def _gen3(ich):
if has_stereo(ich):
raise ValueError
gra = graph(ich, stereo=False)
gra = automol.graph.explicit(gra)
geo = automol.graph.embed.geometry(gra)
return geo
def hydrogen_bonded_idxs(geo, dist_thresh=5.3, angle_thresh=1.92, grxn=None):
""" Compare bond lengths in structure to determine if there
is a hydrogen bond.
:param geo: geometry object
:type geo: geo object (tuple of tuples)
:param grxn: reaction object (geo indexing)
:type grxn: automol.reac.Reaction object
:param dist_thresh: cutoff value for hbond length (Bohr)
:type dist_thresh: float
:param angle_thresh: cutoff value for hbond angle (Radian)
:type angle_thresh: float
:rtype: tuple
"""
# Initialize the hydrogen bond list to None
hydrogen_bond = None
if count(geo) > 1:
# Get the forming/breaking bond idxs if possible
if grxn is not None:
frm_bnd_keys = automol.graph.ts.forming_bond_keys(
grxn.forward_ts_graph)
brk_bnd_keys = automol.graph.ts.breaking_bond_keys(
grxn.forward_ts_graph)
rxn_keys = set()
for key in frm_bnd_keys:
rxn_keys = rxn_keys | key
for key in brk_bnd_keys:
rxn_keys = rxn_keys | key
rxn_h_idxs = tuple(rxn_keys)
else:
rxn_h_idxs = ()
# Get all potential indices for HB interactions
gra = graph(geo)
dist_mat = distance_matrix(geo)
adj_atm_dct = automol.graph.atoms_neighbor_atom_keys(gra)
h_idxs = automol.graph.atom_keys(gra, sym='H')
acceptor_idxs = list(
automol.graph.resonance_dominant_radical_atom_keys(gra))
acceptor_idxs.extend(list(automol.graph.atom_keys(gra, sym='O')))
# Loop over indices, ignoring H-idxs in reacting bonds
hb_idxs = tuple(idx for idx in h_idxs if idx not in rxn_h_idxs)
for h_idx in hb_idxs:
for acceptor_idx in acceptor_idxs:
donor_idx = list(adj_atm_dct[h_idx])[0]
if acceptor_idx in adj_atm_dct[donor_idx]:
continue
if dist_mat[h_idx][acceptor_idx] < dist_thresh:
ang = central_angle(geo, donor_idx, h_idx, acceptor_idx)
if ang > angle_thresh:
hydrogen_bond = (
donor_idx,
h_idx,
acceptor_idx,
)
dist_thresh = dist_mat[h_idx][acceptor_idx]
return hydrogen_bond
def components_graph(geo, stereo=True):
""" Generate a list of molecular graphs where each element is a graph that
consists of fully connected (bonded) atoms. Stereochemistry is included
if requested.
:param geo: molecular geometry
:type geo: automol geometry data structure
:param stereo: parameter to include stereochemistry information
:type stereo: bool
:rtype: automol molecular graph data structure
"""
return automol.graph.connected_components(graph(geo, stereo=stereo))
def expand_stereo(ich):
""" Obtain all possible stereoisomers compatible with an InChI string.
:param ich: InChI string
:type ich: str
:rtype: list[str]
"""
gra = graph(ich)
sgrs = automol.graph.stereomers(gra)
ste_ichs = [automol.graph.stereo_inchi(sgr) for sgr in sgrs]
return ste_ichs
def is_complete(ich):
""" Determine if the InChI string is complete
(has all stereo-centers assigned).
Currently only checks species that does not have any
resonance structures.
