From: cruttkie <cru...@ip...> - 2016-02-09 08:42:29
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Hi, I am using CDK to find substructures within an AtomContainer and write them out as SMILES. The problem I have with this workflow is related to the loss of aromaticity information when writing those substructure SMILES in case the substructure has matched within an aromatic ring for example. Is there a way to write out SMARTS instead of SMILES? If not, do you think it is a nice idea to adapt the SmilesGenerator to write out SMARTS including aromaticity information? Best regards, Christoph -- Christoph Ruttkies Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle, Germany email: cru...@ip... phone: +49-345-5582-1471 fax: +49-345-5582-1409 |
From: John M <joh...@gm...> - 2016-02-09 09:42:57
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Hi Christoph, We don't currently have a SMARTS writer but if you want to write aromatic SMILES you just need to tell the generator. It takes exactly what you put it, so I can set the arom flags myself on a substrcture and then create the SMILES: > * IAtomContainer mol = new AtomContainer();* > * IAtom a1 = new Atom("C");* > * a1.setImplicitHydrogenCount(0);* > * a1.setIsAromatic(true);* > * IAtom a2 = new Atom("O");* > * a2.setImplicitHydrogenCount(0);* > * a2.setIsAromatic(true);* > * IAtom a3 = new Atom("C");* > * a3.setImplicitHydrogenCount(0);* > * a3.setIsAromatic(true);* > * IBond b1 = new Bond(a1, a2);* > * b1.setIsAromatic(true);* > * IBond b2 = new Bond(a2, a3);* > * b2.setIsAromatic(true);* > * mol.addAtom(a1);* > * mol.addAtom(a2);* > * mol.addAtom(a3);* > * mol.addBond(b1);** mol.addBond(b2);* > > * SmilesGenerator smigen = SmilesGenerator.generic()* > * .aromatic();** > String smi = smigen.create(mol);* [c]o[c] Note you have to watch out for hydrogens! *[nH]1ccc2c1cccc2 *is indole but as a SMARTS won't match Cn1ccc2c1cccc2. Thanks, John Regards, John W May joh...@gm... On 9 February 2016 at 08:42, cruttkie <cru...@ip...> wrote: > Hi, > > I am using CDK to find substructures within an AtomContainer and write > them out as SMILES. The problem I have with this workflow is related to > the loss of aromaticity information when writing those substructure > SMILES in case the substructure has matched within an aromatic ring for > example. > > Is there a way to write out SMARTS instead of SMILES? If not, do you > think it is a nice idea to adapt the SmilesGenerator to write out SMARTS > including aromaticity information? > > Best regards, > Christoph > > -- > > Christoph Ruttkies > Group Bioinformatics & Mass Spectrometry > Leibniz Institute of Plant Biochemistry > Weinberg 3 > 06120 Halle, Germany > > email: cru...@ip... > phone: +49-345-5582-1471 > fax: +49-345-5582-1409 > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user > |