObj.path,label='',shape='ellipse',color='',style='filled',fontname='Helvetica',fontsize=12,fontcolor='blue') - for cmpt,memb in meshEntry.items(): - #if memb.has_key - if memb in ["pool","cplx","reaction"]: - for poolObj in find_index(memb,'pool'): - #G.add_node(poolObj.path) - G.add_node(poolObj.path,label = poolObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 9,fontcolor = 'blue') - for cplxObj in find_index(memb,'cplx'): - G.add_node(cplxObj.path) - G.add_node(cplxObj.path,label = cplxObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 12,fontcolor = 'blue') - #G.add_edge((cplxObj.parent).path,cplxObj.path) - for reaObj in find_index(memb,'reaction'): - #G.add_node(reaObj.path) - G.add_node(reaObj.path,label='',shape='circle',color='') - - for inn,out in srcdesConnection.items(): - if (inn.className =='ZombieReac'): arrowcolor = 'green' - elif(inn.className =='ZombieEnz'): arrowcolor = 'red' - else: arrowcolor = 'blue' - if isinstance(out,tuple): - if len(out[0])== 0: - print (inn.className + ':' +inn.name + " doesn't have input message") - else: - for items in (items for items in out[0] ): - G.add_edge(element(items[0]).path,inn.path) - if len(out[1]) == 0: - print (inn.className + ':' + inn.name + "doesn't have output mssg") - else: - for items in (items for items in out[1] ): - G.add_edge(inn.path,element(items[0]).path) - elif isinstance(out,list): - if len(out) == 0: - print ("Func pool doesn't have sumtotal") - else: - for items in (items for items in out ): - G.add_edge(element(items[0]).path,inn.path) - position = graphviz_layout(G) - xcord, ycord = [],[] - for item in position.items(): - xy = item[1] - xroundoff = round(xy[0],0) - yroundoff = round(xy[1],0) - xcord.append(xroundoff) - ycord.append(yroundoff) - - xmin = min(xcord) - xmax = max(xcord) - ymin = min(ycord) - ymax = max(ycord) - for item in position.items(): - xy = item[1] - anno = Annotator(item[0]+'/info') - Ax = (xy[0]-xmin)/(xmax-xmin) - Ay = (xy[1]-ymin)/(ymax-ymin) - #anno.x = round(Ax,1) - #anno.y = round(Ay,1) - #not roundingoff to max and min the co-ordinates for bigger model would overlay the co-ordinates - anno.x = xy[0] - anno.y = xy[1] -def find_index(value, key): - """ Value.get(key) to avoid expection which would raise if empty value in dictionary for a given key """ - if value.get(key) != None: - return value.get(key) - else: - raise ValueError('no dict with the key found') diff --git a/plugins/kkitQGraphics.py b/plugins/kkitQGraphics.py deleted file mode 100644 index 1f18019..0000000 --- a/plugins/kkitQGraphics.py +++ /dev/null @@ -1,718 +0,0 @@ - -__author__ = "HarshaRani" -__credits__ = ["Upi Lab"] -__license__ = "GPL3" -__version__ = "1.0.0" -__maintainer__ = "HarshaRani" -__email__ = "hrani@ncbs.res.in" -__status__ = "Development" -__updated__ = "Sep 19 2017" - -''' -sep 19: add GroupItem class -''' -#import sys -#sys.path.insert(0, '/home/harsha/trunk/gui') -import config -from PyQt4 import QtGui, QtCore, Qt -from moose import * -from PyQt4.QtGui import QPixmap, QImage, QGraphicsPixmapItem -from constants import * -from os import path - -class KineticsDisplayItem(QtGui.QGraphicsWidget): - """Base class for display elemenets in kinetics layout""" - name = ITEM - defaultFontName = "Helvetica" - defaultFontSize = 10 - def __init__(self, mooseObject, parent=None): - QtGui.QGraphicsObject.__init__(self,parent) - self.mobj = mooseObject - self.gobj = None - self.pressed = False - self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable,True) - self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True) - self.setAcceptHoverEvents(True) - self.setFocusPolicy(QtCore.Qt.StrongFocus) - if QtCore.QT_VERSION >= 0x040600: - self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges,1) - self.setFlag(QtGui.QGraphicsItem.ItemIgnoresTransformations, False) - - def getParentMooseObject(self): - return moose.element(self.mobj).parent - - def getParentGraphicsObject(self): - return self.parentItem() - - def setDisplayProperties(self, dinfo): - self.setGeometry(dinfo.x, dinfo.y) - - def paint(self, painter=None, option=None, widget = None): - #If item is selected - if self.hasFocus() or self.isSelected(): - painter.setPen(QtGui.QPen(QtGui.QPen(QtCore.Qt.black, 1.8,Qt.Qt.DashLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin))) - painter.drawRect(self.boundingRect()) - # def mouseDoubleClickEvent(self, event): - # self.emit(QtCore.SIGNAL("qgtextDoubleClick(PyQt_PyObject)"),element(self.mobj)) - - def itemChange(self,change,value): - #pass - #if change == QtGui.QGraphicsItem.ItemPositionChange: - #print "itemChange ---->",self.mobj - # self.emit(QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.mobj) - if change == QtGui.QGraphicsItem.ItemSelectedChange and value == True: - self.emit(QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),element(self.mobj)) - return QtGui.QGraphicsItem.itemChange(self,change,value) - -class FuncItem(KineticsDisplayItem): - name = ITEM - """Class for displaying Functions""" - #fontMetrics = None - font =QtGui.QFont(KineticsDisplayItem.defaultFontName) - font.setPointSize(KineticsDisplayItem.defaultFontSize) - fontMetrics = QtGui.QFontMetrics(font) - def __init__(self, mobj, parent): - super(FuncItem, self).__init__(mobj, parent) - self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True) - iconmap_file = (path.join(config.settings[config.KEY_ICON_DIR], 'classIcon/Function.png')) - self.funcImage = QImage(iconmap_file).scaled(15,33) - self.bg = QtGui.QGraphicsRectItem(self) - self.bg.setAcceptHoverEvents(True) - self.gobj = QtGui.QGraphicsPixmapItem(QtGui.QPixmap.fromImage(self.funcImage),self.bg) - #self.gobj = QtGui.QGraphicsPixmapItem(QtGui.QPixmap('../icons/classIcon/Function.png')) - self.gobj.setAcceptHoverEvents(True) - self.gobj.mobj = self.mobj - classname = self.mobj.className - funcdoc = (element(self.mobj.path)).expr - self.gobj.setToolTip(funcdoc) - #self.bg.setPen(Qt.QColor(100,100,10,10)) - - def setDisplayProperties(self,x,y,textcolor,bgcolor): - """Set the display properties of this item.""" - #With Respect to BuffPool (as parent which is in old genesis) then function are placed at 0,30 (which is below the BuffPool) - #else if droped from the GUI then placed wrt position - #self.setGeometry(0, 30,self.gobj.boundingRect().width(),self.gobj.boundingRect().height()) - #self.setGeometry(x,y) - poolt = ["ZombieBufPool","BufPool","ZombiePool","Pool"] - if self.gobj.mobj.parent.className in poolt: - self.setGeometry(0, 30,self.gobj.boundingRect().width(),self.gobj.boundingRect().height()) - else: - self.setGeometry(x,y,self.gobj.boundingRect().width(),self.gobj.boundingRect().height()) - self.bg.setBrush(QtGui.QBrush(bgcolor)) - self.setFlag(QtGui.QGraphicsItem.ItemIsMovable,False) - def refresh(self,scale): - # fontsize = PoolItem.defaultFontsize*scale - # font =QtGui.QFont("Helvetica") - # font.setPointSize(fontsize) - # self.gobj.setFont(font) - pass - def boundingRect(self): - ''' reimplimenting boundingRect for redrawning ''' - return QtCore.QRectF(0,0,self.gobj.boundingRect().width(),self.gobj.boundingRect().height()) - - def updateSlot(self): - pass - # #This func will adjust the background color with respect to text size - # self.gobj.setText(self.mobj.name) - # self.bg.setRect(0, 0, self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '), self.gobj.boundingRect().height()) - - def updateColor(self,bgcolor): - #self.bg.setBrush(QtGui.QBrush(QtGui.QColor(bgcolor))) - pass - - def updateRect(self,ratio): - pass - # width = self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' ') - # height = self.gobj.boundingRect().height() - # adjustw = width*ratio - # adjusth = height*ratio - # self.bgColor.setRect(width/2-abs(adjustw/2),height/2-abs(adjusth/2),adjustw, adjusth) - #self.bg.setRect(0,0,self.gobj.boundingRect().width()*ratio+PoolItem.fontMetrics.width(' '), self.gobj.boundingRect().height()*ratio) - def returnColor(self): - return (self.bg.brush().color()) - - def updateValue(self,gobj): - self.gobj.setToolTip(funcdoc) - # self._gobj = gobj - # #if type(self._gobj) is moose.ZombiePool: - # if (isinstance(self._gobj,PoolBase)): - # self._conc = self.mobj.conc - # self._n = self.mobj.n - # doc = "Conc\t: "+str(self._conc)+"\nn\t: "+str(self._n) - # self.gobj.setToolTip(doc) - - -class PoolItem(KineticsDisplayItem): - name = ITEM - """Class for displaying pools. Uses a QGraphicsSimpleTextItem to - display the name.""" - #fontMetrics = None - font = QtGui.QFont(KineticsDisplayItem.defaultFontName) - font.setPointSize(KineticsDisplayItem.defaultFontSize) - fontMetrics = QtGui.QFontMetrics(font) - def __init__(self, mobj, parent): - KineticsDisplayItem.__init__(self, mobj, parent) - self.bg = QtGui.QGraphicsRectItem(self) - self.bg.setAcceptHoverEvents(True) - self.gobj = QtGui.QGraphicsSimpleTextItem(self.mobj.name, self.bg) - self.gobj.mobj = self.mobj - classname = self.mobj.className - # classname = 'PoolBase' - # doc = moose.element('/classes/%s' % (classname)).docs - # print "docs ",self.gobj.mobj, " ",doc - # doc = doc.split('Description:')[-1].split('Name:')[0].strip() - self._conc = self.mobj.conc - self._n = self.mobj.n - doc = "Conc\t: "+str(self._conc)+"\nn\t: "+str(self._n) - self.gobj.setToolTip(doc) - self.gobj.setFont(PoolItem.font) - if not PoolItem.fontMetrics: - PoolItem.fontMetrics = QtGui.QFontMetrics(self.gobj.font()) - self.bg.setRect(0, - 0, - self.gobj.boundingRect().width() - +PoolItem.fontMetrics.width(' '), - self.gobj.boundingRect().height()) - self.bg.setPen(Qt.QColor(0,0,0,0)) - self.gobj.setPos(PoolItem.fontMetrics.width(' '), 0) - def setDisplayProperties(self,x,y,textcolor,bgcolor): - """Set the display properties of this item.""" - self.setGeometry(x, y,self.gobj.boundingRect().width() - +PoolItem.fontMetrics.width(''), - self.gobj.boundingRect().height()) - self.bg.setBrush(QtGui.QBrush(bgcolor)) - - def refresh(self,scale): - fontsize = KineticsDisplayItem.defaultFontSize*scale - font = QtGui.QFont(KineticsDisplayItem.defaultFontName) - if (fontsize < 1): - fontsize = self.gobj.font().pointSize() - font.setPointSize(fontsize) - #self.gobj.setFont(PoolItem.font) - self.gobj.setFont(font) - - def boundingRect(self): - ''' reimplimenting boundingRect for redrawning ''' - return QtCore.QRectF(0,0,self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '),self.gobj.boundingRect().height()) - - def updateSlot(self): - #This func will adjust the background color with respect to text size - self.gobj.setText(self.mobj.name) - self.bg.setRect(0, 0, self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '), self.gobj.boundingRect().height()) - self.setGeometry(self.pos().x(),self.pos().y(),self.gobj.boundingRect().width() - +PoolItem.fontMetrics.width(''), - self.gobj.boundingRect().height()) - def updateColor(self,bgcolor): - self.bg.setBrush(QtGui.QBrush(QtGui.QColor(bgcolor))) - #pass - - def updateRect(self,ratio=1.0): - width = self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' ') - height = self.gobj.boundingRect().height() - adjustw = width*ratio - adjusth = height*ratio - self.bg.setRect(width/2-abs(adjustw/2),height/2-abs(adjusth/2),adjustw, adjusth) - #self.bg.setRect(0,0,self.gobj.boundingRect().width()*ratio+PoolItem.fontMetrics.width(' '), self.gobj.boundingRect().height()*ratio) - - def returnColor(self): - return (self.bg.brush().color()) - - def updateValue(self,gobj): - self._gobj = gobj - #if type(self._gobj) is moose.ZombiePool: - if (isinstance(self._gobj,PoolBase)): - self._conc = self.mobj.conc - self._n = self.mobj.n - doc = "Conc\t: "+str(self._conc)+"\nn\t: "+str(self._n) - self.gobj.setToolTip(doc) - -class PoolItemCircle(PoolItem): - name = ITEM - def __init__(self,*args,**kwargs): - PoolItem.__init__(self, *args, **kwargs) - self.setFlag(QtGui.QGraphicsItem.ItemIsMovable,True) - self.bgColor = QtGui.QGraphicsEllipseItem(self) - self.bgColor.setFlag(QtGui.QGraphicsItem.ItemStacksBehindParent,True) - self.bgColor.setRect(((self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '))/2)-5,self.gobj.boundingRect().height()/2-5,10,10) - - def setDisplayProperties(self,x,y,textcolor,bgcolor): - self.setGeometry(x, y,self.gobj.boundingRect().width() - +PoolItem.fontMetrics.width(' '), - self.gobj.boundingRect().height()) - self.bgColor.setBrush(QtGui.QBrush(QtGui.QColor(bgcolor.red(),bgcolor.green(),bgcolor.blue(),255))) - - def updateRect(self,ratio): - width = self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' ') - height = self.gobj.boundingRect().height() - adjustw = width*ratio - adjusth = height*ratio - self.bgColor.setRect(width/2-abs(adjustw/2),height/2-abs(adjusth/2),adjustw, adjusth) - self.updateValue(self.gobj) - - def returnEllispeSize(self): - self.bgColor.setRect(((self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '))/2)-5,self.gobj.boundingRect(). - height()/2-5,10,10) - - def refresh(self,scale): - fontsize = KineticsDisplayItem.defaultFontSize*scale - font =QtGui.QFont(KineticsDisplayItem.defaultFontName) - if (fontsize < 1): - fontsize = self.gobj.font().pointSize() - font.setPointSize(fontsize) - self.gobj.setFont(font) - - def MooseRef(self): - return self.gobj.mobj - -class TableItem(KineticsDisplayItem): - defaultWidth = 30 - defaultHeight = 30 - defaultPenWidth = 2 - name = ITEM - def __init__(self, *args, **kwargs): - KineticsDisplayItem.__init__(self, *args, **kwargs) - - points = [QtCore.QPointF(0,TableItem.defaultWidth/2), - QtCore.QPointF(TableItem.defaultHeight/2-2,0), - QtCore.QPointF(TableItem.defaultWidth/2+2,0), - QtCore.QPointF(TableItem.defaultWidth,TableItem.defaultHeight/2), - ] - - path = QtGui.QPainterPath() - path.moveTo(points[0]) - for p in points[1:]: - path.lineTo(p) - path.moveTo(p) - path.moveTo(0,0) - path.lineTo(TableItem.defaultWidth,0) - path.moveTo(-(TableItem.defaultWidth/3),TableItem.defaultHeight/4) - path.lineTo((TableItem.defaultWidth+10),TableItem.defaultHeight/4) - - self.gobj = QtGui.QGraphicsPathItem(path, self) - #self.gobj.setToolTip("Need to see what to show unlike conc/nint for pool") - tabledoc = (element(self.mobj.path)).outputValue - self.gobj.setToolTip(str(tabledoc)) - self.gobj.setPen(QtGui.QPen(QtCore.Qt.black, 2,Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) - self.gobj.mobj = self.mobj - - def refresh( self,scale): - defaultWidth = TableItem.defaultWidth*scale - defaultHeight = TableItem.defaultHeight*scale - points = [QtCore.QPointF(0,defaultWidth/2), - QtCore.QPointF(defaultHeight/2-2,0), - QtCore.QPointF(defaultWidth/2+2,0), - QtCore.QPointF(defaultWidth,defaultHeight/2) - ] - path = QtGui.QPainterPath() - path.moveTo(points[0]) - for p in points[1:]: - path.lineTo(p) - path.moveTo(p) - path.moveTo(0,0) - path.lineTo(defaultWidth,0) - path.moveTo(-(defaultWidth/3),defaultHeight/4) - path.lineTo((defaultWidth+10),defaultHeight/4) - self.gobj.setPath(path) - TablePen = self.gobj.pen() - defaultpenwidth = TableItem.defaultPenWidth - tableWidth = TableItem.defaultPenWidth*scale - TablePen.setWidth(tableWidth) - self.gobj.setPen(TablePen) - - def setDisplayProperties(self, x,y,textcolor,bgcolor): - #TODO check the table bounding reactangle b'cos selection looks ugly - """Set the display properties of this item.""" - self.setGeometry(x,y, - self.gobj.boundingRect().width(), - self.gobj.boundingRect().height()) - -class ReacItem(KineticsDisplayItem): - defaultWidth = 30 - defaultHeight = 30 - defaultPenWidth = 2 - name = ITEM - def __init__(self, *args, **kwargs): - KineticsDisplayItem.