Scientific & technical presentation Calculator Plugins January 2011

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.

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)

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.

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 ,5Cc1ccnc(Cl)c1C([O-])=O ,12[NH3+]Cc1cccc2N=C[N-]S(=O)(=O)c ,8[NH3+]C(Cc1cnc[nH]1)C([O-])=O Calculations are performed on all molecules in the file

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:

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.

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

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.

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

Elemental Analysis Plugin

IUPAC Name Plugin

trainable pK a Plugin

Major Microspecies Plugin

Isoelectric Point Plugin

trainable logP Plugin

logD Plugin

Charge Plugin

Polarizability Plugin

Orbital Electronegativity Plugin

Tautomers Plugin

Stereoisomers Plugin

Conformers Plugin

Molecular Dynamics Plugin

3D Alignment Plugin

Topology Analysis Plugin

Geometry Plugin

Polar Surface Area Plugin

Molecular Surface Area Plugin

Markush Enumeration Plugin

H Bond Donor/Acceptor Plugin

Huckel Analysis Plugin

Refractivity Plugin

Resonance Plugin

Structural Frameworks Plugin

Displaying Plugin Results In MarvinSpace

Visit other technical presentations MarvinSketch/View MarvinSpace Calculator Plugins JChem Base JChem Cartridge Standardizer Screen JKlustor Fragmenter Reactor

References Built-in plugin descriptions: Developers guide with API usage examples: Plugin framework API (chemaxon.marvin.plugin): Built-in plugins API (chemaxon.marvin.calculations):