:param ich: InChI string
:type ich: str
:rtype: bool
"""
gra = graph(ich, stereo=False)
ste_atm_keys = automol.graph.stereogenic_atom_keys(gra)
ste_bnd_keys = automol.graph.stereogenic_bond_keys(gra)
graph_has_stereo = bool(ste_atm_keys or ste_bnd_keys)
_complete = equivalent(
ich, standard_form(ich)) and not (has_stereo(ich) ^ graph_has_stereo)
return _complete
def torsional_symmetry_numbers(zma,
tors_names,
frm_bnd_key=None,
brk_bnd_key=None):
""" symmetry numbers for torsional dihedrals
"""
dih_edg_key_dct = _dihedral_edge_keys(zma)
assert set(tors_names) <= set(dih_edg_key_dct.keys())
edg_keys = tuple(map(dih_edg_key_dct.__getitem__, tors_names))
gra = graph(zma, stereo=False)
bnd_sym_num_dct = automol.graph.bond_symmetry_numbers(
gra, frm_bnd_key, brk_bnd_key)
tors_sym_nums = []
for edg_key in edg_keys:
if edg_key in bnd_sym_num_dct.keys():
sym_num = bnd_sym_num_dct[edg_key]
else:
sym_num = 1
tors_sym_nums.append(sym_num)
tors_sym_nums = tuple(tors_sym_nums)
return tors_sym_nums
def torsion_leading_atom(zma, key1, key2, zgra=None):
""" Obtain the leading atom for a torsion coordinate about a torsion axis.
The leading atom is the atom whose dihedral defines the torsional
coordinate, which must always be the first dihedral coordinate
for this bond.
A bond is properly decoupled if all other dihedrals along this
bond depend on the leading atom.
:param zma: the z-matrix
:type zma: automol Z-Matrix data structure
:param key1: the first key in the torsion axis (rotational bond)
:type key1: int
:param key2: the second key in the torsion axis (rotational bond)
:type key2: int
:param gra: an automol graph data structure, aligned to the z-matrix;
used to check connectivity when necessary
:rtype: int
"""
key_mat = key_matrix(zma)
krs1 = [(key, row) for key, row in enumerate(key_mat)
if row[:2] == (key1, key2)]
krs2 = [(key, row) for key, row in enumerate(key_mat)
if row[:2] == (key2, key1)]
lead_key_candidates = []
for krs in (krs1, krs2):
if krs:
keys, rows = zip(*krs)
start_key = keys[0]
assert all(row[-1] == start_key for row in rows[1:]), (
"Torsion coordinate along bond {:d}-{:d} not decoupled:\n{}"
.format(key1, key2, string(zma, one_indexed=False)))
if rows[0][-1] is not None:
lead_key_candidates.append(start_key)
if not lead_key_candidates:
lead_key = None
elif len(lead_key_candidates) == 1:
lead_key = lead_key_candidates[0]
else:
# If we get to this point, then the z-matrix includes dihedrals across
# the key1-key2 bond in both directions and we have to choose which
# dihedral to use. This mans there will be two lead_key_candidates.
zgra = graph(zma) if zgra is None else zgra
# Let key0 be the lead key and let (key1, key2, key3) be its key row in
# the z-matrix. For the torsion coordinate, key0-key1-key2-key3 should
# all be connected in a line. For subsidiary dihedral coordinates, key3
# will be connected to key1 instead of key2.
# A simple solution is therefore to choose the lead key based on
# whether or not key2 and key3 are connected, which is what this code
# does.
bnd_keys = automol.graph.bond_keys(zgra)
lead_key = next((k for k in lead_key_candidates if
frozenset(key_mat[k][-2:]) in bnd_keys), None)
# If that fails, choose the key that appears earlier. It's possible
# that it would be better to choose the later one, in which case we
# would replace the min() here with a max().
if lead_key is None:
lead_key = min(lead_key_candidates)
return lead_key
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 = graph(geo, stereo=False)
term_atms = {}
all_hyds = []
neighbor_dct = automol.graph.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 = automol.graph.unsaturated_atom_keys(gra)
if not saddle:
rad_atms = automol.graph.sing_res_dom_radical_atom_keys(gra)
res_rad_atms = automol.graph.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 hyds in term_atms.values():
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 = graph(geo, stereo=False)
term_atms = {}
all_hyds = []
neighbor_dct = automol.graph.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 = automol.graph.unsaturated_atom_keys(gra)
if not saddle:
rad_atms = automol.graph.sing_res_dom_radical_atom_keys(gra)
res_rad_atms = automol.raph.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
print('terminal atom accepted:', 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 = remove(geo, remove_atms)
return geo, factor, remove_atms