__init__(self, *args, **kwargs) - points = [QtCore.QPointF(ReacItem.defaultWidth/4, 0), - QtCore.QPointF(0, ReacItem.defaultHeight/4), - QtCore.QPointF(ReacItem.defaultWidth, ReacItem.defaultHeight/4), - QtCore.QPointF(3*ReacItem.defaultWidth/4, ReacItem.defaultHeight/2)] - path = QtGui.QPainterPath() - path.moveTo(points[0]) - for p in points[1:]: - path.lineTo(p) - path.moveTo(p) - self.gobj = QtGui.QGraphicsPathItem(path, self) - self.gobj.setPen(QtGui.QPen(QtCore.Qt.black, 2,Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) - self.gobj.mobj = self.mobj - #classname = self.mobj.className - # classname = 'ReacBase' - # doc = moose.element('/classes/%s' % (classname)).docs - # print "docs ",self.gobj.mobj, " ",doc - # doc = doc.split('Description:')[-1].split('Name:')[0].strip() - self._Kf = self.gobj.mobj.Kf - self._Kb = self.gobj.mobj.Kb - doc = "Kf\t: "+str(self._Kf)+"\nKb\t: "+str(self._Kb) - self.gobj.setToolTip(doc) - - def updateValue(self,gobj): - self._gobj = gobj - #if ( type(self._gobj) is moose.ZombieReac or type(self_gobj) is moose.Reac): - if (isinstance(self._gobj,ReacBase)): - self._Kf = self._gobj.Kf - self._Kb = self._gobj.Kb - doc = "Kf\t: "+str(self._Kf)+"\nKb\t: "+str(self._Kb) - self.gobj.setToolTip(doc) - - def refresh( self,scale): - defaultWidth = ReacItem.defaultWidth*scale - defaultHeight = ReacItem.defaultHeight*scale - points = [QtCore.QPointF(defaultWidth/4, 0), - QtCore.QPointF(0,defaultHeight/4), - QtCore.QPointF(defaultWidth, defaultHeight/4), - QtCore.QPointF(3*defaultWidth/4,defaultHeight/2)] - path = QtGui.QPainterPath() - path.moveTo(points[0]) - for p in points[1:]: - path.lineTo(p) - path.moveTo(p) - - self.gobj.setPath(path) - ReacPen = self.gobj.pen() - defaultpenwidth = ReacItem.defaultPenWidth - reacWidth = defaultpenwidth*scale - ReacPen.setWidth(reacWidth) - self.gobj.setPen(ReacPen) - - def setDisplayProperties(self, x,y,textcolor,bgcolor): - """Set the display properties of this item.""" - self.setGeometry(x,y, - self.gobj.boundingRect().width(), - self.gobj.boundingRect().height()) - -class EnzItem(KineticsDisplayItem): - defaultWidth = 20 - defaultHeight = 10 - name = ITEM - def __init__(self, *args, **kwargs): - KineticsDisplayItem.__init__(self, *args, **kwargs) - self.gobj = QtGui.QGraphicsEllipseItem(0, 0, - EnzItem.defaultWidth, - EnzItem.defaultHeight, self) - self.gobj.mobj = self.mobj - # classname = 'EnzBase' - # doc = moose.element('/classes/%s' % (classname)).docs - # doc = doc.split('Description:')[-1].split('Name:')[0].strip() - self._Km = self.gobj.mobj.Km - self._Kcat = self.gobj.mobj.kcat - doc = "Km\t: "+str(self._Km)+"\nKcat\t: "+str(self._Kcat) - self.gobj.setToolTip(doc) - - def updateValue(self,gobj): - self._gobj = gobj - if ( isinstance(self.gobj,EnzBase)): - self._Km = self._gobj.Km - self._Kcat = self._gobj.kcat - doc = "Km\t: "+str(self._Km)+"\nKcat\t: "+str(self._Kcat) - self.gobj.setToolTip(doc) - - def updateColor(self,bgcolor): - self.gobj.setBrush(QtGui.QBrush(QtGui.QColor(bgcolor))) - - def setDisplayProperties(self,x,y,textcolor,bgcolor): - """Set the display properties of this item.""" - self.setGeometry(x,y, - self.gobj.boundingRect().width(), - self.gobj.boundingRect().height()) - self.gobj.setBrush(QtGui.QBrush(bgcolor)) - - def refresh(self,scale): - defaultWidth = EnzItem.defaultWidth*scale - defaultHeight = EnzItem.defaultHeight*scale - self.gobj.setRect(0,0,defaultWidth,defaultHeight) - -class MMEnzItem(EnzItem): - name = ITEM - def __init__(self,*args, **kwargs): - EnzItem.__init__(self,*args, **kwargs) - -class CplxItem(KineticsDisplayItem): - defaultWidth = 10 - defaultHeight = 10 - name = ITEM - def __init__(self, *args, **kwargs): - KineticsDisplayItem.__init__(self, *args, **kwargs) - self.gobj = QtGui.QGraphicsRectItem(0,0, CplxItem.defaultWidth, CplxItem.defaultHeight, self) - self.gobj.mobj = self.mobj - self._conc = self.mobj.conc - self._n = self.mobj.n - doc = "Conc\t: "+str(self._conc)+"\nn\t: "+str(self._n) - self.gobj.setToolTip(doc) - - def updateValue(self,gobj): - self._gobj = gobj - if (isinstance(self._gobj,PoolBase)): - self._conc = self.mobj.conc - self._n = self.mobj.n - doc = "Conc\t: "+str(self._conc)+"\nn\t: "+str(self._n) - self.gobj.setToolTip(doc) - - def setDisplayProperties(self,x,y,textcolor,bgcolor): - """Set the display properties of this item.""" - self.setGeometry(self.gobj.boundingRect().width()/2,self.gobj.boundingRect().height(), - self.gobj.boundingRect().width(), - self.gobj.boundingRect().height()) - self.setFlag(QtGui.QGraphicsItem.ItemIsMovable,False) - - def refresh(self,scale): - defaultWidth = CplxItem.defaultWidth*scale - defaultHeight = CplxItem.defaultHeight*scale - - self.gobj.setRect(0,0,defaultWidth,defaultHeight) -class GRPItem(QtGui.QGraphicsRectItem): - #This is used for displaying Grp Item - name = GROUP - def __init__(self,parent,x,y,w,h,item): - self.grpEmitter = QtCore.QObject() - QtGui.QGraphicsRectItem.__init__(self,x,y,w,h,parent) - self.mobj = item - self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True); - self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable) - self.setAcceptHoverEvents(True) - self.setToolTip(self.mobj.name) - QT_VERSION = str(QtCore.QT_VERSION_STR).split('.') - QT_MINOR_VERSION = int(QT_VERSION[1]) - if config.QT_MINOR_VERSION >= 6: - self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1) - - # def paint(self, painter=None, option=None, widget = None): - # print " self .hasFocus ",self.hasFocus(), " ## ",self.isSelected() - - # if self.isSelected(): - # drawFocus(painter) - # #painter.setPen(QtGui.QPen(QtGui.QPen(QtCore.Qt.black, 1.8,Qt.Qt.DashLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin))) - # #painter.drawRect(self.boundingRect()) - - # def drawFocusRect(self, painter): - # self.focusbrush = QtGui.QBrush() - # self.focuspen = QtGui.QPen(QtCore.Qt.DotLine) - # self.focuspen.setColor(QtCore.Qt.black) - # self.focuspen.setWidthF(1.5) - # painter.setBrush(self.focusbrush) - # painter.setPen(self.focuspen) - # painter.drawRect(self.focusrect) - - def itemChange(self,change,value): - #print " itemchange at GRPItem ",change,value - if change == QtGui.QGraphicsItem.ItemPositionChange: - self.grpEmitter.emit(QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.mobj) - #if change == QtGui.QGraphicsItem. - if change == QtGui.QGraphicsItem.ItemSelectedChange and value == True: - #self.setPen(QtGui.QPen(QtGui.QPen(QtCore.Qt.black, 1.8,Qt.Qt.DashLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin))) - #self.drawRect(self.boundingRect()) - self.grpEmitter.emit(QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),self.mobj) - - return QtGui.QGraphicsItem.itemChange(self,change,value) - -class ComptItem(QtGui.QGraphicsRectItem): - name = COMPARTMENT - def __init__(self,parent,x,y,w,h,item): - self.cmptEmitter = QtCore.QObject() - iParent = item - ''' - self._rect = QtCore.QRectF(x,y,w,h) - self._scene = parent - print "self comptItem",self._scene.sceneContainer ," and",self._scene.sceneContainer.graphicsView - self.mouseOver = False - self.resizeHandleSize = 4.0 - self.mousePressPos = None - self.mouseMovePos = None - self.mouseIsPressed = False - #self.setAcceptsHoverEvents(True) - self.updateResizeHandles() - ''' - if hasattr(iParent, "__iter__"): - self.mobj = iParent[0] - else: - self.mobj = iParent - self.layoutWidgetPt = parent - QtGui.QGraphicsRectItem.__init__(self,x,y,w,h) - - self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True); - self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable) - #self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1) - QT_VERSION = str(QtCore.QT_VERSION_STR).split('.') - QT_MINOR_VERSION = int(QT_VERSION[1]) - if QT_MINOR_VERSION >= 6: - #if config.QT_MINOR_VERSION >= 6: - self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1) - self.setAcceptHoverEvents(True) - self.setToolTip(iParent.name) - ''' - def hoverEnterEvent(self, event): - self.updateResizeHandles() - self.mouseOver = True - self.prepareGeometryChange() - - def hoverLeaveEvent(self, event): - self.mouseOver = False - self.prepareGeometryChange() - - def hoverMoveEvent(self, event): - - if self.topLeft.contains(event.scenePos()) or self.bottomRight.contains(event.scenePos()): - self.setCursor(QtCore.Qt.SizeFDiagCursor) - elif self.topRight.contains(event.scenePos()) or self.bottomLeft.contains(event.scenePos()): - self.setCursor(QtCore.Qt.SizeBDiagCursor) - else: - self.setCursor(QtCore.Qt.SizeAllCursor) - - QtGui.QGraphicsRectItem.hoverMoveEvent(self, event) - - def mousePressEvent(self, event): - """ - Capture mouse press events and find where the mosue was pressed on the object - """ - self.mousePressPos = event.scenePos() - self.mouseIsPressed = True - self.rectPress = copy.deepcopy(self._rect) - - # Top left corner - if self.topLeft.contains(event.scenePos()): - self.mousePressArea = 'topleft' - # top right corner - elif self.topRight.contains(event.scenePos()): - self.mousePressArea = 'topright' - # bottom left corner - elif self.bottomLeft.contains(event.scenePos()): - self.mousePressArea = 'bottomleft' - # bottom right corner - elif self.bottomRight.contains(event.scenePos()): - self.mousePressArea = 'bottomright' - # entire rectangle - else: - self.mousePressArea = None - - QtGui.QGraphicsRectItem.mousePressEvent(self, event) - - def mouseReleaseEvent(self, event): - """ - Capture nmouse press events. - """ - self.mouseIsPressed = False - - self.updateResizeHandles() - self.prepareGeometryChange() - - QtGui.QGraphicsRectItem.mouseReleaseEvent(self, event) - - def mouseMoveEvent(self, event): - """ - Handle mouse move events. - """ - self.mouseMovePos = event.scenePos() - - if self.mouseIsPressed: - # Move top left corner - if self.mousePressArea=='topleft': - self._rect.setTopLeft(self.rectPress.topLeft()-(self.mousePressPos-self.mouseMovePos)) - # Move top right corner - elif self.mousePressArea=='topright': - self._rect.setTopRight(self.rectPress.topRight()-(self.mousePressPos-self.mouseMovePos)) - # Move bottom left corner - elif self.mousePressArea=='bottomleft': - self._rect.setBottomLeft(self.rectPress.bottomLeft()-(self.mousePressPos-self.mouseMovePos)) - # Move bottom right corner - elif self.mousePressArea=='bottomright': - self._rect.setBottomRight(self.rectPress.bottomRight()-(self.mousePressPos-self.mouseMovePos)) - # Move entire rectangle, don't resize - else: - self._rect.moveCenter(self.rectPress.center()-(self.mousePressPos-self.mouseMovePos)) - - self.updateResizeHandles() - self.prepareGeometryChange() - - QtGui.QGraphicsRectItem.mousePressEvent(self, event) - - def boundingRect(self): - """ - Return bounding rectangle - """ - return self._boundingRect - - def updateResizeHandles(self): - """ - Update bounding rectangle and resize handles - """ - self.offset = self.resizeHandleSize*(self._scene.sceneContainer.graphicsView.mapToScene(1,0)-self._scene.sceneContainer.graphicsView.mapToScene(0,1)).x() - - self._boundingRect = self._rect.adjusted(-self.offset, self.offset, self.offset, -self.offset) - - # Note: this draws correctly on a view with an inverted y axes. i.e. QGraphicsView.scale(1,-1) - self.topLeft = QtCore.QRectF(self._boundingRect.topLeft().x(), self._boundingRect.topLeft().y() - 2*self.offset, - 2*self.offset, 2*self.offset) - self.topRight = QtCore.QRectF(self._boundingRect.topRight().x() - 2*self.offset, self._boundingRect.topRight().y() - 2*self.offset, - 2*self.offset, 2*self.offset) - self.bottomLeft = QtCore.QRectF(self._boundingRect.bottomLeft().x(), self._boundingRect.bottomLeft().y(), - 2*self.offset, 2*self.offset) - self.bottomRight = QtCore.QRectF(self._boundingRect.bottomRight().x() - 2*self.offset, self._boundingRect.bottomRight().y(), - 2*self.offset, 2*self.offset) - - def paint(self, painter, option, widget): - """ - Paint Widget - """ - - # show boundingRect for debug purposes - painter.setPen(QtGui.QPen(QtCore.Qt.red, 0, QtCore.Qt.DashLine)) - painter.drawRect(self._boundingRect) - - # Paint rectangle - painter.setPen(QtGui.QPen(QtCore.Qt.black, 0, QtCore.Qt.SolidLine)) - painter.drawRect(self._rect) - - # If mouse is over, draw handles - if self.mouseOver: - # if rect selected, fill in handles - if self.isSelected(): - painter.setBrush(QtGui.QBrush(QtGui.QColor(0,0,0))) - painter.drawRect(self.topLeft) - painter.drawRect(self.topRight) - painter.drawRect(self.bottomLeft) - painter.drawRect(self.bottomRight) - ''' - def pointerLayoutpt(self): - return (self.layoutWidgetPt) - - # def mouseDoubleClickEvent(self, event): - # self.cmptEmitter.emit(QtCore.SIGNAL("qgtextDoubleClick(PyQt_PyObject)"),element(self.mooseObj_)) - - def itemChange(self,change,value): - if change == QtGui.QGraphicsItem.ItemPositionChange: - self.cmptEmitter.emit(QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.mobj) - if change == QtGui.QGraphicsItem.ItemSelectedChange and value == True: - self.cmptEmitter.emit(QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),self.mobj) - return QtGui.QGraphicsItem.itemChange(self,change,value) - - -if __name__ == '__main__': - app = QtGui.QApplication(sys.argv) - a = moose.Pool('pool') - b = moose.Reac('reac') - c = moose.Enz('enzyme') - gview = QtGui.QGraphicsView() - scene = QtGui.QGraphicsScene(gview) - #item = PoolItem(a) - #dinfo = (5, 5, QtGui.QColor('red'), QtGui.QColor('blue')) - #item.setDisplayProperties(dinfo) - reacItem = ReacItem(b) - reacItem.setDisplayProperties(50, 5, QtGui.QColor('yellow'), QtGui.QColor('green')) - enzItem = EnzItem(c) - enzItem.setDisplayProperties(100, 10, QtGui.QColor('blue'), QtGui.QColor('yellow')) - #scene.addItem(item) - scene.addItem(reacItem) - scene.addItem(enzItem) - gview.setScene(scene) - #print 'Position', reacItem.pos() - gview.show() - sys.exit(app.exec_()) diff --git a/plugins/modelBuild.py b/plugins/modelBuild.py deleted file mode 100644 index 260c8af..0000000 --- a/plugins/modelBuild.py +++ /dev/null @@ -1,332 +0,0 @@ -__author__ = "HarshaRani" -__credits__ = ["Upi Lab"] -__license__ = "GPL3" -__version__ = "1.0.0" -__maintainer__ = "HarshaRani" -__email__ = "hrani@ncbs.res.in" -__status__ = "Development" -__updated__ = "Apr 11 2018" - -import moose -from kkitQGraphics import * -from kkitOrdinateUtil import * -from kkitUtil import * -import PyQt4 -from setsolver import * - -def updateCompartmentSize(qGraCompt): - #childBoundingRect = qGraCompt.childrenBoundingRect() - childBoundingRect = calculateChildBoundingRect(qGraCompt) - comptBoundingRect = qGraCompt.boundingRect() - rectcompt = comptBoundingRect.united(childBoundingRect) - comptPen = qGraCompt.pen() - comptWidth = 1 - comptPen.setWidth(comptWidth) - qGraCompt.setPen(comptPen) - if not comptBoundingRect.contains(childBoundingRect): - qGraCompt.setRect(rectcompt.x()-comptWidth,rectcompt.y()-comptWidth,rectcompt.width()+(comptWidth*2),rectcompt.height()+(comptWidth*2)) - -# def checkCreate(string,num,itemAt,qGraCompt,modelRoot,scene,pos,posf,view,qGIMob): -def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layoutPt): - # The variable 'compt' will be empty when dropping cubeMesh,cyclMesh, but rest it shd be - # compartment - # if modelpath.find('/',1) > -1: - # modelRoot = modelpath[0:modelpath.find('/',1)] - # else: - # modelRoot = modelpath - if moose.exists(modelpath+'/info'): - mType = moose.Annotator((moose.element(modelpath+'/info'))).modeltype - itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos)) - pos = view.mapToScene(event_pos) - modelpath = moose.element(modelpath) - if num: - string_num = ret_string+str(num) - else: - string_num = ret_string - if string == "CubeMesh" or string == "CylMesh": - if string == "CylMesh": - mobj = moose.CylMesh(modelpath.path+'/'+string_num) - else: - mobj = moose.CubeMesh(modelpath.path+'/'+string_num) - - mobj.volume = 1e-15 - mesh = moose.element(mobj.path+'/mesh') - qGItem = ComptItem(scene,pos.toPoint().x(),pos.toPoint().y(),100,100,mobj) - qGItem.setPen(QtGui.QPen(Qt.QColor(66,66,66,100), 1, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)) - view.sceneContainerPt.addItem(qGItem) - qGItem.cmptEmitter.connect(qGItem.cmptEmitter,QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),layoutPt.positionChange1) - qGItem.cmptEmitter.connect(qGItem.cmptEmitter,QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),layoutPt.objectEditSlot) - compartment = qGItem - layoutPt.qGraCompt[mobj]= qGItem - view.emit(QtCore.SIGNAL("dropped"),mobj) - - elif string == "Pool" or string == "BufPool": - #getting pos with respect to compartment otherwise if compartment is moved then pos would be wrong - posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() - if string == "Pool": - poolObj = moose.Pool(mobj.path+'/'+string_num) - else: - poolObj = moose.BufPool(mobj.path+'/'+string_num) - - poolinfo = moose.Annotator(poolObj.path+'/info') - #Compartment's one Pool object is picked to get the font size - - qGItem = PoolItem(poolObj,itemAtView) - layoutPt.mooseId_GObj[poolObj] = qGItem - posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() - bgcolor = getRandColor() - qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),QtGui.QColor('green'),bgcolor) - poolinfo.color = str(bgcolor.getRgb()) - view.emit(QtCore.SIGNAL("dropped"),poolObj) - setupItem(modelpath.path,layoutPt.srcdesConnection) - layoutPt.drawLine_arrow(False) - x,y = roundoff(qGItem.scenePos(),layoutPt) - poolinfo.x = x - poolinfo.y = y - #Dropping is on compartment then update Compart size - if isinstance(mobj,moose.ChemCompt): - compt = layoutPt.qGraCompt[moose.element(mobj)] - updateCompartmentSize(compt) - - elif string == "Reac": - posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() - reacObj = moose.Reac(mobj.path+'/'+string_num) - reacinfo = moose.Annotator(reacObj.path+'/info') - qGItem = ReacItem(reacObj,itemAtView) - qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),"white", "white") - #if mType == "new_kkit": - # reacinfo.x = posWrtComp.x() - # reacinfo.y = posWrtComp.y() - layoutPt.mooseId_GObj[reacObj] = qGItem - view.emit(QtCore.SIGNAL("dropped"),reacObj) - setupItem(modelpath.path,layoutPt.srcdesConnection) - layoutPt.drawLine_arrow(False) - #Dropping is on compartment then update Compart size - if isinstance(mobj,moose.ChemCompt): - compt = layoutPt.qGraCompt[moose.element(mobj)] - updateCompartmentSize(compt) - x,y = roundoff(qGItem.scenePos(),layoutPt) - reacinfo.x = x - reacinfo.y = y - - elif string == "StimulusTable": - posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() - tabObj = moose.StimulusTable(mobj.path+'/'+string_num) - tabinfo = moose.Annotator(tabObj.path+'/info') - qGItem = TableItem(tabObj,itemAtView) - qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),QtGui.QColor('white'),QtGui.QColor('white')) - #if mType == "new_kkit": - #tabinfo.x = posWrtComp.x() - #tabinfo.y = posWrtComp.y() - layoutPt.mooseId_GObj[tabObj] = qGItem - view.emit(QtCore.SIGNAL("dropped"),tabObj) - setupItem(modelpath.path,layoutPt.srcdesConnection) - layoutPt.drawLine_arrow(False) - #Dropping is on compartment then update Compart size - if isinstance(mobj,moose.ChemCompt): - compt = layoutPt.qGraCompt[moose.element(mobj)] - updateCompartmentSize(compt) - x,y = roundoff(qGItem.scenePos(),layoutPt) - tabinfo.x = x - tabinfo.y = y - - elif string == "Function": - posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() - funcObj = moose.Function(mobj.path+'/'+string_num) - funcinfo = moose.Annotator(funcObj.path+'/info') - #moose.connect( funcObj, 'valueOut', mobj ,'setN' ) - poolclass = ["ZombieBufPool","BufPool"] - comptclass = ["CubeMesh","cyclMesh"] - - if mobj.className in poolclass: - funcParent = layoutPt.mooseId_GObj[element(mobj.path)] - elif mobj.className in comptclass: - funcParent = layoutPt.qGraCompt[moose.element(mobj)] - posWrtComp = funcParent.mapFromScene(pos).toPoint() - #posWrtComp = (itemAtView.mapFromScene(pos)).toPoint() - elif mobj.className in "Neutral": - funcParent = layoutPt.qGraGrp[element(mobj)] - - qGItem = FuncItem(funcObj,funcParent) - qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),QtGui.QColor('red'),QtGui.QColor('green')) - layoutPt.mooseId_GObj[funcObj] = qGItem - #if mType == "new_kkit": - #funcinfo.x = posWrtComp.x() - #funcinfo.y = posWrtComp.y() - view.emit(QtCore.SIGNAL("dropped"),funcObj) - setupItem(modelpath.path,layoutPt.srcdesConnection) - layoutPt.drawLine_arrow(False) - #Dropping is on compartment then update Compart size - mooseCmpt = findCompartment(mobj) - if isinstance(mooseCmpt,moose.ChemCompt): - compt = layoutPt.qGraCompt[moose.element(mooseCmpt)] - updateCompartmentSize(compt) - x,y = roundoff(qGItem.scenePos(),layoutPt) - funcinfo.x = x - funcinfo.y = y - - elif string == "Enz" or string == "MMenz": - #If 2 enz has same pool parent, then pos of the 2nd enz shd be displaced by some position, need to check how to deal with it - posWrtComp = pos - enzPool = layoutPt.mooseId_GObj[mobj] - if ((mobj.parent).className == "Enz"): - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have Pool as its parent and not Enzyme Complex'.format(newString =string),QtGui.QMessageBox.Ok) - return - else: - enzparent = findCompartment(mobj) - parentcompt = layoutPt.qGraCompt[enzparent] - if string == "Enz": - enzObj = moose.Enz(moose.element(mobj).path+'/'+string_num) - enzinfo = moose.Annotator(enzObj.path+'/info') - moose.connect( enzObj, 'enz', mobj, 'reac' ) - qGItem = EnzItem(enzObj,parentcompt) - layoutPt.mooseId_GObj[enzObj] = qGItem - posWrtComp = pos - bgcolor = getRandColor() - qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y()-40,QtGui.QColor('green'),bgcolor) - x,y = roundoff(qGItem.scenePos(),layoutPt) - enzinfo.x = x - enzinfo.y = y - enzinfo.color = str(bgcolor.name()) - enzinfo.textColor = str(QtGui.QColor('green').name()) - #if mType == "new_kkit": - #enzinfo.x = posWrtComp.x() - #enzinfo.y = posWrtComp.y() - - #enzinfo.color = str(bgcolor.name()) - e = moose.Annotator(enzinfo) - #e.x = posWrtComp.x() - #e.y = posWrtComp.y() - Enz_cplx = enzObj.path+'/'+string_num+'_cplx'; - cplxItem = moose.Pool(Enz_cplx) - cplxinfo = moose.Annotator(cplxItem.path+'/info') - qGEnz = layoutPt.mooseId_GObj[enzObj] - qGItem = CplxItem(cplxItem,qGEnz) - layoutPt.mooseId_GObj[cplxItem] = qGItem - enzboundingRect = qGEnz.boundingRect() - moose.connect( enzObj, 'cplx', cplxItem, 'reac' ) - qGItem.setDisplayProperties(enzboundingRect.height()/2,enzboundingRect.height()-40,QtGui.QColor('white'),QtGui.QColor('white')) - #cplxinfo.x = enzboundingRect.height()/2 - #cplxinfo.y = enzboundingRect.height()-60 - view.emit(QtCore.SIGNAL("dropped"),enzObj) - - else: - enzObj = moose.MMenz(mobj.path+'/'+string_num) - enzinfo = moose.Annotator(enzObj.path+'/info') - moose.connect(mobj,"nOut",enzObj,"enzDest") - qGItem = MMEnzItem(enzObj,parentcompt) - posWrtComp = pos - bgcolor = getRandColor() - qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y()-30,QtGui.QColor('green'),bgcolor) - #enzinfo.x = posWrtComp.x() - #enzinfo.y = posWrtComp.y() - enzinfo.color = str(bgcolor.name()) - layoutPt.mooseId_GObj[enzObj] = qGItem - view.emit(QtCore.SIGNAL("dropped"),enzObj) - x,y = roundoff(qGItem.scenePos(),layoutPt) - enzinfo.x = x - enzinfo.y = y - setupItem(modelpath.path,layoutPt.srcdesConnection) - layoutPt.drawLine_arrow(False) - - #Dropping is on compartment then update Compart size - if isinstance(enzparent,moose.ChemCompt): - updateCompartmentSize(parentcompt) - if view.iconScale != 1: - view.updateScale(view.iconScale) - -def createObj(scene,view,modelpath,string,pos,layoutPt): - event_pos = pos - num = 0 - ret_string = " " - pos = view.mapToScene(event_pos) - itemAt = view.sceneContainerPt.itemAt(pos) - chemMesh = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]') - deleteSolver(modelpath) - mobj = "" - - if itemAt != None: - itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos)) - itemClass = type(itemAtView).__name__ - if ( itemClass == 'QGraphicsRectItem'): - mobj = itemAtView.parentItem().mobj - elif(itemClass == 'QGraphicsSvgItem'): - mobj = itemAtView.parent().mobj - else: - mobj = itemAtView.mobj - if string == "CubeMesh" or string == "CylMesh": - ret_string,num = findUniqId(moose.element(modelpath),"Compartment",0) - comptexist = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]') - if not len(comptexist): - if itemAt != None: - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' currently single compartment model building is allowed'.format(newString =string),QtGui.QMessageBox.Ok) - return - else: - mobj = moose.element(modelpath) - else: - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' currently single compartment model building is allowed'.format(newString =string),QtGui.QMessageBox.Ok) - return - - elif string == "Pool" or string == "BufPool" or string == "Reac" or string == "StimulusTable": - if itemAt == None: - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have compartment as its parent'.format(newString =string),QtGui.QMessageBox.Ok) - return - else: - mobj = findCompartment(mobj) - ret_string,num = findUniqId(mobj,string,num) - - elif string == "Function": - #mobj = findCompartment(mobj) - ret_string,num = findUniqId(mobj,string,num) - ''' - if itemAt != None: - if ((mobj).className != "BufPool"): - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have BufPool as its parent'.format(newString =string),QtGui.QMessageBox.Ok) - return - else: - ret_string,num = findUniqId(mobj,string,num) - else: - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have BufPool as its parent'.format(newString =string),QtGui.QMessageBox.Ok) - return - ''' - elif string == "Enz" or string == "MMenz": - if itemAt != None: - if ((mobj).className != "Pool" and (mobj).className != "BufPool"): - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have Pool as its parent'.format(newString =string),QtGui.QMessageBox.Ok) - return - else: - ret_string,num = findUniqId(mobj,string,num) - else: - QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have Pool as its parent'.format(newString =string),QtGui.QMessageBox.Ok) - return - - if ret_string != " ": - checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layoutPt) - -def roundoff(scenePos,layoutPt): - xtest = scenePos.x()/layoutPt.defaultScenewidth - xroundoff = round(xtest,1) - - ytest = scenePos.y()/layoutPt.defaultSceneheight - yroundoff = round(ytest,1) - - return(xroundoff,yroundoff) - -def findUniqId(mobj,string,num): - if num == 0: - path = mobj.path+'/'+string; - else: - path = mobj.path+'/'+string+str(num); - if not moose.exists(path): - return(string,num) - else: - num +=1; - return(findUniqId(mobj,string,num)) - -def findCompartment(mooseObj): - if mooseObj.path == '/': - return None - elif isinstance(mooseObj,ChemCompt): - return (mooseObj) - else: - return findCompartment(moose.element(mooseObj.parent)) diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..ebbd809 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,3 @@ +pymoose +pyqt5 +networkx diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..0fbfe08 --- /dev/null +++ b/setup.py @@ -0,0 +1,58 @@ +# -*- coding: utf-8 -*- + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2016, Dilawar Singh" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import os +import sys +from setuptools import setup + +demofiles = [] + +version_ = '0.1.0' + +demoDir = os.path.join(os.path.dirname(__file__), 'demos') + +for d, sd, fs in os.walk( demoDir ): + for f in fs: + filepath = os.path.join( d, f ).replace( demoDir, '' ) + demofiles.append( filepath ) + +setup( + name = "moosegui", + version = version_, + description = "Graphical User Interface of MOOSE simulator", + long_description = open( 'README.md' ).read(), + packages = [ "moosegui", 'moosegui.plugins', "moosegui.demos" + , 'suds', 'suds.bindings', 'suds.sax', 'suds.mx', 'suds.xsd' + , 'suds.umx', 'suds.transport' + ], + package_dir = { + 'moosegui' : 'moosegui' + , 'moosegui.demos' : '.' + , 'moosegui.plugins' : 'moosegui/plugins' + , 'suds' : 'suds' + }, + package_data = { + 'moosegui' : [ 'icons/*', 'colormaps/*' ] + demofiles + , 'moosegui.demos' : [ '*' ] + demofiles + , 'moosegui.plugins' : [ 'datastore/*', 'list.txt' ] + }, + author = open('AUTHOR').read(), + maintainer = 'Dilawar Singh', + maintainer_email = 'dilawars@ncbs.res.in', + url = "http://github.com/BhallaLab/moose-gui", + license='GPLv3', + install_requires = [ 'pymoose', 'pyqt5' ], + entry_points = { + 'console_scripts' : [ + 'moosegui = moosegui.mgui:main' + ], + }, +) diff --git a/sidebar.py b/sidebar.py deleted file mode 100644 index d14b1af..0000000 --- a/sidebar.py +++ /dev/null @@ -1,244 +0,0 @@ - -# -*- coding: utf-8 -*- -from __future__ import print_function - -"""Sidebar for plugins. The sidebar comprises of actions. -Currently mode, connect and settings are defined. -""" - -__author__ = "Aviral Goel" -__credits__ = ["Upi Lab"] -__license__ = "GPL3" -__version__ = "1.0.0" -__maintainer__ = "Aviral Goel" -__email__ = "goel.aviral@gmail.com" -__status__ = "Development" - - -import sys -import os -import SettingsDialog -from PyQt4 import QtGui, Qt -from PyQt4.QtGui import QDialog -from PyQt4.QtGui import QHBoxLayout -from PyQt4.QtGui import QPixmap -from PyQt4.QtGui import QIcon -from PyQt4.QtGui import QPushButton -from PyQt4.QtGui import QAction - - - -ICON_DIRECTORY = "icons" -HAND_ICON_FILENAME = "hand.png" -CONNECTOR_ICON_FILENAME = "straight_connector_with_filled_circles.png" -WRENCH_ICON_FILENAME = "wrench.png" -DELETE_GRAPH_ICON_FILENAME = "add_graph.png" -ADD_GRAPH_ICON_FILENAME = "delete_graph.png" -LIST_ICON_FILENAME = "list.png" - - -def create_action( parent - , callback - , text - , checkable - , checked - , icon_path - ): - pixmap = QPixmap(icon_path) - icon = QIcon(pixmap) - action = QAction(icon, text, parent) - # action.setIcon(icon) - # action.setIconText(text) - action.triggered.connect(callback) - action.setCheckable(checkable) - action.setChecked(checked) - return action - - -def mode_action( parent - , callback = (lambda event: print("Mode Clicked!")) - , text = "Mode" - , checkable = True - , checked = True - , icon_path = os.path.join( ICON_DIRECTORY - , HAND_ICON_FILENAME - ) - ): - return create_action( parent - , callback - , text - , checkable - , checked - , icon_path - ) - -def add_graph_action( parent - , callback = (lambda event: print("Add Graph Clicked!")) - , text = "Add Graph" - , checkable = False - , checked = False - , icon_path = os.path.join( ICON_DIRECTORY - , ADD_GRAPH_ICON_FILENAME - ) - ): - return create_action( parent - , callback - , text - , checkable - , checked - , icon_path - ) - -def delete_graph_action( parent - , callback = (lambda event: print("Delete Graph Clicked!")) - , text = "Delete Graph" - , checkable = False - , checked = False - , icon_path = os.path.join( ICON_DIRECTORY - , DELETE_GRAPH_ICON_FILENAME - ) - ): - return create_action( parent - , callback - , text - , checkable - , checked - , icon_path - ) - -def