def insertion(rct_zmas, prd_zmas, tras):
""" z-matrix for an insertion reaction
"""
ret = {}
dist_name = 'rts'
dist_val = 3.
tra = tras[0]
frm_bnd_keys, _ = automol.graph.trans.formed_bond_keys(tra)
# get the atom on react 1 that is being attacked (bond is forming)
rct1_atm1_key = list(frm_bnd_keys)[0]
# figure out atoms in the chain to define the dummy atom
_, rct2_gra = map(rct_gras.__getitem__, rct_idxs)
rct1_zma, rct2_zma = map(rct_zmas.__getitem__, rct_idxs)
rct1_natms = automol.zmatrix.count(rct1_zma)
rct2_natms = automol.zmatrix.count(rct2_zma)
rct1_atm2_key, rct1_atm3_key, _ = join_atom_keys(rct1_zma, rct1_atm1_key)
# Join the reactant zmas to build the TS zma
x_atm_key = rct1_natms
rct1_x_zma = rct1_x_join(rct1_zma, rct1_atm1_key, rct1_atm2_key,
rct1_atm3_key)
ts_zma = rct1x_rct2_join(rct1_x_zma,
rct2_zma,
dist_name,
dist_val,
rct1_atm1_key,
x_atm_key,
rct1_atm2_key,
join_vals=(85., 85., 170., 85., 170.))
ts_name_dct = automol.zmatrix.standard_names(ts_zma)
dist_name = ts_name_dct[dist_name]
ts_zma = automol.zmatrix.standard_form(ts_zma)
# Generate constraints
# tors_keys = constbuild.bimol()
# CHECK IF THE INSERTION MESSES WITH THE TORSION ASSIGNMENTS
# Shift the TS bond keys
frm_bnd_keys = shift_vals_from_dummy(frm_bnd_keys, ts_zma)
brk_bnd_keys = shift_vals_from_dummy(brk_bnd_keys, ts_zma)
ret = {
'ts_zma': ts_zma,
'bnd_keys': (frm_bnd_keys, brk_bnd_keys),
'const_keys': (frozenset({}), frozenset({}), frozenset({}))
}
return ret
def beta_scission(rct_zmas, prd_zmas, tras):
""" z-matrix for a beta-scission reaction
"""
# Obtain frm and brk keys from arbtrary tras
tra = tras[0]
brk_bnd_keys, = automol.graph.trans.broken_bond_keys(tra)
_ = prd_zmas # Unneeded
# Obtain the TS ZMA
ts_zma, = rct_zmas # wrong since rct_zmas is a lst
ts_zma = automol.zmatrix.standard_form(ts_zma)
brk_bnd_keys = shift_vals_from_dummy(brk_bnd_keys, ts_zma)
ret = {
'ts_zma': ts_zma,
'bnd_keys': (frozenset({}), brk_bnd_keys),
'const_keys': (frozenset({}), frozenset({}), frozenset({}))
}
return ret
def substitution(rct_zmas, prd_zmas, tras):
""" z-matrix for a substitution reaction
Presume that radical substitutions at a pi bond occur instead as
a sequence of addition and elimination.
Also, for now presume that we are only interested in
radical molecule substitutions
"""
ret = None
# Set the name and value for the bond being formed
dist_name = 'rts'
dist_val = 3.
# first determine if this is a radical molecule reaction and then
# if the radical is the first species
# reorder to put it second
rad_cnt = 0
mol_cnt = 0
for idx, rct_zma in enumerate(rct_zmas):
rad_keys = automol.graph.resonance_dominant_radical_atom_keys(
automol.geom.graph(automol.zmatrix.geometry(rct_zma)))
ich = automol.geom.inchi(automol.zmatrix.geometry(rct_zma))
is_co = (ich == 'InChI=1S/CO/c1-2')
if rad_keys and not is_co:
rad_idx = idx
rad_cnt += 1
else:
# mol_idx = idx
mol_cnt += 1
