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Ton van Daelen Accelrys, Inc. ChemAxon - Pipeline Pilot Integration.

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Presentation on theme: "Ton van Daelen Accelrys, Inc. ChemAxon - Pipeline Pilot Integration."— Presentation transcript:

1 Ton van Daelen Accelrys, Inc. ChemAxon - Pipeline Pilot Integration

2 Outline Pipeline Pilot ChemAxon components Integration technologies

3 Pipeline Pilot

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

5 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

6 Calculator Easy access for the most important calculations

7 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 Maximum freedom trough Chemical Terms Expressions for the expert user

8 Reactor Improvements: Upgraded in 1.4 Synthesis code generation Output reaction mapping Advanced options: –Unambiguous only –Ignore rules: Reactivity and Exclude Selectivity Tolerance

9 IUPAC naming components IUPAC Name to Molecule Molecule to IUPAC Name Example roundtrip protocol: New in 1.4

10 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

11 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

12 Tautomerization Component for tautomer generation New in 1.5 Calculation modes: –All tautomers –Canonical tautomer –Generic tautomer –Major tautomer –Dominant tautomer distribution Options: –Protect aromaticity, charge, double bond stereo, tetrahedral stereo –Exclude antiaromatic compounds –Single fragment mode –Consider pH at specific value

13 MolConverter Swiss army knife for molecular format conversion New in 1.5 Input and output can either be –File –Property –Pipeline Pilot Molecule Specified input format or auto- detection Various output formats or custom format string Option to halt or continue on error, error messages put into property 2D cleaning (coordinate generation) only when needed (default). Unconditional 2D or 3D cleaning or no cleaning can also be selected

14 Conformer generation Component for 3D conformer generation New in 1.6 Calculation modes: –Multiple conformers –Lowes energy conformer Options: –Maximum number of conformers –Diversity limit –Optimization limit, hyperfine option –Time limit –Generate with explicit H atoms –Energy unit kcal/mol or KJ/mol, into arbitrary property

15 Pipeline Pilot Integration Web services Pipeline Pilot Perl API Java API Cmd Line Telnet / FTP SOAP ODBCJDBC OracleISISAccord Application Services Application integration layer Data access layer IBM II Data Sources JavaScript SDK.NET SDK Java SDK Native and Java ClientsBrowser Clients SOAP SDK Various Clients Client side Server side

16 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)

17 Integration of SOAP Web Services Simple method example public 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 –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)

18 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

19 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

20 Java Molecular Weight Example private static final double HYDROGEN_WEIGHT = Hydrogen.atomicWeight(); // get molecule and properties, skip data record if molecule is not found Molecule mol = Molecule.findMolecule(data); if (mol == null) return Component.State.ReadyForInputData; PropertyCollection props = mol.getProperties(); // calculate mol weight and exact weight (most common isotopes) double mw = 0.0; for (Atom atom : mol.getAtoms()) { int numImplH = atom.getNumImplicitHydrogens(); mw += atom.getAtomicWeight(); mw += numImplH*HYDROGEN_WEIGHT; } props.define("Java_MW", mw);

21 Conclusions Compatible architectures Pipeline Pilot good prototyping environment for ChemAxons advanced science Multiple deployment options

22 Future Work Integrate more ChemAxon functionality Let us know what your priorities are Acknowledgements –Szilard Dorant –Moises Hassan –Keith Burdick Contact –Alex Allardyce: –Ton van Daelen:

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