Pipelining ChemAxon - Accelrys EUGM 2008
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The document outlines the features and updates of ChemAxon's tools for cheminformatics in the 1.4 version, including access via Pipeline Pilot and open-source Java sources. Key functionalities include structure canonicalization, virtual reaction processing, and advanced database interaction features. It also highlights the significant upgrades made in the latest versions and offers resources for download and support.
Pipelining ChemAxon - Accelrys EUGM 2008
- 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 November 24 1.4 October 22 1.3.1 July 11 1.3 March 5 1.2 Date Version User interest Development
- 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 Use arbitrary Chemical Terms expressions Results stored to arbitrary properties A wide range of ChemAxon functionality can be accessed as Chemical Terms functions New in 1.3
- 6. Canonicalization with Standardizer Simple to use, but now full complexity is also available: Simple actions (checkboxes) Configuration string (simple or XML) Configuration file Upgraded in 1.2
- 7. IUPAC naming components IUPAC Name to Molecule Molecule to IUPAC Name Example “roundtrip” protocol: New in 1.4
- 8. Reactor Improvements: Upgraded in 1.4 Synthesis code generation Output reaction mapping Advanced options: Unambiguous only Ignore rules: Reactivity and Exclude Selectivity Tolerance
- 10. Clustering with LibMCS Maximum Common Substructure (MCS) based clustering 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) Options: New in 1.4
- 11. JChem Base Insert 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* New features: *Under development, currently limited to string database column types Duplicate filtering option (using Pass and Fail ports) Upgraded in 1.2
- 12. JChem Database Search Several search options were added Easier protocol integration and better performance due to concentrated functionality Upgraded in 1.2
- 13. JChem Base demo protocol
- 14. Improved error reporting 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 New in 1.3
- 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 Gy ö rgy Pirok Mikl ós Vargyas Zsolt Moh á csi