Pipelining ChemAxon

Szilard Dorant

Solutions for Cheminformatics

ChemAxon and Pipeline Pilot - What’s new

• New components for current ChemAxon functionality

• Support for new ChemAxon functionality more quickly

• Support from ChemAxon directly

ChemAxon took over the responsibility of maintaining

and supporting the ChemAxon Pipeline Pilot

Component Collection with the continued active help

from SciTegic.

ChemAxon released component collection

version 1.2 in March 2008

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

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)

Molecular Table Viewer

Calculator

Chemical Terms Calculator

• Use arbitrary Chemical Terms

expressions

• Results stored to arbitrary

properties

• Up to 10 expressions can be

calculated in a single component

for maximum efficiency

New in 1.3

Chemical Terms Filter

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

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

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, as of version 1.3 limited to string database column types

• Duplicate filtering option (using Pass and Fail ports)

Upgraded in 1.2

• Several search options were added

• Easier protocol integration and

better performance due to

concentrated functionality

JChem Database Search

Upgraded in 1.2

JChem Base demo protocol

New in 1.2

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

Combinatorial Reactor Example

New in 1.2

Improved error reporting

• 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 "pp_error.txt" in the specified directory

New in 1.3

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)

ChemicalTermsFilter OnInitialize()

ChemicalTermsFilter OnProcess()

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.

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

Acknowledgements

• SciTegic

– Moises Hassan

– Ton van Daelen

– Keith Burdick

• Informatics Matters

– Tim Dudgeon

• ChemAxon

– György Pirok

– Zsolt Mohácsi

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