Dear James, On Fri, Dec 17, 2010 at 5:35 PM, James Davidson <[email protected]> wrote: > > I have been investigating an issue that a colleague of mine identified. > He was working with the RDKit Canon Smiles node in Knime, and found that > for the natural product, Geldanamycin, the double-bond geometry > information was being lost during canonicalisation. I repeated this > result outside of knime: > > from rdkit import Chem > from rdkit.Chem import AllChem > >>>> smi = > r'NC(=O)o...@h]1c(/C)=C/[...@h](C)[C@@H](O)[C@@H](OC)c...@h](C)C\C2=C(/OC)C( > =O)\C=C(\NC(=O)C(\C)=C\C=C/[C@@H]1OC)C2=O' >>>> AllChem.CanonSmiles(smi) > > 'COC1=C2C[C@@H](C)c...@h](OC)[...@h](O)[C@@H](C)C=C(C)[...@h](OC(N)=O)[C@@H]( > OC)C=CC=C(C)C(=O)NC(=CC1=O)C2=O' > > > The simpler example below may be better: > >>>> smi1 = r'O1CC/C=C\CCCC1' # cyclic ether >>>> smi2 = r'OCC/C=C\CCCC' # corresponding acyclic alcohol > >>>> AllChem.CanonSmiles(smi1) > 'C1C=CCCOCCC1' -> stereochemistry lost >>>> AllChem.CanonSmiles(smi2) > 'CCCC/C=C\\CCO' -> stereochemistry retained >> > So, I am guessing that double-bonds in rings are being 'ignored'(?) by > the canonicaliser?
It's actually being done by the molecule cleanup code that is run when a molecule is read. The result is, as far as you're concerned, the same though: there's no stereochemistry on ring double bonds. > For 'classic' aliphatic systems, double-bonds in > 3-7-membered rings can only sensibly exist in the cis orientation, so > 'ignoring' them would be ok. However, for 8-membered and above, cis or > trans are certainly both possible, so it becomes more important to keep > track - particularly if canonical smiles are being used to check for > unique structures, as my colleague was doing with the geldanamycin > example above. yeah, that's clear: for larger ring systems the information should be preserved. That's very easy to do. The more difficult part is going to be making sure the output is actually canonical. I've entered a bug for this (https://sourceforge.net/tracker/?func=detail&aid=3139534&group_id=160139&atid=814650) and I'll take a look to try and get it fixed (and correct). It would be helpful to have some additional test cases; I will generate some, but if you have some examples you could send (or attach to the bug report) it would be quite helpful. Thanks for the report, -greg ------------------------------------------------------------------------------ Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
