Ton van Daelen

Accelrys, Inc.

ChemAxon - Pipeline Pilot Integration

Outline

• Pipeline Pilot

• ChemAxon components

• Integration technologies

Pipeline Pilot

Aggregate and Disseminate Information…

Easily Configurable Apps Into a Web Service CallableBy Any Type Of Interface

An Example of How To Step Forward In The Informatics Evolution

Release history - major changes

• Version 1.6, August 2009– New component: "ChemAxon 3D Conformers"

• Version 1.5, May 2009– New components: "ChemAxon MolConverter", "ChemAxon

Tautomerization", "ChemAxon Markush Enumeration"

• Version 1.4, November 2008– New components: "LibMCS Clustering", "Molecule to IUPAC

Name", "Molecule from IUPAC Name“– Major upgrade of "ChemAxon Reactor" component

• Version 1.3, July 2008– New component: “Chemical Terms Calculator”

• Version 1.2, March 2008– New components: “ChemAxon Reactor”, “Drop JChem Base

Table”, “Create JChem Base Table” – Several components upgraded

Calculator

Easy access for the most important calculations

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 1.3Maximum freedom trough Chemical Terms Expressions for the expert user

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

• File input

• Enumeration type:

– Sequential

– Random

• Number of enumerated structures can be limited (per input structure)

• Valence filter

• Scaffold alignment

• Markush code generation. The scaffold ID can be:

– fetched from data field

– generated (prefix + number)

Markush Enumeration

Enumeration of generic structures New in 1.5

Pipeline Pilot Integration

Web services

Pipeline Pilot

PerlAPI

JavaAPI

Cmd Line

Telnet /FTP

SOAP ODBC JDBC

Oracle ISIS Accord

Application Services

Application integration layer Data access layer

IBM II

Data Sources

JavaScriptSDK

.NETSDK

JavaSDK

Native and Java ClientsBrowser Clients

SOAPSDK

Various Clients

“Client side”

“Server side”

Telnet/FTP Component

• Execute command line applications on remote server (any platform)

• No coding required

• Use files to pass input and output data

• Secure version (SSH)

Integration of SOAP Web Services

• Simple method examplepublic double GetCLogP(string SMILES) {

// ... Do the calculation ...return clogp;

}

• Configuring SOAP Component– SOAP Endpoint - HTTP URL resource– Method Name - Name of function (“GetCLogP”)– Method Namespace - Found in WSDL (often http://tempuri.org/)– SOAP Parameter Names - Name of function parameter (“Name”) – Method Parameter Values - Pipeline Pilot property names– Property Return Names - What to call the returned value

(“Greeting”)

Java on Server component

• Create new PP components– Filters, calculators, readers,

writers

• Single class with three methods– onInitialize

– onProcess

– onFinalize

• Referencing Java classes on server

• Interact with Molecular Toolkit

New Java class: ChemAxonComponent

• Parent class for component classes, implements com.scitegic.pilot.Component

• Error reporting: all exceptions thrown in onInitializeBody(), onProcessBody(), onFinalizeBody() are caught, logged and reported (re-thrown with added information)

• Parameters and context always readily available

• Utility functions for conveniently accessing parameters and properties, e.g.: findStringParameter(String name)

• Reduced code redundancy, better readability

Conclusions

• Compatible architectures

• Pipeline Pilot good prototyping environment for ChemAxon’s advanced science

• Multiple deployment options

Future Work

• Integrate more ChemAxon functionality

• Let us know what your priorities are

• Acknowledgements– Szilard Dorant– Moises Hassan– Keith Burdick

• Contact– Alex Allardyce: aa@chemaxon.com– Ton van Daelen: tvd@accelrys.com