Calculator Plugins

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    Scientific & technical presentation

    Calcu lator Plug ins

    January 2011

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    Calculator Plugin Features

    Key features:

    Calculations can be performed using the graphical user interfaceof

    MarvinSketchand MarvinView

    Predictions can be run in batch modewith cxcalccommand line tool

    Plugin calculations can be used for filtering resultsof database

    searches

    in JChem Base

    in Instant JChem

    in JChem Cartridge

    Define smart reaction rules using plugin calculations in Reactor

    (ChemAxonsvirtual reaction processing tool)

    Java APIfor developers

    Calculator Plugins are modules of ChemAxons Marvin and JChemcheminformatics platforms which calculate chemical propertiesdescriptors from chemical structures.

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    Calculation Interface

    Marvin GUI

    cxcalccommand line tool

    Java API

    Chemical Termsevaluatecommand line toolsearch filtering in JChem Base,_Instant JChemand JChem Cartridgevirtual reaction processing (Reactor)

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    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:

    pKa(strongest acidic and basic pKavalues)

    and major microspecies (pH=7.4) calculation:

    $ cxcalc

    $ cxcalc pka -h

    $ cxcalc pka a 1 b 1 majorms H 7.4 mols.sdfid apKa1 bpKa1 atoms major-ms1 3.23 0.75 10,5 Cc1ccnc(Cl)c1C([O-])=O2 7.17 9.03 9,12 [NH3+]Cc1cccc2N=C[N-]S(=O)(=O)c123 1.85 9.44 10,8 [NH3+]C(Cc1cnc[nH]1)C([O-])=O

    Calculations are performed

    on all molecules in the file

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    Chemical Terms (I.)

    Chemical Terms Lang uageis used to formulate chemical expressions ingeneral.

    The Chem ical Terms Evaluatoris 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:jcsearche mass() > 150 q query.mrv targets.mrv

    accept only search hits with acidic pKa less than 5 on target atommatching query atom with map 1:

    jcsearche apka(hm(1)) < 5 q query.mrv targets.mrv

    The jcsearchprogram is a command-line interface of the JChem chemicalstructure search. Chemical Termsexpressions can be used for filtering searchresults:

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    Chemical Terms (II.)

    Chemical Termsexpressions can bespecified for definingnew database fields inInstant JChem

    logPfield of the databaseis calculated usingChemical Termsexpression logP(). Itinvokes logP plugin tocalculate the values.

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    Chemical Terms (III.)

    bromination - select aromatic carbon with minimal energy:reactr [c:1][H:2]>>[c:1][Br:3]..s:-energyE(ratom(1)) Nc1ccccc1

    Reactoris ChemAxons virtual reaction processing tool. Reaction rules can bespecified using Chemic al Termsexpressions.

    Command line interface of Reactor:

    ReactorGUI:

    Chemical Terms

    expression that definesthe excluding rule ofthe reaction uses pKapluginto calculate pKa

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    Java API

    Plugin calculations can beintegrated easily into any

    Java application.

    For more information on using

    calculator plugin Java APIplease see our CalculatorPlugins for Developerspresentation.

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    Calculator Plugins

    ElementalAnalys is

    IUPACNaming

    Protonat ion

    pKa, Major Microspecies, Isoelectric Point

    Part i t ioning

    logP, logD

    Charge Charge, Polarizability, Orbital Electronegativity

    Isomers

    Tautomers, Stereoisomers

    Conformat ion

    Conformers, Molecular Dynamics, 3D Alignment

    Geometry

    Topology Analysis, Geometry, Polar Surface Area (2D),

    Molecular Surface Area (3D)

    Markushenumerat ion

    Other

    H Bond Donor/Acceptor, Huckel Analysis, Refractivity, Resonance,Structural Frameworks

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    Elemental Analysis Plugin

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    IUPAC Name Plugin

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    t rainablepKaPlugin

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    Major Microspecies Plugin

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    Isoelectric Point Plugin

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    trainable logPPlugin

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    logDPlugin

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    Charge Plugin

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    Polarizability Plugin

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    Orbital Electronegativity Plugin

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    Tautomers Plugin

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    Stereoisomers Plugin

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    Conformers Plugin

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    Molecular Dynamics Plugin

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    3D Alignment Plugin

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    Topology Analysis Plugin

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    Geometry Plugin

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    Polar Surface Area Plugin

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    Molecular Surface Area Plugin

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    Markush Enumeration Plugin

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    H Bond Donor/Acceptor Plugin

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    Huckel Analysis Plugin

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    Refractivity Plugin

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    Resonance Plugin

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    Structural Frameworks Plugin

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    Displaying Plugin Results In MarvinSpace

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    Visit othertechnical presentations

    MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt

    MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt

    Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt

    JChem Base http://www.chemaxon.com/JChem_Base.ppt

    JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt

    Standardizer http://www.chemaxon.com/Standardizer.ppt

    Screen http://www.chemaxon.com/Screen.ppt

    JKlustor http://www.chemaxon.com/JKlustor.ppt

    Fragmenter http://www.chemaxon.com/Fragmenter.ppt

    Reactor http://www.chemaxon.com/Reactor.ppt

    http://www.chemaxon.com/MarvinSketch_View.ppthttp://www.chemaxon.com/MarvinSpace.ppthttp://www.chemaxon.com/Calculator_Plugins.ppthttp://www.chemaxon.com/JChem_Base.ppthttp://www.chemaxon.com/JChem_Cartridge.ppthttp://www.chemaxon.com/Standardizer.ppthttp://www.chemaxon.com/Screen.ppthttp://www.chemaxon.com/JKlustor.ppthttp://www.chemaxon.com/Fragmenter.ppthttp://www.chemaxon.com/Reactor.ppthttp://www.chemaxon.com/Reactor.ppthttp://www.chemaxon.com/Fragmenter.ppthttp://www.chemaxon.com/JKlustor.ppthttp://www.chemaxon.com/Screen.ppthttp://www.chemaxon.com/Standardizer.ppthttp://www.chemaxon.com/JChem_Cartridge.ppthttp://www.chemaxon.com/JChem_Base.ppthttp://www.chemaxon.com/Calculator_Plugins.ppthttp://www.chemaxon.com/Calculator_Plugins.ppthttp://www.chemaxon.com/MarvinSpace.ppthttp://www.chemaxon.com/MarvinSketch_View.ppt
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    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