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Java Solutions for Cheminformatics

Java Solutions for Cheminformatics. Structure based predictions – new plugins Zsolt Moh ácsi , Nóra Máté , József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli. June 2006, UGM. Calculator Plugin Interface. Marvin GUI. Chemical Terms evaluate command line tool search filtering

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Java Solutions for Cheminformatics

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  1. Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté,József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli June2006, UGM

  2. Calculator Plugin Interface Marvin GUI • Chemical Terms • evaluatecommand line tool • search filtering • JChem Cartridge • reaction processing Java API cxcalc command line tool

  3. New Plugins Elemental Analysys Protonation pKa, Major Microspecies, Isoelectric Point Partitioning logP, logD Charge Charge, Polarizability Isomers Tautomers, Resonance, Stereoisomers Conformation Conformers, Molecular Dynamics Geometry Topology Analysis, Geometry, Polar Surface Area, Molecular Surface Area Other H Bond Donor/Acceptor, Huckel Analysis, Refractivity

  4. Tautomerization Plugin

  5. Resonance Plugin

  6. Stereoisomer Plugin

  7. Conformer Plugin

  8. Molecular Dynamics Plugin

  9. Geometry Plugin

  10. Molecular Surface Area Plugin

  11. Using New Plugins With cxcalc Calculate 400 conformers at pH=7.4 of molecule m1 (using major microspecies and conformer plugin): $ cxcalc majorms -H 7.4 -f mol m1.mol | cxcalc conformers -m 400 -f sdf > conformers_at_ph.sdf Calculate the distance of atom 15 and atom 16 in each conformer (using geometry plugin): $ cxcalc distance –a 15-16 conformers_at_ph.sdf id Distance 1 7.86 2 9.08 3 7.15 4 8.06 5 8.54 6 8.52 7 6.24 8 7.07 9 7.48 10 3.33 11 6.31 12 4.14 13 4.79 14 3.26 …

  12. Display Results In MarvinSpace

  13. Use MarvinSpace Display In Custom Plugins plugin.getResultDomain(Object) == CalculatorPlugin.ATOM plugin.getResult(Object, int) instanceof Number

  14. Acknowledgements, Links Acknowledgements • ChemAxon people taking part in development: • Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli (plugin development) • Judit Papp, Miklós Vargyas (MarvinSpace) Links • Calculator plugins • www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins.html • Unlimited predictions online • www.chemaxon.com/demosite/marvin/index.html • Plugin development • www.chemaxon.com/marvin/doc/dev/plugins.html • API documentation • www.chemaxon.com/marvin/doc/api/index.html

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