def inchi_with_sort_from_coordinates(gra, atm_xyz_dct=None):
""" connectivity graph => inchi conversion
(if coordinates are passed in, they are used to determine stereo)
"""
gra = automol.graph.without_dummy_atoms(gra)
gra = automol.graph.dominant_resonance(gra)
atm_keys = list(automol.graph.atom_keys(gra))
bnd_keys = list(automol.graph.bond_keys(gra))
atm_syms = dict_.values_by_key(automol.graph.atom_symbols(gra), atm_keys)
atm_bnd_vlcs = dict_.values_by_key(
automol.graph.atom_bond_valences(gra), atm_keys)
atm_rad_vlcs = dict_.values_by_key(
automol.graph.atom_unsaturated_valences(gra), atm_keys)
bnd_ords = dict_.values_by_key(automol.graph.bond_orders(gra), bnd_keys)
atm_xyzs = (None if atm_xyz_dct is None else
dict_.values_by_key(atm_xyz_dct, atm_keys))
mlf, key_map_inv = _molfile.from_data(
atm_keys, bnd_keys, atm_syms, atm_bnd_vlcs, atm_rad_vlcs, bnd_ords,
atm_xyzs=atm_xyzs)
rdm = _rdkit.from_molfile(mlf)
ich, aux_info = _rdkit.to_inchi(rdm, with_aux_info=True)
nums = _parse_sort_order_from_aux_info(aux_info)
nums = tuple(map(key_map_inv.__getitem__, nums))
return ich, nums
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 inchi(smi):
""" SMILES => InChI
"""
ich = automol.convert.inchi.object_to_hardcoded_inchi_by_key(
'smiles', smi, comp=_compare)
if ich is None:
rdm = _rdkit.from_smiles(smi)
ich = _rdkit.to_inchi(rdm)
return ich
def inchi(smi):
""" Convert a SMILES string into an InChI string.
:param smi: SMILES string
:type smi: str
:rtype: str
"""
ich = object_to_hardcoded_inchi_by_key('smiles', smi, comp=_compare)
if ich is None:
rdm = _rdkit.from_smiles(smi)
ich = _rdkit.to_inchi(rdm)
return ich
def inchi_with_sort_from_geometry(gra, geo=None, geo_idx_dct=None):
""" Generate an InChI string from a molecular graph.
If coordinates are passed in, they are used to determine stereo.
:param gra: molecular graph
:type gra: automol graph data structure
:param geo: molecular geometry
:type geo: automol geometry data structure
:param geo_idx_dct:
:type geo_idx_dct: dict[:]
:rtype: (str, tuple(int))
"""
gra = without_dummy_atoms(gra)
gra = dominant_resonance(gra)
atm_keys = sorted(atom_keys(gra))
bnd_keys = list(bond_keys(gra))
atm_syms = dict_.values_by_key(atom_symbols(gra), atm_keys)
atm_bnd_vlcs = dict_.values_by_key(atom_bond_valences(gra), atm_keys)
atm_rad_vlcs = dict_.values_by_key(atom_unsaturated_valences(gra),
atm_keys)
bnd_ords = dict_.values_by_key(bond_orders(gra), bnd_keys)
if geo is not None:
assert geo_idx_dct is not None
atm_xyzs = coordinates(geo)
atm_xyzs = [
atm_xyzs[geo_idx_dct[atm_key]] if atm_key in geo_idx_dct else
(0., 0., 0.) for atm_key in atm_keys
]
else:
atm_xyzs = None
mlf, key_map_inv = _molfile.from_data(atm_keys,
bnd_keys,
atm_syms,
atm_bnd_vlcs,
atm_rad_vlcs,
bnd_ords,
atm_xyzs=atm_xyzs)
rdm = _rdkit.from_molfile(mlf)
ich, aux_info = _rdkit.to_inchi(rdm, with_aux_info=True)
nums = _parse_sort_order_from_aux_info(aux_info)
nums = tuple(map(key_map_inv.__getitem__, nums))
return ich, nums
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_with_sort_from_geometry(gra, geo=None, geo_idx_dct=None):
""" connectivity graph => inchi conversion
(if coordinates are passed in, they are used to determine stereo)
"""
gra = automol.graph.without_dummy_atoms(gra)
gra = automol.graph.dominant_resonance(gra)
atm_keys = sorted(automol.graph.atom_keys(gra))
bnd_keys = list(automol.graph.bond_keys(gra))
atm_syms = dict_.values_by_key(automol.graph.atom_symbols(gra), atm_keys)
atm_bnd_vlcs = dict_.values_by_key(automol.graph.atom_bond_valences(gra),
atm_keys)
atm_rad_vlcs = dict_.values_by_key(
automol.graph.atom_unsaturated_valences(gra), atm_keys)
bnd_ords = dict_.values_by_key(automol.graph.bond_orders(gra), bnd_keys)
#print('geo test print:', automol.geom.string(automol.graph.geometry(gra)))
if geo is not None:
assert geo_idx_dct is not None
atm_xyzs = automol.geom.coordinates(geo)
atm_xyzs = [atm_xyzs[geo_idx_dct[atm_key]] for atm_key in atm_keys]
else:
atm_xyzs = None
mlf, key_map_inv = _molfile.from_data(atm_keys,
bnd_keys,
atm_syms,
atm_bnd_vlcs,
atm_rad_vlcs,
bnd_ords,
atm_xyzs=atm_xyzs)
rdm = _rdkit.from_molfile(mlf)
ich, aux_info = _rdkit.to_inchi(rdm, with_aux_info=True)
nums = _parse_sort_order_from_aux_info(aux_info)
nums = tuple(map(key_map_inv.__getitem__, nums))
return ich, nums