# prolly should try the rearranging earlier
# if rad_cnt == 1 and mol_cnt == 1:
# if rad_idx == 0:
# rct2_zma, rct1_zma = rct_zmas
# rct_zmas = [rct1_zma, rct2_zma]
# # Confirm the reaction type and build the appropriate Z-Matrix
# rct2_gra = automol.zmatrix.graph(rct_zmas[1], remove_stereo=True)
# rad_atm_keys = automol.graph.resonance_dominant_radical_atom_keys(
# rct2_gra)
# if 0 not in rad_atm_keys:
# rct_zmas[1] = reorder_zma_for_radicals(
# rct_zmas[1], min(rad_atm_keys))
# rct2_gra = automol.zmatrix.graph(rct_zmas[1], remove_stereo=True)
# rad_atm_keys = automol.graph.resonance_dominant_radical_atom_keys(
# rct2_gra)
# # following assert checks to ensure that
# # the first atom in the second reactant is a radical
# # this is required for the remainder of the routine
# assert 0 in rad_atm_keys
# rct_zmas, rct_gras = shifted_standard_zmas_graphs(
# rct_zmas, remove_stereo=True)
# prd_zmas, prd_gras = shifted_standard_zmas_graphs(
# prd_zmas, remove_stereo=True)
# rcts_gra = functools.reduce(automol.graph.union, rct_gras)
# prds_gra = functools.reduce(automol.graph.union, prd_gras)
# tras, rct_idxs, _ = automol.graph.reac.substitution(rcts_gra, prds_gra)
tra = tras[0]
frm_bnd_keys, = automol.graph.trans.formed_bond_keys(tra)
brk_bnd_keys, = automol.graph.trans.broken_bond_keys(tra)
rct1_zma, rct2_zma = rct_zmas
# get the atom on react 1 that is being attacked (bond is forming)
rct1_atm1_key = list(frm_bnd_keys)[0]
# rct1_zma, rct2_zma = map(rct_zmas.__getitem__, rct_idxs)
# _, rct2_gra = map(rct_gras.__getitem__, rct_idxs)
rct1_natms = automol.zmatrix.count(rct1_zma)
rct2_natms = automol.zmatrix.count(rct2_zma)
# figure out atoms in the chain to define the dummy atom
rct1_atm2_key, rct1_atm3_key, _ = join_atom_keys(rct1_zma, rct1_atm1_key)
# Join the reactant zmas to build the TS zma
x_atm_key = rct1_natms
rct1_x_zma = rct1_x_join(rct1_zma, rct1_atm1_key, rct1_atm2_key,
rct1_atm3_key)
ts_zma = rct1x_rct2_join(rct1_x_zma,
rct2_zma,
dist_name,
dist_val,
rct1_atm1_key,
x_atm_key,
rct1_atm2_key,
join_vals=(85., 85., 170., 85., 85.))
# Get the names of the coordinates of the breaking and forming bond
ts_name_dct = automol.zmatrix.standard_names(ts_zma)
form_dist_name = ts_name_dct[dist_name]
# Get the torsional coordinates of the transition state
ts_zma = automol.zmatrix.standard_form(ts_zma)
# tors_keys = constbuild.bimol()
# Shift the TS bond keys
frm_bnd_keys = shift_vals_from_dummy(frm_bnd_keys, ts_zma)
brk_bnd_keys = shift_vals_from_dummy(brk_bnd_keys, ts_zma)
ret = {
'ts_zma': ts_zma,
'bnd_keys': (frm_bnd_keys, brk_bnd_keys),
'const_keys': (frozenset({}), frozenset({}), frozenset({}))
}
return ret
def _hydrogen_abstraction(rct_zmas, prd_zmas, tras):
""" standard hydrogen abstraction
"""
ret = None
dist_name = 'rts'
dist_val = 3.
# Deal with nasty cases which ruin the ordering
rct2_gra = automol.zmatrix.graph(rct_zmas[1], remove_stereo=True)
rad_atm_keys = automol.graph.resonance_dominant_radical_atom_keys(rct2_gra)
# fix for O2 which is recognized as a radical
# in the long run it would be better to put then in the
# resonance_dominant_radical_atom_keys function
if not rad_atm_keys:
ich = automol.graph.inchi(rct2_gra)
if ich == 'InChI=1S/O2/c1-2':
rad_atm_keys = [0]
return None
# hno2 hack
# rad_atm_keys = [0]
if 0 not in rad_atm_keys:
rct_zmas[1] = reorder_zma_for_radicals(rct_zmas[1], min(rad_atm_keys))
rct2_gra = automol.zmatrix.graph(rct_zmas[1], remove_stereo=True)
rad_atm_keys = automol.graph.resonance_dominant_radical_atom_keys(
rct2_gra)
