Merge pull request #26 from choderalab/travis

Add travis continuous integration

.travis.yml

@@ -0,0 +1,55 @@
+language: c
+sudo: false
+
+branches:
+  only:
+    - master
+
+install:
+  - source devtools/travis-ci/install.sh
+  - export PYTHONUNBUFFERED=true
+  # Add org channel
+  - conda config --add channels ${ORGNAME}
+
+script:
+  # Create a test environment
+  - conda create --yes -n test python=$python
+  # Activate the test environment
+  - source activate test
+  # Add conda channels, using old priority scheme where most recent versions win
+  - conda config --set channel_priority false
+  - conda config --add channels conda-forge
+  - conda config --add channels omnia
+  - conda config --add channels https://conda.anaconda.org/omnia/label/dev
+  # Install extras for testing
+  - conda install --yes --quiet pip nose nose-timer
+  # Build the recipe
+  - echo "Building the recipe..."
+  - conda build devtools/conda-recipe
+  # Install the package
+  - echo "Installing the ${PACKAGENAME} package..."
+  - conda install --yes --use-local ${PACKAGENAME}
+  # Test the openmmforcefields package to make sure installed ffxml files are working
+  - echo "Testing the installed openmmforcefields ffxml files..."
+  - cd devtools && nosetests ${PACKAGENAME}.tests.test_amber_import --nocapture --verbosity=2 --with-timer -a '!slow' && cd ..
+  # Test AMBER conversion
+  - conda install --yes --quiet parmed yaml  
+  - echo "Testing AMBER conversion..."
+  - cd amber && python convert_amber.py && cd ..
+  # Test CHARMM conversion
+  - echo "Testing CHARMM conversion..."
+  - cd charmm && python convert_charmm.py && cd ..
+
+os:
+  - osx
+  - linux
+
+env:
+  matrix:
+    - python=2.7  CONDA_PY=2.7
+    - python=3.5  CONDA_PY=3.5
+    - python=3.5  CONDA_PY=3.6
+
+  global:
+    - ORGNAME="omnia"
+    - PACKAGENAME="openmmforcefields"

LICENSE

@@ -1,6 +1,8 @@
 MIT License
 
-Copyright (c) 2016 Chodera lab // Memorial Sloan Kettering Cancer Center
+Copyright (c) 2016-2017 by
+    Chodera lab // Memorial Sloan Kettering Cancer Center
+    Pande group // Stanford University
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,2 +1,10 @@
-# openmm-forcefields
-CHARMM and AMBER forcefields for OpenMM
+[![Build Status](https://travis-ci.org/choderalab/openmm-forcefields.svg?branch=master)](https://travis-ci.org/choderalab/openmm-forcefields?branch=master)
+
+# CHARMM and AMBER forcefields for OpenMM
+
+Conversion tools for and repository of CHARMM and AMBER forcefields for OpenMM.
+
+## Manifest
+
+* `charmm/` - CHARMM forcefield conversion tools
+* `amber/` - AMBER forcefield conversion tools

amber/README.md

@@ -4,11 +4,11 @@
 
 **General**
 
-Script supports command line arguments, and so `python amber2omm.py -h`:
+Script supports command line arguments, and so `python convert_amber.py -h`:
 ```
-usage: amber2omm.py [-h] [--input INPUT] [--input-format INPUT_FORMAT]
-                    [--verbose] [--no-log] [--protein-test] [--nucleic-test]
-                    [--protein-ua-test] [--phospho-protein-test] [--gaff-test]
+usage: convert_amber.py [-h] [--input INPUT] [--input-format INPUT_FORMAT]
+                        [--verbose] [--no-log] [--protein-test] [--nucleic-test]
+                        [--protein-ua-test] [--phospho-protein-test] [--gaff-test]
 
 AMBER --> OpenMM forcefield conversion script
 
@@ -32,7 +32,7 @@ optional arguments:
                         test
 ```
 
-With the defaults as set, all you need to do is have the script and the `files/` directory and call `python amber2omm.py`. `-v` or `--no-log` as wanted.
+With the defaults as set, all you need to do is have the script and the `files/` directory and call `python convert_amber.py`. `-v` or `--no-log` as wanted.
 
