From: Joerg K. W. <we...@in...> - 2004-06-29 16:03:55
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Hi NAJI, > I would like to ask you if we can transform a Smiles file ( where the > smiles don't contain charges ) to a Smiles file where the molecules are > charged (compounds and groups must be represented in their common state > in aqueous solution, at pH=7) I think we are talking about SMARTS, not SMILES. So we are talking on regular expression patterns on graphs. SMILES is only a subset of SMARTS. Sure you can that's what i expect. If you have time you can also invent tautomer transfomation rules with the same mechansim. I would be happy if you will do. Two possibilities: 1. Modify phmodel.txt and store in myPhModel.txt or what you like Then change in src/joelib.properties the line joelib.data.JOEPhModel.resourceFile=joelib/data/plain/phmodel.txt to joelib.data.JOEPhModel.resourceFile=joelib/data/plain/myPhModel.txt 2. If you want to use SMARTS transformations in general you can use the joelib.data.JOEChemTransformation class see tutorial http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html So for each tranformation you want to apply you need such an instance. The pH model uses simply a vector of such rules and applys them all. For N tautomers or biotransformations you can simply call them NxN times. Then you can try to remove duplicates by using a clever hash code or whatever. Or you can try to avoid calculating them NxN by assuming a clever heuristic, ... but's that's another thread, isn't it ? :-) Kind regards, Joerg > For example > CC(N)C(O)=O>> CC([NH3+])C([O-])=O > In the JOELib I observe source\src\joelib\data\plain/phmodel.txt > #charged amine > TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] > #carboxylic acid > TRANSFORM O=C[OQ1-0:1] >> O=C[O-:1] > Therefore, can I change automatically with a programme in Joelib and > with a phmodel.txt file a Smiles file file ( where the smiles don't > contain charges ) to a Smiles file where the molecules are charged > (compounds and groups must be represented in their common state in > aqueous solution, at pH=7) -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |