Merge branch 'master' into testsize

.dockerignore

@@ -17,3 +17,4 @@ docs/_build
 **/tokens
 **/codeship.aes
 **/tmp
+**/Untitled*.ipynb

.gitignore

@@ -20,4 +20,4 @@ moldesign/_static_data/components.ci*
 moldesign/_static_data/aa-variants-v1.ci*
 tmp
 *.bak
-
+Untitled*.ipynb

DockerMakefiles/CLI.yml

@@ -11,19 +11,13 @@ ambertools:
     - miniconda
   build: |
     RUN apt-get update \
-     && apt-get install --no-install-recommends -y libgfortran3 \
-     && apt-get -y clean && apt-get autoremove -y --purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+     && apt-get install --no-install-recommends -y \
+        libgfortran3 gcc gfortran libfftw3-dev libnetcdf-dev \
+     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
     RUN python -c "print('name = molecular-design-toolkit-builder\ninstitution = Autodesk\ncity = San Francisco\nstate or province = CA\ncountry = USA')" > /root/.amberrc
     RUN conda install -qy -c ambermd ambertools=16.21.1
     ENV AMBERHOME=/opt/conda/
 
-nucleic_acid_builder:
-  requires:
-   - ambertools
-  build: |
-    RUN apt-get update \
-     && apt-get install --no-install-recommends -y gcc gfortran libfftw3-dev libnetcdf-dev \
-     && apt-get -y clean && apt-get autoremove -y --purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 
 dssp:

DockerMakefiles/DockerMake.yml

@@ -17,8 +17,7 @@ _ALL_:
   - moldesign_complete_py2
   - moldesign_minimal
   - moldesign_minimal_py2
-  # - moldesign_notebook
-  - nucleic_acid_builder
+  - moldesign_notebook
   - nwchem_build
   - openblas
   - pyscf_build

DockerMakefiles/Moldesign.yml

@@ -5,12 +5,12 @@ moldesign_requirements:
     RUN conda install -qy -c omnia parmed biopython
 
 
-
 moldesign_minimal_requirements:
  description: Base installation of the MDT library. Built from the current directory.
  requires:
   - moldesign_requirements
  build_directory: ../
+ ignorefile: buildfiles/moldesign/moldesign.dockerignore
  build: |
   COPY requirements.txt /tmp/mdtreqs.txt
   RUN apt-get update \
@@ -49,12 +49,30 @@ moldesign_complete_py2:
 
 
 moldesign_notebook:
- description: OUT OF DATE A production-ready, fully outfitted jupyter server container
+ description: A production-ready, fully outfitted jupyter server container
  requires:
   - moldesign_complete
   - notebook
  build: |
-  RUN pip install nbmolviz # == 0.7.0
+  RUN adduser --disabled-password --gecos '' nbuser
+  RUN pip install nbmolviz==0.7.0rc4
+  USER nbuser
+  RUN python -m nbmolviz activate --user
+  USER root
   RUN python -m moldesign copyexamples
-  RUN jupyter nbextension enable --python --sys-prefix widgetsnbextension \
-   && jupyter nbextension enable --python --sys-prefix nbmolviz
+  RUN chmod -R a+rw .
+
+
+
+moldesign_stack:
+ description: An extra-large image with everything needed to run the example notebooks
+ build_directory: buildfiles/moldesign
+ requires:
+  - opsin
+  - symmol_base
+  - ambertools
+  - moldesign_notebook
+ build: |
+   USER nbuser
+   RUN mkdir -p /home/nbuser/.moldesign
+   ADD moldesign.yml /home/nbuser/.moldesign/moldesign.yml

DockerMakefiles/PythonTools.yml

@@ -3,16 +3,12 @@ notebook:
   - python_deploy_base
  build_directory: buildfiles/notebook/
  build: |
-    RUN conda install -yq matplotlib jupyter ipywidgets
+    RUN conda install -yq matplotlib jupyter ipywidgets nbformat
     ENTRYPOINT /run_notebook.sh
     EXPOSE 8888
     RUN mkdir /notebooks
     WORKDIR /notebooks
     COPY run_notebook.sh /run_notebook.sh
-    # workaround below, not sure why it's necessary or even whose fault it is
-    RUN pip uninstall -y backports.ssl_match_hostname backports.shutil_get_terminal_size \
-     && pip install backports.ssl_match_hostname backports.shutil_get_terminal_size
-
 
 pyquante2:
  requires:
@@ -26,6 +22,9 @@ chem_python_conda:
   - deploy_requirements
  description: All of the external python chemistry libraries in one place
  build: |
+   RUN apt-get update \
+    && apt-get install -y libpng12-dev \
+    && cleanapt
    RUN conda install -qy -c openbabel openbabel=2.4.1
    RUN conda install -qy -c omnia \
       biopython=1.68 \