 Output:
 * `ffxml/` with all output XMLs
@@ -158,14 +158,14 @@ An 'overloading' set: HFE +2, +3 and +4 ions for tip3p water.
 
 Should you want to provide a different YAML (shorter version, different completely, whatever you want), script will take it with:
 ```
-python amber2omm.py --input name_of_your_yaml.yaml
+python convert_amber.py --input name_of_your_yaml.yaml
 ```
 
 The outputs of any YAML will be written to `ffxml/`.
 
 You can also provide a leaprc of your choosing via:
 ```
-python amber2omm.py --input name_of_your_leaprc --input-format leaprc
+python convert_amber.py --input name_of_your_leaprc --input-format leaprc
 ```
 
 The output of any leaprc will be written to the `./`.

charmm/README.md

@@ -1,23 +1,22 @@
-This directory contains files and scripts needed to convert the CHARMM forcefield to ffxml files
+# CHARMM forcefield conversion tools for OpenMM
 
-## Manifest
-* ```toppar/``` - All files taken and unzipped from (http://mackerell.umaryland.edu/charmm_ff.html) Jan 2016.
-* ```ffxml/``` - charmm36 ffxml
-* ```charmm36.yaml``` - yaml file needed for convert_charmm.py script. Specifies files to include and exclude.
-* ```convert_charmm.py``` - script to convert charmm top and par files to ffxml.
-
-### Dependencies
-* ParmEd
+This directory contains files and scripts needed to convert the CHARMM forcefield to OpenMM `ffxml` files
 
----
-
-Notes on files that were excluded from conversion.
+## Manifest
+* `toppar/` - CHARMM36 `toppar` files taken and unzipped from (http://mackerell.umaryland.edu/charmm_ff.html) Jan 2016.
+* `ffxml/` - converted OpenMM `ffxml` files for CHARMM36
+* `charmm36.yaml` - yaml input file needed to drive bundling by `convert_charmm.py`
+* `convert_charmm.py` - script to convert CHARMM `top` and `par` files to `ffxml`
 
-There are two glycolipid stream files with duplicate dihedrals with different values. According to discussion with
-Alex MacKerell, the carb glycolipid file should be used so the lipid glycolipid stream file was excluded.
+## Dependencies
+* [`ParmEd`](https://github.com/parmed/parmed) - for parameter/topology conversion
 
-```toppar_all36_prot_aldehydes.str``` and ```toppar_all36_na_modifications.str``` have different values for the angle of
-atom types O CD CT2. These files should not be used in the same system so both were excluded. A new atom type is needed
-to correct this. If  needed, CGenFF can be used for aldehydes or the user can convert these files at their own risk.
+## Notes
 
+Notes on files that were excluded from conversion:
 
+* There are two glycolipid stream files with duplicate dihedrals with different values.
+According to discussion with Alex MacKerell, the carb glycolipid file should be used so the lipid glycolipid stream file was excluded.
+* `toppar_all36_prot_aldehydes.str` and `toppar_all36_na_modifications.str` have different values for the angle of atom types O CD CT2.
+These files should not be used in the same system so both were excluded.  A new atom type is needed to correct this.
+If needed, [CGenFF](https://cgenff.paramchem.org/) can be used for aldehydes or the user can convert these files at their own risk.

charmm/convert_charmm.py

@@ -37,7 +37,7 @@
     source.append(OrderedDict())
     source[-1]['Source'] = fi
     md5 = hashlib.md5()
-    with open(fi) as f:
+    with open(fi, 'rb') as f:
         md5.update(f.read())
     md5 = md5.hexdigest()
     source[-1]['md5hash'] = md5
@@ -64,5 +64,3 @@
 params = CharmmParameterSet(*charmm_files)
 params_omm = openmm.OpenMMParameterSet.from_parameterset(params)
 params_omm.write('ffxml/charmm36.xml', provenance=provenance)
-
-