# following assert checks to ensure that the first atom
# in the second reactant is a radical
# this is required for the remainder of the routine
assert 0 in rad_atm_keys
# Shift Graph now?
rct_zmas, rct_gras = shifted_standard_zmas_graphs(rct_zmas,
remove_stereo=True)
prd_zmas, prd_gras = shifted_standard_zmas_graphs(prd_zmas,
remove_stereo=True)
# fix to put radical atom first
# ultimately need to fix this for multiple radical centers
# end of fix
tra = tras[0]
rct1_gra, rct2_gra = rct_gras
rct1_zma, rct2_zma = rct_zmas
rct1_natms = automol.zmatrix.count(rct1_zma)
frm_bnd_keys, = automol.graph.trans.formed_bond_keys(tra)
brk_bnd_keys, = automol.graph.trans.broken_bond_keys(tra)
rct2_atm1_key = _xor(frm_bnd_keys, brk_bnd_keys)
if not rct2_atm1_key == rct1_natms:
rct2_gra = automol.graph.move_idx_to_top(rct2_gra, rct2_atm1_key,
rct1_natms)
rct2_zma = automol.geom.zmatrix(automol.graph.geometry(rct2_gra))
rct_zmas = [rct1_zma, rct2_zma]
rct_zmas, _ = shifted_standard_zmas_graphs(rct_zmas,
remove_stereo=True)
_, rct2_zma = rct_zmas
new_bnd_key = []
for key in frm_bnd_keys:
if key == rct2_atm1_key:
key = rct1_natms
new_bnd_key.append(key)
frm_bnd_keys = frozenset(new_bnd_key)
rct_gras = (rct1_gra, rct2_gra)
rct1_atm1_key = next(iter(frm_bnd_keys & brk_bnd_keys))
# if rct1 and rct2 are isomorphic, we may get an atom key on rct2.
# in that case, determine the equivalent atom from rct1
if rct1_atm1_key in automol.graph.atom_keys(rct2_gra):
atm_key_dct = automol.graph.full_isomorphism(rct2_gra, rct1_gra)
assert atm_key_dct
rct1_atm1_key = atm_key_dct[rct1_atm1_key]
rct1_atm2_key, rct1_atm3_key, _ = join_atom_keys(rct1_zma, rct1_atm1_key)
# Join the reactant zmas to build the TS zma
x_atm_key = rct1_natms
rct1_x_zma = rct1_x_join(rct1_zma, rct1_atm1_key, rct1_atm2_key,
rct1_atm3_key)
ts_zma = rct1x_rct2_join(rct1_x_zma,
rct2_zma,
dist_name,
dist_val,
rct1_atm1_key,
x_atm_key,
rct1_atm2_key,
join_vals=(85., 85., 170., 85., 170.))
# Standardize the ZMA
ts_zma = automol.zmatrix.standard_form(ts_zma)
# Generate constraints
# tors_keys = constbuild.bimol()
# Shift the TS bond keys
frm_bnd_keys = shift_vals_from_dummy(frm_bnd_keys, ts_zma)
brk_bnd_keys = shift_vals_from_dummy(brk_bnd_keys, ts_zma)
ret = {
'ts_zma': ts_zma,
'bnd_keys': (frm_bnd_keys, brk_bnd_keys),
'const_keys': (frozenset({}), frozenset({}), frozenset({}))
}
return ret
def _sigma_hydrogen_abstraction(rct_zmas, prd_zmas):
print('323543534343422')
ret = None
dist_name = 'rts'
dist_val = 3.
# in the future, we can get the rxn_idxs directly from
# graph.reac.hydrogen_abstraction, because it returns them now
rxn_idxs = automol.formula.reac.argsort_hydrogen_abstraction(
list(map(automol.convert.zmatrix.formula, rct_zmas)),
list(map(automol.convert.zmatrix.formula, prd_zmas)))
if rxn_idxs is not None:
rct_idxs, prd_idxs = rxn_idxs
rct_zmas = list(map(rct_zmas.__getitem__, rct_idxs))
prd_zmas = list(map(prd_zmas.__getitem__, prd_idxs))
rct_zmas, rct_gras = shifted_standard_zmas_graphs(rct_zmas,
remove_stereo=True)
prd_zmas, prd_gras = shifted_standard_zmas_graphs(prd_zmas,
remove_stereo=True)
tras, _, _ = automol.graph.reac.hydrogen_abstraction(
rct_gras, prd_gras)
if tras:
tra = tras[0]
rct1_gra, rct2_gra = rct_gras
rct1_zma, rct2_zma = rct_zmas
rct1_natms = automol.zmatrix.count(rct1_zma)
rct2_natms = automol.zmatrix.count(rct2_zma)
frm_bnd_keys, = automol.graph.trans.formed_bond_keys(tra)
brk_bnd_keys, = automol.graph.trans.broken_bond_keys(tra)
rct1_atm1_key = next(iter(frm_bnd_keys & brk_bnd_keys))
rct2_atm1_key = next(iter(frm_bnd_keys - brk_bnd_keys))
