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Scientific & technical presentation Calculator Plugins. January 20 11. 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:

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Scientific technical presentation calculator plugins

Scientific & technical presentation

Calculator Plugins

January 2011


Calculator plugin features

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


Calculation interface

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


Marvin gui

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.


Command line access cxcalc

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

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


Chemical terms i

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


Chemical terms ii

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

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


Java api

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

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


Elemental analys i s plugin

Elemental Analysis Plugin


Scientific technical presentation calculator plugins

IUPAC Name Plugin


Trainable p k a plugin

trainablepKa Plugin


Major microspecies plugin

Major Microspecies Plugin


Isoelectric point plugin

Isoelectric Point Plugin


Trainable log p plugin

trainable logP Plugin


Log d plugin

logD Plugin


Charge plugin

Charge Plugin


Polarizability plugin

Polarizability Plugin


Orbital electronegativity plugin

Orbital Electronegativity Plugin


Tautomer s plugin

Tautomers Plugin


Stereoisomer s plugin

Stereoisomers Plugin


Conformer s plugin

Conformers Plugin


Molecular dynamics plugin

Molecular Dynamics Plugin


3d alignment plugin

3D Alignment Plugin


Topology analysis plugin

Topology Analysis Plugin


Geometry plugin

Geometry Plugin


Polar surface area plugin

Polar Surface Area Plugin


Molecular surface area plugin

Molecular Surface Area Plugin


Markush enumeration plugin

Markush Enumeration Plugin


H bond donor acceptor plugin

H Bond Donor/Acceptor Plugin


Huckel analysis plugin

Huckel Analysis Plugin


Refractivity plugin

Refractivity Plugin


Resonance plugin

Resonance Plugin


Structural frameworks plugin

Structural Frameworks Plugin


Displaying plugin results in marvinspace

Displaying Plugin Results In MarvinSpace


Scientific technical presentation calculator plugins

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

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


References

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


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