def insertion_scan_coordinate(rxn, zma):
""" Obtain the scan coordinate for an insertion
:param rxn: a Reaction object
:returns: the name of the scan coordinate in the z-matrix
:rtype: str
"""
frm_bnd_key, _ = insertion_forming_bond_keys(rxn)
scan_name = automol.zmat.distance_coordinate_name(zma, *frm_bnd_key)
return scan_name
def insertion_ts_zmatrix(rxn, ts_geo):
""" z-matrix for an insertion transition state geometry
:param rxn: a Reaction object
:param ts_geo: a transition state geometry
"""
rxn = rxn.copy()
rxn.forward_ts_graph = rxn.forward_ts_graph
# 1. Get keys to linear or near-linear atoms
lin_idxs = list(automol.geom.linear_atoms(ts_geo))
# 2. Add dummy atoms over the linear atoms
rcts_gra = ts.reactants_graph(rxn.forward_ts_graph)
geo, dummy_key_dct = automol.geom.insert_dummies_on_linear_atoms(
ts_geo, lin_idxs=lin_idxs, gra=rcts_gra)
# 3. Add dummy atoms to the Reaction object as well
rxn = add_dummy_atoms(rxn, dummy_key_dct)
# 4. Generate a z-matrix for the geometry
rng_keys, = ts.forming_rings_atom_keys(rxn.forward_ts_graph)
brk_bnd_key, = ts.breaking_bond_keys(rxn.forward_ts_graph)
# Drop one of the forming bonds from the z-matrix by sorting the ring atom
# keys to exclude it. If one of the forming bonds intersects with the
# breaking bond, choose that one.
_, frm_bnd_key = insertion_forming_bond_keys(rxn)
# Cycle the ring keys such that the atom closest to the breaking bond is
# the beginning of the ring and the other atom is the end
if frm_bnd_key & brk_bnd_key:
key1, = frm_bnd_key & brk_bnd_key
key2, = frm_bnd_key - brk_bnd_key
else:
path = automol.graph.shortest_path_between_groups(
rxn.forward_ts_graph, frm_bnd_key, brk_bnd_key)
key2, = frm_bnd_key - set(path)
rng_keys = automol.graph.cycle_ring_atom_key_to_front(rng_keys,
key1,
end_key=key2)
vma, zma_keys = automol.graph.vmat.vmatrix(rxn.forward_ts_graph,
rng_keys=rng_keys)
zma_geo = automol.geom.from_subset(geo, zma_keys)
zma = automol.zmat.from_geometry(vma, zma_geo)
return zma, zma_keys, dummy_key_dct
