Java Solutions for Cheminformatics

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Scientific technical presentation Calculator
Plugins
January 2011
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Calculator Plugin Features
Calculator Plugins are modules of ChemAxons
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 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

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Calculation Interface
Marvin GUI

• Chemical Terms
• evaluate command line tool
• search filtering in JChem Base, _Instant JChem
  and JChem Cartridge
• virtual reaction processing (Reactor)

Java API
cxcalc command line tool
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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.
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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
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 (pH7.4) calculation
cxcalc pka a 1 b 1 majorms H 7.4
mols.sdf id apKa1 bpKa1 atoms major-ms 1 3.23 0.7
5 10,5 Cc1ccnc(Cl)c1C(O-)O 2 7.17 9.03 9,12
NH3Cc1cccc2NCN-S(O)(O)c12 3 1.85 9.44
10,8 NH3C(Cc1cncnH1)C(O-)O
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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) gt 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() gt 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)) lt 5
q query.mrv targets.mrv
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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.
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Chemical Terms (III.)
Reactor is ChemAxons 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 c1H2gtgtc1Br3..s-ener
gyE(ratom(1)) Nc1ccccc1
Reactor GUI
Chemical Terms expression that defines the
excluding rule of the reaction uses pKa plugin to
calculate pKa
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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.
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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

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Elemental Analysis Plugin
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IUPAC Name Plugin
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trainable pKa Plugin
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Major Microspecies Plugin
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Isoelectric Point Plugin
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trainable logP Plugin
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logD Plugin
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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 other technical presentations
MarvinSketch/View http//www.chemaxon.com/MarvinSk
etch_View.ppt MarvinSpace http//www.chemaxon.com
/MarvinSpace.ppt Calculator Plugins
http//www.chemaxon.com/Calculator_Plugins.ppt JC
hem Base http//www.chemaxon.com/JChem_Base.ppt J
Chem Cartridge http//www.chemaxon.com/JChem_Cartr
idge.ppt Standardizer http//www.chemaxon.com/Sta
ndardizer.ppt Screen http//www.chemaxon.com/Scr
een.ppt JKlustor http//www.chemaxon.com/JKlustor
.ppt Fragmenter http//www.chemaxon.com/Fragmente
r.ppt Reactor http//www.chemaxon.com/Reactor.pp
t
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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/p
lugins.html
Plugin framework API (chemaxon.marvin.plugin) htt
p//www.chemaxon.com/marvin/doc/api/chemaxon/marvi
n/plugin/package-summary.html
Built-in plugins API (chemaxon.marvin.calculation
s) http//www.chemaxon.com/marvin/doc/api/chemaxo
n/marvin/calculations/package-summary.html