8/11/2019 Calculator Plugins
1/38
Scientific & technical presentation
Calcu lator Plug ins
January 2011
8/11/2019 Calculator Plugins
2/38
Calculator Plugin Features
Key features:
Calculations can be performed using the graphical user interfaceof
MarvinSketchand MarvinView
Predictions can be run in batch modewith cxcalccommand line tool
Plugin calculations can be used for filtering resultsof database
searches
in JChem Base
in Instant JChem
in JChem Cartridge
Define smart reaction rules using plugin calculations in Reactor
(ChemAxonsvirtual reaction processing tool)
Java APIfor developers
Calculator Plugins are modules of ChemAxons Marvin and JChemcheminformatics platforms which calculate chemical propertiesdescriptors from chemical structures.
8/11/2019 Calculator Plugins
3/38
Calculation Interface
Marvin GUI
cxcalccommand line tool
Java API
Chemical Termsevaluatecommand line toolsearch filtering in JChem Base,_Instant JChemand JChem Cartridgevirtual reaction processing (Reactor)
8/11/2019 Calculator Plugins
4/38
8/11/2019 Calculator Plugins
5/38
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 pKavalues)
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
8/11/2019 Calculator Plugins
6/38
Chemical Terms (I.)
Chemical Terms Lang uageis used to formulate chemical expressions ingeneral.
The Chem ical Terms Evaluatoris 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:jcsearche mass() > 150 q query.mrv targets.mrv
accept only search hits with acidic pKa less than 5 on target atommatching query atom with map 1:
jcsearche apka(hm(1)) < 5 q query.mrv targets.mrv
The jcsearchprogram is a command-line interface of the JChem chemicalstructure search. Chemical Termsexpressions can be used for filtering searchresults:
8/11/2019 Calculator Plugins
7/38
Chemical Terms (II.)
Chemical Termsexpressions can bespecified for definingnew database fields inInstant JChem
logPfield of the databaseis calculated usingChemical Termsexpression logP(). Itinvokes logP plugin tocalculate the values.
8/11/2019 Calculator Plugins
8/38
Chemical Terms (III.)
bromination - select aromatic carbon with minimal energy:reactr [c:1][H:2]>>[c:1][Br:3]..s:-energyE(ratom(1)) Nc1ccccc1
Reactoris ChemAxons virtual reaction processing tool. Reaction rules can bespecified using Chemic al Termsexpressions.
Command line interface of Reactor:
ReactorGUI:
Chemical Terms
expression that definesthe excluding rule ofthe reaction uses pKapluginto calculate pKa
8/11/2019 Calculator Plugins
9/38
Java API
Plugin calculations can beintegrated easily into any
Java application.
For more information on using
calculator plugin Java APIplease see our CalculatorPlugins for Developerspresentation.
8/11/2019 Calculator Plugins
10/38
Calculator Plugins
ElementalAnalys is
IUPACNaming
Protonat ion
pKa, Major Microspecies, Isoelectric Point
Part i t ioning
logP, logD
Charge Charge, Polarizability, Orbital Electronegativity
Isomers
Tautomers, Stereoisomers
Conformat ion
Conformers, Molecular Dynamics, 3D Alignment
Geometry
Topology Analysis, Geometry, Polar Surface Area (2D),
Molecular Surface Area (3D)
Markushenumerat ion
Other
H Bond Donor/Acceptor, Huckel Analysis, Refractivity, Resonance,Structural Frameworks
8/11/2019 Calculator Plugins
11/38
Elemental Analysis Plugin
8/11/2019 Calculator Plugins
12/38
IUPAC Name Plugin
8/11/2019 Calculator Plugins
13/38
t rainablepKaPlugin
8/11/2019 Calculator Plugins
14/38
Major Microspecies Plugin
8/11/2019 Calculator Plugins
15/38
Isoelectric Point Plugin
8/11/2019 Calculator Plugins
16/38
trainable logPPlugin
8/11/2019 Calculator Plugins
17/38
logDPlugin
8/11/2019 Calculator Plugins
18/38
Charge Plugin
8/11/2019 Calculator Plugins
19/38
Polarizability Plugin
8/11/2019 Calculator Plugins
20/38
Orbital Electronegativity Plugin
8/11/2019 Calculator Plugins
21/38
Tautomers Plugin
8/11/2019 Calculator Plugins
22/38
Stereoisomers Plugin
8/11/2019 Calculator Plugins
23/38
Conformers Plugin
8/11/2019 Calculator Plugins
24/38
Molecular Dynamics Plugin
8/11/2019 Calculator Plugins
25/38
3D Alignment Plugin
8/11/2019 Calculator Plugins
26/38
Topology Analysis Plugin
8/11/2019 Calculator Plugins
27/38
Geometry Plugin
8/11/2019 Calculator Plugins
28/38
Polar Surface Area Plugin
8/11/2019 Calculator Plugins
29/38
Molecular Surface Area Plugin
8/11/2019 Calculator Plugins
30/38
Markush Enumeration Plugin
8/11/2019 Calculator Plugins
31/38
H Bond Donor/Acceptor Plugin
8/11/2019 Calculator Plugins
32/38
Huckel Analysis Plugin
8/11/2019 Calculator Plugins
33/38
Refractivity Plugin
8/11/2019 Calculator Plugins
34/38
Resonance Plugin
8/11/2019 Calculator Plugins
35/38
Structural Frameworks Plugin
8/11/2019 Calculator Plugins
36/38
Displaying Plugin Results In MarvinSpace
8/11/2019 Calculator Plugins
37/38
Visit othertechnical 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
http://www.chemaxon.com/MarvinSketch_View.ppthttp://www.chemaxon.com/MarvinSpace.ppthttp://www.chemaxon.com/Calculator_Plugins.ppthttp://www.chemaxon.com/JChem_Base.ppthttp://www.chemaxon.com/JChem_Cartridge.ppthttp://www.chemaxon.com/Standardizer.ppthttp://www.chemaxon.com/Screen.ppthttp://www.chemaxon.com/JKlustor.ppthttp://www.chemaxon.com/Fragmenter.ppthttp://www.chemaxon.com/Reactor.ppthttp://www.chemaxon.com/Reactor.ppthttp://www.chemaxon.com/Fragmenter.ppthttp://www.chemaxon.com/JKlustor.ppthttp://www.chemaxon.com/Screen.ppthttp://www.chemaxon.com/Standardizer.ppthttp://www.chemaxon.com/JChem_Cartridge.ppthttp://www.chemaxon.com/JChem_Base.ppthttp://www.chemaxon.com/Calculator_Plugins.ppthttp://www.chemaxon.com/Calculator_Plugins.ppthttp://www.chemaxon.com/MarvinSpace.ppthttp://www.chemaxon.com/MarvinSketch_View.ppt8/11/2019 Calculator Plugins
38/38
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