def _connected_smiles(ich):
smi = object_from_hardcoded_inchi_by_key('smiles', ich)
if smi is None:
ich = automol.inchi.standard_form(ich)
rdm = _rdkit.from_inchi(ich)
smi = _rdkit.to_smiles(rdm)
return smi
def _connected_formula(ich):
fml = object_from_hardcoded_inchi_by_key('formula', ich)
if fml is None:
ich = automol.inchi.standard_form(ich)
rdm = _rdkit.from_inchi(ich)
fml = _rdkit.to_formula(rdm)
return fml
def recalculate(ich, stereo=False):
""" Recalculate an InChI string.
:param ich: InChI string
:type ich: str
:param stereo: force the same stereochem in recalculated InChI
:type stereo: bool
:rtype: str
"""
# for now, just assert that we have no multi-component strings with
# hardcoded parts -- these are guaranteed to fail
ichs = split(ich)
if len(ichs) > 1:
if any(object_from_hardcoded_inchi_by_key('inchi', ich)
for ich in ichs):
ref_ichs = []
for ich_i in ichs:
ref_ichs.append(recalculate(ich_i))
ref_ichs.sort()
ret = join(ref_ichs)
return ret
# raise error.FailedInchiGenerationError
ret = object_from_hardcoded_inchi_by_key('inchi', ich)
if ret is None:
_options = '-SUU' if stereo else ''
rdm = _rdkit.from_inchi(ich)
ret = _rdkit.to_inchi(rdm, options=_options, with_aux_info=False)
return ret
def _connected_graph(ich, no_stereo=False):
gra = object_from_hardcoded_inchi_by_key('graph', ich)
if gra is None:
ich = automol.inchi.standard_form(ich)
if no_stereo or not automol.inchi.has_stereo(ich):
rdm = _rdkit.from_inchi(ich)
gra = _rdkit.to_connectivity_graph(rdm)
else:
geo = geometry(ich)
gra = automol.convert.geom.graph(geo)
gra = automol.graph.implicit(gra)
return gra
def test__inchi_geometry():
""" test automol.inchi.geometry
"""
ref_ich = 'InChI=1S/H2S/h1H2'
ich = automol.geom.inchi(automol.inchi.geometry(ref_ich))
assert ich == ref_ich
ref_ich = 'InChI=1S/Cl2/c1-2'
ich = automol.geom.inchi(automol.inchi.geometry(ref_ich))
assert ich == ref_ich
ref_ich = 'InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3'
pbm = pybel.from_inchi(ref_ich)
ich = pybel.to_inchi(pbm)
assert ich == ref_ich
rdm = rdkit.from_inchi(ref_ich)
ich = automol.geom.inchi(rdkit.to_geometry(rdm))
assert ich == ref_ich
ref_ich = 'InChI=1S/Ar'
rdm = rdkit.from_inchi(ref_ich)
ich = automol.geom.inchi(rdkit.to_geometry(rdm))
assert ich == ref_ich
def _connected_smiles(ich):
""" Convert a SMILES string into an InChI string.
:param smi: SMILES string
:type smi: str
:rtype: str
"""
smi = object_from_hardcoded_inchi_by_key('smiles', ich)
if smi is None:
ich = standard_form(ich)
rdm = _rdkit.from_inchi(ich)
smi = _rdkit.to_smiles(rdm)
return smi
def _connected_formula(ich):
""" Create a combined molecular from the formulas of a
multi-component InChI string.
:param ich: InChI string
:type ich: str
:rtype: dict[str: int]
"""
fml = object_from_hardcoded_inchi_by_key('formula', ich)
if fml is None:
ich = standard_form(ich)
rdm = _rdkit.from_inchi(ich)
fml = _rdkit.to_formula(rdm)
return fml
def recalculate(ich, force_stereo=False):
""" recalculate InChI string
"""
# for now, just assert that we have no multi-component strings with
# hardcoded parts -- these are guaranteed to fail
ichs = automol.inchi.split(ich)
if len(ichs) > 1:
if any(object_from_hardcoded_inchi_by_key('inchi', ich)
for ich in ichs):
ref_ichs = []
for ich_i in ichs:
ref_ichs.append(recalculate(ich_i))
ref_ichs.sort()
ret = automol.inchi.join(ref_ichs)
return ret
# raise error.FailedInchiGenerationError
ret = object_from_hardcoded_inchi_by_key('inchi', ich)
if ret is None:
_options = '-SUU' if force_stereo else ''
rdm = _rdkit.from_inchi(ich)
ret = _rdkit.to_inchi(rdm, options=_options, with_aux_info=False)
return ret
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
def _gen1(ich):
rdm = _rdkit.from_inchi(ich)
geos = _rdkit.to_conformers(rdm, nconfs)
return geos
