def test_write():
zmat = Topology.open(cwd + '/files/Im11.zmat')
tmp = os.path.join(tmpdir, 'zmat-out.xyz')
zmat.write(tmp)
assert filecmp.cmp(tmp, cwd + '/files/baselines/zmat-out.xyz')
mol = Molecule.from_smiles('C[n+]1cn(cc1)CCCC[B-](F)(F)F')
top = Topology([mol])
tmp = os.path.join(tmpdir, 'smi-out.xyz')
top.write(tmp)
filecmp.cmp(tmp, cwd + '/files/baselines/smi-out.xyz')
def test_write_swm4():
ff = ForceField.open(cwd + '/../forcefield/files/SWM4-NDP.zfp')
mol = Topology.open(cwd + '/files/TIP3P.zmat').molecules[0]
mol.generate_virtual_sites(ff)
mol.generate_drude_particles(ff)
mol.assign_charge_from_ff(ff)
top = Topology([mol], numbers=[10])
tmp = os.path.join(tmpdir, 'swm4-out.psf')
top.write(tmp)
assert filecmp.cmp(tmp, cwd + '/files/baselines/swm4-out.psf')
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.input)
if args.ignore != []:
molecules = [mol for mol in top.molecules if mol.name not in args.ignore]
top = Topology(molecules)
print('Topology info: ', top.n_atom, 'atoms;', top.n_molecule, 'molecules')
if args.qscale != 1:
for atom in top.atoms:
if atom.type in args.qscaleignoreatom or atom.molecule.name in args.qscaleignore:
continue
atom.charge *= args.qscale
box = [
args.box[k] if args.box[k] != -1 else top.cell.size[k] for k in range(3)
]
top.cell.set_box(box)
if top.has_position and set(args.shift) != {0}:
for atom in top.atoms:
atom.position += args.shift
top.write(args.output)
