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 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 _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 _have_no_stereo_assignments(gras):
return all(gra == without_stereo_parities(gra) for gra in gras)