diff --git a/docker_images/DockerMake-dev.yml b/docker_images/DockerMake-dev.yml
index c3cba37..0321ed6 100644
--- 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
index 9d5687d..35429ca 100644
--- a/docker_images/DockerMake.yml
+++ b/docker_images/DockerMake.yml
@@ -79,7 +79,7 @@ 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
@@ -87,7 +87,7 @@ 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
@@ -97,7 +97,7 @@ pyccc:
requires:
- python_install
build: |
- RUN pip install pyccc
+ RUN pip install pyccc==0.6.4
nbmolviz:
@@ -105,7 +105,7 @@ nbmolviz:
- 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
index 3713eaf..efe8801 100644
--- 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",
"About Forum Issues Tutorials Documentation\n",
"\n",
- "\n",
+ "\n",
"
\n",
"\n",
"Example 3: Simulating HIV Protease
\n",
diff --git a/moldesign/_notebooks/.building/Header.ipynb b/moldesign/_notebooks/.building/Header.ipynb
index 9bc40f9..b07f7fb 100644
--- a/moldesign/_notebooks/.building/Header.ipynb
+++ b/moldesign/_notebooks/.building/Header.ipynb
@@ -4,7 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "\n",
+ "\n",
"\n",
"[About](http://moldesign.bionano.autodesk.com/ \"MDT Website\")\n",
" [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
index a574823..e17d47c 100644
--- 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",
"About Forum Issues Tutorials Documentation\n",
"\n",
- "\n",
+ "\n",
"
\n",
"\n",
"Example 1: Build and simulate DNA
\n",
diff --git a/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb b/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb
index 7057e6c..16515fd 100644
--- a/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb
+++ b/moldesign/_notebooks/Example 2. Running Quantum Chemistry.ipynb
@@ -11,7 +11,7 @@
"Tutorials \n",
"Documentation\n",
"\n",
- "\n",
+ "\n",
"
\n",
"Example 2: Orbitals, Wavefunctions, and Potential Energy Surfaces
\n",
"\n",
diff --git a/moldesign/_notebooks/Getting Started.ipynb b/moldesign/_notebooks/Getting Started.ipynb
index 3a05799..52f333a 100644
--- a/moldesign/_notebooks/Getting Started.ipynb
+++ b/moldesign/_notebooks/Getting Started.ipynb
@@ -6,7 +6,7 @@
"collapsed": true
},
"source": [
- "\n",
+ "\n",
"\n",
"
\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
-}
+}
\ No newline at end of file
diff --git a/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb b/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb
index 8e654b4..2f5ae80 100644
--- a/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb
+++ b/moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb
@@ -7,7 +7,7 @@
"\n",
"About Forum Issues Tutorials Documentation\n",
"\n",
- "\n",
+ "\n",
"
\n",
"\n",
"\n",
diff --git a/moldesign/_notebooks/data/butane.xyz b/moldesign/_notebooks/data/butane.xyz
new file mode 100644
index 0000000..8cdabf3
--- /dev/null
+++ 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
new file mode 100644
index 0000000..8a4b3c9
--- /dev/null
+++ 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