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Pipelining ChemAxon
Moises Hassan, Ton van Daelen, Rob Brown
ChemAxon User’s Group Meeting
Budapest, June 6-7 2006
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Pipelining ChemAxon
• ChemAxon components
• Pipeline Pilot architecture
• Implementation
• Timings
• Future Work
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ChemAxon Components
• Viewers– ChemAxon Molecular Table Viewer
• Calculators– ChemAxon Calculator
• Manipulators– ChemAxon Ionize Molecule at pH– ChemAxon MicroSpecies– ChemAxon Standardize
• Filters– ChemAxon Chemical Terms
• JChem Base– Connection– CTAB from DB table– Insert– JChem Search
• JChem Cartridge (under development)
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ChemAxon Molecular Table Viewer
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ChemAxon Molecular Table Viewer
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ChemAxon Calculator
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ChemAxon Micro Species
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ChemAxon Micro Species Report
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ChemAxon Standardize
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ChemAxon Chemical Terms
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ChemAxon JChem Database Search
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ChemAxon Ionize at pH
subprotocol
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Platform Integration Options
Web services
SciTegic Enterprise Server
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
ApacheApache
SOAPSDK
Various Clients
“Client side”
“Server side”
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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) (v6.0)
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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”)
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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
• Commercially released in PP 5.0
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ChemAxon Ionize Java ClassOnInitialize() Method
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ChemAxon Ionize Java ClassOnProcess() Method
continue…
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ChemAxon Ionize Java ClassOnProcess() Method
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Clustering and Visualization with ChemAxon BCUT Values
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Clustering and Visualization with ChemAxon BCUT Values
Equation "BCUT_PC1"
Constant: 1.454383
+ -0.367600 * "ChemAxon_BCUTBurden[1]"
+ -0.417106 * "ChemAxon_BCUTBurden[2]"
+ 0.021342 * "ChemAxon_BCUTBurden[3]"
+ 0.005342 * "ChemAxon_BCUTBurden[4]"
+ -0.530599 * "ChemAxon_BCUTCharge[1]"
+ -0.811792 * "ChemAxon_BCUTCharge[2]"
+ 0.825596 * "ChemAxon_BCUTCharge[3]"
+ 0.525619 * "ChemAxon_BCUTCharge[4]"
+ -0.535487 * "ChemAxon_BCUTHBond[1]"
+ -0.838793 * "ChemAxon_BCUTHBond[2]"
+ 0.281795 * "ChemAxon_BCUTHBond[3]"
+ 0.280152 * "ChemAxon_BCUTHBond[4]"
Equation "BCUT_PC2"
Constant: -2.434596
+ -0.107767 * "ChemAxon_BCUTBurden[1]"
+ 0.524903 * "ChemAxon_BCUTBurden[2]"
+ -0.052277 * "ChemAxon_BCUTBurden[3]"
+ -0.023233 * "ChemAxon_BCUTBurden[4]"
+ -0.482553 * "ChemAxon_BCUTCharge[1]"
+ 0.770592 * "ChemAxon_BCUTCharge[2]"
+ -0.789049 * "ChemAxon_BCUTCharge[3]"
+ 0.468833 * "ChemAxon_BCUTCharge[4]"
+ -0.511670 * "ChemAxon_BCUTHBond[1]"
+ 0.929707 * "ChemAxon_BCUTHBond[2]"
+ -0.006878 * "ChemAxon_BCUTHBond[3]"
+ 0.496791 * "ChemAxon_BCUTHBond[4]"
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Clustering and Visualization with ChemAxon BCUT Values
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Clustering and Visualization with ChemAxon BCUT Values
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Preliminary Execution TimesCommand-line vs. Pipeline Pilot Components
(Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)
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Preliminary Execution TimesCommand-line vs. Pipeline Pilot Components
(Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)
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Preliminary Execution TimesCommand-line vs. Pipeline Pilot Components
(Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)
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Conclusions
• Compatible architectures
• Pipeline Pilot good prototyping environment for ChemAxon’s advanced science
• Multiple deployment options
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Future Work
• Integrate more ChemAxon functionality
• Let us know what your priorities are
• Contact– Alex Allardyce: [email protected]– Ton van Daelen: [email protected]
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Acknowledgements
• Moises Hassan
• Szilard Dorant
• Beta testers– Robert Feinstein, Kelaroo– Christine Clayton, Takeda– Frank Yan, GNF