settings = parser.parseSettings(settings_file) except FileNotFoundError: print("No input file found! See program documentation.") exit() input_files = settings.getInputFiles() topology = top.Topology() # Loop over molecules to process for input_file in range(0, len(input_files)): input_extension = settings.getInputType(input_file) output_extension = settings.getOutputType() # Call appropriate input parser if input_extension == 'pdb': new_molecule = parser.parsePDB(input_files[input_file]) topology.addMolecule(new_molecule) elif input_extension == 'gro': parser.parseGRO(input_file) else: print("File extension not supported.") exit() # Process topology topology = processor.findAtomicDistances(topology) topology = processor.findBonds(topology, settings) topology = processor.findAngles(topology, settings) # Call appropriate output generator if output_extension == 'top': generator.GROMACSDefaults()
def test_parsePDB(self): parsed_pdb = parser.parsePDB('water.pdb') for atom in range(0, len(parsed_pdb)): self.assertEqual(parsed_pdb[atom].x, atom_list[atom].x)