# if rct1 and rct2 are isomorphic, we may get an atom key on rct2.
# in that case, determine the equivalent atom from rct1
if rct1_atm1_key in automol.graph.atom_keys(rct2_gra):
atm_key_dct = automol.graph.full_isomorphism(
rct2_gra, rct1_gra)
assert atm_key_dct
rct1_atm1_key = atm_key_dct[rct1_atm1_key]
rct1_atm2_key, rct1_atm3_key, _ = join_atom_keys(
rct1_zma, rct1_atm1_key)
x_zma = ((('X', (None, None, None), (None, None, None)), ), {})
x_join_val_dct = {
'rx': 1. * qcc.conversion_factor('angstrom', 'bohr'),
'ax': 90. * qcc.conversion_factor('degree', 'radian'),
'dx': 180. * qcc.conversion_factor('degree', 'radian'),
}
x_join_keys = numpy.array(
[[rct1_atm1_key, rct1_atm2_key, rct1_atm3_key]])
x_join_names = numpy.array([['rx', 'ax', 'dx']],
dtype=numpy.object_)
x_join_names[numpy.equal(x_join_keys, None)] = None
x_join_name_set = set(numpy.ravel(x_join_names)) - {None}
x_join_val_dct = {
name: x_join_val_dct[name]
for name in x_join_name_set
}
rct1_x_zma = automol.zmatrix.join(rct1_zma, x_zma, x_join_keys,
x_join_names, x_join_val_dct)
rct1_x_atm_key = rct1_natms
if rct2_atm1_key in automol.graph.atom_keys(rct1_gra):
atm_key_dct = automol.graph.full_isomorphism(
rct1_gra, rct2_gra)
assert atm_key_dct
rct2_atm1_key = atm_key_dct[rct2_atm1_key]
rct2_atm1_key -= rct1_natms
assert rct2_atm1_key == 0
# insert dummy atom as the second atom in reactant 2
insert_keys = numpy.array([[0, None, None], [None, 1, None],
[None, None, 2]])[:rct2_natms]
insert_names = numpy.array([['rx2', None,
None], [None, 'ax2', None],
[None, None, 'dx2']])[:rct2_natms]
insert_val_dct = {
'rx2': 1. * qcc.conversion_factor('angstrom', 'bohr'),
'ax2': 90. * qcc.conversion_factor('degree', 'radian'),
'dx2': 180. * qcc.conversion_factor('degree', 'radian'),
}
insert_name_set = set(numpy.ravel(insert_names)) - {None}
insert_val_dct = {
name: insert_val_dct[name]
for name in insert_name_set
}
rct2_x_zma = automol.zmatrix.insert_dummy_atom(
rct2_zma, 1, insert_keys, insert_names, insert_val_dct)
join_val_dct = {
dist_name: dist_val,
'aabs1': 85. * qcc.conversion_factor('degree', 'radian'),
'aabs2': 85. * qcc.conversion_factor('degree', 'radian'),
'babs1': 170. * qcc.conversion_factor('degree', 'radian'),
'babs2': 85. * qcc.conversion_factor('degree', 'radian'),
'babs3': 170. * qcc.conversion_factor('degree', 'radian'),
}
join_keys = numpy.array(
[[rct1_atm1_key, rct1_x_atm_key, rct1_atm2_key],
[None, rct1_atm1_key, rct1_x_atm_key],
[None, None, rct1_atm1_key]])[:rct2_natms + 1]
join_names = numpy.array([[dist_name, 'aabs1', 'babs1'],
[None, 'aabs2', 'babs2'],
[None, None, 'babs3']])[:rct2_natms + 1]
join_names[numpy.equal(join_keys, None)] = None
join_name_set = set(numpy.ravel(join_names)) - {None}
join_val_dct = {name: join_val_dct[name] for name in join_name_set}
ts_zma = automol.zmatrix.join(rct1_x_zma, rct2_x_zma, join_keys,
join_names, join_val_dct)
ts_name_dct = automol.zmatrix.standard_names(ts_zma)
dist_name = ts_name_dct[dist_name]
ts_zma = automol.zmatrix.standard_form(ts_zma)
rct1_tors_names = automol.zmatrix.torsion_coordinate_names(
rct1_zma)
rct2_tors_names = automol.zmatrix.torsion_coordinate_names(
rct2_zma)
tors_names = (
tuple(map(ts_name_dct.__getitem__, rct1_tors_names)) +
tuple(map(ts_name_dct.__getitem__, rct2_tors_names)))
if 'babs2' in ts_name_dct:
geo1 = automol.convert.zmatrix.geometry(rct1_zma)
if not automol.geom.is_linear(geo1):
tors_name = ts_name_dct['babs2']
tors_names += (tors_name, )
# babs3 should only be included if there is only group
# connected to the radical atom
include = include_babs3(frm_bnd_keys, rct2_gra)
if 'babs3' in ts_name_dct and include:
tors_name = ts_name_dct['babs3']
tors_names += (tors_name, )
frm_bnd_keys = shift_vals_from_dummy(frm_bnd_keys, ts_zma)
brk_bnd_keys = shift_vals_from_dummy(brk_bnd_keys, ts_zma)
# Build reactants graph
atom_keys2 = automol.graph.atom_keys(rct2_gra)
natom2 = len(atom_keys2)
atm_key_dct = dict(
zip(
atom_keys2,
(key + natom2 for key in atom_keys2),
))
new_rct2_gra = automol.graph.relabel(rct2_gra, atm_key_dct)
rcts_gra = automol.graph.union_from_sequence(
(rct1_gra, new_rct2_gra))
ret = (ts_zma, dist_name, frm_bnd_keys, brk_bnd_keys, tors_names,
rcts_gra)
return ret
def addition(rct_zmas, prd_zmas, tras):
""" z-matrix for an addition reaction
"""
dist_name = 'rts'
dist_val = 3.
