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
(ChemAxons virtual reaction processing tool)
Java API for developers
Calculator Plugins are modules of ChemAxons 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:
pK
a
(strongest acidic and basic pK
a
values)
and major microspecies (pH=7.4) calculation:
$ cxcalc
$ cxcalc pka -h
$ 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
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 J Chem

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 ChemAxons virtual reaction processing tool. Reaction rules can be
specified using Chemical Terms expressions.
Command line interface of Reactor:
Reactor GUI:
Chemical Terms
expression that defines
the excluding rule of
the reaction uses pK
a

plugin to calculate pK
a
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
pK
a
, 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 pK
a
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
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