list_action( parent - , callback = (lambda event: print("List Clicked!")) - , text = "Show List" - , checkable = False - , checked = False - , icon_path = os.path.join( ICON_DIRECTORY - , LIST_ICON_FILENAME - ) - ): - return create_action( parent - , callback - , text - , checkable - , checked - , icon_path - ) - -def connector_action( parent - , callback = (lambda event: print("Connector Clicked!")) - , text = "Mode" - , checkable = True - , checked = False - , icon_path = os.path.join( ICON_DIRECTORY - , CONNECTOR_ICON_FILENAME - ) - ): - return create_action( parent - , callback - , text - , checkable - , checked - , icon_path - ) - -def settings_action( parent - , callback = (lambda event: print("Settings Clicked")) - , text = "Mode" - , checkable = False - , checked = False - , icon_path = os.path.join( ICON_DIRECTORY - , WRENCH_ICON_FILENAME - ) - ): - return create_action( parent - , callback - , text - , checkable - , checked - , icon_path - ) - - - # actions - # , left_spacer = False - # , right_spacer = False - -def sidebar(): - return QtGui.QToolBar() - # bar.setOrientation(Qt.Qt.Vertical) - # return bar - # if left_spacer: - # left_spacer = QWidget() - # left_spacer.setSizePolicy( QtGui.QSizePolicy.Expanding - # , QtGui.QSizePolicy.Expanding - # ) - # toolbar.addWidget(left_spacer) - - # for action in actions: - # toolbar.addAction(action(toolbar)) - - # if right_spacer: - # right_spacer = QWidget() - # right_spacer.setSizePolicy( QtGui.QSizePolicy.Expanding - # , QtGui.QSizePolicy.Expanding - # ) - # toolbar.addWidget(right_spacer) - - # return toolbar - - - - -# def connect_action(): - -# def settings_action(): - - - -def main(): - app = QtGui.QApplication(sys.argv) - window = QtGui.QMainWindow() - widget = SettingsDialog.SettingsWidget({ - 'LeakyIaF':['Vm'], - 'Compartment':['Vm','Im'], - 'HHChannel':['Ik','Gk'], - 'ZombiePool':['n','conc'], - 'ZombieBufPool':['n','conc'], - 'HHChannel2D':['Ik','Gk'], - 'CaConc':['Ca'] - }) - d = QDialog() - l = QHBoxLayout() - d.setLayout(l) - l.addWidget(widget) - bar = sidebar() - bar.addAction(mode_action(bar)) - bar.addAction(connector_action(bar)) - bar.addAction(settings_action(bar, d.show)) - window.addToolBar(bar) - window.show() - sys.exit(app.exec_()) - - -if __name__ == "__main__": - main() - -# # spacer widget for left -# # spacer widget for right -# # you can't add the same widget to both left and right. you need two different widgets. -# right_spacer = QtGui.QWidget() -# right_spacer.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding) - -# # here goes the left one -# # toolbar.addWidget(left_spacer) -# # some dummy actions - - - -# ################################################################################ -# # Hand Tool -# ################################################################################ - - - - - diff --git a/suds/__init__.py b/suds/__init__.py index a907102..42eef79 100644 --- a/suds/__init__.py +++ b/suds/__init__.py @@ -25,7 +25,7 @@ # Project properties # -from version import __build__, __version__ +from .version import __build__, __version__ # @@ -34,19 +34,19 @@ class MethodNotFound(Exception): def __init__(self, name): - Exception.__init__(self, u"Method not found: '%s'" % name) + Exception.__init__(self, "Method not found: '%s'" % name) class PortNotFound(Exception): def __init__(self, name): - Exception.__init__(self, u"Port not found: '%s'" % name) + Exception.__init__(self, "Port not found: '%s'" % name) class ServiceNotFound(Exception): def __init__(self, name): - Exception.__init__(self, u"Service not found: '%s'" % name) + Exception.__init__(self, "Service not found: '%s'" % name) class TypeNotFound(Exception): def __init__(self, name): - Exception.__init__(self, u"Type not found: '%s'" % tostr(name)) + Exception.__init__(self, "Type not found: '%s'" % tostr(name)) class BuildError(Exception): msg = """ @@ -71,7 +71,7 @@ def __init__(self, name): class WebFault(Exception): def __init__(self, fault, document): if hasattr(fault, 'faultstring'): - Exception.__init__(self, u"Server raised fault: '%s'" % + Exception.__init__(self, "Server raised fault: '%s'" % fault.faultstring) self.fault = fault self.document = document @@ -104,7 +104,7 @@ def objid(obj): def tostr(object, encoding=None): """ get a unicode safe string representation of an object """ - if isinstance(object, basestring): + if isinstance(object, str): if encoding is None: return object else: @@ -112,7 +112,7 @@ def tostr(object, encoding=None): if isinstance(object, tuple): s = ['('] for item in object: - if isinstance(item, basestring): + if isinstance(item, str): s.append(item) else: s.append(tostr(item)) @@ -122,7 +122,7 @@ def tostr(object, encoding=None): if isinstance(object, list): s = ['['] for item in object: - if isinstance(item, basestring): + if isinstance(item, str): s.append(item) else: s.append(tostr(item)) @@ -131,13 +131,13 @@ def tostr(object, encoding=None): return ''.join(s) if isinstance(object, dict): s = ['{'] - for item in object.items(): - if isinstance(item[0], basestring): + for item in list(object.items()): + if isinstance(item[0], str): s.append(item[0]) else: s.append(tostr(item[0])) s.append(' = ') - if isinstance(item[1], basestring): + if isinstance(item[1], str): s.append(item[1]) else: s.append(tostr(item[1])) @@ -145,7 +145,7 @@ def tostr(object, encoding=None): s.append('}') return ''.join(s) try: - return unicode(object) + return str(object) except: return str(object) @@ -155,7 +155,7 @@ def tostr(object, encoding=None): # if sys.version_info < (3, 0): - from cStringIO import StringIO as BytesIO + from io import StringIO as BytesIO else: from io import BytesIO @@ -165,7 +165,7 @@ class UnicodeMixin(object): # For Python 3, __str__() and __unicode__() should be identical. __str__ = lambda x: x.__unicode__() else: - __str__ = lambda x: unicode(x).encode('utf-8') + __str__ = lambda x: str(x).encode('utf-8') # Used instead of byte literals because they are not supported on Python # versions prior to 2.6. @@ -177,8 +177,8 @@ def byte_str(s='', encoding='utf-8', input_encoding='utf-8', errors='strict'): strings encoded using the given input encoding. """ - assert isinstance(s, basestring) - if isinstance(s, unicode): + assert isinstance(s, str) + if isinstance(s, str): return s.encode(encoding, errors) if s and encoding != input_encoding: return s.decode(input_encoding, errors).encode(encoding, errors) diff --git a/suds/argparser.py b/suds/argparser.py index 67bdb02..ba8e5e1 100644 --- a/suds/argparser.py +++ b/suds/argparser.py @@ -161,7 +161,7 @@ def __check_for_extra_arguments(self, args_required, args_allowed): return if self.__kwargs: - param_name = self.__kwargs.keys()[0] + param_name = list(self.__kwargs.keys())[0] if param_name in self.__params_with_arguments: msg = "got multiple values for parameter '%s'" else: @@ -263,7 +263,7 @@ def __match_ancestry(self, ancestry): if len(stack) == 1: return stack[0], ancestry previous = stack[0] - for frame, n in zip(stack[1:], xrange(len(ancestry))): + for frame, n in zip(stack[1:], range(len(ancestry))): if frame.id() is not ancestry[n]: return previous, ancestry[n:] previous = frame diff --git a/suds/bindings/binding.py b/suds/bindings/binding.py index 45966eb..efe8c6a 100644 --- a/suds/bindings/binding.py +++ b/suds/bindings/binding.py @@ -88,7 +88,7 @@ def param_defs(self, method): @return: A collection of parameter definitions @rtype: [I{pdef},..] """ - raise Exception, 'not implemented' + raise Exception('not implemented') def get_message(self, method, args, kwargs): """ @@ -286,7 +286,7 @@ def bodycontent(self, method, args, kwargs): @return: The XML content for the @rtype: [L{Element},..] """ - raise Exception, 'not implemented' + raise Exception('not implemented') def headercontent(self, method): """ @@ -339,7 +339,7 @@ def replycontent(self, method, body): @return: The body content. @rtype: [L{Element},...] """ - raise Exception, 'not implemented' + raise Exception('not implemented') def body(self, content): """ diff --git a/suds/builder.py b/suds/builder.py index 9264749..a881609 100644 --- a/suds/builder.py +++ b/suds/builder.py @@ -34,7 +34,7 @@ def __init__(self, resolver): def build(self, name): """ build a an object for the specified typename as defined in the schema """ - if isinstance(name, basestring): + if isinstance(name, str): type = self.resolver.find(name) if type is None: raise TypeNotFound(name) diff --git a/suds/cache.py b/suds/cache.py index 91f0c0c..a31ac56 100644 --- a/suds/cache.py +++ b/suds/cache.py @@ -28,7 +28,7 @@ import os from tempfile import gettempdir as tmp try: - import cPickle as pickle + import pickle as pickle except Exception: import pickle @@ -136,7 +136,7 @@ def setduration(self, **duration): @type duration: {unit:value} """ if len(duration) == 1: - arg = duration.items()[0] + arg = list(duration.items())[0] if not arg[0] in self.units: raise Exception('must be: %s' % str(self.units)) self.duration = arg diff --git a/suds/client.py b/suds/client.py index 2a664fe..5ca689c 100644 --- a/suds/client.py +++ b/suds/client.py @@ -37,12 +37,17 @@ from suds.transport.https import HttpAuthenticated from suds.umx.basic import Basic as UmxBasic from suds.wsdl import Definitions -import sudsobject +from . import sudsobject -from cookielib import CookieJar from copy import deepcopy -import httplib -from urlparse import urlparse +try: + from http.cookiejar import CookieJar + import http.client + from urllib.parse import urlparse +except Exception as e: + from cookielib import CookieJar + import httplib + from urlparse import urlparse from logging import getLogger log = getLogger(__name__) @@ -181,7 +186,7 @@ def __unicode__(self): if ( suds.__build__ ): s.append(' build: %s' % suds.__build__) for sd in self.sd: - s.append('\n\n%s' % unicode(sd)) + s.append('\n\n%s' % str(sd)) return ''.join(s) @@ -223,7 +228,7 @@ def create(self, name): else: try: result = self.builder.build(type) - except Exception, e: + except Exception as e: log.error("create '%s' failed", name, exc_info=True) raise BuildError(name, e) timer.stop() @@ -312,20 +317,20 @@ def __find(self, name): """ service = None if not len(self.__services): - raise Exception, 'No services defined' + raise Exception('No services defined') if isinstance(name, int): try: service = self.__services[name] name = service.name - except IndexError: - raise ServiceNotFound, 'at [%d]' % name + except IndexError as e: + raise ServiceNotFound('at [%d]' % name) else: for s in self.__services: if name == s.name: service = s break if service is None: - raise ServiceNotFound, name + raise ServiceNotFound(name) return PortSelector(self.__client, service.ports, name) def __ds(self): @@ -413,13 +418,13 @@ def __find(self, name): """ port = None if not len(self.__ports): - raise Exception, 'No ports defined: %s' % self.__qn + raise Exception('No ports defined: %s' % self.__qn) if isinstance(name, int): qn = '%s[%d]' % (self.__qn, name) try: port = self.__ports[name] - except IndexError: - raise PortNotFound, qn + except IndexError as e: + raise PortNotFound(qn) else: qn = '.'.join((self.__qn, name)) for p in self.__ports: @@ -427,7 +432,7 @@ def __find(self, name): port = p break if port is None: - raise PortNotFound, qn + raise PortNotFound(qn) qn = '.'.join((self.__qn, port.name)) return MethodSelector(self.__client, port.methods, qn) @@ -488,7 +493,7 @@ def __getitem__(self, name): m = self.__methods.get(name) if m is None: qn = '.'.join((self.__qn, name)) - raise MethodNotFound, qn + raise MethodNotFound(qn) return Method(self.__client, m) @@ -519,10 +524,10 @@ def __call__(self, *args, **kwargs): client = clientclass(self.client, self.method) try: return client.invoke(args, kwargs) - except WebFault, e: + except WebFault as e: if self.faults(): raise - return (httplib.INTERNAL_SERVER_ERROR, e) + return (http.client.INTERNAL_SERVER_ERROR, e) def faults(self): """ get faults option """ @@ -613,7 +618,7 @@ def send(self, soapenv): reply = self.options.transport.send(request) timer.stop() metrics.log.debug('waited %s on server reply', timer) - except TransportError, e: + except TransportError as e: content = e.fp and e.fp.read() or '' return self.process_reply(reply=content, status=e.httpcode, description=tostr(e), original_soapenv=original_soapenv) @@ -623,12 +628,12 @@ def send(self, soapenv): def process_reply(self, reply, status=None, description=None, original_soapenv=None): if status is None: - status = httplib.OK - if status in (httplib.ACCEPTED, httplib.NO_CONTENT): + status = http.client.OK + if status in (http.client.ACCEPTED, http.client.NO_CONTENT): return failed = True try: - if status == httplib.OK: + if status == http.client.OK: log.debug('HTTP succeeded:\n%s', reply) else: log.debug('HTTP failed - %d - %s:\n%s', status, description, @@ -657,19 +662,19 @@ def process_reply(self, reply, status=None, description=None, # An INSTANCE MUST use a "500 Internal Server Error" HTTP status # code if the response message is a SOAP Fault. replyroot = None - if status in (httplib.OK, httplib.INTERNAL_SERVER_ERROR): + if status in (http.client.OK, http.client.INTERNAL_SERVER_ERROR): replyroot = _parse(reply) plugins.message.parsed(reply=replyroot) fault = self.get_fault(replyroot) if fault: - if status != httplib.INTERNAL_SERVER_ERROR: + if status != http.client.INTERNAL_SERVER_ERROR: log.warn("Web service reported a SOAP processing " "fault using an unexpected HTTP status code %d. " "Reporting as an internal server error.", status) if self.options.faults: raise WebFault(fault, replyroot) - return (httplib.INTERNAL_SERVER_ERROR, fault) - if status != httplib.OK: + return (http.client.INTERNAL_SERVER_ERROR, fault) + if status != http.client.OK: if self.options.faults: # (todo) # Use a more specific exception class here. @@ -688,7 +693,7 @@ def process_reply(self, reply, status=None, description=None, failed = False if self.options.faults: return result - return (httplib.OK, result) + return (http.client.OK, result) finally: if failed and original_soapenv: log.error(original_soapenv) @@ -717,7 +722,7 @@ def headers(self): @rtype: dict """ action = self.method.soap.action - if isinstance(action, unicode): + if isinstance(action, str): action = action.encode('utf-8') stock = {'Content-Type':'text/xml; charset=utf-8', 'SOAPAction':action} result = dict(stock, **self.options.headers) @@ -742,7 +747,7 @@ class SimClient(SoapClient): @classmethod def simulation(cls, kwargs): """ get whether loopback has been specified in the I{kwargs}. """ - return kwargs.has_key(SimClient.injkey) + return SimClient.injkey in kwargs def invoke(self, args, kwargs): """ diff --git a/suds/mx/__init__.py b/suds/mx/__init__.py index dc8154b..be26f3b 100644 --- a/suds/mx/__init__.py +++ b/suds/mx/__init__.py @@ -43,7 +43,7 @@ def __init__(self, tag=None, value=None, **kwargs): Object.__init__(self) self.tag = tag self.value = value - for k,v in kwargs.items(): + for k,v in list(kwargs.items()): setattr(self, k, v) def __getattr__(self, name): @@ -52,8 +52,7 @@ def __getattr__(self, name): v = None setattr(self, name, v) else: - raise AttributeError, \ - 'Content has no attribute %s' % name + raise AttributeError('Content has no attribute %s' % name) else: v = self.