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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

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

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




pKa, Major Microspecies, Isoelectric Point


logP, logD


Charge, Polarizability, Orbital Electronegativity


Tautomers, Stereoisomers


Conformers, Molecular Dynamics, 3D Alignment


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

Molecular Surface Area (3D)



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

Trainable p k a plugin
trainablepKa Plugin

Trainable log p plugin
trainable logP Plugin

Log d plugin
logD Plugin

Tautomer s plugin
Tautomers Plugin

Stereoisomer s plugin
Stereoisomers Plugin

Conformer s plugin
Conformers Plugin

Scientific technical presentation calculator plugins

Visit othertechnical presentations



Calculator Plugins

JChem Base

JChem Cartridge







Built-in plugin descriptions:

Developer’s guide with API usage examples:

Plugin framework API (chemaxon.marvin.plugin):

Built-in plugins’ API (chemaxon.marvin.calculations):