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Pipelining ChemAxon

Pipelining ChemAxon. Szilard Dorant. Solutions for Cheminformatics. The Component Collection: Quick facts. Provides access to ChemAxon tools from Pipeline Pilot Free of charge Open source : Java sources are also included Available from ChemAxon or Accelrys Latest version : 1.4

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Pipelining ChemAxon

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  1. Pipelining ChemAxon Szilard Dorant Solutions for Cheminformatics

  2. The Component Collection: Quick facts • Provides access to ChemAxon tools from Pipeline Pilot • Free of charge • Open source : Java sources are also included • Available from ChemAxon or Accelrys • Latest version : 1.4 • Released in November 2008 • Requires JChem / Marvin 5.0.1 or better • Tested against Pipeline Pilot 6.1.1

  3. What’s new in 2008* • Direct support and development from ChemAxon • 3 major releases – one about every 4 months • 6 early access releases • 12 new user components • Several components significantly upgraded *As of November 2008

  4. Available functionality • Standardizer: structure canonicalization • Chemical Terms expressions for filtering and calculations (including logP, logD, pKa, HBD, HBA, Isoelectric point, PSA and more) • Reactor: “smart” virtual reaction processing • Maximum Common Substructure (MCS) based clustering • IUPAC Name <-> Molecule conversion (both directions) • JChem chemical database: insertion, search and retrieval of structures; create and drop structure tables • Marvin applets: structure visualization and editing • Major microspecies (major protonation form) • Microspecies distribution • Burden eigenvalue descriptor (BCUT)

  5. Chemical Terms Calculator New in 1.3 • Use arbitrary Chemical Terms expressions • Results stored to arbitrary properties • A wide range of ChemAxon functionality can be accessed as Chemical Terms functions

  6. Canonicalization with Standardizer Upgraded in 1.2 Simple to use, but now full complexity is also available: • Simple actions (checkboxes) • Configuration string (simple or XML) • Configuration file

  7. IUPAC naming components New in 1.4 • IUPAC Name to Molecule • Molecule to IUPAC Name • Example “roundtrip” protocol:

  8. Reactor Upgraded in 1.4 Improvements: • Synthesis code generation • Output reaction mapping • Advanced options: • Unambiguous only • Ignore rules: • Reactivity and Exclude • Selectivity • Tolerance

  9. Combinatorial Reactor Example

  10. Clustering with LibMCS Maximum Common Substructure (MCS) based clustering New in 1.4 Options: • Size of smallest common substructure to consider • Three levels of heuristics: • Exact (no heuristics) • Fast • Very Fast • Bond type, atom type, charge can optionally be ignored • Disallow “breaking” rings (default)

  11. JChem Base Insert Upgraded in 1.2 New features: • Returns cd_id (primary key) values • Two input modes: • read structure source from a specified property • if property not specified uses PP input molecule • Insert into additional data fields* • Duplicate filtering option (using Pass and Fail ports) *Under development, currently limited to string database column types

  12. JChem Database Search Upgraded in 1.2 • Several search options were added • Easier protocol integration and better performance due to concentrated functionality

  13. JChem Base demo protocol

  14. Improved error reporting New in 1.3 • Helps to track down problems quicker • More information is displayed in the error dialog: Marvin or JChem version, the current structure, etc. • Utility component for displaying ChemAxon environment (from 1.4) • If the environment variable CHEMAXON_PP_LOG_DIR is set, an even more detailed error report will be appended to the file "pp_error.txt" in the specified directory

  15. Planned components • JChem Cartridge for Oracle • Integration with Instant JChem • Tautomer generation • Conformer generation • Conversion of various structure file formats Node release cycle is fast and flexible. Please advise us on priority and additional functionality for future node development.

  16. Resources • Download: • http://www.chemaxon.com/integration/download.html • http://accelrys.org/pipelinepilot/chemistry.html • Technical support forum: • http://www.chemaxon.com/forum/forum88.html • E-mail: • Dorant__at__chemaxon_._com

  17. Acknowledgements • Accelrys • Moises Hassan • Ton van Daelen • Keith Burdick • Informatics Matters • Tim Dudgeon • ChemAxon • György Pirok • Miklós Vargyas • Zsolt Mohácsi

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