![Page 1: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/1.jpg)
Java Solutions for Cheminformatics
Structure based predictions – new plugins
Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli
June 2006, UGM
![Page 2: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/2.jpg)
Calculator Plugin Interface
Marvin GUI
cxcalc command line tool
Java API
Chemical Terms• evaluate command line tool• search filtering• JChem Cartridge• reaction processing
![Page 3: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/3.jpg)
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
![Page 4: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/4.jpg)
Tautomerization Plugin
![Page 5: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/5.jpg)
Resonance Plugin
![Page 6: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/6.jpg)
Stereoisomer Plugin
![Page 7: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/7.jpg)
Conformer Plugin
![Page 8: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/8.jpg)
Molecular Dynamics Plugin
![Page 9: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/9.jpg)
Geometry Plugin
![Page 10: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/10.jpg)
Molecular Surface Area Plugin
![Page 11: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/11.jpg)
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.sdfid Distance1 7.862 9.083 7.154 8.065 8.546 8.527 6.248 7.079 7.4810 3.3311 6.3112 4.1413 4.7914 3.26…
![Page 12: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/12.jpg)
Display Results In MarvinSpace
![Page 13: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/13.jpg)
Use MarvinSpace Display In Custom Plugins
plugin.getResultDomain(Object) == CalculatorPlugin.ATOM
plugin.getResult(Object, int) instanceof Number
![Page 14: Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli](https://reader033.vdocuments.site/reader033/viewer/2022061306/5514652a550346414e8b5b20/html5/thumbnails/14.jpg)
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