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 _is_compatible(sgr):
atm_ste_par_dct = _assigned(atom_stereo_parities(sgr))
bnd_ste_par_dct = _assigned(bond_stereo_parities(sgr))
_compat_atm_assgns = (set(known_atm_ste_par_dct.items()) <=
set(atm_ste_par_dct.items()))
_compat_bnd_assgns = (set(known_bnd_ste_par_dct.items()) <=
set(bnd_ste_par_dct.items()))
return _compat_atm_assgns and _compat_bnd_assgns
def substereomers(gra):
""" all stereomers compatible with this graph's assignments
"""
_assigned = functools.partial(
dict_.filter_by_value, func=lambda x: x is not None)
known_atm_ste_par_dct = _assigned(atom_stereo_parities(gra))
known_bnd_ste_par_dct = _assigned(bond_stereo_parities(gra))
def _is_compatible(sgr):
atm_ste_par_dct = _assigned(atom_stereo_parities(sgr))
bnd_ste_par_dct = _assigned(bond_stereo_parities(sgr))
_compat_atm_assgns = (set(known_atm_ste_par_dct.items()) <=
set(atm_ste_par_dct.items()))
_compat_bnd_assgns = (set(known_bnd_ste_par_dct.items()) <=
set(bnd_ste_par_dct.items()))
return _compat_atm_assgns and _compat_bnd_assgns
sgrs = tuple(filter(_is_compatible, stereomers(gra)))
return sgrs
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
# GEO = (
# ('C', (-4.3870588134, -1.233231672517, 0.143749726309016)),
# ('C', (3.430304171771, -2.162836645393, 0.06129774977456508)),
# ('C', (-2.228277354885, 0.1940343942502, -1.0788747507898575)),
# ('C', (1.642516616594, -0.2666792157215, -1.1217150146524835)),
# ('C', (-0.128929182575, 1.167922277159, 0.6891116967734786)),
# ('O', (2.44416862025, 4.3088944278, 2.2811617948010614)),
# ('O', (-0.4839163664245, -1.530973627393, -2.314392676447687)),
# ('O', (0.1546996690877, 3.88389710099, 0.8186943317590577)),
# ('H', (-3.69835752847, -2.73865502820, 1.385388988006255)),
# ('H', (-5.55611791656, 0.04579783881378, 1.2732325623382277)),
# ('H', (-5.59710374244, -2.09637223693, -1.2950602194746856)),
# ('H', (2.43356758828, -3.46358524781, 1.3249230383597128)),
# ('H', (4.89255603965, -1.19599087753, 1.1592100844834574)),
# ('H', (4.37095524985, -3.286477042474, -1.3988006492215568)),
# ('H', (-2.909935258917, 1.611421581693, -2.430728150238205)),
# ('H', (2.608452006545, 0.954321649398, -2.49176226302396)),
# ('H', (-0.2313534706629, 0.353123800972, 2.5932645521380446)),
# ('H', (3.243829672371, 5.45538852286, 1.0816218339892072)))
XGR = set_stereo_from_geometry(SGR, GEO, geo_idx_dct=GEO_IDX_DCT)
print(automol.geom.string(GEO))
REF_ATM_STE_PAR_DCT = dict_.filter_by_value(atom_stereo_parities(GRA),
lambda x: x is not None)
ATM_STE_PAR_DCT = dict_.filter_by_value(atom_stereo_parities(XGR),
lambda x: x is not None)
print(REF_ATM_STE_PAR_DCT)
print(ATM_STE_PAR_DCT)
def atom_stereo_keys(sgr):
""" keys to atom stereo-centers
"""
atm_ste_keys = dict_.keys_by_value(atom_stereo_parities(sgr),
lambda x: x in [True, False])
return atm_ste_keys