def isomorphism(gra1, gra2, backbone_only=False, stereo=True, dummy=True):
""" Obtain an isomorphism between two graphs
This should eventually replace the other isomorphism functions.
:param backbone_only: Compare backbone atoms only?
:type backbone_only: bool
:param stereo: Consider stereo?
:type stereo: bool
:param dummy: Consider dummy atoms?
:type dummy: bool
:returns: The isomorphism mapping `gra1` onto `gra2`
:rtype: dict
"""
if backbone_only:
gra1 = implicit(gra1)
gra2 = implicit(gra2)
if not stereo:
gra1 = without_stereo_parities(gra1)
gra2 = without_stereo_parities(gra2)
if not dummy:
gra1 = without_dummy_atoms(gra1)
gra2 = without_dummy_atoms(gra2)
return _isomorphism(gra1, gra2)
def is_stereo_compatible(tra, sgr1, sgr2):
""" is this transformation compatible with the reactant/product stereo
assignments?
"""
cgr1 = without_stereo_parities(sgr1)
cgr2 = without_stereo_parities(sgr2)
atm_key_dct = _full_isomorphism(apply(tra, cgr1), cgr2)
# determine the stereo centers which are preserved in the transformation
sgr1 = _relabel(sgr1, atm_key_dct)
atm_keys = sorted(atom_stereo_keys(sgr1) & atom_stereo_keys(sgr2))
bnd_keys = sorted(bond_stereo_keys(sgr1) & bond_stereo_keys(sgr2))
atm_pars1 = dict_.values_by_key(atom_stereo_parities(sgr1), atm_keys)
atm_pars2 = dict_.values_by_key(atom_stereo_parities(sgr2), atm_keys)
bnd_pars1 = dict_.values_by_key(bond_stereo_parities(sgr1), bnd_keys)
bnd_pars2 = dict_.values_by_key(bond_stereo_parities(sgr2), bnd_keys)
atm_ngb_keys_dct1 = atom_neighbor_keys(sgr1)
atm_ngb_keys_dct2 = atom_neighbor_keys(sgr2)
ret = True
for atm_key, par1, par2 in zip(atm_keys, atm_pars1, atm_pars2):
atm_ngb_keys1 = stereo_sorted_atom_neighbor_keys(
sgr1, atm_key, atm_ngb_keys_dct1[atm_key])
atm_ngb_keys2 = stereo_sorted_atom_neighbor_keys(
sgr2, atm_key, atm_ngb_keys_dct2[atm_key])
if _permutation_parity(atm_ngb_keys1, atm_ngb_keys2):
ret &= (par1 == par2)
else:
ret &= (par1 != par2)
for bnd_key, par1, par2 in zip(bnd_keys, bnd_pars1, bnd_pars2):
atm1_key, atm2_key = bnd_key
atm1_ngb_key1 = stereo_sorted_atom_neighbor_keys(
sgr1, atm1_key, atm_ngb_keys_dct1[atm1_key] - {atm2_key})[0]
atm2_ngb_key1 = stereo_sorted_atom_neighbor_keys(
sgr1, atm2_key, atm_ngb_keys_dct1[atm2_key] - {atm1_key})[0]
atm1_ngb_key2 = stereo_sorted_atom_neighbor_keys(
sgr2, atm1_key, atm_ngb_keys_dct2[atm1_key] - {atm2_key})[0]
atm2_ngb_key2 = stereo_sorted_atom_neighbor_keys(
sgr2, atm2_key, atm_ngb_keys_dct2[atm2_key] - {atm1_key})[0]
if not ((atm1_ngb_key1 != atm1_ngb_key2) ^
(atm2_ngb_key1 != atm2_ngb_key2)):
ret &= (par1 == par2)
else:
ret &= (par1 != par2)
return ret
def set_stereo_from_geometry(gra, geo, geo_idx_dct=None):
""" set graph stereo from a geometry
(coordinate distances need not match connectivity -- what matters is the
relative positions at stereo sites)
"""
gra = without_stereo_parities(gra)
last_gra = None
atm_keys = sorted(atom_keys(gra))
geo_idx_dct = (geo_idx_dct if geo_idx_dct is not None else
{atm_key: idx
for idx, atm_key in enumerate(atm_keys)})
# set atom and bond stereo, iterating to self-consistency
atm_keys = set()
bnd_keys = set()
while last_gra != gra:
last_gra = gra
atm_keys.update(stereogenic_atom_keys(gra))
bnd_keys.update(stereogenic_bond_keys(gra))
gra = _set_atom_stereo_from_geometry(gra, atm_keys, geo, geo_idx_dct)
gra = _set_bond_stereo_from_geometry(gra, bnd_keys, geo, geo_idx_dct)
return gra
def atom_groups(gra, atm, stereo=False):
""" return a list of groups off of one atom
"""
if not stereo:
gra = without_stereo_parities(gra)
adj_atms = atoms_neighbor_atom_keys(gra)
keys = []
for atmi in adj_atms[atm]:
key = [atm, atmi]
key.sort()
key = frozenset(key)
keys.append(key)
gras = remove_bonds(gra, keys)
return connected_components(gras)
def stereomers(tsg):
""" Expand all possible stereo assignments for the reactants in this TS
graph. (Ignores stereo assignments already present, if any.)
