Removed old build-only test.

tests/test_build.py

-
-import pdbfixer
-import simtk.openmm 
-import Bio.PDB
-
-import os
-import sys
-import numpy
-
-def test_build():
-    # These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm
-    build_pdbcodes = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ'] # structures to be built 
-    simulate_pdbcodes = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ'] # structures to be simulated
-
-    # Set up PDB retrieval.
-    from Bio.PDB import PDBList
-    pdblist = PDBList(server=PDBList.alternative_download_url)
-
-    success = True
-
-    for pdbcode in pdbcodes:
-        print pdbcode
-
-        try:
-            print "Attempting to retrieve PDB code '%s' from %s..." % (pdbcode, PDBList.alternative_download_url)
-            input_pdb_filename = pdblist.retrieve_pdb_file(pdbcode, pdir='.')
-        except Exception as e:
-            print str(e)
-            print "Could not download PDB code '%s'" % pdbcode
-            continue
-
-        output_pdb_filename = 'output.pdb'
-
-        # PDB setup parameters.
-        # TODO: Try several combinations?
-        from simtk import unit
-        pH = 7.0
-        ionic = 50.0 * unit.millimolar
-        box = 10.0 * unit.angstrom
-        positiveIon = 'Na+'
-        negativeIon = 'Cl-'
-
-        infile = open(input_pdb_filename)
-        outfile = open(output_pdb_filename, 'w')
-
-        try:
-            from pdbfixer.pdbfixer import PDBFixer, PdbStructure
-            from simtk.openmm import app
-            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)
-            success = False
-
-    if not success:
-        raise Exception("build test failed on one or more PDB files.")
-
-if __name__ == '__main__':
-    test_build()