def to_inchi(str_data, in_format):
mol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
conv.ReadString(mol, str_data)
conv.SetOutFormat('inchi')
inchi = conv.WriteString(mol).rstrip()
conv.SetOptions('K', conv.OUTOPTIONS)
inchikey = conv.WriteString(mol).rstrip()
return (inchi, inchikey)
class Converter:
def __init__(self, can=False):
self._OBconverter = OBConversion()
self._OBconverter.SetOutFormat('smi')
options = 'in'
if can:
options += 'c'
self._OBconverter.SetOptions(options, OBConversion.OUTOPTIONS)
def getSmiles(self, mol):
smiles = self._OBconverter.WriteString(mol.OBMol)[:-1]
if '@' in smiles:
smiles = self._OBconverter.WriteString(mol.OBMol)[:-1]
return smiles
def to_inchi(str_data, in_format):
mol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
# Hackish for now, convert to xyz first...
conv.SetOutFormat('xyz')
conv.ReadString(mol, str_data)
xyz = conv.WriteString(mol)
# Now convert to inchi and inchikey.
mol = OBMol()
conv.SetInFormat('xyz')
conv.ReadString(mol, xyz)
conv.SetOutFormat('inchi')
inchi = conv.WriteString(mol).rstrip()
conv.SetOptions("K", conv.OUTOPTIONS)
inchikey = conv.WriteString(mol).rstrip()
return (inchi, inchikey)
def get_inchikey_gen():
ob_conversion = OBConversion()
ob_conversion.SetInAndOutFormats("inchi", "inchi")
ob_conversion.SetOptions("K", ob_conversion.OUTOPTIONS)
def get_inchikey(ser):
try:
if 'inchikey' in ser:
return ser.inchikey
if ser.inchi is None or ser.inchi == '':
raise Exception('Empty inchi')
mol = OBMol()
ob_conversion.ReadString(mol, ser.inchi)
return ob_conversion.WriteString(mol).strip('\n')
except Exception as e:
LOG.warning(e)
return '{}-{}-{}'.format(ser.formula, ser['name'], ser['id'])
return get_inchikey