__dict__[name] return v diff --git a/suds/mx/appender.py b/suds/mx/appender.py index e60dc79..8e50a06 100644 --- a/suds/mx/appender.py +++ b/suds/mx/appender.py @@ -208,7 +208,7 @@ def append(self, parent, content): child = self.node(content) child.setText(p.get()) parent.append(child) - for item in p.items(): + for item in list(p.items()): cont = Content(tag=item[0], value=item[1]) Appender.append(self, child, cont) @@ -240,7 +240,7 @@ def append(self, parent, content): return child = self.node(content) parent.append(child) - for item in d.items(): + for item in list(d.items()): cont = Content(tag=item[0], value=item[1]) Appender.append(self, child, cont) diff --git a/suds/mx/literal.py b/suds/mx/literal.py index 44f38a3..1e46624 100644 --- a/suds/mx/literal.py +++ b/suds/mx/literal.py @@ -131,9 +131,8 @@ def end(self, parent, content): if current == content.type: self.resolver.pop() else: - raise Exception, \ - 'content (end) mismatch: top=(%s) cont=(%s)' % \ - (current, content) + raise Exception('content (end) mismatch: top=(%s) cont=(%s)' % \ + (current, content)) def node(self, content): # diff --git a/suds/mx/typer.py b/suds/mx/typer.py index aa52ad3..9a6c145 100644 --- a/suds/mx/typer.py +++ b/suds/mx/typer.py @@ -33,10 +33,10 @@ class Typer: types = { int : ('int', NS.xsdns), - long : ('long', NS.xsdns), + int : ('long', NS.xsdns), float : ('float', NS.xsdns), str : ('string', NS.xsdns), - unicode : ('string', NS.xsdns), + str : ('string', NS.xsdns), Text : ('string', NS.xsdns), bool : ('boolean', NS.xsdns), } diff --git a/suds/options.py b/suds/options.py index de49326..9fc6e15 100644 --- a/suds/options.py +++ b/suds/options.py @@ -132,9 +132,9 @@ def __init__(self, **kwargs): Definition('extraArgumentErrors', bool, True), Definition('faults', bool, True), Definition('transport', Transport, None, TpLinker()), - Definition('service', (int, basestring), None), - Definition('port', (int, basestring), None), - Definition('location', basestring, None), + Definition('service', (int, str), None), + Definition('port', (int, str), None), + Definition('location', str, None), Definition('soapheaders', (), ()), Definition('wsse', Security, None), Definition('doctor', Doctor, None), diff --git a/suds/plugin.py b/suds/plugin.py index 0616568..fc23961 100644 --- a/suds/plugin.py +++ b/suds/plugin.py @@ -22,6 +22,7 @@ from suds import * from logging import getLogger +import collections log = getLogger(__name__) @@ -205,7 +206,7 @@ def __getattr__(self, name): plugins.append(p) return PluginDomain(ctx, plugins) else: - raise Exception, 'plugin domain (%s), invalid' % name + raise Exception('plugin domain (%s), invalid' % name) class PluginDomain: @@ -250,8 +251,8 @@ def __call__(self, **kwargs): for plugin in self.domain.plugins: try: method = getattr(plugin, self.name, None) - if method and callable(method): + if method and isinstance(method, collections.Callable): method(ctx) - except Exception, pe: + except Exception as pe: log.exception(pe) return ctx diff --git a/suds/properties.py b/suds/properties.py index 7103232..23ec820 100644 --- a/suds/properties.py +++ b/suds/properties.py @@ -67,23 +67,23 @@ def validate(self, pA, pB): """ if pA in pB.links or \ pB in pA.links: - raise Exception, 'Already linked' + raise Exception('Already linked') dA = pA.domains() dB = pB.domains() for d in dA: if d in dB: - raise Exception, 'Duplicate domain "%s" found' % d + raise Exception('Duplicate domain "%s" found' % d) for d in dB: if d in dA: - raise Exception, 'Duplicate domain "%s" found' % d - kA = pA.keys() - kB = pB.keys() + raise Exception('Duplicate domain "%s" found' % d) + kA = list(pA.keys()) + kB = list(pB.keys()) for k in kA: if k in kB: - raise Exception, 'Duplicate key %s found' % k + raise Exception('Duplicate key %s found' % k) for k in kB: if k in kA: - raise Exception, 'Duplicate key %s found' % k + raise Exception('Duplicate key %s found' % k) return self def teardown(self): @@ -177,7 +177,7 @@ def validate(self, value): if len(self.classes) and \ not isinstance(value, self.classes): msg = '"%s" must be: %s' % (self.name, self.classes) - raise AttributeError,msg + raise AttributeError(msg) def __repr__(self): @@ -251,7 +251,7 @@ def update(self, other): """ if isinstance(other, Properties): other = other.defined - for n,v in other.items(): + for n,v in list(other.items()): self.set(n, v) return self @@ -372,7 +372,7 @@ def keys(self, history=None): history = [] history.append(self) keys = set() - keys.update(self.definitions.keys()) + keys.update(list(self.definitions.keys())) for x in self.links: if x in history: continue @@ -408,7 +408,7 @@ def prime(self): @return: self @rtype: L{Properties} """ - for d in self.definitions.values(): + for d in list(self.definitions.values()): self.defined[d.name] = d.default return self @@ -434,10 +434,10 @@ def __get(self, name, *df): def str(self, history): s = [] s.append('Definitions:') - for d in self.definitions.values(): + for d in list(self.definitions.values()): s.append('\t%s' % repr(d)) s.append('Content:') - for d in self.defined.items(): + for d in list(self.defined.items()): s.append('\t%s' % str(d)) if self not in history: history.append(self) diff --git a/suds/sax/__init__.py b/suds/sax/__init__.py index bef7825..d249533 100644 --- a/suds/sax/__init__.py +++ b/suds/sax/__init__.py @@ -45,7 +45,7 @@ def splitPrefix(name): @return: A tuple containing the (2) parts of I{name} @rtype: (I{prefix}, I{name}) """ - if isinstance(name, basestring) and ':' in name: + if isinstance(name, str) and ':' in name: return tuple(name.split(':', 1)) return None, name diff --git a/suds/sax/attribute.py b/suds/sax/attribute.py index c775e20..a655430 100644 --- a/suds/sax/attribute.py +++ b/suds/sax/attribute.py @@ -171,4 +171,4 @@ def __unicode__(self): v = self.value.escape() else: v = self.value - return u'%s="%s"' % (n, v) + return '%s="%s"' % (n, v) diff --git a/suds/sax/date.py b/suds/sax/date.py index ac534c4..8ad4346 100644 --- a/suds/sax/date.py +++ b/suds/sax/date.py @@ -65,7 +65,7 @@ def __init__(self, value): self.value = value.date() elif isinstance(value, datetime.date): self.value = value - elif isinstance(value, basestring): + elif isinstance(value, str): self.value = self.__parse(value) else: raise ValueError("invalid type for Date(): %s" % type(value)) @@ -115,7 +115,7 @@ def __init__(self, value): """ if isinstance(value, datetime.datetime): self.value = value - elif isinstance(value, basestring): + elif isinstance(value, str): self.value = self.__parse(value) else: raise ValueError("invalid type for DateTime(): %s" % type(value)) @@ -173,7 +173,7 @@ def __init__(self, value): """ if isinstance(value, datetime.time): self.value = value - elif isinstance(value, basestring): + elif isinstance(value, str): self.value = self.__parse(value) else: raise ValueError("invalid type for Time(): %s" % type(value)) diff --git a/suds/sax/document.py b/suds/sax/document.py index 8697e08..d666e31 100644 --- a/suds/sax/document.py +++ b/suds/sax/document.py @@ -52,7 +52,7 @@ def append(self, node): the document root element. @type node: (L{Element}|str|None) """ - if isinstance(node, basestring): + if isinstance(node, str): self.__root = Element(node) return if isinstance(node, Element): diff --git a/suds/sax/element.py b/suds/sax/element.py index 502d90d..a75811e 100644 --- a/suds/sax/element.py +++ b/suds/sax/element.py @@ -158,7 +158,7 @@ def clone(self, parent=None): root.append(a.clone(self)) for c in self.children: root.append(c.clone(self)) - for item in self.nsprefixes.items(): + for item in list(self.nsprefixes.items()): root.addPrefix(item[0], item[1]) return root @@ -567,11 +567,11 @@ def findPrefix(self, uri, default=None): @return: A mapped prefix. @rtype: basestring """ - for item in self.nsprefixes.items(): + for item in list(self.nsprefixes.items()): if item[1] == uri: prefix = item[0] return prefix - for item in self.specialprefixes.items(): + for item in list(self.specialprefixes.items()): if item[1] == uri: prefix = item[0] return prefix @@ -592,11 +592,11 @@ def findPrefixes(self, uri, match='eq'): @rtype: [basestring,...] """ result = [] - for item in self.nsprefixes.items(): + for item in list(self.nsprefixes.items()): if self.matcher[match](item[1], uri): prefix = item[0] result.append(prefix) - for item in self.specialprefixes.items(): + for item in list(self.specialprefixes.items()): if self.matcher[match](item[1], uri): prefix = item[0] result.append(prefix) @@ -617,7 +617,7 @@ def promotePrefixes(self): c.promotePrefixes() if self.parent is None: return - for p,u in self.nsprefixes.items(): + for p,u in list(self.nsprefixes.items()): if p in self.parent.nsprefixes: pu = self.parent.nsprefixes[p] if pu == u: @@ -730,7 +730,7 @@ def str(self, indent=0): result = [] result.append('%s<%s' % (tab, self.qname())) result.append(self.nsdeclarations()) - for a in [unicode(a) for a in self.attributes]: + for a in [str(a) for a in self.attributes]: result.append(' %s' % a) if self.isempty(): result.append('/>') @@ -755,7 +755,7 @@ def plain(self): result = [] result.append('<%s' % self.qname()) result.append(self.nsdeclarations()) - for a in [unicode(a) for a in self.attributes]: + for a in [str(a) for a in self.attributes]: result.append(' %s' % a) if self.isempty(): result.append('/>') @@ -785,7 +785,7 @@ def nsdeclarations(self): if self.expns is not None: d = ' xmlns="%s"' % self.expns s.append(d) - for item in self.nsprefixes.items(): + for item in list(self.nsprefixes.items()): (p,u) = item if self.parent is not None: ns = self.parent.resolvePrefix(p) @@ -884,13 +884,13 @@ def __len__(self): return len(self.children) def __getitem__(self, index): - if isinstance(index, basestring): + if isinstance(index, str): return self.get(index) if index < len(self.children): return self.children[index] def __setitem__(self, index, value): - if isinstance(index, basestring): + if isinstance(index, str): self.set(index, value) else: if index < len(self.children) and isinstance(value, Element): @@ -927,7 +927,7 @@ def __init__(self, parent): self.pos = 0 self.children = parent.children - def next(self): + def __next__(self): """ Get the next child. @return: The next child. @@ -999,7 +999,7 @@ def pset(self, n): @rtype: set """ s = set() - for ns in n.nsprefixes.items(): + for ns in list(n.nsprefixes.items()): if self.permit(ns): s.add(ns[1]) return s @@ -1078,7 +1078,7 @@ def refitMappings(self): for n in self.branch: n.nsprefixes = {} n = self.node - for u, p in self.prefixes.items(): + for u, p in list(self.prefixes.items()): n.addPrefix(p, u) def permit(self, ns): diff --git a/suds/sax/enc.py b/suds/sax/enc.py index d15988d..3787037 100644 --- a/suds/sax/enc.py +++ b/suds/sax/enc.py @@ -46,7 +46,7 @@ def needsEncoding(self, s): @return: True if needs encoding. @rtype: boolean """ - if isinstance(s, basestring): + if isinstance(s, str): for c in self.special: if c in s: return True @@ -60,7 +60,7 @@ def encode(self, s): @return: The encoded string. @rtype: str """ - if isinstance(s, basestring) and self.needsEncoding(s): + if isinstance(s, str) and self.needsEncoding(s): for x in self.encodings: s = re.sub(x[0], x[1], s) return s @@ -73,7 +73,7 @@ def decode(self, s): @return: The decoded string. @rtype: str """ - if isinstance(s, basestring) and '&' in s: + if isinstance(s, str) and '&' in s: for x in self.decodings: s = s.replace(x[0], x[1]) return s diff --git a/suds/sax/parser.py b/suds/sax/parser.py index 2f48b3b..bc4548c 100644 --- a/suds/sax/parser.py +++ b/suds/sax/parser.py @@ -47,10 +47,10 @@ def __init__(self): def startElement(self, name, attrs): top = self.top() - node = Element(unicode(name)) + node = Element(str(name)) for a in attrs.getNames(): - n = unicode(a) - v = unicode(attrs.getValue(a)) + n = str(a) + v = str(attrs.getValue(a)) attribute = Attribute(n,v) if self.mapPrefix(node, attribute): continue @@ -63,19 +63,19 @@ def mapPrefix(self, node, attribute): skip = False if attribute.name == 'xmlns': if len(attribute.value): - node.expns = unicode(attribute.value) + node.expns = str(attribute.value) skip = True elif attribute.prefix == 'xmlns': prefix = attribute.name - node.nsprefixes[prefix] = unicode(attribute.value) + node.nsprefixes[prefix] = str(attribute.value) skip = True return skip def endElement(self, name): - name = unicode(name) + name = str(name) current = self.top() if len(current.charbuffer): - current.text = Text(u''.join(current.charbuffer)) + current.text = Text(''.join(current.charbuffer)) del current.charbuffer if len(current): current.trim() @@ -85,7 +85,7 @@ def endElement(self, name): raise Exception('malformed document') def characters(self, content): - text = unicode(content) + text = str(content) node = self.top() node.charbuffer.append(text) diff --git a/suds/sax/text.py b/suds/sax/text.py index ebdbc62..3323f80 100644 --- a/suds/sax/text.py +++ b/suds/sax/text.py @@ -22,7 +22,7 @@ from suds.sax import * -class Text(unicode): +class Text( type("") ): """ An XML text object used to represent text content. @ivar lang: The (optional) language flag. @@ -30,7 +30,8 @@ class Text(unicode): @ivar escaped: The (optional) XML special character escaped flag. @type escaped: bool """ - __slots__ = ('lang', 'escaped') + + slots = ['lang', 'escaped'] @classmethod def __valid(cls, *args): @@ -75,7 +76,7 @@ def trim(self): return Text(post, lang=self.lang, escaped=self.escaped) def __add__(self, other): - joined = u''.join((self, other)) + joined = ''.join((self, other)) result = Text(joined, lang=self.lang, escaped=self.escaped) if isinstance(other, Text): result.escaped = self.escaped or other.escaped @@ -91,12 +92,12 @@ def __repr__(self): def __getstate__(self): state = {} - for k in self.__slots__: + for k in self.slots: state[k] = getattr(self, k) return state def __setstate__(self, state): - for k in self.__slots__: + for k in self.slots: setattr(self, k, state[k]) @@ -112,5 +113,5 @@ def unescape(self): return self def __add__(self, other): - joined = u''.join((self, other)) + joined = ''.join((self, other)) return Raw(joined, lang=self.lang) diff --git a/suds/servicedefinition.py b/suds/servicedefinition.py index 19ed243..6418d59 100644 --- a/suds/servicedefinition.py +++ b/suds/servicedefinition.py @@ -80,7 +80,7 @@ def addports(self): timer.start() for port in self.service.ports: p = self.findport(port) - for op in port.binding.operations.values(): + for op in list(port.binding.operations.values()): m = p[0].method(op.name) binding = m.binding.input method = (m.name, binding.param_defs(m)) @@ -138,7 +138,7 @@ def paramtypes(self): def publictypes(self): """Get all public types.""" - for t in self.wsdl.schema.types.values(): + for t in list(self.wsdl.schema.types.values()): if t in self.params: continue if t in self.types: continue item = (t, t) @@ -152,7 +152,7 @@ def nextprefix(self): WSDL document. """ used = [ns[0] for ns in self.prefixes] - used += [ns[0] for ns in self.wsdl.root.nsprefixes.items()] + used += [ns[0] for ns in list(self.wsdl.root.nsprefixes.items())] for n in range(0,1024): p = 'ns%d'%n if p not in used: @@ -235,6 +235,6 @@ def description(self): def __unicode__(self): try: return self.description() - except Exception, e: + except Exception as e: log.exception(e) return tostr(e) diff --git a/suds/serviceproxy.py b/suds/serviceproxy.py index 1b6a62f..f1da926 100644 --- a/suds/serviceproxy.py +++ b/suds/serviceproxy.py @@ -70,7 +70,7 @@ def get_enum(self, name): return self.__client__.factory.create(name) def __unicode__(self): - return unicode(self.__client__) + return str(self.