:param tsg: The TS graph, without stereo assignments.
:returns: All possible TS graphs with stereo assignments for the reactants.
"""
rcts_gra = reactants_graph(tsg)
frm_bnd_keys = forming_bond_keys(tsg)
brk_bnd_keys = breaking_bond_keys(tsg)
rcts_gra = without_stereo_parities(rcts_gra)
rcts_sgrs = _stereomers(rcts_gra)
ste_tsgs = tuple(
graph(rcts_sgr, frm_bnd_keys, brk_bnd_keys) for rcts_sgr in rcts_sgrs)
return ste_tsgs
def compatible_reverse_stereomers(ste_tsg):
""" Given a TS graph with stereo assignments, expand all possible reverse
graphs compatble with the forward graph.
:param ste_tsg: The TS graph, with stereo assignments.
:returns: All possible reverse TS graphs.
"""
frm_bnd_keys = forming_bond_keys(ste_tsg)
brk_bnd_keys = breaking_bond_keys(ste_tsg)
_, des_ste_atm_keys = nonconserved_atom_stereo_keys(ste_tsg)
_, des_ste_bnd_keys = nonconserved_bond_stereo_keys(ste_tsg)
cons_atm_keys = sorted(atom_stereo_keys(ste_tsg) - des_ste_atm_keys)
cons_bnd_keys = sorted(bond_stereo_keys(ste_tsg) - des_ste_bnd_keys)
# 1. Determine index-based stereo assignments for conserved stereo centers
idx_tsg = to_index_based_stereo(ste_tsg)
cons_idx_atm_pars = dict_.values_by_key(
atom_stereo_parities(idx_tsg), cons_atm_keys)
cons_idx_bnd_pars = dict_.values_by_key(
bond_stereo_parities(idx_tsg), cons_bnd_keys)
# 2. Determine all possible index-based stereo assignments for the reverse
# reaction.
prds_gra = without_stereo_parities(products_graph(ste_tsg))
prds_sgrs = _stereomers(prds_gra)
prds_idx_sgrs = list(map(_to_index_based_stereo, prds_sgrs))
rev_idx_tsgs_pool = [
graph(p, brk_bnd_keys, frm_bnd_keys) for p in prds_idx_sgrs]
# 3. Find possibilities which match the assignments for the conserved
# stereo centers.
rev_idx_tsgs = []
for rev_idx_tsg in rev_idx_tsgs_pool:
rev_cons_idx_atm_pars = dict_.values_by_key(
atom_stereo_parities(rev_idx_tsg), cons_atm_keys)
rev_cons_idx_bnd_pars = dict_.values_by_key(
bond_stereo_parities(rev_idx_tsg), cons_bnd_keys)
if (rev_cons_idx_atm_pars == cons_idx_atm_pars and
rev_cons_idx_bnd_pars == cons_idx_bnd_pars):
rev_idx_tsgs.append(rev_idx_tsg)
