Hi Lewis, Dealing with all the strange chemical representations that show up "in the wild" is an ongoing struggle.
Your first example is pretty clearly intended to be an azide and we can certainly add a rule to normalize that one to what the RDKit expects it to be (there already is a rule for C-N=N#N, but that doesn't help here.). That won't happen before the next feature release though. I'm not really sure what the intent was for the two four-coordinate neutral Ns in the second molecule, so I think it's unlikely that we'd add a standard cleanup for one. However! The good news is that there's a pretty easy (and efficient) way to fix this yourself. We added a new method to chemical reactions in the 2021.09 release which allows you to modify a molecule in place (subject to some constraints). This is ideal for doing cleanup transformations like these. This gist shows how to write reaction rules for your cases (I guessed for what the Ns are supposed to be) and then use them: https://gist.github.com/greglandrum/8fd229bc6bf6c734d1c21da7f2bebebb Hope this helps, -greg On Wed, Dec 15, 2021 at 12:21 AM Lewis Martin <lewis.marti...@gmail.com> wrote: > Hi All, > Reading molecules from a bulk download of SureChEMBL, I come across a fair > few molecules that fail to parse. Not sure whether they SHOULD parse or > not. > > Here is an example: https://www.surechembl.org/chemical/SCHEMBL386 > with SMILES code: COC(=O)C1=C(C=CC=C1)C1=CC=C(C[N+]#[N]=[N-])C=C1 > > Even reading the SMILES code one can see that there are too many bonds in > there - a nitrogen triply bonded and doubly bonded to other atoms. > > Another example: https://www.surechembl.org/chemical/SCHEMBL33957 > smiles: NC(N)=[NH]C1=NC(CSCC[NH]=CNS(=O)(=O)C2=CC=C(Br)C=C2)=CS1 > > Again, valence for a nitrogen is off. > > Should I expect to parse these with RDKit? Might there be some way around > this? It's a significant fraction of the molecules in SureChEMBL. > > Thanks team! > Lewis > _______________________________________________ > Rdkit-discuss mailing list > Rdkitemail@example.com > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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