Scientific & technical presentation Calculator Plugins January 2011.

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

(ChemAxon’s virtual reaction processing tool)• Java API for developers

Calculator Plugins are modules of ChemAxon’s 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:

pKa (strongest acidic and basic pKa values)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

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 ChemAxon’s virtual reaction processing tool. Reaction rules can bespecified using Chemical Terms expressions.

Command line interface of Reactor:

Reactor GUI:

Chemical Terms expression that defines the excluding rule of the reaction uses pKa plugin to calculate pKa

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– 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)

• Markush enumeration

• Other– H Bond Donor/Acceptor, Huckel Analysis, Refractivity, Resonance,

Structural Frameworks

Elemental Analysis Plugin

IUPAC Name Plugin

trainable pKa 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 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

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