Hello,
Below I show a smiles string from MOE and the smiles string calculated from
RDKit and the InChI string calculated by RDkit(2020_1).
The error on conversion to inchi string is confusing me after entering both
smiles strings into a viewer I don't see any undefined stereo center.
O=C(/C=C/c1ccccc1)c1ccc(OC/C=C(/CC/C=C(\C)/C)\C)cc1
CC(C)=CCC/C(C)=C/COc1ccc(C(=O)/C=C/c2ccccc2)cc1
[18:10:42] WARNING: Omitted undefined stereo
InChI=1S/C25H28O2/c1-20(2)8-7-9-21(3)18-19-27-24-15-13-23(14-16-24)25(26)17-12-22-10-5-4-6-11-22/h4-6,8,10-18H,7,9,19H2,1-3H3
while len(line) != 0:
fields = line.replace('","',' ').split()
mol1 = fields[0].replace('"','')
mol_name = fields[1]
try:
mol = Chem.MolFromSmiles(mol1,sanitize=False) #, removeHs=False)
except:
mol = None
if mol is None:
print("mol1 failed:",mol1)
output.write("mol1 failes:",mol1)
else:
rkditsmiout.write('\"'+Chem.MolToSmiles(mol,
isomericSmiles=True)+'\"\n')
print(Chem.MolToSmiles(mol, isomericSmiles=True))
rkditsmiout.write('\"'+Chem.inchi.MolToInchi(mol)+'\"\n')
print(Chem.inchi.MolToInchi(mol))
count += 1
print(count)
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
