def elimination_ts_geometry(rxn, rct_geos,
max_dist_err=2e-1, log=False):
""" geometry for an elimination transition state
:param rxn: a Reaction object
:param rct_geos: the reactant geometries
"""
assert rxn.class_ == ReactionClass.Typ.ELIMINATION
assert rxn.has_standard_keys()
frm_bnd_key, = ts.forming_bond_keys(rxn.forward_ts_graph)
frm_bnd_dist = 1.6
frm_rng_keys, = ts.forming_rings_atom_keys(rxn.forward_ts_graph)
dist_dct = automol.geom.ts.distances(rct_geos, angstrom=True)
dist_dct[frm_bnd_key] = frm_bnd_dist
gra = ts.reactants_graph(rxn.forward_ts_graph)
dist_range_dct = automol.graph.embed.distance_ranges_from_coordinates(
gra, dist_dct, rings_keys=[frm_rng_keys], 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)
return geo
def hydrogen_migration_ts_geometry(rxn, rct_geos,
max_dist_err=2e-1, log=False):
""" geometry for a hydrogen migration transition state
:param rxn: a Reaction object
:param rct_geos: the reactant geometries
"""
assert rxn.class_ == par.ReactionClass.HYDROGEN_MIGRATION
assert rxn.has_standard_keys()
frm_bnd_key, = ts.forming_bond_keys(rxn.forward_ts_graph)
frm_bnd_dist = 1.7
dist_dct = automol.geom.ts.distances(rct_geos, angstrom=True)
dist_dct[frm_bnd_key] = frm_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 = 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)
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 insertion_ts_geometry(rxn, rct_geos,
max_dist_err=2e-1, log=False):
""" geometry for an insertion transition state
:param rxn: a Reaction object
:param rct_geos: the reactant geometries
"""
assert rxn.class_ == ReactionClass.Typ.INSERTION
assert rxn.has_standard_keys()
# set the formed bond distance based on the number of hydrogens
frm_bnd_dist_dct = {
0: 1.9,
1: 1.6,
2: 1.2,
}
tsg = rxn.forward_ts_graph
frm_bnd_key1, frm_bnd_key2 = ts.forming_bond_keys(tsg)
hcnt1 = automol.graph.atom_count_by_type(tsg, 'H', keys=frm_bnd_key1)
hcnt2 = automol.graph.atom_count_by_type(tsg, 'H', keys=frm_bnd_key2)
frm_bnd_dist1 = frm_bnd_dist_dct[hcnt1]
frm_bnd_dist2 = frm_bnd_dist_dct[hcnt2]
a123 = 170.
frm_rng_keys, = ts.forming_rings_atom_keys(tsg)
dist_dct = automol.geom.ts.distances(rct_geos, angstrom=True)
dist_dct[frm_bnd_key1] = frm_bnd_dist1
dist_dct[frm_bnd_key2] = frm_bnd_dist2
gra = ts.reactants_graph(tsg)
dist_range_dct = automol.graph.embed.distance_ranges_from_coordinates(
gra, dist_dct, rings_keys=[frm_rng_keys], angstrom=True)
# Join on the end without hydrogen, if there is one
if hcnt1 <= hcnt2:
key2, key3 = sorted(frm_bnd_key1)
else:
key2, key3 = sorted(frm_bnd_key2)
geo1, geo2 = rct_geos
geo_init = automol.geom.ts.join(geo1, geo2, key2=key2, key3=key3,
r23=frm_bnd_dist1, a123=a123)
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)
return geo
def forming_bond_keys(rxn, rev=False):
""" Obtain forming 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.forming_bond_keys(tsg)
def substitution_ts_geometry(rxn, rct_geos,
max_dist_err=2e-1, log=False):
""" geometry for a substitution transition state
:param rxn: a Reaction object
:param rct_geos: the reactant geometries
"""
assert rxn.class_ == ReactionClass.Typ.SUBSTITUTION
assert rxn.has_standard_keys()
# set the formed bond distance based on the number of hydrogens
frm_bnd_dist_dct = {
0: 1.9,
1: 1.6,
2: 1.2,
}
tsg = rxn.forward_ts_graph
a123 = 170.
a234 = 95.
frm_bnd_key, = ts.forming_bond_keys(tsg)
hcnt = automol.graph.atom_count_by_type(tsg, 'H', keys=frm_bnd_key)
frm_bnd_dist = frm_bnd_dist_dct[hcnt]
dist_dct = automol.geom.ts.distances(rct_geos, angstrom=True)
dist_dct[frm_bnd_key] = frm_bnd_dist
# key2 the hydrogen atom and key3 is the attacking atom; this is guaranteed
# to be true since the Reaction has been standardized
key2, key3 = sorted(frm_bnd_key)
ang_dct = {(None, key2, key3): a123, (key2, key3, None): a234}
gra = ts.reactants_graph(tsg)
dist_range_dct = automol.graph.embed.distance_ranges_from_coordinates(
gra, dist_dct, ang_dct=ang_dct, degree=True, angstrom=True)
geo1, geo2 = rct_geos
geo_init = automol.geom.ts.join(geo1, geo2, key2=key2, key3=key3,
r23=frm_bnd_dist, a123=a123, a234=a234)
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)
return geo
def addition_ts_geometry(rxn, rct_geos,
max_dist_err=2e-1, log=False):
""" geometry for an addition transition state
:param rxn: a Reaction object
:param rct_geos: the reactant geometries
"""
assert rxn.class_ == ReactionClass.Typ.ADDITION
assert rxn.has_standard_keys()
frm_bnd_key, = ts.forming_bond_keys(rxn.forward_ts_graph)
frm_bnd_dist = 1.9
a123 = 85.
a234 = 85.
d1234 = 85.
dist_dct = automol.geom.ts.distances(rct_geos, angstrom=True)
dist_dct[frm_bnd_key] = frm_bnd_dist
# key2 the hydrogen atom and key3 is the attacking atom; this is guaranteed
# to be true since the Reaction has been standardized
key2, key3 = sorted(frm_bnd_key)
ang_dct = {(None, key2, key3): a123, (key2, key3, None): a234}
dih_dct = {(None, key2, key3, None): d1234}
gra = ts.reactants_graph(rxn.forward_ts_graph)
dist_range_dct = automol.graph.embed.distance_ranges_from_coordinates(
gra, dist_dct, ang_dct=ang_dct, dih_dct=dih_dct, degree=True,
angstrom=True)
geo1, geo2 = rct_geos
geo_init = automol.geom.ts.join(geo1, geo2, key2=key2, key3=key3,
r23=frm_bnd_dist, a123=a123, a234=a234,
d1234=d1234)
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