__client__) def __getattr__(self, name): builtin = name.startswith('__') and name.endswith('__') diff --git a/suds/store.py b/suds/store.py index 58ebf4a..ab0b0bd 100644 --- a/suds/store.py +++ b/suds/store.py @@ -566,7 +566,7 @@ def open(self, url): protocol, location = self.__split(url) content = self.__find(location) if protocol == 'suds' and content is None: - raise Exception, 'location "%s" not in document store' % location + raise Exception('location "%s" not in document store' % location) return content def __find(self, location): diff --git a/suds/sudsobject.py b/suds/sudsobject.py index 9894009..9489c87 100644 --- a/suds/sudsobject.py +++ b/suds/sudsobject.py @@ -121,7 +121,7 @@ def object(cls, classname=None, dict={}): inst = subclass() else: inst = Object() - for a in dict.items(): + for a in list(dict.items()): setattr(inst, a[0], a[1]) return inst @@ -156,7 +156,7 @@ def __delattr__(self, name): self.__keylist__.remove(name) except Exception: cls = self.__class__.__name__ - raise AttributeError, "%s has no attribute '%s'" % (cls, name) + raise AttributeError("%s has no attribute '%s'" % (cls, name)) def __getitem__(self, name): if isinstance(name, int): @@ -189,7 +189,7 @@ def __init__(self, sobject): self.keylist = self.__keylist(sobject) self.index = 0 - def next(self): + def __next__(self): keylist = self.keylist nkeys = len(self.keylist) while self.index < nkeys: @@ -278,7 +278,7 @@ def process(self, object, h, n=0, nl=False): if len(object) == 0: return "" return self.print_collection(object, h, n + 2) - if isinstance(object, basestring): + if isinstance(object, str): return '"%s"' % (tostr(object),) return "%s" % (tostr(object),) @@ -333,7 +333,7 @@ def print_dictionary(self, d, h, n, nl=False): s.append("\n") s.append(self.indent(n)) s.append("{") - for item in d.items(): + for item in list(d.items()): s.append("\n") s.append(self.indent(n+1)) if isinstance(item[1], (list,tuple)): diff --git a/suds/transport/__init__.py b/suds/transport/__init__.py index 6ffea2d..e5f7551 100644 --- a/suds/transport/__init__.py +++ b/suds/transport/__init__.py @@ -54,7 +54,7 @@ def __init__(self, url, message=None): self.message = message def __unicode__(self): - return u"""\ + return """\ URL: %s HEADERS: %s MESSAGE: @@ -89,7 +89,7 @@ def __init__(self, code, headers, message): self.message = message def __unicode__(self): - return u"""\ + return """\ CODE: %s HEADERS: %s MESSAGE: diff --git a/suds/transport/http.py b/suds/transport/http.py index c3f2512..16ab7f4 100644 --- a/suds/transport/http.py +++ b/suds/transport/http.py @@ -22,12 +22,27 @@ from suds.transport import * import base64 -from cookielib import CookieJar -import httplib +try: + from http.cookiejar import CookieJar +except Exception as e: + from cookielib import CookieJar + +try: + import http.client +except Exception as e: + import httplib + import socket import sys -import urllib2 -from urlparse import urlparse +try: + import urllib.request, urllib.error, urllib.parse +except Exception as e: + import urllib + +try: + from urllib.parse import urlparse +except Exception as e: + from urlparse import urlparse from logging import getLogger log = getLogger(__name__) @@ -62,10 +77,10 @@ def open(self, request): try: url = self.__get_request_url(request) log.debug('opening (%s)', url) - u2request = urllib2.Request(url) + u2request = urllib.request.Request(url) self.proxy = self.options.proxy return self.u2open(u2request) - except urllib2.HTTPError, e: + except urllib.error.HTTPError as e: raise TransportError(str(e), e.code, e.fp) def send(self, request): @@ -74,7 +89,7 @@ def send(self, request): msg = request.message headers = request.headers try: - u2request = urllib2.Request(url, msg, headers) + u2request = urllib.request.Request(url, msg, headers) self.addcookies(u2request) self.proxy = self.options.proxy request.headers.update(u2request.headers) @@ -85,10 +100,10 @@ def send(self, request): headers = fp.headers.dict else: headers = fp.headers - result = Reply(httplib.OK, headers, fp.read()) + result = Reply(http.client.OK, headers, fp.read()) log.debug('received:\n%s', result) - except urllib2.HTTPError, e: - if e.code in (httplib.ACCEPTED, httplib.NO_CONTENT): + except urllib.error.HTTPError as e: + if e.code in (http.client.ACCEPTED, http.client.NO_CONTENT): result = None else: raise TransportError(e.msg, e.code, e.fp) @@ -140,7 +155,7 @@ def u2opener(self): """ if self.urlopener is None: - return urllib2.build_opener(*self.u2handlers()) + return urllib.request.build_opener(*self.u2handlers()) return self.urlopener def u2handlers(self): @@ -152,7 +167,7 @@ def u2handlers(self): """ handlers = [] - handlers.append(urllib2.ProxyHandler(self.proxy)) + handlers.append(urllib.request.ProxyHandler(self.proxy)) return handlers def u2ver(self): @@ -165,7 +180,7 @@ def u2ver(self): try: part = urllib2.__version__.split('.', 1) return float('.'.join(part)) - except Exception, e: + except Exception as e: log.exception(e) return 0 diff --git a/suds/transport/https.py b/suds/transport/https.py index 080315a..babcc76 100644 --- a/suds/transport/https.py +++ b/suds/transport/https.py @@ -21,7 +21,10 @@ from suds.transport import * from suds.transport.http import HttpTransport -import urllib2 +try: + import urllib.request, urllib.error, urllib.parse +except Exception as e: + import urllib class HttpAuthenticated(HttpTransport): @@ -55,7 +58,7 @@ def __init__(self, **kwargs): """ HttpTransport.__init__(self, **kwargs) - self.pm = urllib2.HTTPPasswordMgrWithDefaultRealm() + self.pm = urllib.request.HTTPPasswordMgrWithDefaultRealm() def open(self, request): self.addcredentials(request) @@ -77,7 +80,7 @@ def credentials(self): def u2handlers(self): handlers = HttpTransport.u2handlers(self) - handlers.append(urllib2.HTTPBasicAuthHandler(self.pm)) + handlers.append(urllib.request.HTTPBasicAuthHandler(self.pm)) return handlers diff --git a/suds/transport/options.py b/suds/transport/options.py index c4c1552..70d8b40 100644 --- a/suds/transport/options.py +++ b/suds/transport/options.py @@ -53,6 +53,6 @@ def __init__(self, **kwargs): Definition('proxy', dict, {}), Definition('timeout', (int,float), 90), Definition('headers', dict, {}), - Definition('username', basestring, None), - Definition('password', basestring, None)] + Definition('username', str, None), + Definition('password', str, None)] Skin.__init__(self, domain, definitions, kwargs) diff --git a/suds/umx/__init__.py b/suds/umx/__init__.py index f672320..e94109b 100644 --- a/suds/umx/__init__.py +++ b/suds/umx/__init__.py @@ -40,7 +40,7 @@ def __init__(self, node, **kwargs): self.node = node self.data = None self.text = None - for k,v in kwargs.items(): + for k,v in list(kwargs.items()): setattr(self, k, v) def __getattr__(self, name): @@ -49,8 +49,7 @@ def __getattr__(self, name): v = None setattr(self, name, v) else: - raise AttributeError, \ - 'Content has no attribute %s' % name + raise AttributeError('Content has no attribute %s' % name) else: v = self.__dict__[name] return v diff --git a/suds/umx/core.py b/suds/umx/core.py index 9ffa3bd..9a1d0f3 100644 --- a/suds/umx/core.py +++ b/suds/umx/core.py @@ -95,7 +95,7 @@ def postprocess(self, content): return None else: return Text('', lang=lang) - if isinstance(content.text, basestring): + if isinstance(content.text, str): return Text(content.text, lang=lang) else: return content.text diff --git a/suds/wsdl.py b/suds/wsdl.py index 8a5e558..b78d4bc 100644 --- a/suds/wsdl.py +++ b/suds/wsdl.py @@ -31,8 +31,12 @@ from suds.reader import DocumentReader import re -import soaparray -from urlparse import urljoin +from . import soaparray + +try: + from urllib.parse import urljoin +except Exception as e: + from urlparse import urljoin from logging import getLogger log = getLogger(__name__) @@ -232,7 +236,7 @@ def add_methods(self, service): for p in service.ports: binding = p.binding ptype = p.binding.type - operations = p.binding.type.operations.values() + operations = list(p.binding.type.operations.values()) for name in [op.name for op in operations]: m = Facade('Method') m.name = name @@ -249,8 +253,8 @@ def add_methods(self, service): def set_wrapped(self): """ set (wrapped|bare) flag on messages """ - for b in self.bindings.values(): - for op in b.operations.values(): + for b in list(self.bindings.values()): + for op in list(b.operations.values()): for body in (op.soap.input.body, op.soap.output.body): body.wrapped = False if not self.options.unwrap: @@ -482,7 +486,7 @@ def resolve(self, definitions): @param definitions: A definitions object. @type definitions: L{Definitions} """ - for op in self.operations.values(): + for op in list(self.operations.values()): if op.input is None: op.input = Message(Element('no-input'), definitions) else: @@ -505,7 +509,7 @@ def resolve(self, definitions): qref = qualify(f.message, self.root, definitions.tns) msg = definitions.messages.get(qref) if msg is None: - raise Exception, "msg '%s', not-found" % f.message + raise Exception("msg '%s', not-found" % f.message) f.message = msg def operation(self, name): @@ -519,7 +523,7 @@ def operation(self, name): """ try: return self.operations[name] - except Exception, e: + except Exception as e: raise MethodNotFound(name) def __gt__(self, other): @@ -654,7 +658,7 @@ def resolve(self, definitions): @type definitions: L{Definitions} """ self.resolveport(definitions) - for op in self.operations.values(): + for op in list(self.operations.values()): self.resolvesoapbody(definitions, op) self.resolveheaders(definitions, op) self.resolvefaults(definitions, op) @@ -683,8 +687,7 @@ def resolvesoapbody(self, definitions, op): """ ptop = self.type.operation(op.name) if ptop is None: - raise Exception, \ - "operation '%s' not defined in portType" % op.name + raise Exception("operation '%s' not defined in portType" % op.name) soap = op.soap parts = soap.input.body.parts if len(parts): @@ -720,15 +723,14 @@ def resolveheaders(self, definitions, op): ref = qualify(mn, self.root, definitions.tns) message = definitions.messages.get(ref) if message is None: - raise Exception, "message'%s', not-found" % mn + raise Exception("message'%s', not-found" % mn) pn = header.part for p in message.parts: if p.name == pn: header.part = p break if pn == header.part: - raise Exception, \ - "message '%s' has not part named '%s'" % (ref, pn) + raise Exception("message '%s' has not part named '%s'" % (ref, pn)) def resolvefaults(self, definitions, op): """ @@ -741,8 +743,7 @@ def resolvefaults(self, definitions, op): """ ptop = self.type.operation(op.name) if ptop is None: - raise Exception, \ - "operation '%s' not defined in portType" % op.name + raise Exception("operation '%s' not defined in portType" % op.name) soap = op.soap for fault in soap.faults: for f in ptop.faults: @@ -751,8 +752,7 @@ def resolvefaults(self, definitions, op): continue if hasattr(fault, 'parts'): continue - raise Exception, \ - "fault '%s' not defined in portType '%s'" % (fault.name, self.type.name) + raise Exception("fault '%s' not defined in portType '%s'" % (fault.name, self.type.name)) def operation(self, name): """ @@ -854,7 +854,7 @@ def setlocation(self, url, names=None): @type names: [str,..] """ for p in self.ports: - for m in p.methods.values(): + for m in list(p.methods.values()): if names is None or m.name in names: m.location = url diff --git a/suds/xsd/__init__.py b/suds/xsd/__init__.py index 5c5dd8c..cf48a2a 100644 --- a/suds/xsd/__init__.py +++ b/suds/xsd/__init__.py @@ -59,8 +59,8 @@ def isqref(object): return (\ isinstance(object, tuple) and \ len(object) == 2 and \ - isinstance(object[0], basestring) and \ - isinstance(object[1], basestring)) + isinstance(object[0], str) and \ + isinstance(object[1], str)) class Filter: diff --git a/suds/xsd/deplist.py b/suds/xsd/deplist.py index b686675..81d82bc 100644 --- a/suds/xsd/deplist.py +++ b/suds/xsd/deplist.py @@ -77,7 +77,7 @@ def sort(self): while len(self.stack): try: top = self.top() - ref = top[1].next() + ref = next(top[1]) refd = self.index.get(ref) if refd is None: log.debug('"%s" not found, skipped', Repr(ref)) @@ -137,4 +137,4 @@ def pop(self): x = ('x', ()) L = DepList() L.add(c, e, d, b, f, a, x) - print [x[0] for x in L.sort()] + print([x[0] for x in L.sort()]) diff --git a/suds/xsd/query.py b/suds/xsd/query.py index 62929c9..360dca6 100644 --- a/suds/xsd/query.py +++ b/suds/xsd/query.py @@ -54,7 +54,7 @@ def execute(self, schema): @return: The item matching the search criteria. @rtype: L{sxbase.SchemaObject} """ - raise Exception, 'not-implemented by subclass' + raise Exception('not-implemented by subclass') def filter(self, result): """ diff --git a/suds/xsd/schema.py b/suds/xsd/schema.py index 33a0948..4f9dfe5 100644 --- a/suds/xsd/schema.py +++ b/suds/xsd/schema.py @@ -104,7 +104,7 @@ def autoblend(self): @return: self @rtype: L{SchemaCollection} """ - namespaces = self.namespaces.keys() + namespaces = list(self.namespaces.keys()) for s in self.children: for ns in namespaces: tns = s.root.get('targetNamespace') @@ -261,27 +261,27 @@ def merge(self, schema): @returns: self @rtype: L{Schema} """ - for item in schema.attributes.items(): + for item in list(schema.attributes.items()): if item[0] in self.attributes: continue self.all.append(item[1]) self.attributes[item[0]] = item[1] - for item in schema.elements.items(): + for item in list(schema.elements.items()): if item[0] in self.elements: continue self.all.append(item[1]) self.elements[item[0]] = item[1] - for item in schema.types.items(): + for item in list(schema.types.items()): if item[0] in self.types: continue self.all.append(item[1]) self.types[item[0]] = item[1] - for item in schema.groups.items(): + for item in list(schema.groups.items()): if item[0] in self.groups: continue self.all.append(item[1]) self.groups[item[0]] = item[1] - for item in schema.agrps.items(): + for item in list(schema.agrps.items()): if item[0] in self.agrps: continue self.all.append(item[1]) diff --git a/suds/xsd/sxbase.py b/suds/xsd/sxbase.py index 28ab814..38ce14a 100644 --- a/suds/xsd/sxbase.py +++ b/suds/xsd/sxbase.py @@ -463,7 +463,7 @@ def description(self): return () def __unicode__(self): - return unicode(self.str()) + return str(self.str()) def __repr__(self): s = [] @@ -520,7 +520,7 @@ def __init__(self, sx): self.items = sx.rawchildren self.index = 0 - def next(self): + def __next__(self): """ Get the I{next} item in the frame's collection. @return: The next item or None @@ -571,7 +571,7 @@ def top(self): else: raise StopIteration() - def next(self): + def __next__(self): """ Get the next item. @return: A tuple: the next (child, ancestry). @@ -580,15 +580,15 @@ def next(self): """ frame = self.top() while True: - result = frame.next() + result = next(frame) if result is None: self.pop() - return self.next() + return next(self) if isinstance(result, Content): ancestry = [f.sx for f in self.stack] return result, ancestry self.push(result) - return self.next() + return next(self) def __iter__(self): return self diff --git a/suds/xsd/sxbasic.py b/suds/xsd/sxbasic.py index 1f55fd9..8a84d90 100644 --- a/suds/xsd/sxbasic.py +++ b/suds/xsd/sxbasic.py @@ -26,7 +26,10 @@ from suds.sax import Namespace from suds.transport import TransportError from suds.reader import DocumentReader -from urlparse import urljoin +try: + from urllib.parse import urljoin +except Exception as e: + from urlparse import urljoin from logging import getLogger log = getLogger(__name__) @@ -667,7 +670,7 @@ def __applytns(self, root): root.set(TNS, tns) else: if self.schema.tns[1] != tns: - raise Exception, '%s mismatch' % TNS + raise Exception('%s mismatch' % TNS) def