From: Miguel R. C. <mig...@un...> - 2005-07-01 12:14:48
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My work consist of trying to reproduce a mass spectrum. For this, I need reaction tools. I have implemented a reaction package which I use and I would like submit to cdk and to know what the people think and its opinions about this. I have tried that its input is very simple. And it is like so. 1: Reaction reaction = new Reaction(); 2: reaction.addReactant(molecule?); 3: Object[] params = {new Integer(0)}; 4: reaction.setParameters(params); 5: reaction.setNameReaction(“NameOfReaction”); 6: reaction.startReaction(); 7: ReactionParameters rp = reaction.getReactionParameters(); //not necessary for the reaction 8: ReactionSpecification rs = reaction.getReactionSpecification(); //not necessary for the reaction 9: Molecule fragmentedMolecules = reaction.getProducts().getMolecules(); 1: implemented already by cdk 2: also by cdk 3: Its function is to specific a parameter (Temperature or bond to reaction) which has importance in the process. 4: set the parameter. 5: set the name of the reaction 6: starts the reaction 7: get the parameters 8: get the specific specifications of the reactions (title, vendor, reference, etc..) 9: get the products of the reactions. The structure of this package contains: link image: http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reaction/reactionPackage a ReactionsType which is a extends of Reaction and controls the process. It loads the corresponding class, determined according to the name of the reaction. a ReactionsTools which has some tools for the reactions . the diverse reactions class extends of ReactionsType. Each reaction contains an Analysator method (determinate if is possible the reaction) and the constructor method (make the process) a ReactionsFactory which load the reactions.xml file a ReactionsModel interface of the structure reactions a reactions.xml which has all imformation of the reactions which is structured so: 1°------------ <entry id="electronimpactpbd" term="Electron impact for pi-Bond Dissociation"> <annotation> <documentation> <metadata name="dc:creator" content="IUPAC"/> <metadata name="dc:identifier" content="COMPENDIUM:E01999"/> <metadata name="dc:contributor" content="mrc"/> <metadata name="dc:date" content="2005-03-13"/> </documentation> </annotation> <metadataLocation dictRef="reactions-metadata:Location"> <metadata dictRef="reactions-metadata:LocationClass" content="org.openscience.massspectra.reaction.ElectronImpactPBD"/> </metadataLocation> <metadataParameters dictRef="reactions-metadata:Parameters"> <metadata dictRef="parameters:Number" content="1"/> <parameter> <metadata dataType="xsd:Integer" content="Position Bond"/> </parameter> </metadataParameters> 2°------- <definition></definition> <description> Term used to describe ionization of any species by electrons accelerated between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. In this case pi-Bond Dissociation. </description> <metadataList dictRef="reaction-metadata:Classification"> <metadata dictRef="reaction-metadata:reactionClass" content="reaction-processor-metadata:electronionization"/> </metadataList> <exemplesReaction> <imagedata dictRef="reactions-metadata:CML" content="examples/ElectronImpactPBD1.cml"/> </exemplesReaction> </entry> The first part is used for the reaction package. Id(name of reaction), localization and Parameters which can be define. The second part has the function to create a web page which is dictionary about reaction. Its contains definition and an example of each reaction and etc... I think that it should be a good information for the community if they search if a predicted reaction there is possible in cdk like descriptors-qsar . link webpage: http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reaction/copy_of_reactionDictionary If someone hat some suggestion!! rojas -- Miuel Rojas Cherto(mig...@un...) Junior Research Group for Applied Bioinformatics(http://almost.cubic.uni-koeln.de/jrg) Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 |
From: Miguel R. C. <mig...@un...> - 2005-07-01 12:42:33
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sorry The right links http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reaction/reactionPackage http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reaction/copy_of_reactionDictionary -- Miuel Rojas Cherto(mig...@un...) Junior Research Group for Applied Bioinformatics(http://almost.cubic.uni-koeln.de/jrg) Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 |