Transcript Java Solutions for Cheminformatics

Scientific & technical presentation
Calculator Plugins
January 2011
Calculator Plugin Features
Calculator Plugins are modules of ChemAxon’s 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
(ChemAxon’s virtual reaction processing tool)
• Java API for developers
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
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.
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
Calculation specific help is also available:
Calculations are performed
$ cxcalc pka -h
on all molecules in the file
pKa (strongest acidic and basic pKa values)
and major microspecies (pH=7.4) calculation:
$ cxcalc pka
id apKa1
1
3.23
2
7.17
3
1.85
–a 1 –b
bpKa1
0.75
9.03
9.44
1 majorms –H 7.4 mols.sdf
atoms
major-ms
10,5
Cc1ccnc(Cl)c1C([O-])=O
9,12
[NH3+]Cc1cccc2N=C[N-]S(=O)(=O)c12
10,8
[NH3+]C(Cc1cnc[nH]1)C([O-])=O
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
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() > 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
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.)
Reactor is ChemAxon’s 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 “[c:1][H:2]>>[c:1][Br:3]..s:-energyE(ratom(1))” “Nc1ccccc1”
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