description(self): diff --git a/suds/xsd/sxbuiltin.py b/suds/xsd/sxbuiltin.py index 3fc82aa..2cc1d33 100644 --- a/suds/xsd/sxbuiltin.py +++ b/suds/xsd/sxbuiltin.py @@ -62,7 +62,7 @@ class XBoolean(XBuiltin): @staticmethod def translate(value, topython=True): if topython: - if isinstance(value, basestring): + if isinstance(value, str): return XBoolean.translation[0].get(value) else: if isinstance(value, (bool, int)): @@ -78,7 +78,7 @@ class XInteger(XBuiltin): @staticmethod def translate(value, topython=True): if topython: - if isinstance(value, basestring) and len(value): + if isinstance(value, str) and len(value): return int(value) else: if isinstance(value, int): @@ -94,10 +94,10 @@ class XLong(XBuiltin): @staticmethod def translate(value, topython=True): if topython: - if isinstance(value, basestring) and len(value): - return long(value) + if isinstance(value, str) and len(value): + return int(value) else: - if isinstance(value, (int, long)): + if isinstance(value, int): return str(value) return value @@ -110,7 +110,7 @@ class XFloat(XBuiltin): @staticmethod def translate(value, topython=True): if topython: - if isinstance(value, basestring) and len(value): + if isinstance(value, str) and len(value): return float(value) else: if isinstance(value, float): @@ -126,7 +126,7 @@ class XDate(XBuiltin): @staticmethod def translate(value, topython=True): if topython: - if isinstance(value, basestring) and len(value): + if isinstance(value, str) and len(value): return Date(value).value else: if isinstance(value, dt.date): @@ -142,7 +142,7 @@ class XTime(XBuiltin): @staticmethod def translate(value, topython=True): if topython: - if isinstance(value, basestring) and len(value): + if isinstance(value, str) and len(value): return Time(value).value else: if isinstance(value, dt.time): @@ -158,7 +158,7 @@ class XDateTime(XBuiltin): @staticmethod def translate(value, topython=True): if topython: - if isinstance(value, basestring) and len(value): + if isinstance(value, str) and len(value): return DateTime(value).value else: if isinstance(value, dt.datetime): diff --git a/test_model.py b/test_model.py new file mode 100644 index 0000000..a82d2d9 --- /dev/null +++ b/test_model.py @@ -0,0 +1,882 @@ +"""camkii_pp1_scheme.py + +See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1069645/ + +""" + +__author__ = "Dilawar Singh" +__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore" +__credits__ = ["NCBS Bangalore"] +__license__ = "GNU GPL" +__version__ = "1.0.0" +__maintainer__ = "Dilawar Singh" +__email__ = "dilawars@ncbs.res.in" +__status__ = "Development" + +import params as _p +import datetime +import moose +import moose.utils as mu +import numpy as np +import re +import sys +import time +import math +from collections import defaultdict + +import logging +logging.basicConfig(level=logging.DEBUG, + format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s', + datefmt='%m-%d %H:%M', + filename='__log__.txt', + filemode='a' + ) +console = logging.StreamHandler() +console.setLevel(logging.INFO) +formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s') +console.setFormatter(formatter) +_logger = logging.getLogger('') +_logger.addHandler(console) + +class Args: pass +args = Args() + +print( '[INFO] Using moose from %s' % moose.__file__ ) +print( '[INFO] Using moose from %s' % moose.__version__ ) + +# global data-structures +model_path_ = '/model' +molecules_ = {} +tables_ = defaultdict( list ) +curr_subsec_ = None +compt_ = None + +N = 6.023e23 + +gainers_ , loosers_ = [], [] +dephospho_ = [] + +def pool_name( root, name ): + global molecules_ + molName = '%s.%s' % (root.name, name ) + return molName + + +def conc_to_n( conc ): + val = conc * float( args['volume'] ) * N + assert val > 0.0 + return val + + +def num_subunits( name ): + m = re.search( r'x(?P\d)y(?P\d)', name ) + try: + xs, ys = int(m.group('xs')), int(m.group( 'ys' )) + except Exception as e: + mu.warn( 'Failed to get subunit numbers in %s' % name ) + raise e + return xs + ys + + +def inv_conc_to_N( conc ): + return conc / (float(args['volume']) * N ) + +def n_to_conc( n ): + global args + return n / (N * args['volume'] ) + + +def add_pool( root, name ): + global molecules_ + pname = pool_name( root, name ) + ppath = '%s/%s' % (root.path, name) + if moose.exists( ppath ): + _logger.warn( 'Already exists %s' % ppath ) + return moose.element( ppath ) + else: + p = moose.Pool( ppath ) + p.name = pname + molecules_[pname] = p + return p + + +def init_pools( compt ): + global args + # Ring with 6 subunits. + for st in range(7): + state = 'x%dy%d' % (st, 6 - st ) + p = add_pool( compt, state ) + p.nInit = 0 + + if args['enable_subunit_exchange']: + # Ring with 7 subunits + for st in range(8): + state = 'x%dy%d' % (st, 7 - st ) + p = add_pool( compt, state ) + p.nInit = 0 + molecules_[p.name] = p + + if args['enable_subunit_exchange']: + # Add subunit x and y. + # NOTE: These guys are shared across multiple sub_sections.. + x = add_pool( compt, 'x' ) + x.nInit = 0 + molecules_[x.name] = x + + y = add_pool( compt, 'y' ) + y.nInit = 0 + molecules_[y.name] = y + else: + _logger.info( "Subunit exchange is disabled" ) + + + for p in [ 'I1', 'PP1', 'PP1_', 'I1P', 'I1P_', 'I1PPP1' ]: + if p in [ 'I1' ]: + c = moose.BufPool( '%s/%s' % (compt.path, p) ) + c.name = pool_name( compt, p ) + molecules_[c.name] = c + else: + c = moose.Pool( '%s/%s' % (compt.path, p) ) + c.name = pool_name( compt, p ) + molecules_[c.name] = c + + molecules_[c.name].nInit = 0 + + if args['enable_subunit_exchange']: + # Here we are using concInit rather than nInit to setup the number of + # molecules. This is because when Dsolve is used, setting nInit causes + # problem: they don't get divided into different voxels. + molecules_[ pool_name(compt, 'x0y7') ].concInit = args[ 'camkii_conc' ] / 2.0 + molecules_[ pool_name(compt, 'x0y6') ].concInit = args[ 'camkii_conc' ] / 2.0 + else: + molecules_[ pool_name(compt, 'x0y6') ].concInit = args['camkii_conc'] + + if args['enable_subunit_exchange']: + _logger.debug('CaMKII = %f (6sym) %f (7sym)' % ( + molecules_[ pool_name(compt,'x0y6')].nInit, + molecules_[pool_name(compt,'x0y7')].nInit ) + ) + else: + _logger.debug('CaMKII = %d (6sym)' % ( + molecules_[pool_name(compt,'x0y6')].nInit ) + ) + + molecules_[ pool_name(compt, 'PP1') ].concInit = args['pp1_conc'] + _logger.debug('Total PP1 %s' % molecules_[pool_name(compt,'PP1')].nInit ) + + # TODO: Much of it only make sense if stochastic solver is used. + molecules_[ pool_name(compt,'I1') ].concInit = _p.conc_i1_free + pp1CamKIICplx = moose.Pool( '%s/camkii_pp1_cplx' % compt.path ) + pp1CamKIICplx.name = pool_name( compt, pp1CamKIICplx.name ) + pp1CamKIICplx.concInit = 0 + molecules_[ pp1CamKIICplx.name ] = pp1CamKIICplx + + for k in sorted(molecules_): + _logger.debug( 'Molecule: %s (%f)' % (k, molecules_[k].nInit ) ) + + +def add_table( moose_elem, field, tableName = None): + global tables_ + tablePath = '%s/tab%s' % (moose_elem.path, field) + if moose.exists( tablePath ): + return None + t = moose.Table2( tablePath ) + moose.connect( t, 'requestOut', moose_elem, 'get'+field[0].upper()+field[1:]) + tables_[ moose_elem.name ].append( t ) + _logger.debug( 'Added table on %s' % moose_elem.path ) + + +def add_reaction( reacPath ): + if moose.exists( reacPath ): + mu.warn( 'Reaction %s already exists' % reacPath ) + return moose.element( reacPath ) + else: + r = moose.Reac( reacPath ) + return r + + +def looseX( pool, xs ): + # Only pool with 7 subunits can loose subunit. + assert num_subunits( pool.name ) == 7, 'Only CaMKII(7) can gain subunit' + global curr_subsec_ + loosers_.append( ('x', pool.name) ) + r = add_reaction( '%s/%s.loose_x' % (pool.path, pool.name)) + r.numKf = _p.rate_loosex + r.numKb = 0.0 + moose.connect( r, 'sub', pool, 'reac' ) + toPoolName = 'x%dy%d' % (xs-1, 7 - xs ) + toPool = molecules_[ curr_subsec_ + '.' + toPoolName ] + moose.connect( r, 'prd', toPool, 'reac' ) + moose.connect( r, 'prd', molecules_[curr_subsec_ + '.x'], 'reac' ) + assert num_subunits(pool.name) == num_subunits(toPool.name) + 1 + _logger.debug( 'Reaction: %s -> %s + x' % ( pool.name, toPool.name) ) + + +def looseY( pool, ys ): + # Only pool with 7 subunits can loose subunit. + assert num_subunits( pool.name ) == 7, 'Only CaMKII(7) can gain subunit' + global curr_subsec_ + loosers_.append( ('y', pool.name) ) + r = add_reaction( '%s/%s.loose_y' % (pool.path, pool.name) ) + r.numKf = _p.rate_loosey + r.numKb = 0.0 + moose.connect( r, 'sub', pool, 'reac' ) + toPoolName = 'x%dy%d' % (7-ys, ys - 1 ) + toPool = molecules_[ curr_subsec_ + '.' + toPoolName ] + moose.connect( r, 'prd', toPool, 'reac' ) + moose.connect( r, 'prd', molecules_[curr_subsec_ + '.y'], 'reac' ) + _logger.debug( 'Reaction: %s -> %s + y' % ( pool.name, toPool.name ) ) + assert num_subunits( pool.name) == num_subunits( toPool.name) + 1 + + +def gainX( pool, xs ): + # Only pool with 6 subunits can gain subunit. + global curr_subsec_ + gainers_.append( ('x', pool.name) ) + r = add_reaction( '%s/%s.gainx' % (pool.path, pool.name)) + r.numKf = _p.rate_gainx + r.numKb = 0.0 + moose.connect( r, 'sub', pool, 'reac' ) + moose.connect( r, 'sub', molecules_['%s.x' % curr_subsec_ ], 'reac' ) + toPoolName = 'x%dy%d' % (xs+1, 6 - xs ) + toPool = molecules_[ curr_subsec_ + '.' + toPoolName ] + moose.connect( r, 'prd', toPool, 'reac' ) + _logger.debug( 'Reaction: %s + x -> %s' % ( pool.name, toPool.name ) ) + assert num_subunits( pool.name ) == 6, 'Only CaMKII(6) can gain subunit' + assert num_subunits( pool.name) == num_subunits( toPool.name) - 1 + + +def gainY( pool, ys ): + # Only pool with 6 subunits can gain subunit. + global curr_subsec_ + gainers_.append( ('y', pool.name) ) + r = add_reaction( '%s/%s.gainy' % (pool.path, pool.name) ) + r.numKf = _p.rate_gainy + r.numKb = 0.0 + moose.connect( r, 'sub', pool, 'reac' ) + moose.connect( r, 'sub', molecules_['%s.y' % curr_subsec_], 'reac' ) + toPoolName = 'x%dy%d' % ( 6-ys, ys+1 ) + toPool = molecules_[ curr_subsec_ + '.' + toPoolName ] + moose.connect( r, 'prd', toPool, 'reac' ) + _logger.debug( 'Reaction: %s, y -> %s' % ( pool.name, toPool.name ) ) + assert num_subunits( pool.name ) == 6, 'Only CaMKII(6) can gain subunit' + assert num_subunits( pool.name) == num_subunits( toPool.name) - 1 + + +def ca_input( root ): + """Input calcium pulse + + When using stochastic solver, any event less than 100 or so seconds would + not work. + """ + global args + # Input calcium + ca = moose.Pool( '%s/ca' % root.path ) + ca.concInit = _p.ca_basal + ca.name = pool_name( root, ca.name ) + molecules_[ ca.name ] = ca + + _logger.info("Setting up input calcium : init = %s" % ca.concInit ) + + # _logger.debug("Baselevel ca conc = %s" % _p.resting_ca_conc) + concFunc = moose.Function( "%s/cafunc" % ca.path ) + concFunc.expr = args[ 'ca_expr' ] + moose.connect( concFunc, 'valueOut', ca, 'setConc' ) + _logger.info( "Ca conc expression = %s " % concFunc.expr ) + + +def i1_to_i1p( root ): + global molecules_ + global curr_subsec_ + i1p_const = moose.BufPool( '%s/i1p_const' % molecules_[curr_subsec_ + '.' + 'I1'].path) + i1p_const.name = pool_name( root, i1p_const.name ) + molecules_[i1p_const.name] = i1p_const + + f = moose.Function( '%s/i12i1p' % molecules_[pool_name(root, 'I1P')].path ) + f.x.num = 2 + f.expr = 'x1*(1+(x0/{kh2})^3)/(x0/{kh2})^3'.format(kh2=conc_to_n(_p.K_H2)) + frmName = pool_name( root, 'I1' ) + toName = pool_name( root, 'I1P_' ) + moose.connect( molecules_[pool_name(root,'ca')], 'nOut', f.x[0], 'input' ) + moose.connect( molecules_[frmName], 'nOut', f.x[1], 'input' ) + moose.connect( f, 'valueOut', molecules_[toName], 'setN' ) + _logger.debug('Reaction: %s -> %s, Expr = %s' % (frmName, toName, f.expr )) + + # A slow reaction between I1P and I1P_ which synchornize both pools. + r = add_reaction( '%s/sync' % molecules_[pool_name(root,'I1P')].path ); + frmPool = molecules_[ pool_name( root, 'I1P_' ) ] + toPool = molecules_[ pool_name( root, 'I1P' ) ] + moose.connect( r, 'sub', frmPool, 'reac' ) + moose.connect( r, 'prd', toPool, 'reac' ) + r.Kf = r.Kb = 1.0 + _logger.debug( 'Reaction: %s -> %s' % ( frmPool.name, toPool.name ) ) + + +def pp1_activation( root ): + """Here we setup the reactions PP1 + + I1P binds with PP1 and give rise to complex I1PPP1 (which is inavtivated PP1) + I1P + PP1 <- -> I1PPP1 + """ + activePP1 = molecules_[pool_name(root, 'PP1')] + i1pPool = molecules_[ pool_name( root, 'I1P' ) ] + inactive_pp1 = molecules_[ pool_name( root, 'I1PPP1' ) ] + r = add_reaction( '%s/reac_inactivate_pp1' % activePP1.path ) + + moose.connect( r, 'sub', activePP1, 'reac' ) + moose.connect( r, 'prd', inactive_pp1, 'reac') + k3, k4, s = 1e5, 0.0001, 1 + kfFun = moose.Function( '%s/kffunc' % r.path ) + kfFun.expr = '{scale}*{k3}*x0'.format( k3 = k3, scale = s ) + moose.connect( i1pPool, 'nOut', kfFun.x[0], 'input' ) + moose.connect( kfFun, 'valueOut', r, 'setNumKf' ) + r.numKb = s * k4 + + _logger.debug( 'Reaction: %s + %s -> %s' % ( activePP1.name, i1pPool.name, + inactive_pp1.name ) ) + + +def dephosphorylate( root, frmPool, toPool ): + global molecules_ + global curr_subsec_ + dephospho_.append( frmPool.name ) + + _logger.info( 'Not using Michealson Menten scheme for dephosphorylate' ) + inter = moose.Pool( '%s/pp1_%s_cplx' % (frmPool.path, frmPool.name) ) + inter.name = curr_subsec_ + '.' + inter.name + inter.nInit = 0 + r = add_reaction( '%s/%s.add_pp1' % (frmPool.path, frmPool.name) ) + moose.connect( r, 'sub', frmPool, 'reac' ) + moose.connect( r, 'sub', molecules_[curr_subsec_+ '.' + 'PP1'], 'reac' ) + moose.connect( r, 'prd', inter, 'reac' ) + r.Kf = _p.k_2 / _p.K_M + r.Kb = 0.0 + + rr = add_reaction( '%s/%s_dephospho' % (frmPool.path,frmPool.name) ) + moose.connect( rr, 'sub', inter, 'reac' ) + moose.connect( rr, 'prd', molecules_[curr_subsec_ + '.' + 'PP1'], 'reac' ) + moose.connect( rr, 'prd', toPool, 'reac' ) + rr.Kf = 1.0 + rr.Kb = 0.0 + _logger.debug( "Reac (dephospho): %s -> %s" % (frmPool.name, toPool.name )) + + +def phosphorylation_first_step( root, nc ): + # CaMKII to x1y0 is slow. + subPool = molecules_[ pool_name( root, 'x0y%d' % nc ) ] + prdPool = molecules_[ pool_name( root, 'x1y%d' % (nc-1) ) ] + r0 = add_reaction( '%s/reac_0to1_%d' % (subPool.path, nc) ) + r0.numKb = 0 + moose.connect( r0, 'sub', subPool, 'reac' ) + moose.connect( r0, 'prd', prdPool, 'reac' ) + # The rate expression of this reaction depends on Ca++ + f = moose.Function( '%s/func_kf' % r0.path ) + f.expr = '{nc}*{k1}*(x0/{kh1})^6/(1 + (x0/{kh1})^3)^2'.format( + k1 = _p.k_1, kh1= conc_to_n(_p.K_H1), nc = nc + ) + f.x.num = 1 + moose.connect( molecules_[pool_name(root,'ca')], 'nOut', f.x[0], 'input' ) + moose.connect( f, 'valueOut', r0, 'setNumKf' ) + _logger.debug( 'Reaction: %s -> %s' % (subPool.name, prdPool.name ) ) + + +def phosphorylation_first_step_subunit( compt ): + """ + NOTE: Phosphorylation of detached subunit is much faster than the subunits in + holoenzyme. Why? + + Phosphorylation of detached subunit is not possible. To phosphorylate, the + subunit must have a neighbour i.e. two subunit must come together first. + + """ + return + + # Previously I was phosphrylating the subunits. + global molecules_ + global curr_subsec_ + subPool = molecules_[ pool_name( compt, 'y') ] + prdPool = molecules_[ pool_name( compt, 'x') ] + r0 = add_reaction( '%s/reac_y2x' % compt.path ) + r0.numKb = 0 + moose.connect( r0, 'sub', subPool, 'reac' ) + moose.connect( r0, 'prd', prdPool, 'reac' ) + # The