def do(self):
# Get the molecular graph of the molecule in the selection
parent = context.application.cache.node
graph = create_molecular_graph([parent], parent)
if graph.molecule.size == 0:
raise UserError("Could not get molecular graph.", "Make sure that the selected frame contains a molecule.")
# Guessed and original geometry
opt_coords = tune_geometry(graph, graph.molecule).coordinates
org_coords = graph.molecule.coordinates
coords_to_zeobuilder(org_coords, opt_coords, graph.molecule.atoms, parent)
def test_example_periodic(self):
mol = Molecule.from_file("input/caplayer.cml")
unit_cell = UnitCell(
numpy.array([
[14.218, 7.109, 0.0],
[ 0.0 , 12.313, 0.0],
[ 0.0 , 0.0 , 10.0],
])*angstrom,
numpy.array([True, True, False]),
)
dm = mol.distance_matrix
dm = dm + dm.max()*numpy.identity(len(dm))
mol = tune_geometry(mol.graph, mol, unit_cell)
mol.write_to_file("output/caplayer.xyz")
def test_tune_geometry(self):
for input_mol in self.iter_molecules(allow_multi=False):
output_mol = tune_geometry(input_mol.graph, input_mol)
output_mol.title = input_mol.title
output_mol.write_to_file("output/tune_%s.xyz" % input_mol.title)