DockerMakefiles/SymMol.yml

@@ -17,14 +17,17 @@ symmol_build:
      && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
     RUN mv /src/symmol/symmol /usr/local/bin
 
-symmol:
-  requires:
-    - deploybase
+symmol_base:
   build: |
     RUN apt-get update \
      && apt-get install -y --no-install-recommends \
            gfortran libgfortran3\
      && cleanapt
   copy_from:
     symmol_build:
-      /usr/local/bin/symmol: /usr/local/bin
+      /usr/local/bin/symmol: /usr/local/bin
+
+symmol:
+  requires:
+    - deploybase
+    - symmol_base

DockerMakefiles/buildfiles/moldesign/moldesign.dockerignore

@@ -0,0 +1,22 @@
+**/*.pyc
+**/*.pyo
+.idea
+**/.ipynb_checkpoints/
+**/pyquante.log
+**/_docker_make_tmp
+**/lastfailed
+dist
+build
+**/*.egg-info
+**/__pycache__
+moldesign/_static_data/components.ci*
+moldesign/_static_data/aa-variants-v1.ci*
+**/*.bak
+**/.coverage
+docs/_build
+**/tokens
+**/codeship.aes
+**/tmp
+**/Untitled*.ipynb
+DockerMakefiles
+docs

DockerMakefiles/buildfiles/moldesign/moldesign.yml

@@ -0,0 +1,4 @@
+run_local:
+  nab: true
+  opsin: true
+  symmol: true

DockerMakefiles/buildfiles/notebook/run_notebook.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-jupyter notebook --ip=0.0.0.0 --no-browser --port=8888 $@
+jupyter notebook --ip=0.0.0.0 --no-browser --port=8888 --allow-root $@

DockerMakefiles/requirements.txt

@@ -1 +1,2 @@
-DockerMake >= 0.5.6
+DockerMake >= 0.6.0rc2
+

codeship-services.yml

@@ -10,8 +10,8 @@ docker_make:
 publisher:
   encrypted_env_file: deployment/tokens.crypt
   build:
-    context: ./deployment
-    dockerfile: ./moldesign-complete-cache.dockerfile
+    context: .  # this one builds at the root of the repository
+    dockerfile: ./deployment/moldesign-complete-cache.dockerfile
   add_docker: true
   working_dir: /opt/molecular-design-toolkit
   volumes:
@@ -50,8 +50,8 @@ test_moldesign_minimal_py2:
 test_moldesign_complete:
   encrypted_env_file: deployment/tokens.crypt
   build:
-    context: ./deployment
-    dockerfile: moldesign-complete-cache.dockerfile
+    context: ./   # this one builds at the root of the repository
+    dockerfile: ./deployment/moldesign-complete-cache.dockerfile
   cached: false  # do not cache this! It gets built before the cache is triggered
   working_dir: /opt/molecular-design-toolkit/
   add_docker: true

codeship-steps.yml

@@ -2,13 +2,7 @@
   service: docker_make
   type: serial
   steps:
-    - command:
-       docker-make -p -n --dockerfile-dir /makefiles
-         nwchem_build
-         pyscf_build
-         deploybase
-         python_deploy_base
-         python_deploy_base_py2
+    - command: docker-make -p -n --dockerfile-dir /makefiles nwchem_build pyscf_build deploybase python_deploy_base python_deploy_base_py2
       name: write_dockerfiles
     - command: cp buildfiles/deploybase/cleanapt buildfiles/notebook/run_notebook.sh /makefiles
       name: copy_contexts
@@ -70,15 +64,22 @@
   steps:
    - command: deployment/print_environment.sh
 
