def prod_beta_scission(gra):
""" products of beta scission
"""
prod_gras = tuple()
rad_idxs = resonance_dominant_radical_atom_keys(gra)
single_bonds = bonds_of_order(gra, mbond=1)
for rad_idx in rad_idxs:
rad_neighs = atoms_neighbor_atom_keys(gra)[rad_idx]
for single_bond in single_bonds:
bond = frozenset(single_bond)
if rad_neighs & bond and rad_idx not in bond:
gra2 = remove_bonds(gra, [bond])
disconn_gras = automol.graph.connected_components(gra2)
prod_gras += (disconn_gras, )
return _unique_gras(prod_gras)
def rot_permutated_geoms(geo, frm_bnd_keys=(), brk_bnd_keys=()):
""" Convert an input geometry to a list of geometries
corresponding to the rotational permuations of all the terminal groups.
:param geo: molecular geometry
:type geo: automol molecular geometry data structure
:param frm_bnd_keys: keys denoting atoms forming bond in TS
:type frm_bnd_keys: frozenset(int)
:param brk_bnd_keys: keys denoting atoms breaking bond in TS
:type brk_bnd_keys: frozenset(int)
:rtype: tuple(automol geom data structure)
"""
# Set saddle based on frm and brk keys existing
saddle = bool(frm_bnd_keys or brk_bnd_keys)
gra = automol.convert.geom.graph(geo, stereo=False)
term_atms = {}
all_hyds = []
neighbor_dct = atoms_neighbor_atom_keys(gra)
ts_atms = []
for bnd in frm_bnd_keys:
ts_atms.extend(list(bnd))
for bnd in brk_bnd_keys:
ts_atms.extend(list(bnd))
# determine if atom is a part of a double bond
unsat_atms = unsaturated_atom_keys(gra)
if not saddle:
rad_atms = sing_res_dom_radical_atom_keys(gra)
res_rad_atms = resonance_dominant_radical_atom_keys(gra)
rad_atms = [atm for atm in rad_atms if atm not in res_rad_atms]
else:
rad_atms = []
gra = gra[0]
for atm in gra:
if gra[atm][0] == 'H':
all_hyds.append(atm)
for atm in gra:
if atm in unsat_atms and atm not in rad_atms:
pass
else:
if atm not in ts_atms:
nonh_neighs = []
h_neighs = []
neighs = neighbor_dct[atm]
for nei in neighs:
if nei in all_hyds:
h_neighs.append(nei)
else:
nonh_neighs.append(nei)
if len(nonh_neighs) < 2 and len(h_neighs) > 1:
term_atms[atm] = h_neighs
geo_final_lst = [geo]
for atm in term_atms:
hyds = term_atms[atm]
geo_lst = []
for geom in geo_final_lst:
geo_lst.extend(_swap_for_one(geom, hyds))
geo_final_lst = geo_lst
return geo_final_lst
def end_group_symmetry_factor(geo, frm_bnd_keys=(), brk_bnd_keys=()):
""" Determine sym factor for terminal groups in a geometry
:param geo: molecular geometry
:type geo: automol molecular geometry data structure
:param frm_bnd_keys: keys denoting atoms forming bond in TS
:type frm_bnd_keys: frozenset(int)
:param brk_bnd_keys: keys denoting atoms breaking bond in TS
:type brk_bnd_keys: frozenset(int)
:rtype: (automol geom data structure, float)
"""
# Set saddle based on frm and brk keys existing
saddle = bool(frm_bnd_keys or brk_bnd_keys)
gra = automol.convert.geom.graph(geo, stereo=False)
term_atms = {}
all_hyds = []
neighbor_dct = atoms_neighbor_atom_keys(gra)
ts_atms = []
for bnd in frm_bnd_keys:
ts_atms.extend(list(bnd))
for bnd in brk_bnd_keys:
ts_atms.extend(list(bnd))
# determine if atom is a part of a double bond
unsat_atms = unsaturated_atom_keys(gra)
if not saddle:
rad_atms = sing_res_dom_radical_atom_keys(gra)
res_rad_atms = resonance_dominant_radical_atom_keys(gra)
rad_atms = [atm for atm in rad_atms if atm not in res_rad_atms]
else:
rad_atms = []
gra = gra[0]
for atm in gra:
if gra[atm][0] == 'H':
all_hyds.append(atm)
for atm in gra:
if atm in unsat_atms and atm not in rad_atms:
pass
else:
if atm not in ts_atms:
nonh_neighs = []
h_neighs = []
neighs = neighbor_dct[atm]
for nei in neighs:
if nei in all_hyds:
h_neighs.append(nei)
else:
nonh_neighs.append(nei)
if len(nonh_neighs) == 1 and len(h_neighs) > 1:
term_atms[atm] = h_neighs
factor = 1.
remove_atms = []
for atm in term_atms:
hyds = term_atms[atm]
if len(hyds) > 1:
factor *= len(hyds)
remove_atms.extend(hyds)
geo = trans.remove_coordinates(geo, remove_atms)
return geo, factor, remove_atms