Merge pull request #143 from peastman/registeratom

Fixed code that was broken by changes to OpenMM

.travis.yml

@@ -11,15 +11,22 @@ install:
   - export PATH=$HOME/miniconda/bin:$PATH
   - export PATH=$HOME/miniconda/bin:$PATH
 
 
 script:
 script:
-  # Add conda channel
-  - conda config --add channels $ORGNAME
+  # Create a test environment
+  - conda create --yes -n test python=$python
+  # Activate the test environment
+  - source activate test
+  # Add org channel
+  - conda config --add channels ${ORGNAME}
+  # Add omnia dev channels
+  - conda config --add channels https://conda.anaconda.org/omnia/label/dev
   # Build the recipe
   # Build the recipe
   - conda build devtools/conda-recipe
   - conda build devtools/conda-recipe
-  # Test the local installation
-  - source activate _test
+  # Install the package
+  - conda install --yes --use-local ${PACKAGENAME}-dev
+  # Install testing dependencies
   - conda install --yes --quiet nose nose-timer
   - conda install --yes --quiet nose nose-timer
-  # Run tests
-  - cd devtools && nosetests $PACKAGENAME --nocapture --verbosity=2 --with-doctest --with-timer -a "\!slow" && cd ..
+  # Test the package
+  - cd devtools && nosetests $PACKAGENAME --nocapture --verbosity=2 --with-timer --with-doctest -a '!slow' && cd ..
 
 
 env:
 env:
   matrix:
   matrix:

devtools/conda-recipe/meta.yaml

@@ -10,12 +10,12 @@ requirements:
   build:
   build:
     - python
     - python
     - setuptools
     - setuptools
-    - openmm-dev
+    - openmm
     - numpy
     - numpy
 
 
   run:
   run:
     - python
     - python
-    - openmm-dev
+    - openmm
     - numpy
     - numpy
 
 
 test:
 test:

devtools/travis-ci/install.sh

@@ -5,8 +5,8 @@ cd $HOME
 # Install Miniconda
 # Install Miniconda
 MINICONDA=Miniconda2-latest-Linux-x86_64.sh
 MINICONDA=Miniconda2-latest-Linux-x86_64.sh
 MINICONDA_HOME=$HOME/miniconda
 MINICONDA_HOME=$HOME/miniconda
-MINICONDA_MD5=$(curl -s http://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
-wget -q http://repo.continuum.io/miniconda/$MINICONDA
+MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget -q https://repo.continuum.io/miniconda/$MINICONDA
 if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
 if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
     echo "Miniconda MD5 mismatch"
     echo "Miniconda MD5 mismatch"
     exit 1
     exit 1

pdbfixer/pdbfixer.py

@@ -1112,7 +1112,7 @@ class PDBFixer(object):
                             sigma = radii[element.symbol]
                             sigma = radii[element.symbol]
                         else:
                         else:
                             sigma = 0.5
                             sigma = 0.5
-                        nonbonded.typeMap[typeName] = (0.0, sigma, 0.0)
+                        nonbonded.registerAtom({'type':typeName, 'charge':'0', 'sigma':str(sigma), 'epsilon':'0'})
                 indexInResidue[atom.index] = len(template.atoms)
                 indexInResidue[atom.index] = len(template.atoms)
                 template.atoms.append(app.ForceField._TemplateAtomData(atom.name, typeName, element))
                 template.atoms.append(app.ForceField._TemplateAtomData(atom.name, typeName, element))
             for atom in residue.atoms():
             for atom in residue.atoms():