Chem Axon — Pipeline Pilot Integration Ton van

Chem. Axon - Pipeline Pilot Integration Ton van Daelen Accelrys, Inc.

Outline • Pipeline Pilot • Chem. Axon components • Integration technologies

Pipeline Pilot

Aggregate and Disseminate Information… An Example of How To Step Forward In The Informatics Evolution Easily Configurable Apps Into a Web Service Callable By Any Type Of Interface

Release history - major changes • Version 1. 6, August 2009 – New component: "Chem. Axon 3 D Conformers" • Version 1. 5, May 2009 – New components: "Chem. Axon Mol. Converter", "Chem. Axon Tautomerization", "Chem. Axon Markush Enumeration" • Version 1. 4, November 2008 – New components: "Lib. MCS Clustering", "Molecule to IUPAC Name", "Molecule from IUPAC Name“ – Major upgrade of "Chem. Axon Reactor" component • Version 1. 3, July 2008 – New component: “Chemical Terms Calculator” • Version 1. 2, March 2008 – New components: “Chem. Axon Reactor”, “Drop JChem Base Table”, “Create JChem Base Table” – Several components upgraded

Calculator Easy access for the most important calculations

Chemical Terms Calculator Maximum freedom trough Chemical Terms Expressions for the expert user • Use arbitrary Chemical Terms expressions • Results stored to arbitrary properties • A wide range of Chem. Axon functionality can be accessed as Chemical Terms functions New in 1. 3

Clustering with Lib. MCS Maximum Common Substructure (MCS) based clustering Options: • 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) New in 1. 4

Markush Enumeration of generic structures • 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) New in 1. 5

Pipeline Pilot Integration Browser Clients Native and Java Clients Java. Script SDK . NET SDK Java SDK Various Clients “Client side” SOAP SDK Web services Pipeline Pilot Java API Perl API SOAP Cmd Line Telnet / FTP ODBC Data access layer Application integration layer Oracle Application Services JDBC ISIS Accord IBM II Data Sources “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 example public double Get. CLog. P(string SMILES) { //. . . Do the calculation. . . return clogp; } • Configuring SOAP Component – – – SOAP Endpoint Method Namespace SOAP Parameter Names Method Parameter Values Property Return Names (“Greeting”) - HTTP URL resource - Name of function (“Get. CLog. P”) - Found in WSDL (often http: //tempuri. org/) - Name of function parameter (“Name”) - Pipeline Pilot property names - What to call the returned value

Java on Server component • Create new PP components – Filters, calculators, readers, writers • Single class with three methods – on. Initialize – on. Process – on. Finalize • Referencing Java classes on server • Interact with Molecular Toolkit

New Java class: Chem. Axon. Component • Parent class for component classes, implements com. scitegic. pilot. Component • Error reporting: all exceptions thrown in on. Initialize. Body(), on. Process. Body(), on. Finalize. Body() 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. : find. String. Parameter(String name) • Reduced code redundancy, better readability

Conclusions • Compatible architectures • Pipeline Pilot good prototyping environment for Chem. Axon’s advanced science • Multiple deployment options

Future Work • Integrate more Chem. Axon 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