Scientific & technical presentation Calculator Plugins January 2011.
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Transcript of 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