def test_compress():
top = Topology.open(cwd + '/files/10-H2O-5-C3H6.lmp', improper_center=3)
molecules = top.molecules
for mol in molecules[4:]:
for atom in mol.atoms:
atom.charge *= 2
top = Topology.open(cwd + '/files/Im11.zmat')
molecules += top.molecules
top = Topology.open(cwd + '/files/10-H2O-5-C3H6.lmp', improper_center=3)
molecules += top.molecules
top = Topology.open(cwd + '/files/Im11.zmat')
molecules += top.molecules
top = Topology()
top.update_molecules(molecules)
mols_unique = top.get_unique_molecules()
for mol, count in mols_unique.items():
print(str(mol), count)
assert list(mols_unique.values()) == [4, 6, 5, 1, 10, 5, 1]
if mol.n_atom > 1 and mol.n_bond == 0:
if mol.has_position:
logger.warning(f'{str(mol)} carries no bond. Guessing connectivity from FF')
mol.guess_connectivity_from_ff(ff, angle_tolerance=15, pbc='xyz', cell=top.cell)
else:
logger.warning(f'{str(mol)} carries no bond. Make sure the topology is correct')
if ff.is_polarizable:
mol.generate_drude_particles(ff)
if ff.has_virtual_site:
mol.generate_virtual_sites(ff)
mol.assign_mass_from_ff(ff)
mol.assign_charge_from_ff(ff)
if args.packmol:
top.update_molecules(list(mol_count.keys()))
top.scale_with_packmol(list(mol_count.values()))
sys.exit(0)
logger.info('Exporting ...')
top.update_molecules(list(mol_count.keys()), list(mol_count.values()))
if args.trj is None:
logger.warning('Trajectory file not provided. '
'Will use positions and cell from the topology')
else:
_positions_set = False
if len(frame.positions) == top.n_atom:
top.set_positions(frame.positions)
_positions_set = True
type=float,
help='overwrite the box dimensions')
parser.add_argument('--shift',
nargs=3,
default=[0, 0, 0],
type=float,
help='shift the positions of all atoms')
args = parser.parse_args()
top = Topology.open(args.topology)
if args.topignore != []:
molecules = [
mol for mol in top.molecules if mol.name not in args.topignore
]
top = Topology()
top.update_molecules(molecules)
print('Topology info: ', top.n_atom, 'atoms;', top.n_molecule, 'molecules')
trj = Trajectory.open(args.input)
print('Trajectory info: ', trj.n_atom, 'atoms;', trj.n_frame, 'frames')
if (top.n_atom != trj.n_atom):
raise Exception(
'Number of atoms in topology and trajectory files do not match')
trj_out = Trajectory.open(args.output, 'w')
if args.ignore != []:
subset = [
atom.id for atom in top.atoms if atom.type not in args.ignoreatom
and atom.molecule.name not in args.ignore
]