PowerPoint bemutat

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Scientific technical presentation JChem Base
version 5.3, February 2010
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Introduction to JChem Base

• High performance Java based tools for
• storage, search and retrieval of chemical
  structures and associated data
• The components can be integrated into
• web-based or standalone applications
• in association with other ChemAxon tools

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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

• File formats
• SMILES
• MDL molfile (v2000 and v3000)
• MDL SDF
• RXN
• RDF
• MRV
• IUPAC name, InChI
• Markush DARC
• CDX
• Integration
• extensive API for
• Java
• .NET
• JChem Cartridge for Oracle

• Database engines
• Oracle
• MySQL
• MS SQL Server
• PostgreSQL
• MS Access
• IBM DB2
• Derby
• etc.
• Operating systems
• Windows
• Linux
• Mac OS X
• Solaris
• etc.

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JSP example application

• Features
• Substructure, Superstructure, Full, Exact
  fragment, Similarity and Perfect 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
• AJAX in JChem Webservices

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Structure search features

• Wide range of query atoms
• Query properties
• R-group queries
• Full SMARTS support
• Coordination compounds
• Link nodes
• Pseudo atoms, lone pairs
• Relative stereo
• Reaction search features
• Hit coloring, position variation
• Polymers

See detailed information on structure search
www.chemaxon.com/conf/Structural_Search.ppt
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Search options

• Some selected structure search options
• Stereo on/off
• Ignore charge/isotope/radical/valence/polymers,
  etc.
• Vague bond matching options
• Chemical Terms filter
• Tautomer search
• Inverse hit list
• Maximum search time / number of hits
• Combine with non-structure conditions
• Ordering of results
• etc.

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Performance (1)
Compound registration
Substructure search in PubChem (19.5 million
compounds)
JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB
RAM Oracle 10.2.0.3
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Performance (2)

• Similarity searchTanimoto gt0.9
• JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB
  RAM Oracle 10.2.0.

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Markush structures

• Markush structure registration and search
• Markush features
• R-groups
• Atom lists, bond lists
• Position variation bond
• Link nodes and repeating units
• Homology variation (alkyl, aryl, etc.)
• Compatible Markush enumeration plugin

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Administration with JChemManager

• User interface for
• creating tables
• import
• export
• deleting rows
• dropping tables
• Most functions are also available from command
  line.

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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 Table Options dialog
  of JChem Manager (jcman)

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Custom Standardization Example
Standardizer http//www.chemaxon.com/conf/Standard
izer.ppt
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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
• More than one property table can be used, each
  property table represents a particular JChem
  environment.

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Table types

• Control allowed chemical structures and available
  operations
• Molecule
• Reaction
• Markush
• Query
• Any structure

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The structure of JChem tables
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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)

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Future plans

• Graphical user interface for R-group
  decomposition
• Arbitrary table structure (Java and .NET API for
  JChem index)
• Maximum common substructure search type
• Additional layer JChem Server (later also as
  grid)
• Compound registration system API

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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
• http//www.chemaxon.com/products/jchem-base
• Online tryout
• http//www.chemaxon.com/jchem/examples.html
• API documentation
• http//www.chemaxon.com/jchem/doc/api/index.html
• Brochure
• www.chemaxon.com/brochures/JChemBase.pdf

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