There is a fair bit of information associated with the original PR: https://github.com/cdk/cdk/pull/916
It's my understanding that hydrogens are not automatically adjusted, that is, modifying the charge on an atom requires adjusting the hydrogen count. In this comment are references to more information regarding the different matching modes: https://github.com/cdk/cdk/pull/916#issuecomment-1273164172 Best Uli On Mon, Nov 25, 2024 at 4:59 AM Jonas Schaub via Cdk-user < cdk-user@lists.sourceforge.net> wrote: > Hi Egon, > > > > I also started playing with SMIRKS only a few days ago but I think you > need to specify the neutral charge and hydrogen saturation in the product > explicitly. I tried “[O-:1]>>[O;+0;H1:1]” and it produced the output you > are looking for (O=C(O)C). > > > > > let's say we have multiple carboxylic acids and amine groups, how would > one enumerate all possible charge states? Is that possible with just SMIRKS? > > > > If you use the transform mode “Unique”, you will get as many structures > returned as there are matches to your SMIRKS in the molecule. So in each > returned structure, one carboxylic acid would be neutralised. But I guess > this is only the first step towards what you are looking for. I am actually > faced with a similar problem right now, i.e. enumerating all possible > transformation combinations for one molecule and multiple SMIRKS… > > > > Hope this was of help. > > > > Kind regards, > > Jonas > > > > *From:* Egon Willighagen <egon.willigha...@gmail.com> > *Sent:* Saturday, November 23, 2024 6:52 PM > *To:* CDK users list <cdk-user@lists.sourceforge.net> > *Subject:* [Cdk-user] SMIRKS in 2.10-SNAPSHOT > > > > > Hi John, all, > > > > I am playing with SMIRKS but it's pretty new to me. > > > > Transform neutralAcid = Smirks.compile("[O-:1]>>[O:1]"); > > IAtomContainer cdkStruct = parser.parseSmiles("CC(=O)[O-]"); > Iterable<IAtomContainer> iterable = neutralAcid.apply(cdkStruct, > Transform.Mode.Exclusive); > for (IAtomContainer neutral : iterable) { > String neutralSmiles = generator.createSMILES(neutral); > > System.out.println(neutralSmiles); > } > > > > (I hope I did not make any copy/paste typos) > > > > Why am I not getting this as output: CC(=O)O ? > > > > (Actually, let's assume I can get that working, let's say we have multiple > carboxylic acids and amine groups, how would one enumerate all possible > charge states? Is that possible with just SMIRKS?) > > > > Egon > > > > -- > > [NL] WikiPathways in actie voor MetaKids: We zamelen geld in voor MetaKids > met een actie rond WikiPathways, zie https://sr24.wikipathways.org/. > Doneer via > https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids > > > > [EN] WikiPathways in action for MetaKids: We are fundraising for the Dutch > charity MetaKids by improving metabolic disorder pathways, see > https://sr24.wikipathways.org/. Donate at > https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids > > > > -- > > E.L. Willighagen > Department of Translational Genomics > > NUTRIM Institute of Nutrition and Translational Research in Metabolism > Maastricht University > Blog: https://chem-bla-ics.linkedchemistry.info/ > Mastodon: https://social.edu.nl/@egonw > PubList: https://orcid.org/0000-0001-7542-0286 > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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