# Old sort procedure (maybe move?)
count1 = automol.zmatrix.count(rct_zmas[0])
if len(rct_zmas) == 2:
count2 = automol.zmatrix.count(rct_zmas[1])
if count1 == 1 or count1 < count2:
rct2_zma, rct1_zma = rct_zmas
rct_zmas = [rct1_zma, rct2_zma]
rct1_zma, rct2_zma = rct_zmas
rct1_gra = automol.zmatrix.graph(rct1_zma)
rct2_gra = automol.zmatrix.graph(rct2_zma)
rct2_natms = automol.zmatrix.count(rct2_zma)
rct1_natms = automol.zmatrix.count(rct1_zma)
tra = tras[0]
frm_bnd_keyss, = automol.graph.trans.formed_bond_keys(tra)
rct1_atm1_key, rct2_atm_key = sorted(frm_bnd_keyss)
# Shift rct2_zma so that it's forming site is the first atom
if rct2_atm_key != rct1_natms:
rct2_geo = automol.zmatrix.geometry(rct2_zma)
rct2_geo = automol.geom.swap_coordinates(rct2_geo,
rct2_atm_key - rct1_natms, 0)
rct2_zma = automol.geom.zmatrix(rct2_geo)
rct_zmas, rct_gras = shifted_standard_zmas_graphs([rct1_zma, rct2_zma],
remove_stereo=True)
_, rct2_zma = rct_zmas
rct2_atm_key = rct1_natms
frm_bnd_keys = frozenset({rct1_atm1_key, rct2_atm_key})
# Replace old routine with new one based on unsaturated atoms
# Start of new routine
rct1_unsat_keys = automol.graph.unsaturated_atom_keys(rct1_gra)
# get neighbor keys for rct1_atm1_key
neighbor_dct = automol.graph.atom_neighbor_keys(rct1_gra)
atm1_nghbr_keys = neighbor_dct[rct1_atm1_key]
# shift keys for unsaturated atoms and for atm1_nghbr keys
# to include dummy atoms
# second atom key
# choose rct1_atm2 as first unsaturated neighbor to rct1_atm1
rct1_atm2_key = None
for key in atm1_nghbr_keys:
if key in rct1_unsat_keys:
rct1_atm2_key = key
break
# if no unsaturated neighbor, choose any atm1_nghbr
if rct1_atm2_key is None:
for key in atm1_nghbr_keys:
rct1_atm2_key = key
break
# third atom key
# if atm1 has two neighbors choose third atom key as second neighbor
rct1_atm3_key = []
for key in atm1_nghbr_keys:
if key != rct1_atm2_key:
rct1_atm3_key = key
break
# else choose it as second neighbor to atm 2
if not rct1_atm3_key:
atm2_nghbr_keys = neighbor_dct[rct1_atm2_key]
for key in atm2_nghbr_keys:
if key != rct1_atm1_key:
rct1_atm3_key = key
break
# check if rct1_atm1, rct1_atm2, rct1_atm3 are colinear
# if they are choose a dummy atom
rct1_geo = automol.zmatrix.geometry(rct1_zma)
if rct1_atm3_key:
rct1_sub_geo = (rct1_geo[rct1_atm1_key], rct1_geo[rct1_atm2_key],
rct1_geo[rct1_atm3_key])
else:
rct1_sub_geo = (rct1_geo[rct1_atm1_key], rct1_geo[rct1_atm2_key])
if automol.geom.is_linear(rct1_sub_geo) or not rct1_atm3_key:
# have to regenerate atm2_nghbr_keys to include dummy atom keys!
rct1_key_mat = automol.zmatrix.key_matrix(rct1_zma)
rct1_keys = [row[0] for row in rct1_key_mat]
if rct1_keys[rct1_atm2_key] is not None:
atm2_nghbr_keys = [rct1_keys[rct1_atm2_key]]
else:
atm2_nghbr_keys = []
for idx, rct1_key in enumerate(rct1_keys):
if rct1_key == rct1_atm2_key:
atm2_nghbr_keys.append(idx)
new_atm3 = False
for atm_key in atm2_nghbr_keys:
if atm_key not in (rct1_atm3_key, rct1_atm1_key):
rct1_atm3_key = atm_key
new_atm3 = True
break
if not new_atm3:
