def _gen3(ich):
if has_stereo(ich):
raise ValueError
gra = graph(ich, stereo=False)
gra = explicit(gra)
geo = automol.graph.embed.geometry(gra)
return geo
def _connected_geometry(ich):
""" 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
:rtype: automol molecular geometry data structure
"""
geo = object_from_hardcoded_inchi_by_key('geom', ich)
if geo is None:
ich = standard_form(ich)
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 = explicit(gra)
geo = automol.graph.embed.geometry(gra)
return geo
for gen_ in [_gen1, _gen1, _gen1, _gen2, _gen3]:
success = False
# geo = gen_(ich)
# geo_ich = automol.convert.geom.inchi(geo)
# same_conn = automol.inchi.same_connectivity(ich, geo_ich)
# conn = automol.geom.connected(geo)
# has_stereo = automol.inchi.has_stereo(ich)
try:
geo = gen_(ich)
geo_ich = inchi(geo)
# Check connectivity
same_conn = same_connectivity(ich, geo_ich)
conn = connected(geo)
_has_stereo = has_stereo(ich)
ich_equiv = equivalent(ich, geo_ich)
if (same_conn and conn) and (not _has_stereo or ich_equiv):
success = True
break
except (RuntimeError, TypeError, ValueError):
continue
if not success:
raise error.FailedGeometryGenerationError
return geo
def conformers(ich, nconfs):
""" 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 = object_from_hardcoded_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
# def _gen2(ich):
# pbm = _pybel.from_inchi(ich)
# geos = _pybel.to_conformers(pbm)
# return geos
for gen_ in [_gen1]:
success = False
try:
geos = gen_(ich)
for geo in geos:
geo_ich = 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
def _inchi_connected_graph(ich, stereo=True):
""" Generate a molecular graph from an InChI string where
all all atoms are connected by at least one bond.
:param ich: InChI string
d :type ich: str
:param remove_stereo: parameter to include stereochemistry information
:type remove_stereo: bool
:rtype: automol molecular graph
"""
gra = object_from_hardcoded_inchi_by_key('graph', ich)
if gra is None:
ich = standard_form(ich)
if not stereo or not has_stereo(ich):
rdm = _rdkit.from_inchi(ich)
gra = _rdkit.to_connectivity_graph(rdm)
else:
geo = geometry(ich)
gra = graph(geo, stereo=stereo)
gra = implicit(gra)
return gra