Pipelining ChemAxon

2008 Accelrys EUGM

Pipelining ChemAxon

Szilard Dorant

Solutions for Cheminformatics

2008 Accelrys EUGM

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

2008 Accelrys EUGM

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

Version Date

1.2 March 5

1.3 July 11

1.3.1 October 22

1.4 November 24

User interestDevelopment

*As of November 2008

2008 Accelrys EUGM

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)

2008 Accelrys EUGM

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

2008 Accelrys EUGM

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

2008 Accelrys EUGM

IUPAC naming components

• IUPAC Name to Molecule

• Molecule to IUPAC Name

• Example “roundtrip” protocol:

New in 1.4

2008 Accelrys EUGM

Reactor

Improvements:

Upgraded in 1.4

• Synthesis code generation

• Output reaction mapping

• Advanced options:– Unambiguous only

– Ignore rules:• Reactivity and Exclude• Selectivity• Tolerance

2008 Accelrys EUGM

Combinatorial Reactor Example

2008 Accelrys EUGM

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

2008 Accelrys EUGM

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

2008 Accelrys EUGM

• Several search options were added

• Easier protocol integration and better performance due to concentrated functionality

JChem Database Search

Upgraded in 1.2

2008 Accelrys EUGM

JChem Base demo protocol

2008 Accelrys EUGM

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

2008 Accelrys EUGM

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.

2008 Accelrys EUGM

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

2008 Accelrys EUGM

Acknowledgements

• Accelrys– Moises Hassan– Ton van Daelen– Keith Burdick

• Informatics Matters– Tim Dudgeon

• ChemAxon– György Pirok– Miklós Vargyas– Zsolt Mohácsi