# if there are no dummy atoms connected to the rct1_atm2 then
# search for dummy atom keys connected to rct1_atm1
# now regenerate atm1_nghbr_keys to include dummy atom keys!
if rct1_keys[rct1_atm1_key] is not None:
atm1_nghbr_keys = [rct1_keys[rct1_atm1_key]]
else:
atm1_nghbr_keys = []
for idx, rct1_key in enumerate(rct1_keys):
if rct1_key == rct1_atm1_key:
atm1_nghbr_keys.append(idx)
new_atm3 = False
for atm_key in atm1_nghbr_keys:
if atm_key not in (rct1_atm3_key, rct1_atm2_key):
rct1_atm3_key = atm_key
new_atm3 = True
break
join_val_dct = {
dist_name: dist_val,
'aabs1': 85. * qcc.conversion_factor('degree', 'radian'),
'aabs2': 85. * qcc.conversion_factor('degree', 'radian'),
'babs1': 85. * qcc.conversion_factor('degree', 'radian'),
'babs2': 85. * qcc.conversion_factor('degree', 'radian'),
'babs3': 85. * qcc.conversion_factor('degree', 'radian'),
}
rct1_natom = automol.zmatrix.count(rct1_zma)
rct2_natom = automol.zmatrix.count(rct2_zma)
if rct1_natom == 1 and rct2_natom == 1:
raise NotImplementedError
if rct1_natom == 2 and rct2_natom == 1:
join_keys = numpy.array([[rct1_atm1_key, rct1_atm2_key, None]])
join_names = numpy.array([[dist_name, 'aabs1', None]])
elif rct1_natom == 2 and rct2_natom == 2:
join_keys = numpy.array([[rct1_atm1_key, rct1_atm2_key, rct1_atm3_key],
[None, rct1_atm1_key, rct1_atm2_key]])
join_names = numpy.array([[dist_name, 'aabs1', None],
[None, 'aabs2', 'babs2']])
else:
join_keys = numpy.array([[rct1_atm1_key, rct1_atm2_key, rct1_atm3_key],
[None, rct1_atm1_key, rct1_atm2_key],
[None, None, rct1_atm1_key]])[:rct2_natms]
join_names = numpy.array([[dist_name, 'aabs1', 'babs1'],
[None, 'aabs2', 'babs2'],
[None, None, 'babs3']])[:rct2_natms]
join_name_set = set(numpy.ravel(join_names)) - {None}
join_val_dct = {name: join_val_dct[name] for name in join_name_set}
ts_zma = automol.zmatrix.join(rct1_zma, rct2_zma, join_keys, join_names,
join_val_dct)
ts_name_dct = automol.zmatrix.standard_names(ts_zma)
dist_name = ts_name_dct[dist_name]
ts_zma = automol.zmatrix.standard_form(ts_zma)
# bimol_tors_names = constbuild.bimol()
frm_bnd_keys = shift_vals_from_dummy(frm_bnd_keyss, ts_zma)
# Build return
ret = {
'ts_zma': ts_zma,
'bnd_keys': (frm_bnd_keys, frozenset({})),
'const_keys': (frozenset({}), frozenset({}), frozenset({}))
}
return ret
def hydrogen_migration(rct_zmas_lst, prd_zmas_lst, tras):
""" z-matrix for a hydrogen migration reaction
tras in the ZMATRIX coordinate system
"""
# Find the zma and traj pair that has min dist among rxn coord
init_zma, min_tra = min_dist(rct_zmas_lst, tras)
_ = prd_zmas_lst # unneeded for TS build
frm_bnd_keys, = automol.graph.trans.formed_bond_keys(min_tra)
brk_bnd_keys, = automol.graph.trans.broken_bond_keys(min_tra)
# Build a properly ordered zma
count = 0
while True:
# figure out which idx in frm_bnd_keys corresponds to the hydrogen
symbols = automol.vmatrix.symbols(automol.zmatrix.var_(init_zma))
dist_coo_key = tuple(reversed(sorted(frm_bnd_keys)))
for idx in dist_coo_key:
if symbols[idx] == 'H':
h_idx = idx
else:
a1_idx = idx
brk_dist_coo_key = tuple(reversed(sorted(brk_bnd_keys)))
for idx in brk_dist_coo_key:
if symbols[idx] != 'H':
a2_idx = idx
# determine if the zmatrix needs to be rebuilt by x2z
# determines if the hydrogen atom is used to define other atoms
init_keys = automol.zmatrix.key_matrix(init_zma)
rebuild = False
for i, _ in enumerate(init_keys):
if i > h_idx and any(idx == h_idx for idx in init_keys[i]):
rebuild = True
break
