From: <eg...@us...> - 2008-10-30 10:51:11
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Revision: 12883 http://cdk.svn.sourceforge.net/cdk/?rev=12883&view=rev Author: egonw Date: 2008-10-30 10:51:08 +0000 (Thu, 30 Oct 2008) Log Message: ----------- Fixed strings Modified Paths: -------------- cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java Modified: cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java =================================================================== --- cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java 2008-10-30 07:07:38 UTC (rev 12882) +++ cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java 2008-10-30 10:51:08 UTC (rev 12883) @@ -33,21 +33,21 @@ public class SomeCDKFunctionOne implements IFunction { - private final static String functionname = "getCoffeeCanStatus"; + private final static String functionname = "calculateMass"; private final static String description = - "Returns the amount of coffee left in the can."; + "Calculates the mass of this molecule."; private final static String descriptiondetails = - "Returns the amount of coffee left in the can. Requires no input. Finishes immediately."; + "Returns the mass, and expects SMILES as input."; public FunctionInformation getFunctionInformation() { FunctionInformation info = new FunctionInformation( functionname, description, descriptiondetails, - "<xs:schema xmlns:xs='http://www.w3.org/2001/XMLSchema' targetNamespace='urn:xws:getCoffeeCanStatus:input' xmlns='urn:xws:getCoffeeCanStatus:input' elementFormDefault='qualified'/>", - "<xs:schema xmlns:xs='http://www.w3.org/2001/XMLSchema' targetNamespace='urn:xws:getCoffeeCanStatus:output' xmlns='urn:xws:getCoffeeCanStatus:output' elementFormDefault='qualified'>" + - "<xs:element name='coffeecanstatus' minOccurs='1' maxOccurs='1' type='xs:integer'>" + - "<!-- The amount of coffe in the can (0 - 100) -->" + + "<xs:schema xmlns:xs='http://www.w3.org/2001/XMLSchema' targetNamespace='urn:xws:cdk:input' xmlns='urn:xws:cdk:input' elementFormDefault='qualified'/>", + "<xs:schema xmlns:xs='http://www.w3.org/2001/XMLSchema' targetNamespace='urn:xws:cdk:output' xmlns='urn:xws:cdk:output' elementFormDefault='qualified'>" + + "<xs:element name='mass' minOccurs='1' maxOccurs='1' type='xs:float'>" + + "<!-- The mass. -->" + "</xs:element>" + "</xs:schema>", false @@ -60,15 +60,13 @@ Element output = null; try { - output = JavaDOMTools.createElement("coffeecanstatus"); - output.setTextContent(""+5); + output = JavaDOMTools.createElement("mass"); + output.setTextContent(""+5.0); } catch (Exception e) { - System.out.println("ERROR IN GetCoffeeCanStatus.run: creating element failed: " + e.getMessage()); + System.out.println("ERROR IN CDK.getMass.run: creating element failed: " + e.getMessage()); output = null; } - ps.setResult(output, "The coffee can status (" + - 5 + - ")"); + ps.setResult(output, "Done"); } } \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2009-01-17 13:27:15
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Revision: 13900 http://cdk.svn.sourceforge.net/cdk/?rev=13900&view=rev Author: egonw Date: 2009-01-17 12:05:39 +0000 (Sat, 17 Jan 2009) Log Message: ----------- Set the proper namespace Modified Paths: -------------- cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java Modified: cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java =================================================================== --- cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java 2009-01-17 11:24:24 UTC (rev 13899) +++ cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java 2009-01-17 12:05:39 UTC (rev 13900) @@ -75,6 +75,7 @@ double mass = AtomContainerManipulator.getNaturalExactMass(mol); System.out.println(" mass: " + mass); output = JavaDOMTools.createElement("mass"); + output.setAttribute("xmlns", "urn:xws:cdk:input"); output.setTextContent(""+mass); } catch (Exception e) { System.out.println("ERROR IN CDK.getMass.run: creating element failed: " + e.getMessage()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2009-04-25 18:03:08
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Revision: 14569 http://cdk.svn.sourceforge.net/cdk/?rev=14569&view=rev Author: egonw Date: 2009-04-25 18:03:04 +0000 (Sat, 25 Apr 2009) Log Message: ----------- Take into hydrogens too Modified Paths: -------------- cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java Modified: cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java =================================================================== --- cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java 2009-04-25 18:02:25 UTC (rev 14568) +++ cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/SomeCDKFunctionOne.java 2009-04-25 18:03:04 UTC (rev 14569) @@ -29,9 +29,12 @@ import net.bioclipse.xws.component.adhoc.function.IFunction; import net.bioclipse.xws.component.xmpp.process.IProcessStatus; +import org.openscience.cdk.atomtype.CDKAtomTypeMatcher; +import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.smiles.SmilesParser; +import org.openscience.cdk.tools.CDKHydrogenAdder; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.xws.ResourceAsStringTool; import org.w3c.dom.Element; @@ -48,6 +51,14 @@ ResourceAsStringTool.getAsString("org/openscience/cdk/xws/schema/mass.xml"); private final static SmilesParser parser = new SmilesParser(NoNotificationChemObjectBuilder.getInstance()); + private static CDKAtomTypeMatcher atMatcher = + CDKAtomTypeMatcher.getInstance( + NoNotificationChemObjectBuilder.getInstance() + ); + private static CDKHydrogenAdder hAdder = + CDKHydrogenAdder.getInstance( + NoNotificationChemObjectBuilder.getInstance() + ); public FunctionInformation getFunctionInformation() { @@ -72,6 +83,14 @@ try { IMolecule mol = parser.parseSmiles(SMILES); System.out.println("Molecule: " + mol); + IAtomType[] types = atMatcher.findMatchingAtomType(mol); + for (int i=0; i<mol.getAtomCount(); i++) { + if (types[i] != null) { + mol.getAtom(i).setAtomTypeName(types[i].getAtomTypeName()); + hAdder.addImplicitHydrogens(mol, mol.getAtom(i)); + } + } + AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); double mass = AtomContainerManipulator.getNaturalExactMass(mol); System.out.println(" mass: " + mass); output = JavaDOMTools.createElement("mass"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |