Notebook fixes

Dev
Autodesk · Jul 26, 2016 · c9fac8d · c9fac8d
2 parents 7d632d6 + 45121dd
commit c9fac8d
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Showing 10 changed files with 64 additions and 12 deletions.
diff --git a/docker_images/DockerMake-dev.yml b/docker_images/DockerMake-dev.yml
@@ -56,3 +56,11 @@ dev_deploys:
       && pip install git+https://github.com/Autodesk/py-cloud-compute-cannon@dev
      ENTRYPOINT python -m moldesign intro
 
+master_deploy:
+  requires:
+    - deploy_test_base
+  description: Install from master branch
+  build: |
+    RUN pip install biopython jupyter
+    RUN pip install git+https://github.com/Autodesk/molecular-design-toolkit@master
+
diff --git a/docker_images/DockerMake.yml b/docker_images/DockerMake.yml
@@ -79,15 +79,15 @@ devtools:
 
 ############################################
 # moldesign
-# Note - this image installs from GITHUB MASTER so that we can test it before pushing to pypi
+# Note - this image installs from github so we can test it before submitting to pypi
 moldesign:
  requires:  # TODO: remove biopython dependency (it's in C ...)
   - python_install
  build_directory: moldesign
  build: |
   RUN apt-get update && apt-get install -y gcc gfortran python-dev git \
    && pip install biopython \
-   && pip install git+https://github.com/Autodesk/molecular-design-toolkit@master \
+   && pip install git+https://github.com/Autodesk/molecular-design-toolkit@0.7.2 \
    && apt-get -y remove --purge gcc gfortran python-dev git \
    && apt-get -y autoremove --purge \
    && apt-get -y clean
@@ -97,15 +97,15 @@ pyccc:
  requires:
   - python_install
  build: |
-  RUN pip install pyccc
+  RUN pip install pyccc==0.6.4
 
 
 nbmolviz:
  requires:
   - python_install
  build: |
   RUN pip install nbmolviz
-  RUN jupyter nbextension enable --python --sys-prefix nbmolviz &&
+  RUN jupyter nbextension enable --python --sys-prefix nbmolviz==0.6.5 &&
       jupyter nbextension enable --python --sys-prefix widgetsnbextensions
 
 

diff --git a/moldesign/_notebooks/.building/Example 3. Simulate HIV Protease.ipynb b/moldesign/_notebooks/.building/Example 3. Simulate HIV Protease.ipynb
@@ -7,7 +7,7 @@
     "\n",
     "<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://forum.bionano.autodesk.com/c/Molecular-Design-Toolkit\" target=\"_blank\" title=\"Forum\">Forum</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" target=\"_blank\" title=\"Issues\">Issues</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://bionano.autodesk.com/MolecularDesignToolkit/explore.html\" target=\"_blank\" title=\"Tutorials\">Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://autodesk.github.io/molecular-design-toolkit/\" target=\"_blank\" title=\"Documentation\">Documentation</a></span>\n",
     "</span>\n",
-    "![Molecular Design Toolkit](img/top.png)\n",
+    "![Molecular Design Toolkit](img/Top.png)\n",
     "<br>\n",
     "\n",
     "<center><h1>Example 3: Simulating HIV Protease </h1> </center>\n",

diff --git a/moldesign/_notebooks/.building/Header.ipynb b/moldesign/_notebooks/.building/Header.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "![Molecular Design Toolkit](img/top.png)\n",
+    "![Molecular Design Toolkit](img/Top.png)\n",
     "\n",
     "[About](http://moldesign.bionano.autodesk.com/ \"MDT Website\")\n",
     "&nbsp;&nbsp;&nbsp;[Tutorials](http://example.com/ \"Title\")\n",

diff --git a/moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb b/moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb
@@ -7,7 +7,7 @@
     "\n",
     "<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://forum.bionano.autodesk.com/c/Molecular-Design-Toolkit\" target=\"_blank\" title=\"Forum\">Forum</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" target=\"_blank\" title=\"Issues\">Issues</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://bionano.autodesk.com/MolecularDesignToolkit/explore.html\" target=\"_blank\" title=\"Tutorials\">Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://autodesk.github.io/molecular-design-toolkit/\" target=\"_blank\" title=\"Documentation\">Documentation</a></span>\n",
     "</span>\n",
-    "![Molecular Design Toolkit](img/top.png)\n",
+    "![Molecular Design Toolkit](img/Top.png)\n",
     "<br>\n",
     "\n",
     "<center><h1>Example 1: Build and simulate DNA </h1> </center>\n",

diff --git a/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb b/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb
@@ -11,7 +11,7 @@
     "<a href=\"http://bionano.autodesk.com/MolecularDesignToolkit/explore.html\" target=\"_blank\" title=\"Tutorials\">Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\n",
     "<a href=\"http://autodesk.github.io/molecular-design-toolkit/\" target=\"_blank\" title=\"Documentation\">Documentation</a></span>\n",
     "</span>\n",
-    "![Molecular Design Toolkit](img/top.png)\n",
+    "![Molecular Design Toolkit](img/Top.png)\n",
     "<br>\n",
     "<center><h1>Example 2: Orbitals, Wavefunctions, and Potential Energy Surfaces </h2> </center>\n",
     "\n",

diff --git a/moldesign/_notebooks/Getting Started.ipynb b/moldesign/_notebooks/Getting Started.ipynb
@@ -6,7 +6,7 @@
     "collapsed": true
    },
    "source": [
-    "![Molecular Design Toolkit](img/header.png)\n",
+    "![Molecular Design Toolkit](img/Header.png)\n",
     "\n",
     "<br>\n",
     "\n",
@@ -67,7 +67,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 2.0
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -79,4 +79,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}
diff --git a/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb b/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb
@@ -7,7 +7,7 @@
     "\n",
     "<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://forum.bionano.autodesk.com/c/Molecular-Design-Toolkit\" target=\"_blank\" title=\"Forum\">Forum</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" target=\"_blank\" title=\"Issues\">Issues</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://bionano.autodesk.com/MolecularDesignToolkit/explore.html\" target=\"_blank\" title=\"Tutorials\">Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://autodesk.github.io/molecular-design-toolkit/\" target=\"_blank\" title=\"Documentation\">Documentation</a></span>\n",
     "</span>\n",
-    "![Molecular Design Toolkit](img/top.png)\n",
+    "![Molecular Design Toolkit](img/Top.png)\n",
     "<br>\n",
     "\n",
     "\n",

diff --git a/moldesign/_notebooks/data/butane.xyz b/moldesign/_notebooks/data/butane.xyz
@@ -0,0 +1,16 @@
+14
+
+C          1.07084       -0.13841       -0.05668
+C          0.57475        0.27291        1.32171
+C          1.06176        1.66053        1.74189
+C          0.56567        2.76742        0.82323
+H          0.68453        0.52482       -0.83667
+H          0.73394       -1.15211       -0.29441
+H          2.16362       -0.12102       -0.09931
+H         -0.51968        0.24172        1.34052
+H          0.92655       -0.46188        2.05688
+H          0.70996        1.86405        2.76119
+H          2.15619        1.67604        1.77485
+H         -0.52710        2.77659        0.77811
+H          0.90257        3.74271        1.18778
+H          0.95198        2.64830       -0.19366
diff --git a/moldesign/_notebooks/data/octane.xyz b/moldesign/_notebooks/data/octane.xyz
@@ -0,0 +1,28 @@
+26
+
+C          1.07494       -0.21101        0.01832
+C          0.64681       -0.10289        1.47390
+C          1.11981        1.21007        2.10489
+C          0.54543        2.44755        1.40516
+C         -0.98571        2.48972        1.42790
+C         -1.56009        2.58505        2.84631
+C         -1.08709        3.83368        3.59660
+C         -1.51522        5.10924        2.88714
+H          0.64941        0.59283       -0.59180
+H          0.73256       -1.15552       -0.41263
+H          2.16324       -0.16064       -0.06360
+H         -0.43925       -0.20173        1.54857
+H          1.06498       -0.94409        2.04010
+H          0.84650        1.21636        3.16757
+H          2.21232        1.25761        2.07891
+H          0.96356        3.34867        1.87191
+H          0.89227        2.49389        0.36840
+H         -1.33254        3.33049        0.81951
+H         -1.40383        1.60461        0.93147
+H         -2.65260        2.58063        2.79232
+H         -1.28678        1.69371        3.42497
+H         -1.50526        3.82283        4.61054
+H         -0.00103        3.82560        3.72021
+H         -2.60352        5.15001        2.80004
+H         -1.17283        5.98829        3.43950
+H         -1.08969        5.17732        1.88027