1. Scientific & technical presentation Calculator Plugins January 2011

2. Calculator Plugin Features Key features: Calculations can be performed using the graphical user interface of MarvinSketch and MarvinView Predictions can be run in batch mode with cxcalc command line tool Plugin calculations can be used for filtering results of database searches in JChem Base in Instant JChem in JChem Cartridge Define smart reaction rules using plugin calculations in Reactor (ChemAxons virtual reaction processing tool) Java API for developers Calculator Plugins are modules of ChemAxons Marvin and JChem cheminformatics platforms which calculate chemical properties descriptors from chemical structures.

3. Calculation Interface Marvin GUI cxcalc command line tool Java API Chemical Terms evaluate command line tool search filtering in JChem Base, _Instant JChem and JChem Cartridge virtual reaction processing (Reactor)

4. Marvin GUI Results are displayed in a separate result display window Parameter panel allows you to set options for the calculation. Plugins are listed in the Tools menu.

5. Command line access: cxcalc Plugin calculations can be run by the command line tool cxcalc. The calculations can be performed singly or in batch mode. All calculations are listed in the help text: Calculation specific help is also available: pK a (strongest acidic and basic pK a values) and major microspecies (pH=7.4) calculation: $ cxcalc $ cxcalc pka -h $ cxcalc pka –a 1 –b 1 majorms –H 7.4 mols.sdf idapKa1bpKa1atomsmajor-ms 13.230.7510,5Cc1ccnc(Cl)c1C([O-])=O 27.179.039,12[NH3+]Cc1cccc2N=C[N-]S(=O)(=O)c12 31.859.4410,8[NH3+]C(Cc1cnc[nH]1)C([O-])=O Calculations are performed on all molecules in the file

6. Chemical Terms (I.) Chemical Terms Language is used to formulate chemical expressions in general. The Chemical Terms Evaluator is designed to evaluate mathematical expressions on molecules using built-in chemical and general purpose functions: basic pKa value on atom 5 (0-based): evaluate –e bpka(5) test.mrv true if partial charge on atom 5 is greater than on atom 0: evaluate –e charge(5) > charge(0) test.mrv perform search on targets with mol mass greater than 150: jcsearch –e mass() > 150 –q query.mrv targets.mrv accept only search hits with acidic pKa less than 5 on target atom matching query atom with map 1: jcsearch –e apka(hm(1)) < 5 –q query.mrv targets.mrv The jcsearch program is a command-line interface of the JChem chemical structure search. Chemical Terms expressions can be used for filtering search results:

7. Chemical Terms (II.) Chemical Terms expressions can be specified for defining new database fields in Instant JChem logP field of the database is calculated using Chemical Terms expression logP(). It invokes logP plugin to calculate the values.

8. Chemical Terms (III.) bromination - select aromatic carbon with minimal energy: react –r [c:1][H:2]>>[c:1][Br:3]..s:-energyE(ratom(1)) Nc1ccccc1 Reactor is ChemAxons virtual reaction processing tool. Reaction rules can be specified using Chemical Terms expressions. Command line interface of Reactor: Reactor GUI: Chemical Terms expression that defines the excluding rule of the reaction uses pK a plugin to calculate pK a

9. Java API Plugin calculations can be integrated easily into any Java application. For more information on using calculator plugin Java API please see our Calculator Plugins for Developers presentation.

10. Calculator Plugins Elemental Analysis IUPAC Naming Protonation –pK a, Major Microspecies, Isoelectric Point Partitioning –logP, logD Charge –Charge, Polarizability, Orbital Electronegativity Isomers –Tautomers, Stereoisomers Conformation –Conformers, Molecular Dynamics, 3D Alignment Geometry –Topology Analysis, Geometry, Polar Surface Area (2D), Molecular Surface Area (3D) Markush enumeration Other –H Bond Donor/Acceptor, Huckel Analysis, Refractivity, Resonance, Structural Frameworks

11. Elemental Analysis Plugin

12. IUPAC Name Plugin

13. trainable pK a Plugin

14. Major Microspecies Plugin

15. Isoelectric Point Plugin

16. trainable logP Plugin

17. logD Plugin

18. Charge Plugin

19. Polarizability Plugin

20. Orbital Electronegativity Plugin

21. Tautomers Plugin

22. Stereoisomers Plugin

23. Conformers Plugin

24. Molecular Dynamics Plugin

25. 3D Alignment Plugin

26. Topology Analysis Plugin

27. Geometry Plugin

28. Polar Surface Area Plugin

29. Molecular Surface Area Plugin

30. Markush Enumeration Plugin

31. H Bond Donor/Acceptor Plugin

32. Huckel Analysis Plugin

33. Refractivity Plugin

34. Resonance Plugin

35. Structural Frameworks Plugin

36. Displaying Plugin Results In MarvinSpace

37. Visit other technical presentations MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt http://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt http://www.chemaxon.com/MarvinSpace.ppt Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt http://www.chemaxon.com/Calculator_Plugins.ppt JChem Base http://www.chemaxon.com/JChem_Base.ppt http://www.chemaxon.com/JChem_Base.ppt JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt http://www.chemaxon.com/JChem_Cartridge.ppt Standardizer http://www.chemaxon.com/Standardizer.ppt http://www.chemaxon.com/Standardizer.ppt Screen http://www.chemaxon.com/Screen.ppt http://www.chemaxon.com/Screen.ppt JKlustor http://www.chemaxon.com/JKlustor.ppt http://www.chemaxon.com/JKlustor.ppt Fragmenter http://www.chemaxon.com/Fragmenter.ppt http://www.chemaxon.com/Fragmenter.ppt Reactor http://www.chemaxon.com/Reactor.ppt http://www.chemaxon.com/Reactor.ppt

38. References Built-in plugin descriptions: http://www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins.html Developers guide with API usage examples: http://www.chemaxon.com/marvin/doc/dev/plugins.html Plugin framework API (chemaxon.marvin.plugin): http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/plugin/package-summary.html Built-in plugins API (chemaxon.marvin.calculations): http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/calculations/package-summary.html