Transcript ChemAxon Presentation

ChemAxon - Pipeline Pilot
Integration
Ton van Daelen
Accelrys, Inc.
Outline
• Pipeline Pilot
• ChemAxon 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: "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
Maximum freedom trough Chemical Terms
Expressions for the expert user
• 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
Clustering with LibMCS
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
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
JavaScript
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 GetCLogP(string SMILES) {
// ... Do the calculation ...
return clogp;
}
• Configuring SOAP Component
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SOAP Endpoint
Method Name
Method Namespace
SOAP Parameter Names
Method Parameter Values
Property Return Names
(“Greeting”)
- HTTP URL resource
- Name of function (“GetCLogP”)
- 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
– 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: [email protected]
– Ton van Daelen: [email protected]