# rebuild zmat and go through while loop again if needed
# shifts order of cartesian coords and rerun x2z to get a new zmat
# else go to next stage
if rebuild:
re_zma, frm_bnd_keys, brk_bnd_keys = reorder_zmatrix_for_redef(
init_zma, a1_idx, h_idx, frm_bnd_keys, brk_bnd_keys)
rct_zma = [re_zma]
count += 1
if count == 6:
break
else:
rct_zma = init_zma
break
if not rct_zma:
return None
# Determine the backbone atoms to redefine the z-matrix entry
_, gras = shifted_standard_zmas_graphs([rct_zma], remove_stereo=True)
gra = functools.reduce(automol.graph.union, gras)
xgr1, = automol.graph.connected_components(gra)
chains_dct = automol.graph.atom_longest_chains(xgr1)
idx_found = True
a3_idx = chains_dct[a2_idx][1]
if a3_idx in (h_idx, a1_idx):
idx_found = False
a2_neighbors = _atom_neighbor_keys(xgr1)[a2_idx]
for idx in a2_neighbors:
if idx not in (h_idx, a1_idx):
a3_idx = idx
idx_found = True
if not idx_found:
a3_idx = chains_dct[a1_idx][1]
if a3_idx in (h_idx, a2_idx):
a1_neighbors = _atom_neighbor_keys(xgr1)[a1_idx]
for idx in a1_neighbors:
if idx not in (h_idx, a2_idx):
a3_idx = idx
# Set the values of the coordinates of the migrating H atom
rct_geo = automol.zmatrix.geometry(rct_zma)
distance = automol.geom.distance(rct_geo, h_idx, a1_idx)
angle = automol.geom.central_angle(rct_geo, h_idx, a1_idx, a2_idx)
dihedral = automol.geom.dihedral_angle(rct_geo, h_idx, a1_idx, a2_idx,
a3_idx)
dihed_is_180 = numpy.isclose(abs(dihedral), (numpy.pi),
rtol=(5.0 * numpy.pi / 180.))
dihed_is_0 = numpy.isclose(dihedral, (0.0), rtol=(5.0 * numpy.pi / 180.))
dihed_is_360 = numpy.isclose(abs(dihedral), (2 * numpy.pi),
rtol=(5.0 * numpy.pi / 180.))
if dihed_is_180 or dihed_is_0 or dihed_is_360:
dihedral -= (15.0 * numpy.pi / 180.)
# Reset the keys for the migrating H atom
new_idxs = (a1_idx, a2_idx, a3_idx)
key_dct = {h_idx: new_idxs}
ts_zma = automol.zmatrix.set_keys(rct_zma, key_dct)
h_names = automol.zmatrix.name_matrix(ts_zma)[h_idx]
ts_zma = automol.zmatrix.set_values(ts_zma, {
h_names[0]: distance,
h_names[1]: angle,
h_names[2]: dihedral
})
# standardize the ts zmat and get tors and dist coords
coo_dct = automol.zmatrix.coordinates(ts_zma)
for coo_name, coo_key in coo_dct.items():
dist_coo_key_rev = dist_coo_key[::-1]
if coo_key[0] in (dist_coo_key, dist_coo_key_rev):
dist_name = coo_name
break
# if migrating H atom is not the final zmat entry, shift it to the end (if
# needed)
if h_idx != automol.zmatrix.count(ts_zma) - 1:
ts_zma, h_idx, frm_bnd_keys, brk_bnd_keys = shift_row_to_end(
ts_zma, h_idx, frm_bnd_keys, brk_bnd_keys)
ts_name_dct = automol.zmatrix.standard_names(ts_zma)
dist_name = ts_name_dct[dist_name]
ts_zma = automol.zmatrix.standard_form(ts_zma)
# Build the torsional coordinates
const_bnd_keys, _, _ = constbuild.hydrogen_migration(
ts_zma, rct_zma, h_idx, frm_bnd_keys, brk_bnd_keys)
# tors_bnd_keys = [coord_idxs(ts_zma, name) for name in tors_names]
# Build the bond coordinates
frm_bnd_keys = shift_vals_from_dummy(frm_bnd_keys, ts_zma)
brk_bnd_keys = shift_vals_from_dummy(brk_bnd_keys, ts_zma)
const_bnd_keys = shift_vals_from_dummy(const_bnd_keys, ts_zma)
# Set the return
ret = {
'ts_zma': ts_zma,
'bnd_keys': (frm_bnd_keys, brk_bnd_keys),
'const_keys': (const_bnd_keys, frozenset({}), frozenset({}))
}
return ret
def concerted_unimol_elimination(rct_zmas, prd_zmas, tras):
""" z-matrix for a concerted unimolecular elimination reaction
"""
# Find the zma and traj pair that has min dist among rxn coord
_ = prd_zmas # Unneeded
