Added draft .travis.yml

.travis.yml

+language: python
+python:
+  - "2.7"
+install:
+    - sudo apt-get update -qq
+    - sudo apt-get install -qq python-dev python-pip python-yaml g++
+    - sudo pip install conda
+    - sudo conda init
+    - conda config --add channels http://conda.binstar.org/rmcgibbo
+    - conda create --yes --name test numpy scipy biopython pyflakes openmm
+    
+script:
+    - python setup.py install
+    - nosetests tests/test_build.py
+    - nosetests tests/test_simulate.py
+
+after_script:
+    - pyflakes pdbfixer/*.py
+

tests/test_build.py

+from Bio.PDB import PDBList
+from simtk import unit
+from pdbfixer.pdbfixer import *
+import os
+import sys
+
+pdbcodes = ['1PGB', '1VII']
+
+for pdbcode in pdbcodes:
+    pdblist = PDBList()
+    input_pdb_filename = pdblist.retrieve_pdb_file(pdbcode, pdir='.')
+    output_pdb_filename = 'output.pdb'
+
+    pH = 7.0
+    ionic = 50.0 * unit.millimolar
+    box = 10.0 * unit.angstrom
+    positiveIon = 'Na+'
+    negativeIon = 'Cl-'
+
+    print "Running PDBFixer..."
+    infile = open(input_pdb_filename)
+    outfile = open(output_pdb_filename, 'w')
+
+    try:
+        fixer = PDBFixer(PdbStructure(infile))
+        fixer.findMissingResidues()
+        fixer.findNonstandardResidues()
+        fixer.replaceNonstandardResidues()
+        fixer.findMissingAtoms()
+        fixer.addMissingAtoms()
+        fixer.removeHeterogens(False)
+        fixer.addMissingHydrogens(pH)
+        #fixer.addSolvent(box*unit.nanometer, positiveIon, negativeIon, ionic*unit.molar)
+        app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
+        infile.close()
+        outfile.close()
+
+        # Delete input file.
+        os.remove(input_pdb_filename)
+        os.remove(output_pdb_filename)
+
+    except Exception as e:
+        print str(e)
+        sys.exit(1)
+
+
+# Signal success.
+sys.exit(0)
+
+    

tests/test_simulate.py

+from Bio.PDB import PDBList
+from simtk import unit
+from pdbfixer.pdbfixer import *
+import os
+import sys
+
+pdbcodes = ['1PGB', '1VII']
+
+for pdbcode in pdbcodes:
+    pdblist = PDBList()
+    input_pdb_filename = pdblist.retrieve_pdb_file(pdbcode, pdir='.')
+    output_pdb_filename = 'output.pdb'
+
+    pH = 7.0
+    ionic = 50.0 * unit.millimolar
+    box = 10.0 * unit.angstrom
+    positiveIon = 'Na+'
+    negativeIon = 'Cl-'
+
+    print "Running PDBFixer..."
+    infile = open(input_pdb_filename)
+    outfile = open(output_pdb_filename, 'w')
+
+    try:
+        fixer = PDBFixer(PdbStructure(infile))
+        fixer.findMissingResidues()
+        fixer.findNonstandardResidues()
+        fixer.replaceNonstandardResidues()
+        fixer.findMissingAtoms()
+        fixer.addMissingAtoms()
+        fixer.removeHeterogens(False)
+        fixer.addMissingHydrogens(pH)
+        #fixer.addSolvent(box*unit.nanometer, positiveIon, negativeIon, ionic*unit.molar)
+        app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
+        infile.close()
+        outfile.close()
+
+        # Delete input file.
+        os.remove(input_pdb_filename)
+        os.remove(output_pdb_filename)
+
+    except Exception as e:
+        print str(e)
+        sys.exit(1)
+
+
+# Signal success.
+sys.exit(0)
+
+