[WIP] Overhaul parameterization scheme used for small molecules

.travis.yml

@@ -1,72 +1,74 @@
-language: c
-sudo: false
-addons:
-  apt:
-    sources:
-    - ubuntu-toolchain-r-test
-    packages:
-      #- g++
-      #- gfortran
-      #- valgrind
-      #- csh
-      #- g++-multilib
-      #- gcc-multilib
+language: python
+
+# Run jobs on container-based infrastructure, can be overridden per job
+dist: xenial
+
 branches:
-  except:
-    - /^(?i:notest)-.*$/
+  only:
+    - master
 
-install:
-  #add random sleep from 1-10s to try to prevent overloading the anaconda servers
-  - sleep $[ ( $RANDOM % 10 )  + 1 ]s
-  - env
+matrix:
+  include:
+    - os: osx
+      language: generic
+      env: PYTHON_VER=3.6 OPENEYE=true
+    - os: osx
+      language: generic
+      env: PYTHON_VER=3.7 OPENEYE=true
+
+    - os: linux
+      python: 3.6
+      env: PYTHON_VER=3.6 OPENEYE=true
+    - os: linux
+      sudo: required
+      python: 3.7
+      env: PYTHON_VER=3.7 OPENEYE=true
+
+env:
+  global:
+    - OE_LICENSE="$HOME/oe_license.txt"
+
+before_install:
+  # Additional info about the build
+  - uname -a
+  - df -h
+  - ulimit -a
+  # Install Conda and dependencies
   - source devtools/travis-ci/install.sh
-  - export PYTHONUNBUFFERED=true
-  - export CC=gcc
-  - export CXX=g++
+  # Add nighly openmm dev builds
+  - conda config --add channels omnia-dev
+  # Add openeye beta builds
+  - conda config --add channels openeye/label/beta
+  # Report Python version
+  - python -V
   # Unpack encrypted OpenEye license file
   - if [ "$TRAVIS_SECURE_ENV_VARS" == true ]; then openssl aes-256-cbc -K $encrypted_e49582a90fb5_key -iv $encrypted_e49582a90fb5_iv -in devtools/travis-ci/oe_license.txt.enc -out $OE_LICENSE -d; fi
-  - if [ "$TRAVIS_SECURE_ENV_VARS" == false ]; then echo "OpenEye license will not be installed in forks."; fi
+  - if [ "$TRAVIS_SECURE_ENV_VARS" == false ] ; then echo "OpenEye license will not be installed in pull request."; fi
 
-script:
-  # Create a test environment
-  - conda create --yes -n test python=$python
-  # Activate the test environment
+install:
+  # Create test environment for package
+  - conda create --yes -n test python=$PYTHON_VER pip pytest pytest-cov
   - source activate test
-  # Add omnia
-  - conda config --add channels omnia --add channels conda-forge
-  # Add omnia beta and dev channels
-  - conda config --add channels omnia/label/beta
-  - conda config --add channels omnia/label/dev
-  # Add OpenEye channel
-  - conda config --add channels openeye
-  # Update conda
-  - conda update --yes --all
-  # List conda environment
+
+  # Use OpenEye toolkits beta version for partial bond orders
+  - if [[ "$OPENEYE" == true ]]; then conda install --yes -c openeye/label/beta openeye-toolkits && python -c "import openeye; print(openeye.__version__)"; fi
+
+  # Install pip only modules
+  - pip install codecov
+  - pip install coverage==4.4
+
+  # Build and install package
+  - conda build --python=$PYTHON_VER devtools/conda-recipe
+  - conda install --yes --use-local perses-dev
+
+  # Report on environment
   - conda list
-  # Build the recipe
-  - conda build devtools/conda-recipe
-  # Install the package
-  - conda install --yes --use-local ${PACKAGENAME}-dev
-  # Install testing dependencies
-  - conda install --yes --quiet nose nose-timer
-  # Test the package
-  - cd devtools && nosetests perses --nocapture --verbosity=3 --with-timer -a '!advanced' && cd ..
 
-env:
-  matrix:
-    - python=3.5 CONDA_PY=35 TESTSYSTEMS="ValenceSmallMoleculeLibraryTestSystem"
-    - python=3.6 CONDA_PY=36 TESTSYSTEMS="ValenceSmallMoleculeLibraryTestSystem"
+script:
+  - pytest -v -s --cov=perses-dev perses-dev/tests/
 
-  global:
-    - ORGNAME="omnia"
-    - OE_LICENSE="$HOME/oe_license.txt"
-    - PACKAGENAME="perses"
-    # Location of decrypted OpenEye license file
-    - OE_LICENSE="$HOME/oe_license.txt"
-    - OPENEYE_CHANNEL="-i https://pypi.anaconda.org/OpenEye/simple"
-    # encrypted BINSTAR_TOKEN for push of dev package to binstar
-    - secure: "RRvLDPu9mPoNaRWIseaJdgShOXI+PaHPWKAIJvW7VYWcAS6iEN7W4Fj4zD5hkocQxc3ou97EtkgID+ApH10bSGKxCykyU0urSY9jsSOJX2m0AE19X0dVr6ySIQkwCWE6kUMVlvQYQo80fM2EMElD+btr4G9XBAhArAO7HvZHkoQ="
+notifications:
+    email: false
 
 after_success:
-  - echo "after_success"
-  - if [ "$TRAVIS_SECURE_ENV_VARS" == true ]; then source devtools/travis-ci/after_success.sh; fi
+  - codecov

devtools/conda-recipe/meta.yaml

@@ -23,10 +23,10 @@ requirements:
     - numexpr
     - autograd
     - pymbar
-    - openmm >=7.3.1
+    - openmm >=7.4.0
     - parmed
     - openmoltools
-    - openmmtools
+    - openmmtools >=0.18.1
     - numba
     - netcdf4
     - matplotlib
@@ -40,8 +40,10 @@ requirements:
     - distributed
     - progressbar2
     - yank
-    - parmed
+    - ambermini
+    - tinydb
     - tqdm
+    - nose
 
 about:
   home: https://github.com/choderalab/perses

devtools/travis-ci/install.sh

@@ -25,6 +25,7 @@ bash $MINICONDA -b -p $MINICONDA_HOME
 # Configure miniconda
 export PIP_ARGS="-U"
 export PATH=$MINICONDA_HOME/bin:$PATH
+conda config --add channels omnia
 conda config --add channels conda-forge
 conda config --set always_yes yes
 conda install conda conda-build jinja2 anaconda-client

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - numexpr
   - autograd
   - pymbar
-  - openmm >=7.3.1
+  - openmm >=7.4.0
   - openmoltools # may need to sort out ambermini/ambertools/parmed dependencies (we don't want ambertools)
   - openmmtools # may need to sort out ambermini/ambertools/parmed dependencies
   - numba

perses/bias/bias_engine.py

@@ -98,6 +98,7 @@ def _create_implicit_solvent_openmm(self, mol):
         positions : np.array, Quantity nm
            array of atomic positions
         """
+        # TODO: Replace this with a SystemGenerator
         molecule_name = oeiupac.OECreateIUPACName(mol)
         openmoltools.openeye.enter_temp_directory()
         _ , tripos_mol2_filename = openmoltools.openeye.molecule_to_mol2(mol, tripos_mol2_filename=molecule_name + '.tripos.mol2', conformer=0, residue_name='MOL')

perses/constants.py

@@ -0,0 +1,6 @@
+################################################################################
+# CONSTANTS
+################################################################################
+
+from openeye import oechem
+OESMILES_OPTIONS = oechem.OESMILESFlag_DEFAULT | oechem.OESMILESFlag_ISOMERIC