Scientific & technical presentation Calculator Plugins

1. Scientific & technical presentation Calculator Plugins January 2011

2. Calculator Plugin Features Calculator Plugins are modules of ChemAxon’s Marvin and JChem cheminformatics platforms which calculate chemical properties descriptors from chemical structures. Key features: • Calculations can be performed using the graphical user interface of MarvinSketch and MarvinView • Predictions can be run in batch mode with cxcalccommand 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(ChemAxon’svirtual reaction processing tool) • Java API for developers

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

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

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: $ cxcalc Calculations are performed on all molecules in the file Calculation specific help is also available: $ cxcalc pka -h pKa (strongest acidic and basic pKa values) and major microspecies (pH=7.4) calculation: $ cxcalc pka –a 1 –b 1 majorms –H 7.4 mols.sdf id apKa1 bpKa1 atoms major-ms 1 3.23 0.75 10,5 Cc1ccnc(Cl)c1C([O-])=O 2 7.17 9.03 9,12 [NH3+]Cc1cccc2N=C[N-]S(=O)(=O)c12 3 1.85 9.44 10,8 [NH3+]C(Cc1cnc[nH]1)C([O-])=O

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 The jcsearch program is a command-line interface of the JChem chemical structure search. Chemical Terms expressions can be used for filtering search results: 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

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

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 ElementalAnalysis IUPACNaming Protonation pKa, 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) Markushenumeration Other H Bond Donor/Acceptor, Huckel Analysis, Refractivity, Resonance, Structural Frameworks

11. Elemental Analysis Plugin

12. IUPAC Name Plugin

13. trainablepKa 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 othertechnical presentations MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpacehttp://www.chemaxon.com/MarvinSpace.ppt Calculator Pluginshttp://www.chemaxon.com/Calculator_Plugins.ppt JChem Basehttp://www.chemaxon.com/JChem_Base.ppt JChem Cartridgehttp://www.chemaxon.com/JChem_Cartridge.ppt Standardizerhttp://www.chemaxon.com/Standardizer.ppt Screenhttp://www.chemaxon.com/Screen.ppt JKlustorhttp://www.chemaxon.com/JKlustor.ppt Fragmenterhttp://www.chemaxon.com/Fragmenter.ppt Reactor http://www.chemaxon.com/Reactor.ppt

38. References Built-in plugin descriptions: http://www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins.html Developer’s 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