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)
