def is_stereo_compatible(tra, sgr1, sgr2):
""" is this transformation compatible with the applyant/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 atom_stereo_coordinates(sgr):
""" stereo-specific coordinates for this molecular graph
"""
assert sgr == _explicit(sgr)
last_xgr = None
xgr = _without_stereo_parities(sgr)
# first, get a set of non-stereo-specific coordinates for the graph
atm_xyz_dct = _atom_coordinates(xgr)
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()
while last_xgr != xgr:
last_xgr = xgr
atm_keys.update(stereogenic_atom_keys(xgr))
bnd_keys.update(stereogenic_bond_keys(xgr))
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
}
xgr, atm_xyz_dct = _correct_atom_stereo_coordinates(
xgr, atm_ste_par_dct, atm_xyz_dct)
xgr, atm_xyz_dct = _correct_bond_stereo_coordinates(
xgr, bnd_ste_par_dct, atm_xyz_dct)
return atm_xyz_dct
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(xgr):
""" 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(xgr))
known_bnd_ste_par_dct = _assigned(_bond_stereo_parities(xgr))
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(xgr)))
return sgrs
def bond_stereo_keys(sgr):
""" keys to bond stereo-centers
"""
bnd_ste_keys = dict_.keys_by_value(_bond_stereo_parities(sgr),
lambda x: x in [True, False])
return bnd_ste_keys