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 = guess_geometry(graph).coordinates
org_coords = graph.molecule.coordinates
coords_to_zeobuilder(org_coords, opt_coords, graph.molecule.atoms, parent)
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
unitcell = context.application.model.universe.cell
unitcell_reciproke = context.application.model.universe.cell_reciproke
unitcell_active = context.application.model.universe.cell_active # not entirely sure where to set this in zeobuilder
opt_coords = guess_geometry(graph, unitcell_active, unitcell, unitcell_reciproke).coordinates
org_coords = graph.molecule.coordinates
coords_to_zeobuilder(org_coords, opt_coords, graph.molecule.atoms, parent, graph)
def test_guess_geometry(self):
for input_mol in self.iter_molecules(allow_multi=False):
output_mol = guess_geometry(input_mol.graph)
output_mol.title = input_mol.title
output_mol.write_to_file("output/guess_%s.xyz" % input_mol.title)
def test_guess_geometry(self):
for input_mol in self.iter_molecules(allow_multi=False):
output_mol = guess_geometry(input_mol.graph)
output_mol.title = input_mol.title
output_mol.write_to_file("output/guess_%s.xyz" % input_mol.title)
