Thank you very much - this is what I been expecting... 2009/5/26 Greg Landrum <[email protected]>
> On Tue, May 26, 2009 at 9:51 AM, Evgueni Kolossov <[email protected]> > wrote: > > > > One additional question about this subject: > > If we have molecules in both tautomeric forms:'C[N+](=O)([O-])' and > > CN(=O)(=O)' > > than what we will have after SmilesToMol() and MolToSmiles() (which will > > sanitise molecule)? > > There's no difference between the results, the sanitization step done > by MolToSmiles() or by reading molecules in from a mol block "fixes" > the system by generating the zwitterionic form: > -------------------- > [2]>>> m = Chem.MolFromSmiles('CN(=O)(=O)') > > [3]>>> print Chem.MolToMolBlock(m) > > RDKit > > 4 3 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 > 2 3 1 0 > 2 4 2 0 > M CHG 2 2 1 3 -1 > M END > > > [4]>>> m2 = Chem.MolFromSmiles('C[N+](=O)([O-])') > > [5]>>> print Chem.MolToMolBlock(m) > > RDKit > > 4 3 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 > 2 3 1 0 > 2 4 2 0 > M CHG 2 2 1 3 -1 > M END > > -------------------- > > -greg >
