def smiles_to_inchi_inchikey(smiles,verbose=0):
error_counter=0
warning_counter=0
inchis=[]
inchis2=[]
inchiKeys=[]
for elem in smiles:
mol=Chem.MolFromSmiles(elem)
if(mol!=None):
inchi, retcode, message, logs, aux =rdinchi.MolToInchi(mol)
inchiKey=rdinchi.InchiToInchiKey(inchi)
inchis.append(inchi)
inchiKeys.append(inchiKey)
try:
mol, retcode, message, logs=rdinchi.InchiToMol(inchi)
if(mol!=None):
inchi2, retcode, message, logs, aux =rdinchi.MolToInchi(mol)
inchis2.append(inchi2)
else:
inchis2.append("XXX")
if(verbose!=0):
print(elem+ ": InChI cannot converted to mol object, added XXX instead!")
except:
if(verbose!=0):
print(retcode)
print(message)
print("Smiles:"+elem)
inchis2.append("XXX")
else:
inchis.append("XXX")
inchiKeys.append("XXX")
inchis2.append("XXX")
if(verbose!=0):
print(elem+ ": can not converted added XXX instead! ")
error_counter=error_counter+1
for i1,i2 in zip(inchis,inchis2):
if(i1!=i2):
if(verbose!=0):
print("Warning:"+i1+" - "+i2)
warning_counter=warning_counter+1
print("\nGeneration of InChI and InChIKey from SMILES is completed.")
print("Total errors:"+str(error_counter))
print("Total warnings:"+str(warning_counter)+"\n")
return inchis,inchiKeys
def MolFromInchi(inchi,
sanitize=True,
removeHs=True,
logLevel=None,
treatWarningAsError=False):
"""Construct a molecule from a InChI string
Keyword arguments:
sanitize -- set to True to enable sanitization of the molecule. Default is
True
removeHs -- set to True to remove Hydrogens from a molecule. This only
makes sense when sanitization is enabled
logLevel -- the log level used for logging logs and messages from InChI
API. set to None to diable the logging completely
treatWarningAsError -- set to True to raise an exception in case of a
molecule that generates warning in calling InChI API. The resultant
molecule and error message are part of the excpetion
Returns:
a rdkit.Chem.rdchem.Mol instance
"""
try:
mol, retcode, message, log = rdinchi.InchiToMol(
inchi, sanitize, removeHs)
except ValueError as e:
logger.error(str(e))
return None
if logLevel is not None:
if logLevel not in logLevelToLogFunctionLookup:
raise ValueError("Unsupported log level: %d" % logLevel)
log = logLevelToLogFunctionLookup[logLevel]
if retcode == 0:
log(message)
if retcode != 0:
if retcode == 1:
logger.warning(message)
else:
logger.error(message)
if treatWarningAsError and retcode != 0:
raise InchiReadWriteError(mol, message)
return mol