Dear Christian, 2010/6/28 Christian de Bouillé <ambin...@wanadoo.fr>: > > How can I escape to this error ? > as I cannot change the smiles >
To review for the mailing list. The molecule in question is: CC[NH+](CC)CC.O1c2ccccc2O[P-]1123Oc4ccccc4O1.O2c1ccccc1O3 What I said before: > I'm not sure what your question is. The error message is pretty clear: > the P in your molecule has a valence of 7. The RDKit expects P to have > a valence of either 3 or 5. The anion in this compound, trisphat, is > an example of a hypervalent phosphorous, which the RDKit does not > currently accept. > > If enough people think it's important, we can discuss how to molecules > like this can be supported by the RDKit. To continue and try to answer Christian's question: it is currently impossible to really work with this hypervalent molecule in the RDKit. The only real solution is to tell the RDKit that P is allowed to have 7 substituents. If you really want to do this you can edit the file $RDBASE/Code/GraphMol/atomic_data.cpp and change the allowed valence list for P from "3 5" to "3 5 7". After you do this, you will need to rebuild the code. Best Regards, -greg ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
