def _connected_geometry(ich, check=True):
""" Generate a molecular geometry from an InChI string where
all atoms are connected by at least one bond.
:param ich: InChI string
:type ich: str
:param check: check stereo and connectivity?
:type check: bool
:rtype: automol molecular geometry data structure
"""
# print("inchi in:", ich)
geo = hardcoded_object_from_inchi_by_key('geom', ich)
if geo is None:
def _gen1(ich):
rdm = rdkit_.from_inchi(ich)
geo, = rdkit_.to_conformers(rdm, nconfs=1)
return geo
def _gen2(ich):
pbm = pybel_.from_inchi(ich)
geo = pybel_.to_geometry(pbm)
return geo
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
for gen_ in [_gen1, _gen1, _gen1, _gen2, _gen3]:
success = False
try:
geo = gen_(ich)
geo_ich = automol.geom.inchi(geo)
# Check connectivity
same_conn = same_connectivity(ich, geo_ich)
conn = automol.geom.connected(geo)
_has_stereo = has_stereo(ich)
ich_equiv = equivalent(ich, geo_ich)
checks_pass = ((same_conn and conn)
and (not _has_stereo or ich_equiv))
# print('original inchi', ich)
# print('geometry inchi', geo_ich)
if not check or checks_pass:
success = True
break
except (RuntimeError, TypeError, ValueError):
continue
if not success:
raise error.FailedGeometryGenerationError('Failed InChI:', ich)
return geo
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 conformers(ich, nconfs=1):
""" Generate a list of molecular geometries for various conformers
of a species from an InChI string.
:param ich: InChI string
:type ich: str
:param nconfs: number of conformer structures to generate
:type: int
:rtype: automol molecular geometry data structure
"""
geo = hardcoded_object_from_inchi_by_key('geom', ich)
if geo is None:
ich = standard_form(ich)
def _gen1(ich):
rdm = rdkit_.from_inchi(ich)
geos = rdkit_.to_conformers(rdm, nconfs)
return geos
for gen_ in [_gen1]:
success = False
try:
geos = gen_(ich)
for geo in geos:
geo_ich = automol.geom.inchi(geo)
if same_connectivity(
ich, geo_ich) and (not has_stereo(ich)
or equivalent(ich, geo_ich)):
success = True # fix
break
except (RuntimeError, TypeError, ValueError):
continue
if not success:
raise error.FailedGeometryGenerationError
return geos