Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli June 2006, UGM
Jan 09, 2016
Java Solutions for Cheminformatics
Structure based predictions – new plugins
Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli
June 2006, UGM
Calculator Plugin Interface
Marvin GUI
cxcalc command line tool
Java API
Chemical Terms• evaluate command line tool• search filtering• JChem Cartridge• reaction processing
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
Tautomerization Plugin
Resonance Plugin
Stereoisomer Plugin
Conformer Plugin
Molecular Dynamics Plugin
Geometry Plugin
Molecular Surface Area Plugin
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…
Display Results In MarvinSpace
Use MarvinSpace Display In Custom Plugins
plugin.getResultDomain(Object) == CalculatorPlugin.ATOM
plugin.getResult(Object, int) instanceof Number
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