Merge pull request #171 from Autodesk/vizfixes

Vizfixes

moldesign/_tests/test_gaussian_math.py

@@ -177,7 +177,7 @@ def _assert_numerical_analytical_overlaps_match(g1, g2):
     with np.errstate(under='ignore'):
         prodvals = g1(allpoints) * g2(allpoints)
     numsum = prodvals.sum() * grid.dx * grid.dy * grid.dz
-    helpers.assert_almost_equal(numsum, olap, decimal=5)
+    helpers.assert_almost_equal(numsum, olap, decimal=4)
 
 
 @pytest.mark.parametrize('withunits', [False, True])

moldesign/helpers/widgets.py

@@ -59,7 +59,7 @@ def not_installed_method(*args, **kwargs):
 
 
 try:
-    from nbmolviz.uibase import Logger, display_log
+    from nbmolviz.uielements import Logger, display_log
     exports_names('Logger', 'display_log')
 
 except ImportError:

moldesign/molecules/bonds.py

@@ -25,6 +25,7 @@
 from . import toplevel
 from .. import units as u
 from .. import mathutils
+from .. import geom
 
 
 @toplevel
@@ -95,6 +96,12 @@ def order(self, order):
                 if atom.molecule is self.molecule:
                     atom.bond_graph[nbr] = order
 
+    @property
+    def exists(self):
+        """ bool: whether or not this bond exists
+        """
+        return self.order is not None
+
     @property
     def type(self):
         return self.a1.symbol + self.SYMBOLS.get(self.order, u'?̶') + self.a2.symbol
@@ -129,6 +136,11 @@ def partner(self, atom):
     def length(self):
         return self.a1.distance(self.a2)
 
+    @length.setter
+    def length(self, value):
+        geom.set_distance(self.a1, self.a2, value,
+                          adjustmol=self.exists and not self.is_cyclic)
+
     @property
     def name(self):
         """ str: name of the bond """
@@ -151,6 +163,26 @@ def molecule(self):
     def midpoint(self):
         return (self.a1.position + self.a2.position) / 2.0
 
+    @property
+    def is_cyclic(self):
+        """
+        bool: True if this bond is in one or more rings
+        """
+        visited = set([self.a2])
+
+        def check_for_cycles(atom):
+            visited.add(atom)
+            for nbr in atom.bond_graph:
+                if nbr is self.a2 and atom is not self.a1:
+                    return True
+                if nbr not in visited:
+                    in_cycle = check_for_cycles(nbr)
+                    if in_cycle:
+                        return True
+            return False  # if here, not in a cycle
+        check_for_cycles(self.a1)
+
+
     def align(self, other, centered=True):
         """ Rotates the entire molecule to align this bond with another object.
 

moldesign/orbitals/wfn.py

@@ -19,7 +19,7 @@
 import numpy as np
 import copy
 
-from . import MolecularOrbitals
+from . import Orbital, MolecularOrbitals
 from ..utils import DotDict
 
 
@@ -73,8 +73,12 @@ def __init__(self, mol, num_electrons,
             self.positions = positions.copy()
 
         if self.aobasis is not None:
-            self.orbitals['atomic'] = self.aobasis
             self.aobasis.wfn = self
+            atomic_orbs = [Orbital(c, basis=self.aobasis, wfn=self, name=bf.name)
+                           for c,bf in zip(np.identity(len(self.aobasis)), self.aobasis)]
+            self.orbitals.atomic = MolecularOrbitals(atomic_orbs, wfn=self,
+                                                     basis=self.aobasis,
+                                                     orbtype='atomic')
             for orb in self.aobasis.orbitals:
                 orb.wfn = self
 

moldesign/units/quantity.py

@@ -125,7 +125,10 @@ def __deepcopy__(self, memo):
         return result
 
     def __hash__(self):
-        return hash((self._magnitude, str(self.units)))
+        m = self._magnitude
+        if isinstance(m, np.ndarray) and m.shape == ():
+            m = float(m)
+        return hash((m, str(self.units)))
 
     def __setitem__(self, key, value):
         from . import array as quantityarray

moldesign/utils/descriptors.py

@@ -19,29 +19,36 @@
 
 class Alias(object):
     """
-    Descriptor that calls a child object's method.
+    Descriptor that delegates to a child's attribute or method.
     e.g.
     >>> class A(object):
     >>>     childkeys = Alias('child.keys')
     >>>     child = dict()
     >>>
     >>> a = A()
     >>> a.child['key'] = 'value'
-    >>> a.childkeys() #calls a.child.keys(), returns ['key']
+    >>> a.childkeys() # calls a.child.keys(), returns ['key']
     ['key']
     """
-    def __init__(self, objmethod):
-        objname, methodname = objmethod.split('.')
+    def __init__(self, objattr):
+        objname, attrname = objattr.split('.')
         self.objname = objname
-        self.methodname = methodname
+        self.attrname = attrname
 
     def __get__(self, instance, owner):
         if instance is None:
             assert owner is not None
-            return _unbound_getter(self.objname, self.methodname)
+            return _unbound_getter(self.objname, self.attrname)
         else:
             proxied = getattr(instance, self.objname)
-            return getattr(proxied,self.methodname)
+            return getattr(proxied, self.attrname)
+
+    def __set__(self, instance, value):
+        if instance is None:
+            raise NotImplementedError()
+        else:
+            proxied = getattr(instance, self.objname)
+            setattr(proxied, self.attrname, value)
 
 
 def _unbound_getter(objname, methodname):

moldesign/widgets.py

@@ -19,11 +19,12 @@
 from .helpers.widgets import nbmolviz_installed
 
 if nbmolviz_installed:
-    from nbmolviz.widgets import BondSelector, GeometryBuilder, ResidueSelector, Symmetrizer
+    from nbmolviz.widgets import (BondSelector, GeometryBuilder, ResidueSelector, Symmetrizer,
+                                  AtomSelector)
     from nbmolviz.widgets.computeconfig import configure, about
 else:
     from .helpers.widgets import not_installed_method
-    BondSelector = GeometryBuilder = ResidueSelector = Symmetrizer = configure = about = \
-        not_installed_method
+    BondSelector = GeometryBuilder = ResidueSelector = AtomSelector = Symmetrizer = configure \
+        = about = not_installed_method
 
-__all__ = 'BondSelector GeometryBuilder ResidueSelector Symmetrizer'.split()
+__all__ = 'BondSelector GeometryBuilder ResidueSelector Symmetrizer AtomSelector'.split()