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() generator.GROMACSAtomtypes(topology.getAtomTypes(), settings) generator.GROMACSNonbonded(topology.getAtomTypes(), settings) for molecule in topology.getMolecules(): generator.GROMACSMoleculetype(molecule, settings) generator.GROMACSAtoms(molecule, settings) generator.GROMACSBonds(molecule.getBonds(), settings) generator.GROMACSAngles(molecule.getAngles(), settings) generator.GROMACSSystem(settings) generator.GROMACSMolecules(topology, settings)
def test_findAtomicDistances(self): atomic_distances = processor.findAtomicDistances(atom_list) for dist in range(0, len(atomic_distances)): self.assertAlmostEqual(atomic_distances[dist][0], distances[dist][0], 2) self.assertAlmostEqual(atomic_distances[dist][1], distances[dist][1], 2) self.assertAlmostEqual(atomic_distances[dist][2], distances[dist][2], 2)