Hi Lewis, SureChEMBL is getting its structures from:
- USPTO attached molfiles (deposited structures) - names using tools including OPSIN, ChemAxon, Lexichem, ACD. - images using tools including OSRA, imago, CLiDE. As Nicolas points out, issues like this one can occur when auto generating structures from names and images. It is the case for the 2 structures you mention. We have plans to review all the tools we are using to generate the structures as we know about some new ones out there. Cheers, Eloy On Thu, 16 Dec 2021 at 09:28, Nicolas Bosc <nb...@ebi.ac.uk> wrote: > Hi Lewis, > > Currently structures are generated automatically in SureChEMBL so this > kind of error unfortunately happens… > > My colleagues will address this issue as soon as possible. > > Cheers, > Nicolas > ----------------------------------------------- > Dr Nicolas Bosc > Data Mining and Analysis Scientist > ChEMBL group > EMBL-EBI > Wellcome Genome Campus > Hinxton, Cambridge, CB10 1SD > United Kingdom > > nb...@ebi.ac.uk > +44 1223 492519 > > > On 15 Dec 2021, at 20:42, Lewis Martin <lewis.marti...@gmail.com> wrote: > > Thanks a lot Greg! That is indeed very helpful. > > Just to know that the molecule is odd is helpful too. The mol blocks > appear to be V2000 format and have names like "Mrv0541 03021215572D" > which says ChemAxon Marvin to me, but I'm still unsure why SureChEMBL would > use such a representation (it doesn't look like a faithful transcription > from the source patent). Off-topic, but if anyone happens to have an > insight or connection with SureChEMBL, please do reach out! > > Cheers > Lewis > > > > > On Wed, Dec 15, 2021 at 4:24 PM Greg Landrum <greg.land...@gmail.com> > wrote: > >> 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 >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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