As a recent change in the ChemAxon - SciTegic collaboration, ChemAxon took over the responsibility for developing the ChemAxon Pipeline Pilot component collection with continued active support from our partner. A new, improved collection package has been released since then by ChemAxon in March 2008. The presentation covers the new components, improvements of existing components and plans for future development. Free download of component collection is here: http://www.chemaxon.com/integration/download.html

1. Pipelining ChemAxon
Szilard Dorant
Solutions for Cheminformatics

2. ChemAxon and Pipeline Pilot - What’s new
ChemAxon took over the responsibility of maintaining
and supporting the ChemAxon Pipeline Pilot
Component Collection with the continued active help
from SciTegic.
• New components for current ChemAxon functionality
• Support for new ChemAxon functionality more quickly
• Support from ChemAxon directly
ChemAxon released component collection
version 1.2 in March 2008

3. The Component Collection: Quick facts
• Free of charge
• Open source : Java sources are also included
• Available from ChemAxon or SciTegic
• Latest version : 1.3
– Released in July 2008
– Requires JChem 3.2 / Marvin 4.1.2 or better
– Tested against Pipeline Pilot 6.1.1

4. Available functionality
• Standardizer
• Chemical Terms expressions for filtering and calculations
(including logP, logD, pKa, HBD, HBA, Isoelectric point, PSA
and more)
• Reactor
• JChem chemical database: insertion, search and retrieval of
structures; create and drop structure tables
• Marvin sketcher and viewer (structure editing and display)
• Major microspecies (major protonation form)
• Microspecies distribution
• Burden eigenvalue descriptor (BCUT)

5. Molecular Table Viewer

6. Calculator

7. Chemical Terms Calculator
• Use arbitrary Chemical Terms New in 1.3
expressions
• Results stored to arbitrary
properties
• Up to 10 expressions can be
calculated in a single component
for maximum efficiency

8. Chemical Terms Filter

9. 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

10. Database Connection
• Provides a convenient way to define a JDBC connection
parameter set within a protocol
• Other ChemAxon components refer to this parameter set by a
symbolic name (e.g. “myConnection”)
• Multiple instances may be used in a protocol if needed
• Each component creates its own JDBC connection to the
database according to these parameters

11. JChem Base Insert
New features: Upgraded in 1.2
• Duplicate filtering option (using Pass and Fail ports)
• 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*
*Under development, as of version 1.3 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
New in 1.2

14. Reactor
Features:
• Reaction scheme can be specified
as file or string (reaction SMARTS)
• Sequential or combinatorial mode
• Product or reaction output
• Select products to include
• Inserts product number and
reaction number into specified tags
• Four tagger components available
to distinguish inputs of multi-
reactant reactions New in 1.2

15. Combinatorial Reactor Example
New in 1.2

16. Improved error reporting
New in 1.3
• Helps to track down problems quicker
• More information is displayed in the error dialog:
Marvin / JChem version, the current structure,
etc.
• If the environment variable
CHEMAXON_PP_LOG_DIR is set, an even
more detailed error report will be appended to
the file quot;pp_error.txtquot; in the specified directory

17. The “Java (On Server)” Component
• Most members of the ChemAxon collection are
based on this generic PP component
• A single “Component” interface with three
methods to implement:
– onInitialize(): initialize once
– onProcess(): runs for each input or each output
– onFinalize(): cleanup
• Java API provided for accessing
– component parameters and the data records
– SciTegic Molecule objects (Molecular Toolkit)

18. ChemicalTermsFilter OnInitialize()

19. ChemicalTermsFilter OnProcess()

20. Planned components
• JChem Cartridge for Oracle
• Instant JChem end user desktop cheminformatics
solution
• Name to structure conversion
• Tautomer and conformer generation
• Conversion of various structure file formats
• MCS based clustering
Node release cycle is fast and flexible. Please advise us on priority
and additional functionality for future node development.

21. Resources
• Download the component collection:
– http://www.chemaxon.com/integration/download.html
– http://accelrys.org/pipelinepilot/chemistry.html
• Support, feedback:
– dorant@chemaxon.com
– support@chemaxon.com

22. Acknowledgements
• SciTegic
– Moises Hassan
– Ton van Daelen
– Keith Burdick
• Informatics Matters
– Tim Dudgeon
• ChemAxon
– György Pirok
– Zsolt Mohácsi

23. Find out more
• Product descriptions & links
www.chemaxon.com/products.html
• Forum
www.chemaxon.com/forum
• Presentations and posters
www.chemaxon.com/conf
• Download
www.chemaxon.com/download.html