From: Rajarshi G. <rg...@in...> - 2007-06-21 22:43:38
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Hi, is there a way that the SMILESGenerator can be forced to create a SMILES string using atom ordering rather than generating a canonical SMILES string? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Build a system that even a fool can use and only a fool will want to use it. |
From: Stefan K. <sk...@ip...> - 2007-06-22 08:04:51
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On Friday 22 June 2007 00:43, Rajarshi Guha wrote: > Hi, is there a way that the SMILESGenerator can be forced to create a > SMILES string using atom ordering rather than generating a canonical > SMILES string? No. And not just in CDK: If you start with a given atom, you have to contin= ue=20 with the nearest atom and so on. So to have the atoms in a smiles in an=20 arbitrary order is not possible. The only thing you can change is the start= =20 atom. This is set in line 326 in SmilesGenerator class, which should be no= =20 problem to change to start=3Dmolecule.getAtom(0); Stefan > > ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > Build a system that even a fool can use and > only a fool will want to use it. > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel =2D-=20 Stefan Kuhn BSc MA IPB Halle AG Bioinformatik & Massenspektrometrie Weinberg 3 06120 Halle http://www.ipb-halle.de http://msbi.bic-gh.de sk...@ip...=A0Tel. +49 (0) 345 5582 1474=A0Fax.+49 (0) 345 5582 1409 |
From: Christoph S. <er...@do...> - 2007-06-25 14:39:26
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Stefan Kuhn wrote: > On Friday 22 June 2007 00:43, Rajarshi Guha wrote: >> Hi, is there a way that the SMILESGenerator can be forced to create a >> SMILES string using atom ordering rather than generating a canonical >> SMILES string? > No. And not just in CDK: If you start with a given atom, you have to continue > with the nearest atom and so on. So to have the atoms in a smiles in an > arbitrary order is not possible. That may not be completely true. You can use "." and bond identifiers "." (normally used for ring closures) to encode all kind of weird things. C1CC.CCC1 is n-hexane, as a start. C1.C12.C23.C34.C45.C56.O6 gives hexanol. C1.C12.C236.O6.C34.C45.C5 gives hexan-3-ol, to demonstrate a branching. Try these smiles on http://www.daylight.com/daycgi/depict Not nice, but it works. Not sure if you can encode a molecule with arbitrary atom order by this, but it looks like. Haven't thought it through. Cheers, Chris -- PD Dr. Christoph Steinbeck Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Stefan K. <sk...@ip...> - 2007-06-25 16:16:34
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On Monday 25 June 2007 16:38, Christoph Steinbeck wrote: > Stefan Kuhn wrote: > > On Friday 22 June 2007 00:43, Rajarshi Guha wrote: > >> Hi, is there a way that the SMILESGenerator can be forced to create a > >> SMILES string using atom ordering rather than generating a canonical > >> SMILES string? > > > > No. And not just in CDK: If you start with a given atom, you have to > > continue with the nearest atom and so on. So to have the atoms in a > > smiles in an arbitrary order is not possible. > > That may not be completely true. You can use "." and bond identifiers > "." (normally used for ring closures) to encode all kind of weird things. True. My fault. Although I would not do this and I believe the original=20 poster was not clear about the consequences of trying an=20 arbitrary-order-smiles. > > C1CC.CCC1 is n-hexane, as a start. > > C1.C12.C23.C34.C45.C56.O6 gives hexanol. > > C1.C12.C236.O6.C34.C45.C5 gives hexan-3-ol, to demonstrate a branching. > > Try these smiles on http://www.daylight.com/daycgi/depict > > Not nice, but it works. Not sure if you can encode a molecule with > arbitrary atom order by this, but it looks like. Haven't thought it > through. > > Cheers, > > Chris =2D-=20 Stefan Kuhn BSc MA IPB Halle AG Bioinformatik & Massenspektrometrie Weinberg 3 06120 Halle http://www.ipb-halle.de http://msbi.bic-gh.de sk...@ip...=C2=A0Tel. +49 (0) 345 5582 1474=C2=A0Fax.+49 (0) 345 558= 2 1409 |