-- type: serial
-  name: complete_tests
-  services:
-   - test_moldesign_complete
-   - test_moldesign_complete_py2
-   - test_moldesign_minimal
-   - test_moldesign_minimal_py2
-  steps:
-   - command: deployment/codeship_runtests.sh
+- service: test_moldesign_complete
+  name: test_moldesign_complete
+  command: deployment/codeship_runtests.sh
+
+- service: test_moldesign_complete_py2
+  name: test_moldesign_complete_py2
+  command: deployment/codeship_runtests.sh
+
+- service: test_moldesign_minimal
+  name: test_moldesign_minimal
+  command: deployment/codeship_runtests.sh
+
+- service: test_moldesign_minimal_py2
+  name: test_moldesign_minimal_py2
+  command: deployment/codeship_runtests.sh
+
 
 - name: publish
   service: publisher

deployment/build-env.dockerfile

@@ -1,5 +1,6 @@
 FROM python:2.7-slim
-
+# This is the environment that "docker-make" will run in on the CI server
+# The expected build context is the root of the MDT repository
 RUN apt-get update && apt-get install -y curl
 
 # Install docker CLI only, not the full engine

deployment/moldesign-complete-cache.dockerfile

@@ -1,5 +1,8 @@
+# this is meant to built at the ROOT of the repository
+
 FROM moldesign_complete:dev
-ADD requirements.txt provision_testrunner_image.sh /tmp/
+ADD DockerMakefiles /opt/molecular-design-toolkit/DockerMakefiles
+ADD deployment/requirements.txt deployment/provision_testrunner_image.sh /tmp/
 RUN cd /tmp && ./provision_testrunner_image.sh
 RUN pip install twine
 WORKDIR /opt/molecular-design-toolkit

moldesign/_tests/test_pdbfixer_xface.py

@@ -22,6 +22,7 @@
 
 import moldesign as mdt
 from moldesign import units as u
+from .helpers import get_data_path
 
 import pytest
 
@@ -91,6 +92,23 @@ def test_mutation_nomenclature_string_only(pdb3aid):
     assert len(mut25) == 2
     assert [r.resname for r in mut25] == ['MET', 'MET']
 
+def test_mutation_topology(pdb1yu8):
+    """ Test the topology of the backbone atoms for a mutated molecule. """
+    molecule = pdb1yu8 
+    mutation_residues = ["X.13G"]
+    mutated_molecule = mdt.mutate_residues(molecule, mutation_residues)
+    # Check that the number of bonds for backbone atoms match.
+    for res, mut_res in zip(molecule.residues, mutated_molecule.residues):
+        if not res.backbone:
+            continue 
+        for atom in res.backbone:
+            bonds = [bond for bond in molecule.bond_graph[atom] if bond.name in res.backbone]
+            mut_atom = mutated_molecule.chains["X"].residues[mut_res.name].atoms[atom.name]
+            mut_bonds = mutated_molecule.bond_graph[mut_atom]
+            mut_bonds = [bond for bond in mutated_molecule.bond_graph[mut_atom] \
+                if bond.name in mut_res.backbone]
+            assert len(bonds) == len(mut_bonds)
+
 
 @pytest.mark.screening
 def test_multiple_mutations(pdb3aid):

moldesign/compute/configuration.py

@@ -190,11 +190,19 @@ def init_config():
 
     for pkg, do_remote in list(config.run_remote.items()):
         if do_remote:
-            getattr(packages, pkg).force_remote = True
+            try:
+                getattr(packages, pkg).force_remote = True
+            except AttributeError:
+                print('WARNING: unknown key "%s" in %s' % (pkg, path),
+                      file=sys.stderr)
 
     for pkg, do_local in list(config.run_local.items()):
         if do_local:
-            getattr(packages, pkg).run_local = True
+            try:
+                getattr(packages, pkg).run_local = True
+            except AttributeError:
+                print('WARNING: unknown key "%s" in %s' % (pkg, path),
+                      file=sys.stderr)
 
 
 def _check_override(tagname, expected, path):

moldesign/compute/packages.py

@@ -256,7 +256,7 @@ def make_job(self, **kwargs):
 
 nwchem = InterfacedExecutable('nwchem.exe', None, 'nwchem', version_flag=None)
 opsin = InterfacedExecutable('opsin', None, 'opsin', version_flag=None)
-nab = InterfacedExecutable('nab', '16', 'nucleic_acid_builder', version_flag=None)
+nab = InterfacedExecutable('nab', '16', 'ambertools', version_flag=None)
 symmol = InterfacedExecutable('symmol', None, 'symmol', version_flag=None)
 tleap = InterfacedExecutable('tleap', '16', 'ambertools', version_flag=None)
 antechamber = InterfacedExecutable('antechamber', '16', 'ambertools', version_flag=None)