rct_zma, min_tra = min_dist(rct_zmas, tras)
frm_bnd_keys, = automol.graph.trans.formed_bond_keys(min_tra)
brk_bnd_keys = automol.graph.trans.broken_bond_keys(min_tra)
brk_bnd_key1, brk_bnd_key2 = brk_bnd_keys
count = 1
while True:
init_zma = rct_zma
print('init_zma\n', automol.zmatrix.string(init_zma))
# print('init_geo\n', automol.geom.string(automol.zmatrix.geometry(init_zma)))
# Get index for migrating atom (or bond-form atom in group)
brk_bnd_key1, brk_bnd_key2 = brk_bnd_keys
for bnd_key in (brk_bnd_key1, brk_bnd_key2):
if bnd_key & frm_bnd_keys:
mig_key = next(iter(bnd_key & frm_bnd_keys))
for key in frm_bnd_keys:
if key != mig_key:
a1_idx = key
# Get chain for redefining the rc1_atm1_key z-matrix entries
_, gras = shifted_standard_zmas_graphs([init_zma], remove_stereo=True)
gra = functools.reduce(automol.graph.union, gras)
xgr1, = automol.graph.connected_components(gra)
atm1_neighbors = _atom_neighbor_keys(xgr1)[a1_idx]
for idx in atm1_neighbors:
num_keys = len(_atom_neighbor_keys(xgr1)[idx])
if idx != mig_key and num_keys > 1:
a2_idx = idx
atm2_neighbors = _atom_neighbor_keys(xgr1)[a2_idx]
for idx in atm2_neighbors:
if idx not in (mig_key, a1_idx):
a3_idx = idx
mig_redef_keys = (a1_idx, a2_idx, a3_idx)
print('mig key', mig_key)
print('mig redef keys', mig_redef_keys)
print('frm keys', frm_bnd_keys)
print('brk keys', brk_bnd_keys)
# determine if the zmatrix needs to be rebuilt by x2z
# determines if the hydrogen atom is used to define other atoms
rebuild = False
if any(idx > mig_key for idx in mig_redef_keys):
rebuild = True
# rebuild zmat and go through while loop again if needed
# shift order of cartesian coords & rerun x2z to get a new zmat
# else go to next stage
if rebuild:
# multiple bond keys need to be passed
reord_zma, frm_bnd_keys, brk_bnd_keys = reorder_zmatrix_for_redef(
init_zma, a1_idx, mig_key, frm_bnd_keys, brk_bnd_keys)
rct_zma = reord_zma
count += 1
if count == 3:
finish_build = False
break
print('rebuild')
else:
rct_zma = init_zma
finish_build = True
print('no rebuild')
break
# If z-mat with good order not found, exit function
if not finish_build:
return None
# determine the new coordinates
rct_geo = automol.zmatrix.geometry(rct_zma)
distance = automol.geom.distance(rct_geo, mig_key, a1_idx)
angle = automol.geom.central_angle(rct_geo, mig_key, a1_idx, a2_idx)
dihedral = automol.geom.dihedral_angle(rct_geo, mig_key, a1_idx, a2_idx,
a3_idx)
# Reset the keys for the migrating H atom
new_idxs = (a1_idx, a2_idx, a3_idx)
key_dct = {mig_key: new_idxs}
ts_zma = automol.zmatrix.set_keys(rct_zma, key_dct)
# Reset the values in the value dict
mig_names = automol.zmatrix.name_matrix(ts_zma)[mig_key]
ts_zma = automol.zmatrix.set_values(ts_zma, {
mig_names[0]: distance,
mig_names[1]: angle,
mig_names[2]: dihedral
})
# standardize the ts zmat and get tors and dist coords
coo_dct = automol.zmatrix.coordinates(ts_zma)
dist_coo_key = tuple(reversed(sorted(frm_bnd_keys)))
dist_name = next(coo_name for coo_name, coo_keys in coo_dct.items()
if dist_coo_key in coo_keys)
ts_name_dct = automol.zmatrix.standard_names(ts_zma)
dist_name = ts_name_dct[dist_name]
ts_zma = automol.zmatrix.standard_form(ts_zma)
brk_bnd_keys = frozenset({
shift_vals_from_dummy(brk_bnd_key1, ts_zma),
shift_vals_from_dummy(brk_bnd_key2, ts_zma)
})
frm_bnd_keys = shift_vals_from_dummy(frm_bnd_keys, ts_zma)
# Set the return
ret = {
'ts_zma': ts_zma,
'bnd_keys': (frm_bnd_keys, brk_bnd_keys),
'const_keys': (frozenset({}), frozenset({}), frozenset({}))
}
return ret