rate expression of this reaction depends on Ca++ + f = moose.Function( '%s/func_kf' % r0.path ) + f.expr = '{k1}*(x0/{kh1})^3/(1 + (x0/{kh1})^3)'.format( + k1 = _p.k_1 , kh1= conc_to_n(_p.K_H1) + ) + f.x.num = 1 + moose.connect( molecules_[ pool_name(compt, 'ca') ], 'nOut', f.x[0], 'input' ) + moose.connect( f, 'valueOut', r0, 'setNumKf' ) + _logger.info( 'Phosphorylation of subunit y in voxel %s' % compt.name ) + _logger.debug( 'Reaction: %s -> %s' % (subPool.name, prdPool.name ) ) + + +def camkii_activation_deactivation( root ): + """All reaction involved in activating CaMKII""" + + phosphorylation_first_step( root, 6 ) + + if args['enable_subunit_exchange']: + phosphorylation_first_step( root, 7 ) + + # Phosphorylation of CaMKII occurs in various stages: + # x0y0 -> x1y0 -> x2y0 -> x3y0 -> x4y0 -> x5y0 -> CaMKII* + for pp in range(1, 6): + frm, to = 'x%dy%d' % (pp, 6-pp), 'x%dy%d' % (pp + 1, 6-pp-1) + frmName, toName = [pool_name(root, x) for x in [frm, to]] + r = add_reaction( '%s/phospho_%s_%s' % (root.path, frmName, toName)) + # And its rate is controlled by another function + f = moose.Function( '%s/funcKf' % r.path ) + f.expr = '{k1}*(x0/{kh1})^3/(1 + (x0/{kh1})^3)'.format( + k1 = _p.k_1, kh1= conc_to_n(_p.K_H1) + ) + f.x.num = 1 + moose.connect( molecules_[pool_name(root,'ca')], 'nOut', f.x[0], 'input' ) + moose.connect( f, 'valueOut', r, 'setNumKf' ) + r.numKb = 0 + moose.connect( r, 'sub', molecules_[frmName], 'reac') + moose.connect( r, 'prd', molecules_[toName], 'reac') + _logger.debug("Reaction: %s -> %s, numKf=%s" % (frmName, toName, f.expr )) + + # The symmetry of 7 kicks in only when args['enable_subunit_exchange'] is enabled. + if args['enable_subunit_exchange']: + for pp in range(1, 7): + frm, to = 'x%dy%d' % (pp, 7-pp), 'x%dy%d' % (pp + 1, 7-pp-1) + frmName, toName = [ pool_name(root, x) for x in [frm, to] ] + r = add_reaction( '%s/phospho_%s_%s' % (root.path, frm, to)) + # And its rate is controlled by another function + f = moose.Function( '%s/funcKf' % r.path ) + f.expr = '{k1}*(x0/{kh1})^3/(1 + (x0/{kh1})^3)'.format( + k1 = _p.k_1, kh1= conc_to_n(_p.K_H1) + ) + f.x.num = 1 + moose.connect( molecules_[pool_name(root,'ca')], 'nOut', f.x[0], 'input' ) + moose.connect( f, 'valueOut', r, 'setNumKf' ) + r.numKb = 0 + moose.connect( r, 'sub', molecules_[frmName], 'reac') + moose.connect( r, 'prd', molecules_[toName], 'reac') + _logger.debug("Reaction: %s -> %s (numKf = %s)" % (frmName, toName, f.expr )) + + gainX( molecules_[ pool_name(root, 'x0y6') ], 0 ) + gainY( molecules_[ pool_name(root, 'x6y0') ], 0 ) + + for nP in range(1, 7): + if args['enable_subunit_exchange']: + gainX( molecules_[ pool_name(root, 'x%dy%d' % (nP, 6-nP) )], nP ) + gainY( molecules_[ pool_name(root, 'x%dy%d' % (6-nP, nP) )], nP ) + + frmPool = molecules_[ pool_name(root, 'x%dy%d' % (nP, 6-nP)) ] + toPool = molecules_[ pool_name( root, 'x%dy%d' % (nP-1, 6-nP+1)) ] + dephosphorylate( root, frmPool, toPool ) + + if args['enable_subunit_exchange']: + for nP in range(1, 8): + looseX( molecules_[ pool_name(root,'x%dy%d' % (nP, 7-nP)) ], nP ) + looseY( molecules_[ pool_name(root,'x%dy%d' % (7-nP, nP)) ], nP ) + + frmPool = molecules_[ pool_name(root, 'x%dy%d' % (nP, 7-nP)) ] + toPool = molecules_[ pool_name(root, 'x%dy%d' % (nP-1, 7-nP+1)) ] + dephosphorylate( root, frmPool, toPool ) + + if False: + # A reaction between PP1 and PP1_ which synchornize both pools. + r = add_reaction( '%s/sync' % molecules_[pool_name(root,'PP1_')].path ); + a = molecules_[ pool_name( root, 'PP1_' ) ] + b = molecules_[ pool_name( root, 'PP1' ) ] + moose.connect( r, 'sub', a, 'reac' ) + moose.connect( r, 'prd', b, 'reac' ) + r.Kf = 0.1 + r.Kb = 0 + _logger.debug( "Reac %s -> %s" % (a.name, b.name )) + +def remove_extra( pool, limit ): + null = moose.BufPool( '%s/null' % pool.path ) + null.nInit = 0.0 + nullReac = moose.Reac( '%s/null_reac' % pool.path ) + nullReac.numKb = 0.0 + moose.connect( nullReac, 'sub', pool, 'reac' ) + moose.connect( nullReac, 'prd', null, 'reac' ) + nullF = moose.Function( '%s/func_null' % pool.path ) + nullF.expr = '(x0 > %f)?1e-2:0' % limit + _logger.debug( 'Removing extra from pool %s' % pool.path ) + _logger.debug( '\tExpression on nullR %s' % nullF.expr ) + moose.connect( pool, 'nOut', nullF.x[0], 'input' ) + moose.connect( nullF, 'valueOut', nullReac, 'setNumKf' ) + + +def add_turnover( root ): + # Added turnover of CaMKII + global curr_subsec_ + global args + + r = add_reaction( '%s/%s.turnover6' % (root.path, curr_subsec_) ) + moose.connect( r, 'sub', molecules_[pool_name(root,'x6y0')], 'reac' ) + moose.connect( r, 'prd', molecules_[pool_name(root,'x0y6')], 'reac' ) + r.Kf = args[ 'turnover_rate' ] + _logger.info( "Turnover rate for CaMKII(6) %g" % r.Kf ) + r.Kb = 0.0 + + if args['enable_subunit_exchange']: + rr = add_reaction( '%s/%s.turnover7' % (root.path, curr_subsec_) ) + moose.connect( rr, 'sub', molecules_[pool_name(root,'x7y0')], 'reac' ) + moose.connect( rr, 'prd', molecules_[pool_name(root,'x0y7')], 'reac' ) + rr.Kf = args[ 'turnover_rate' ] + _logger.info( "Turnover rate for CaMKII(7) %g" % rr.Kf ) + rr.Kb = 0.0 + + +def print_compt( compt ): + reacs = moose.wildcardFind( '%s/##[TYPE=ZombieReac]' % compt.path ) + reacs += moose.wildcardFind( '%s/##[TYPE=Reac]' % compt.path ) + _logger.debug( 'Total %s reactions ' % len(reacs )) + dot = [ "digraph system { " ] + molecules = [] + rtext = '' + for r in reacs: + subs = [] + for ss in r.neighbors['sub']: + for s in ss: + subs.append( '"%s"' % s.path ) + molecules.append( '"%s" [label="%s",shape=circle,diffConst="%g"]; ' % ( + s.path, "", s.diffConst ) ) + rtext += '\t' + ' , '.join( subs ) + molecules.append( '"%s" [label="", shape=rect];' % r.name ) + rtext += ' -> "%s" -> ' % r.name + tgt = [ ] + # print( '->' ) + for tt in r.neighbors['prd']: + for t in tt: + # print(t.path[-20:]) + tgt.append( '"%s"' % t.path ) + molecules.append( '"%s" [label="%s",shape=circle,diffConst="%g"]; ' % ( + t.path, t.name, t.diffConst ) ) + rtext += ' , '.join( tgt ) + rtext += '\n' + # print( '\n') + try: + _logger.debug( 'Volume of compartment : %g, ' % compt.volume ) + except Exception as e: + _logger.warn( ' Compartment does not have volume' ) + + _logger.info( 'Total reactions %d' % len( set( reacs ) ) ) + _logger.info( 'Total species %d' % len( set(molecules) ) ) + dot.append( '\t\n'.join( molecules ) ) + dot.append( rtext ) + dot.append( "}" ) + with open( '%s.dot' % sys.argv[0], 'w' ) as f: + f.write( "\n".join( dot ) ) + + +def setup_solvers( compt, stochastic ): + global args + stoich = moose.Stoich( "%s/stoich" % compt.path) + if stochastic: + _logger.info("Setting up Stochastic solver in %s" % compt.path ) + s = moose.Gsolve('%s/gsolve' % compt.path) + s.useClockedUpdate = True + else: + s = moose.Ksolve('%s/ksolve' % compt.path) + _logger.info( 'Using method %s' % s.method ) + + stoich.compartment = moose.element(compt.path) + stoich.ksolve = s + stoich.path = '%s/##' % compt.path + + +def is_close( val, ref, rtol): + if abs(val - ref)/float(ref) <= rtol: + return True + return False + + +def assert_close( val, ref, rtol): + if is_close( val, ref, rtol ): + return True + _logger.warn('FAILED' + , "Expected %s, got %s, relative tolerance: %s" % (ref, val, rtol) + ) + return False + + +def make_model( root, **kwargs): + global args + _logger.info( 'Making model under %s' % root ) + init_pools( root ) + ca_input( root ) + i1_to_i1p( root ) + pp1_activation( root ) + camkii_activation_deactivation( root ) + if args['enable_subunit_exchange']: + _logger.info( 'Subunit exchange is enabled' ) + if True: + dephosphorylate( root, molecules_[ pool_name( root, 'x') ], molecules_[ pool_name( root, 'y' ) ] ) + else: + _logger.warn( 'x is not dephosphorylated to y in this version' ) + # And y phosphorylate into x + phosphorylation_first_step_subunit( root ) + else: + _logger.info( 'No subunit exchage in voxel %s' % root.name ) + add_turnover( root ) + + + +def verify( ): + global compt_ + # pools = moose.wildcardFind( '%s/##[TYPE=Pool]' % model_path_ ) + pools = moose.wildcardFind( '%s/##[TYPE=ZombiePool]' % model_path_ ) + assert len(pools) > 0 + allMolecules = np.sum( [ x.nInit for x in pools ] ) + _logger.debug( 'All molecules in systems %d' % allMolecules ) + +def setupTables( plotlist = [ ] ): + """Create tables. + Once can add table when pools are created. But when Dsolve is used, table + must be created after setting the solvers. If number of voxels are n (>1 ), + each pool is divided into n but Tables are not replicated. + Is it a bug BhallaLab/moose-core#159 + + If plotlist is empty, create table on all Pools/BuffPools + """ + + global tables_ + global model_path_ + + allPools = moose.wildcardFind( '%s/##[TYPE=ZombiePool]' % model_path_ ) + allPools += moose.wildcardFind( '%s/##[TYPE=ZombieBufPool]' % model_path_ ) + if not plotlist: + plotlist = allPools + + for i, p in enumerate( plotlist ): + add_table( p, 'n' ) + + # Now renamed the tables for better plotting. + tables = [ ] + for k in tables_: + for i, tab in enumerate( tables_[ k ] ): + tab.columnName = '%s[%d].N' % ( k, i ) + tables.append( tab ) + return tables + +def setup_diffusion_of_pool( voxel1, voxel2, species, diff_const = 1e-12 ): + """Setup diffusion between voxels """ + global molecules_ + global compt_ + pool1 = molecules_[ '%s.%s' % (voxel1.name, species ) ] + pool2 = molecules_[ '%s.%s' % (voxel2.name, species ) ] + r = moose.Reac( '%s/diff_%s' % (voxel1.path, species ) ) + moose.connect( r, 'sub', pool1, 'reac' ) + moose.connect( r, 'prd', pool2, 'reac' ) + _logger.info( + 'Diffusion reaction between %s <-> %s' % (pool1.name, pool2.name) + ) + # The rate constant is given by D / l / l. For diffusion coefficients of 1 + # uM^2/sec in a + d = diff_const / (( compt_.x1 - compt_.x0 ) ** 2) + _logger.debug( 'Diffusion coefficient (%s) %f -> rate %f' % (species, diff_const, d) ) + r.numKf = d + r.numKb = d + +def setup_diffusion( voxels, species ): + """Setup diffusion across voxels """ + global args + + if len( voxels ) < 2: + _logger.info( 'Not enough voxels to setup diffusion' ) + return + + if False: + # A <-> B <-> C where <-> is diffusion between two compartments. + for i, v2 in enumerate( voxels[1:] ): + v1 = voxels[i] + setup_diffusion_of_pool( v1, v2 + , species, args[ 'diff_dict'].get( species, 0.0 ) + ) + else: + # A <-> B <-> C <-> A where <-> is diffusion between two compartments. + for i, v1 in enumerate( voxels ): + v2 = voxels[ (i+1) % len(voxels) ] + setup_diffusion_of_pool( v1, v2, species, args[ 'diff_dict'].get( species, 0.0 ) ) + + +def main( compt_name, **kwargs ): + global args + global model_path_ + global curr_subsec_ + global compt_ + moose.Neutral( model_path_ ) + args = kwargs + + voxels = [ ] + l = args[ 'voxel_length' ] + nVoxels = args[ 'num_voxels' ] + radius = 30e-9 + args[ 'volume' ] = math.pi * radius * radius * l + args[ 'camkii_conc' ] = n_to_conc( args[ 'camkii' ] / nVoxels ) + args[ 'pp1_conc' ] = n_to_conc( args[ 'pp1' ] / nVoxels ) + args[ 'psd_volume' ] = 0.0 + + if isinstance( args['diff_dict'], str ): + args[ 'diff_dict' ] = eval( args[ 'diff_dict' ] ) + _logger.info( 'Diffusion dict %s' % args[ 'diff_dict' ] ) + + compt_ = moose.CylMesh( '%s/%s' % (model_path_, compt_name ) ) + compt_.x1 = l + compt_.r0 = compt_.r1 = radius + + _logger.info( 'Volume of compt %g' % compt_.volume ) + for i in range( args[ 'num_voxels' ] ): + curr_subsec_ = 'sw%d' % i + voxel = moose.Neutral( '%s/%s' % ( compt_.path, curr_subsec_ ) ) + _logger.info( "Creating voxles %d" % i ) + _logger.debug( '==== Created subsystem inside %s' % voxel.name ) + make_model( voxel, **kwargs ) + voxels.append( voxel ) + + for x in args[ 'diff_dict' ].keys( ): + _logger.info( "Setting up diffusion for %s" % x ) + try: + setup_diffusion( voxels, x ) + except Exception as e: + _logger.warn( 'Could not enable diffusion for %s' % x ) + _logger.warn( '\tError was %s' % e ) + + + setup_solvers( compt_, stochastic = True ) + print_compt( compt_ ) + + # Now add solvers and other goodies in compartment. + moose.setClock(18, args['record_dt'] ) # Table2 + tables = setupTables( ) + + st = moose.Streamer( '/model/streamer' ) + st.outfile = args['outfile'] + _logger.info( 'Added streamer with outfile %s' % st.outfile ) + st.addTables( tables ) + t1 = time.time() + stamp = datetime.datetime.now().isoformat() + # moose.setClock( 10, 0.003 ) + # moose.setClock( 15, 0.03 ) + # moose.setClock( 16, 0.03 ) + moose.reinit() + print( '== Gainers' ) + print( sorted( gainers_ ) ) + print( '== Loosers' ) + print( sorted( loosers_ ) ) + print( '== Dephosphorylated' ) + print( sorted( dephospho_ ) ) + + # sanity tests + verify( ) + runtime = 24 * 3600 * float( args[ 'simtime' ] ) + _logger.info('Running for %d seconds' % runtime ) + t = time.time( ) + moose.start( runtime, 1 ) + print( '[INFO] Time taken %f' % (time.time() - t ) ) + + # append parameters to streamer file. + with open( st.outfile, 'a' ) as f: + f.write( "# %s" % str( args ) ) + print( '[INFO] Appended simulation parameters to file' ) + + _logger.info( 'Total time taken %s' % (time.time() - t1 ) ) + + + +if __name__ == '__main__': + import argparse + # Argument parser. + description = 'CaMKII/PP1 switch. Most parameters are in params.py file.' + parser = argparse.ArgumentParser(description=description) + + parser.add_argument('--simtime', '-st' + , required = False + , default = _p.run_time + , type = float + , help = 'Run time for simulation (days)' + ) + + parser.add_argument('--outfile', '-o' + , required = False + , default = '%s.dat' % sys.argv[0] + , help = 'Outfile to save the data in (csv) file.' + ) + + parser.add_argument('--camkii', '-ck' + , required = False + , default = _p.N_CaMK + , type = float + , help = 'No of CaMKII molecules in each voxel.' + ) + + parser.add_argument('--pp1', '-pp' + , required = False + , type = float + , default = _p.N_PP1 + , help = 'No of PP1 molecules in each voxel.' + ) + + parser.add_argument('--turnover-rate', '-tr' + , required = False + , type = float + , default = _p.turnover_rate + , help = 'Turnover rate of CaMKKII (in per second)' + ) + + parser.add_argument('--record-dt', '-dt' + , required = False + , default = 60 + , type = float + , help = 'Record dt for plot' + ) + + parser.add_argument('--enable-subunit-exchange', '-SE' + , required = False + , default = False + , action = 'store_true' + , help = 'Enable subunit exchange.' + ) + + parser.add_argument('--num-switch', '-ns' + , required = False + , default = _p.num_switch + , type = int + , help = 'No of switches in system' + ) + + parser.add_argument('--num-voxels', '-nv' + , required = False + , default = _p.num_voxels + , type = int + , help = 'No of voxels in one switch.' + ) + + parser.add_argument('--diff-dict', '-dd' + , required = False + , default = '%s' % _p.diff_consts + , type = str + , help = 'Diffusion coefficients as python dictionary' + ) + + parser.add_argument('--voxel-length', '-nl' + , required = False + , default = _p.voxel_length + , type = float + , help = 'Length of individial voxel' + ) + + parser.add_argument('--ca-expr', '-ca' + , required = False + , default = _p.ca_expr + , help = 'Calcium expression (muParser/moose expression)' + ) + + parser.add_argument('--michaelis-menten', '-mm' + , required = False + , default = False + , action = 'store_true' + , help = 'Use Michealson-Menten scheme for dephosphorylated.' + ) + + parser.parse_args( namespace = args ) + main( 'camkii_pp1_0', **vars(args) )