Merge branch 'master' into missing-terminal-parsing

# Conflicts:
#	DockerMakefiles/DockerMake.yml
#	DockerMakefiles/Moldesign.yml
#	DockerMakefiles/buildfiles/moldesign/moldesign.yml

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

@@ -18,7 +18,6 @@ _ALL_:
   - moldesign_minimal
   - moldesign_minimal_py2
   - moldesign_notebook
-  - nucleic_acid_builder
   - nwchem_build
   - openblas
   - pyscf_build

DockerMakefiles/Moldesign.yml

@@ -60,17 +60,19 @@ moldesign_notebook:
   RUN python -m nbmolviz activate --user
   USER root
   RUN python -m moldesign copyexamples
+  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:
-  - moldesign_notebook
   - opsin
   - symmol_base
-  - nucleic_acid_builder
+  - ambertools
+  - moldesign_notebook
  build: |
    USER nbuser
-   RUN mkdir -p ~/.moldesign
-   ADD moldesign.yml ~/.moldesign/moldesign.yml
+   RUN mkdir -p /home/nbuser/.moldesign
+   ADD moldesign.yml /home/nbuser/.moldesign/moldesign.yml

DockerMakefiles/PythonTools.yml

@@ -22,6 +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/buildfiles/moldesign/moldesign.yml

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

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/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)

moldesign/interfaces/pdbfixer_interface.py

@@ -97,21 +97,48 @@ def mutate_residues(mol, residue_map):
     # into an MDT structure
     assert temp_mutant.num_residues == mol.num_residues  # shouldn't change number of residues
     residues_to_copy = []
+    old_residue_map = {}
     for oldres, mutant_res in zip(mol.residues, temp_mutant.residues):
         if oldres in residue_map:
             residues_to_copy.append(mutant_res)
             mutant_res.mol = None
             mutant_res.chain = oldres.chain
+            old_residue_map[oldres] = mutant_res
         else:
             residues_to_copy.append(oldres)
 
+    # Bonds between original and mutated backbone atoms will be removed when 
+    # creating the new mutant molecule because the original and mutated atoms 
+    # reference different molecules.
+    #
+    # Make a list of bonds referencing atoms in the original molecule that
+    # is used later to recreate bonds between original and mutated backbone 
+    # atoms.
+    orig_bonds = []
+    for res in residues_to_copy:
+        if not res.backbone:
+            continue 
+        for atom in res.backbone:
+            for bond_atom in atom.bond_graph:
+                if bond_atom.residue in residue_map:
+                    mutant_res = old_residue_map[bond_atom.residue]
+                    mutant_atom = mutant_res.atoms[bond_atom.name]
+                    orig_bonds.append((atom,mutant_atom,atom.bond_graph[bond_atom]))
+
     metadata = {'origin': mol.metadata.copy(),
                 'mutations': mutation_strs}
 
-    return mdt.Molecule(residues_to_copy,
-                        name='Mutant of "%s"' % mol,
-                        metadata=metadata)
+    mutant_mol = mdt.Molecule(residues_to_copy, name='Mutant of "%s"' % mol, metadata=metadata)
+
+    # Add bonds between the original and mutated backbone atoms.
+    for atom,mut_atom,order in orig_bonds:
+        chainID = atom.chain.name
+        residues = mutant_mol.chains[chainID].residues
+        new_atom = residues[atom.residue.name].atoms[atom.name]
+        new_mut_atom = residues[mut_atom.residue.name].atoms[mut_atom.name]
+        new_atom.bond_to(new_mut_atom, order)
 
+    return mutant_mol 
 
 def _pdbfixer_chainnames_to_letter(pdbfixermol):
     for chain in pdbfixermol.chains: