def hydrogen_abstraction_linear_atom_keys(rxn, zma=None):
""" Obtain the linear atom keys for a hydrogen abstraction
:param rxn: a Reaction object
:param zma: a z-matrix; if passed in, the linear atoms will be determined
from this; otherwise they will be determined heuristically from the
reaction object
:returns: the keys of the linear atoms in the graph
:rtype: tuple[int]
"""
tsg = rxn.forward_ts_graph
if zma is not None:
lin_keys = list(automol.zmat.linear_atom_keys(zma))
else:
lin_keys = list(automol.graph.linear_atom_keys(tsg))
_, hyd_key, _ = hydrogen_abstraction_atom_keys(rxn)
lin_keys.append(hyd_key)
lin_keys = tuple(sorted(set(lin_keys)))
return lin_keys
def hydrogen_abstraction_ts_zmatrix(rxn, ts_geo):
""" z-matrix for a hydrogen abstraction 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))
# Add a dummy atom over the transferring hydrogen
att_key, hyd_key, _ = hydrogen_abstraction_atom_keys(rxn)
lin_idxs.append(hyd_key)
if hydrogen_abstraction_is_sigma(rxn):
if att_key not in lin_idxs:
lin_idxs.append(att_key)
lin_idxs = sorted(lin_idxs)
# 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
tsg = rxn.forward_ts_graph
rct1_keys, rct2_keys = rxn.reactants_keys
vma, zma_keys = automol.graph.vmat.vmatrix(tsg, rct1_keys)
vma, zma_keys = automol.graph.vmat.continue_vmatrix(
tsg, rct2_keys, vma, zma_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