def hydrogen_migration_constraint_coordinates(rxn, zma):
""" Obtain the constraint coordinates for a hydrogen migration
:param rxn: a Reaction object
:returns: the names of the constraint coordinates in the z-matrix
:rtype: tuple[str]
"""
att_key, _, _, ngb_key = hydrogen_migration_atom_keys(rxn)
dist_name = automol.zmat.distance_coordinate_name(zma, att_key, ngb_key)
return (dist_name, )
def hydrogen_migration_ts_zmatrix(rxn, ts_geo):
""" z-matrix for a hydrogen migration transition state geometry
:param rxn: a Reaction object
:param ts_geo: a transition state geometry
"""
rxn = rxn.copy()
# 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
# Start the z-matrix from the forming bond ring
rng_keys, = ts.forming_rings_atom_keys(rxn.forward_ts_graph)
_, hyd_key, don_key, _ = hydrogen_migration_atom_keys(rxn)
# Cycle the migrating h to the front of the ring keys and, if
# needed, reverse the ring so that the donating atom is last:
# (migrating h atom, attacking atom, ... , donating atom)
# This ensures that the forming bond coordinate is included in the z-matrix
# and drops the breaking bond coordinate from the z-matrix.
rng_keys = automol.graph.cycle_ring_atom_key_to_front(rng_keys,
hyd_key,
end_key=don_key)
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