# 4. Convert the matching reverse graphs back from index-based stereo
# assignments to absolute stereo assignments.
rev_ste_tsgs = list(map(from_index_based_stereo, rev_idx_tsgs))
return rev_ste_tsgs
def _stereo_corrected_geometry(sgr, geo, geo_idx_dct):
""" correct the stereo parities of a geometry
(works iterately to handle cases of higher-order stereo)
"""
assert sgr == explicit(sgr)
gra = without_stereo_parities(sgr)
if has_stereo(sgr):
full_atm_ste_par_dct = atom_stereo_parities(sgr)
full_bnd_ste_par_dct = bond_stereo_parities(sgr)
atm_keys = set()
bnd_keys = set()
last_gra = None
while last_gra != gra:
last_gra = gra
atm_keys.update(stereogenic_atom_keys(gra))
bnd_keys.update(stereogenic_bond_keys(gra))
atm_ste_par_dct = {
atm_key: full_atm_ste_par_dct[atm_key]
for atm_key in atm_keys
}
bnd_ste_par_dct = {
bnd_key: full_bnd_ste_par_dct[bnd_key]
for bnd_key in bnd_keys
}
geo, gra = _atom_stereo_corrected_geometry(gra, atm_ste_par_dct,
geo, geo_idx_dct)
geo, gra = _bond_stereo_corrected_geometry(gra, bnd_ste_par_dct,
geo, geo_idx_dct)
return geo
def stereomers(gra):
""" all stereomers, ignoring this graph's assignments
"""
bool_vals = (False, True)
def _expand_atom_stereo(sgr):
atm_ste_keys = stereogenic_atom_keys(sgr)
nste_atms = len(atm_ste_keys)
sgrs = [
set_atom_stereo_parities(sgr,
dict(zip(atm_ste_keys, atm_ste_par_vals)))
for atm_ste_par_vals in itertools.product(bool_vals,
repeat=nste_atms)
]
return sgrs
def _expand_bond_stereo(sgr):
bnd_ste_keys = stereogenic_bond_keys(sgr)
nste_bnds = len(bnd_ste_keys)
sgrs = [
set_bond_stereo_parities(sgr,
dict(zip(bnd_ste_keys, bnd_ste_par_vals)))
for bnd_ste_par_vals in itertools.product(bool_vals,
repeat=nste_bnds)
]
return sgrs
last_sgrs = []
sgrs = [without_stereo_parities(gra)]
while sgrs != last_sgrs:
last_sgrs = sgrs
sgrs = list(itertools.chain(*map(_expand_atom_stereo, sgrs)))
sgrs = list(itertools.chain(*map(_expand_bond_stereo, sgrs)))
return tuple(sorted(sgrs, key=frozen))
def from_index_based_stereo(sgr):
""" Convert a graph from index-based stereo assignments back to absolute
stereo assignments, where parities are independent of atom ordering.
:param sgr: a graph with index-based stereo assignments
:returns: a graph with absolute stereo assignments
"""
assert sgr == explicit(sgr), ("Not an explicit graph:\n{}".format(
string(sgr, one_indexed=False)))
gra = without_stereo_parities(sgr)
if has_stereo(sgr):
atm_keys_pool = atom_stereo_keys(sgr)
bnd_keys_pool = bond_stereo_keys(sgr)
idx_atm_ste_par_dct = atom_stereo_parities(sgr)
idx_bnd_ste_par_dct = bond_stereo_parities(sgr)
atm_ngb_keys_dct = atoms_neighbor_atom_keys(sgr)
atm_keys = set()
bnd_keys = set()
last_gra = None
# Do the assignments iteratively to handle higher-order stereo
while last_gra != gra:
last_gra = gra
abs_atm_ste_par_dct = {}
abs_bnd_ste_par_dct = {}
atm_keys.update(stereogenic_atom_keys(gra) & atm_keys_pool)
bnd_keys.update(stereogenic_bond_keys(gra) & bnd_keys_pool)
# Determine absolute stereo assignments for atoms
for atm_key in atm_keys:
abs_srt_keys = atom_stereo_sorted_neighbor_atom_keys(
gra, atm_key, atm_ngb_keys_dct[atm_key])
idx_srt_keys = sorted(abs_srt_keys)
if automol.util.is_even_permutation(idx_srt_keys,
abs_srt_keys):
abs_atm_ste_par_dct[atm_key] = (
idx_atm_ste_par_dct[atm_key])
else:
abs_atm_ste_par_dct[atm_key] = (
not idx_atm_ste_par_dct[atm_key])
# Determine absolute stereo assignments for bonds
for bnd_key in bnd_keys:
atm1_key, atm2_key = sorted(bnd_key)
atm1_abs_srt_keys = atom_stereo_sorted_neighbor_atom_keys(
gra, atm1_key, atm_ngb_keys_dct[atm1_key] - bnd_key)
atm2_abs_srt_keys = atom_stereo_sorted_neighbor_atom_keys(
gra, atm2_key, atm_ngb_keys_dct[atm2_key] - bnd_key)
atm1_idx_srt_keys = sorted(atm1_abs_srt_keys)
atm2_idx_srt_keys = sorted(atm2_abs_srt_keys)
if not ((atm1_idx_srt_keys[0] != atm1_abs_srt_keys[0]) ^
(atm2_idx_srt_keys[0] != atm2_abs_srt_keys[0])):
abs_bnd_ste_par_dct[bnd_key] = (
idx_bnd_ste_par_dct[bnd_key])
else:
abs_bnd_ste_par_dct[bnd_key] = (
not idx_bnd_ste_par_dct[bnd_key])
gra = set_atom_stereo_parities(gra, abs_atm_ste_par_dct)
gra = set_bond_stereo_parities(gra, abs_bnd_ste_par_dct)
atm_ste_keys = atom_stereo_keys(gra)
bnd_ste_keys = bond_stereo_keys(gra)
assert atm_ste_keys == atm_keys_pool, (
"Index-based to absolute stereo conversion failed:\n"
"{} != {}".format(str(atm_ste_keys), str(atm_keys_pool)))
assert bnd_ste_keys == bnd_keys_pool, (
"Index-based to absolute stereo conversion failed:\n"
"{} != {}".format(str(bnd_ste_keys), str(bnd_keys_pool)))
return gra
