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)
