def beta_scission_ts_geometry(rxn, rct_geos,
max_dist_err=2e-1, log=False):
""" geometry for a beta scission transition state
:param rxn: a Reaction object
:param rct_geos: the reactant geometries
"""
assert rxn.class_ == ReactionClass.Typ.BETA_SCISSION
assert rxn.has_standard_keys()
brk_bnd_key, = ts.breaking_bond_keys(rxn.forward_ts_graph)
brk_bnd_dist = 1.5
dist_dct = automol.geom.ts.distances(rct_geos, angstrom=True)
dist_dct[brk_bnd_key] = brk_bnd_dist
gra = ts.reactants_graph(rxn.forward_ts_graph)
dist_range_dct = automol.graph.embed.distance_ranges_from_coordinates(
gra, dist_dct, angstrom=True)
geo_init, = rct_geos
relax_ang = False
relax_tors = False
geo = _geometry_from_info(
gra, rct_geos, geo_init, dist_range_dct,
relax_ang=relax_ang, relax_tors=relax_tors,
max_dist_err=max_dist_err, log=log)
return geo
def ring_forming_scission_ts_geometry(rxn, rct_geos,
max_dist_err=2e-1, log=False):
""" geometry for a ring-forming scission transition state
:param rxn: a Reaction object
:param rct_geos: the reactant geometries
"""
assert rxn.class_ == ReactionClass.Typ.RING_FORM_SCISSION
assert rxn.has_standard_keys()
frm_bnd_key, = ts.forming_bond_keys(rxn.forward_ts_graph)
brk_bnd_key, = ts.breaking_bond_keys(rxn.forward_ts_graph)
frm_bnd_dist = 2.0
brk_bnd_dist = 1.5
d1234 = 180.
dist_dct = automol.geom.ts.distances(rct_geos, angstrom=True)
dist_dct[frm_bnd_key] = frm_bnd_dist
dist_dct[brk_bnd_key] = brk_bnd_dist
# Note that this will not set the angle to exactly 180, because we don't
# yet know the 1-3 and 2-4 distances.
chain_keys = ring_forming_scission_chain(rxn)
key1, key2, key3, key4 = chain_keys[:4]
dih_dct = {(key1, key2, key3, key4): (d1234, None)}
gra = ts.reactants_graph(rxn.forward_ts_graph)
dist_range_dct = automol.graph.embed.distance_ranges_from_coordinates(
gra, dist_dct, dih_dct=dih_dct, degree=True, angstrom=True)
geo_init, = rct_geos
relax_ang = True
relax_tors = True
geo = _geometry_from_info(
gra, rct_geos, geo_init, dist_range_dct,
relax_ang=relax_ang, relax_tors=relax_tors,
max_dist_err=max_dist_err, log=log)
# Rerun the optimization, enforcing planarity on the ring
dist_dct = automol.geom.ts.distances([geo], angstrom=True)
dist_dct[frm_bnd_key] = frm_bnd_dist
dist_dct[brk_bnd_key] = brk_bnd_dist
pla_dct = {}
for key1, key2, key3, key4 in mit.windowed(chain_keys, 4):
pla_dct[(key1, key2, key3, key4)] = (0.0, 0.0)
gra = ts.reactants_graph(rxn.forward_ts_graph)
dist_range_dct = automol.graph.embed.distance_ranges_from_coordinates(
gra, dist_dct, degree=True, angstrom=True)
geo = _geometry_from_info(
gra, [geo], geo, dist_range_dct,
relax_ang=relax_ang, relax_tors=relax_tors,
pla_dct=pla_dct,
max_dist_err=max_dist_err, log=log)
return geo
def breaking_bond_keys(rxn, rev=False):
""" Obtain breaking bonds for the reaction.
:param rxn: the reaction object
:type rxn: Reaction
:param rev: parameter to toggle reaction direction
:type rev: bool
:rtype: frozenset[frozenset[int]]
"""
if rev:
tsg = rxn.backward_ts_graph
else:
tsg = rxn.forward_ts_graph
return ts.breaking_bond_keys(tsg)