I've stumbled onto a molfile which is read properly (MolFromMolBlock) and produces a proper smiles (MolToSmiles). But the smiles generated fails on Chem.MolFromSmiles. Can you help figure this one out? I've attached the molfile in question.
Here is a simple script I used to show this issue. from rdkit import rdBase from rdkit import Chem import sys print rdBase.boostVersion print rdBase.rdkitVersion mb = sys.stdin.read() mol = Chem.MolFromMolBlock(mb) if mol: smi = Chem.MolToSmiles(mol, isomericSmiles=True) print smi newmol = Chem.MolFromSmiles(smi) and the result I get python rdmol.py <254080.mol 1_40 2010.12.1 [Cl-].CC(C)(C)c1[Te+]c(C(C)(C)C)cc(/C=C/C=C2C=C(C(C)(C)C)OC(C(C)(C)C)=C2)c1 [18:13:52] Can't kekulize mol I just rebuilt from subversion source - not sure why this version shows as 2010.12.1 RL: https://rdkit.svn.sourceforge.net/svnroot/rdkit/trunk Repository Root: https://rdkit.svn.sourceforge.net/svnroot/rdkit Repository UUID: 19320e9b-7711-0410-929e-f4fff3a11e9f Revision: 1611 Node Kind: directory Schedule: normal Last Changed Author: glandrum Last Changed Rev: 1611 Last Changed Date: 2011-01-05 00:45:35 -0800 (Wed, 05 Jan 2011) Thanks, TJ O'Donnell
254080.mol
Description: Binary data
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