Szilrd Drnt

1
Scientific technical presentationJChem
Base

• Szilárd Dóránt

Feb 2008
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Contents

• Introduction
• Structural overview
• Compatibility
• Administration
• JChem tables
• Fingerprints
• Structural search

• Structure cache
• Standardization
• Search options
• JSP example
• API examples
• Performance
• Future plans

3
Introduction to JChem Base
High performance Java based tools for -
storage/ - search / - retrieval of chemical
structures and associated data The components
can be integrated into web-based or standalone
applications in association with other ChemAxon
tools.
4
Structural overview
Web browser
Application
Web application
JChem Base API Chemical logic Structure cache
JDBC driver Standard interface to the RDBMS
RDBMS (e.g. Oracle, MySQL, etc.) Storage and
security
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Compatibility and integration
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Administration with JChemManager
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The property table

• The property table stores information about JChem
  structure tables, including
• Fingerprint parameters
• Custom standardization rules
• Other table options and information
• Database-related licence keys
• More than one property table can be used, each
  property table represents a particular JChem
  environment.

8
The structure of JChem tables
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Table types

• Molecules specific structures e.g. single
  molecules, mixtures, salts, polimers
• Reactions single step reactions
• Any structures all types of structures are
  allowed, but no structure type-specific searching

10
Chemical Hashed Fingerprints

• Chemical Hashed Fingerprints encode structural
  patterns in bit strings
• If structure A is a substructure of structure B,
  every bit in Bs fingerprint will be set that is
  set in structure As fingerprint
• Tanimoto similarity of hashed fingerprints can be
  used for diversity analysis and similarity search

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Structural search in database

• Two stage method provides optimal performance
• Rapid pre-screening reduces the number
  of possible hit candidates
• Chemical Hashed Fingerprints are used
  for substructure and superstructure searches
• Hash code is used for duplicate
  filtering (usually during compound
  registration)
• Graph search algorithm is used to determine the
  final hit list

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Structure Cache

• Contains Fingerprints for screening and ChemAxon
  Extended SMILES for ABAS
• Instant access to the structures for the search
  process
• Reduced load on the database server
• Incremental update ensures minimum overhead after
  changes in the table
• Small memory footprint due to
• SMILES compression
• Optimized storage technique
• Approximately 100MB memory needed for 1 million
  typical drug-like structures (using default, 512
  bit long fingerprints)

13
Standardization

• Default standardization includes
• Hydrogen removal
• Aromatization
• Custom standardization can be specified for each
  table by specifying an XML configuration file at
  table creation or in the Regenerate dialog of
  JChem Manager (jcman)

14
Custom Standardization Example
JChem Cartridge http//www.chemaxon.com/JChem_Cart
ridge.ppt
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Database search options
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JSP example application

• Open source, customizable
• Features
• Substructure, Superstructure, Exact and
  Similarity search
• Molecular Descriptor similarity search with
  descriptor coloring
• Substructure hit alignment and coloring, inverse
  hit list
• Chemical Terms filter
• Import / Export
• Export of hits
• Insert / Modify / Delete structures

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API example connecting to a database
ConnectionHandler ch new chemaxon.jchem.db.Conne
ctionHandler() ch.setDriver(oracle.jdbc.driver.
OracleDriver) ch.setUrl(jdbcoraclethin_at_local
host1521mydb) ch.setPropertyTable(JChemProper
ties) ch.setLoginName(scott) ch.setPassword("
tiger") ch.connect() // the java.sql.Connection
object is available if needed Connection
conch.getConnection() // closing the
connection ch.close()
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API example database import
Importer importer new chemaxon.jchem.db.Importer
() importer.setConnectionHandler(conh) importer.
setInput(sample.sdf) // importer.setInput(is)
// alternatively a stream can also be
specified importer.setTableName(SCOTT.STRUCTURES
)
importer.setHaltOnError(false) importer.setDupli
cateImportAllowed(false) //can filter
duplicates // specifying SDFile field - table
field pairs String fieldPairs
DB_Field1SDF_Field1 DB_Field2SDF_Field2 impo
rter.setFieldConnections(fieldPairs) int
importedCount importer.importMols() System.out.
println( Imported importedCount
structures )
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API example database export
Exporter exporter new chemaxon.jchem.db.Exporter
() exporter.setConnectionHandler(conh) exporter
.setTableName(structures) //data fields to
be exported with the structure exporter.setFieldL
ist(cd_id cd_formula name comments) String
fileNameoutput.sdf OutputStream osnew
FileOutputStream(fileName) exporter.setOutputStre
am(os) exporter.setFormat(sdf)
int exportedCount
exporter.writeAll() System.out.println(Exported
exportedCount structures)
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API example database search
JChemSearch searcher new chemaxon.jchem.db.JChem
Search() searcher.setConnectionHandler(ch) searc
her.setSearchType(JChemSearch.SUBSTRUCTURE) search
er.setQueryStructure(c1ccccc1) searcher.setStru
ctureTable(SCOTT.STRUCTURES) // a query that
returns cd_id values can be used for
prefiltering Searcher.setFilterQuery( SELECT
cd_id FROM structures, biodata WHERE
structures.cd_id biodata.cd_id AND
biodata.toxicity esult(true) // otherwise runs in a separate
thread searcher.run() // getting the results as
cd_id values int resultssearcher.getResults()
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API example inserting a structure
// ConnectionHandler, mode, table name and data
field names UpdateHandler uh new
chemaxon.jchem.db.UpdateHandler( ch,
UpdateHandler.INSERT, structures, comment,
stock) uh.setStructure(c1ccccc1) // the
structure // specifying data field
values uh.setValueForAdditionalColumn(1, some
text) uh.setValueForAdditionalColumn(2, new
Double(8.5)) uh.setDuplicateFiltering(true)
// filtering duplicate structures int
iduh.execute(true) // getting back the
cd_id of the inserted structure if ( id 0 )
System.out.println(Inserted, cd_id value
id) else System.out.println(Already
exists with cd_id value (-id)) //
storing update information, the database
connection remains open uh.close()
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Performance (1)

• Compound registration
• Substructure search in a table of 3 million
  compounds
• JChem Base 3.2, Dual Xeon 3GHz, 2GB RAM Oracle
  9.2.0.7.0

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Performance (2)
Similarity searchTanimoto 0.9 JChem
Base 3.2, Dual Xeon 3GHz, 2GB RAM Oracle
9.2.0.7.0
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Future plans

• Additional layer JChem Server (later also as
  grid)
• Tables for storing query structures
• Tables for storing general (Markush) structures
• Partial clean option for hit alignment

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Summary

• ChemAxons JChem Base API provides sophisticated
  high performance tools for the developer to deal
  with chemical structures and associated data.
• Building on the JChem API is convenient,
  because
• Our various tools integrate seamlessly
• Both high and low level API classes are available
• Responsive developer-to-developer support

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Links

• JChem home page
• www.jchem.com
• Live demos
• www.jchem.com/examples
• API documentation
• www.jchem.com/doc/api
• Brochure
• www.chemaxon.com/brochures/JChemBase.pdf

27
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