From: <eg...@us...> - 2006-10-24 13:52:59
|
Revision: 7163 http://svn.sourceforge.net/cdk/?rev=7163&view=rev Author: egonw Date: 2006-10-24 06:52:48 -0700 (Tue, 24 Oct 2006) Log Message: ----------- Setup things for the new GPL qsar-weka module Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/META-INF/qsar.cdkdepends trunk/cdk/src/META-INF/qsar.libdepends trunk/cdk/src/META-INF/test-qsar.cdkdepends Added Paths: ----------- trunk/cdk/src/META-INF/qsar-weka.cdkdepends trunk/cdk/src/META-INF/qsar-weka.libdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2006-10-24 13:44:35 UTC (rev 7162) +++ trunk/cdk/build.xml 2006-10-24 13:52:48 UTC (rev 7163) @@ -442,7 +442,6 @@ <antcall target="compile-module"><param name="module" value="extra"/></antcall> <antcall target="compile-module"><param name="module" value="smiles"/></antcall> <antcall target="compile-module"><param name="module" value="libio-cml"/></antcall> - <antcall target="compile-module"><param name="module" value="libioweka"/></antcall> <antcall target="compile-module"><param name="module" value="libio-openbabel"/></antcall> <antcall target="compile-module"><param name="module" value="pdb-cml"/></antcall> <antcall target="compile-module"><param name="module" value="reaction"/></antcall> @@ -450,6 +449,7 @@ <antcall target="compile-module"><param name="module" value="qsar"/></antcall> <antcall target="compile-module"><param name="module" value="qsar-cml"/></antcall> <antcall target="compile-module"><param name="module" value="qsar-pdb"/></antcall> + <antcall target="compile-module"><param name="module" value="qsar-weka"/></antcall> <antcall target="compile-module"><param name="module" value="forcefield"/></antcall> <antcall target="compile-module"><param name="module" value="builder3d"/></antcall> <antcall target="compile-module"><param name="module" value="svg"/></antcall> Added: trunk/cdk/src/META-INF/qsar-weka.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/qsar-weka.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/qsar-weka.cdkdepends 2006-10-24 13:52:48 UTC (rev 7163) @@ -0,0 +1,10 @@ +cdk-interfaces.jar +cdk-data.jar +cdk-nonotify.jar +cdk-core.jar +cdk-standard.jar +cdk-valencycheck.jar +cdk-extra.jar +cdk-reaction.jar +cdk-charges.jar +cdk-libioweka.jar Added: trunk/cdk/src/META-INF/qsar-weka.libdepends =================================================================== --- trunk/cdk/src/META-INF/qsar-weka.libdepends (rev 0) +++ trunk/cdk/src/META-INF/qsar-weka.libdepends 2006-10-24 13:52:48 UTC (rev 7163) @@ -0,0 +1,7 @@ +Jama-1.0.1.jar +jgrapht-0.6.0.jar +sjava-0.68.jar +vecmath1.2-1.14.jar +xom-1.1.jar +weka.jar + Modified: trunk/cdk/src/META-INF/qsar.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/qsar.cdkdepends 2006-10-24 13:44:35 UTC (rev 7162) +++ trunk/cdk/src/META-INF/qsar.cdkdepends 2006-10-24 13:52:48 UTC (rev 7163) @@ -7,4 +7,4 @@ cdk-extra.jar cdk-reaction.jar cdk-charges.jar -cdk-libioweka.jar +cdk-qsar.jar Modified: trunk/cdk/src/META-INF/qsar.libdepends =================================================================== --- trunk/cdk/src/META-INF/qsar.libdepends 2006-10-24 13:44:35 UTC (rev 7162) +++ trunk/cdk/src/META-INF/qsar.libdepends 2006-10-24 13:52:48 UTC (rev 7163) @@ -4,5 +4,3 @@ sjava-0.68.jar vecmath1.2-1.14.jar xom-1.1.jar -weka.jar - Modified: trunk/cdk/src/META-INF/test-qsar.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-qsar.cdkdepends 2006-10-24 13:44:35 UTC (rev 7162) +++ trunk/cdk/src/META-INF/test-qsar.cdkdepends 2006-10-24 13:52:48 UTC (rev 7163) @@ -11,6 +11,7 @@ cdk-charges.jar cdk-qsar.jar cdk-qsar-pdb.jar +cdk-qsar-weka.jar cdk-smiles.jar cdk-test-core.jar cdk-applications.jar This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2006-10-24 17:09:18
|
Revision: 7172 http://svn.sourceforge.net/cdk/?rev=7172&view=rev Author: egonw Date: 2006-10-24 10:08:45 -0700 (Tue, 24 Oct 2006) Log Message: ----------- Renamed test-libioweka to test-weka (test-qsar-weka is not possible because of second hyphen that would have to end up in the Mqsar-wekaTests.java name :( ). Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java Added Paths: ----------- trunk/cdk/src/META-INF/test-weka.cdkdepends trunk/cdk/src/META-INF/test-weka.datafiles trunk/cdk/src/META-INF/test-weka.devellibdepends trunk/cdk/src/META-INF/test-weka.libdepends trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java Removed Paths: ------------- trunk/cdk/src/META-INF/test-libioweka.cdkdepends trunk/cdk/src/META-INF/test-libioweka.datafiles trunk/cdk/src/META-INF/test-libioweka.devellibdepends trunk/cdk/src/META-INF/test-libioweka.libdepends trunk/cdk/src/org/openscience/cdk/test/MlibiowekaTests.java Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2006-10-24 16:57:46 UTC (rev 7171) +++ trunk/cdk/build.xml 2006-10-24 17:08:45 UTC (rev 7172) @@ -468,7 +468,7 @@ <antcall target="compile-module"><param name="module" value="test-io"/></antcall> <antcall target="compile-module"><param name="module" value="test-extra"/></antcall> <antcall target="compile-module"><param name="module" value="test-smiles"/></antcall> - <antcall target="compile-module"><param name="module" value="test-libioweka"/></antcall> + <antcall target="compile-module"><param name="module" value="test-weka"/></antcall> <antcall target="compile-module"><param name="module" value="test-reaction"/></antcall> <antcall target="compile-module"><param name="module" value="test-forcefield"/></antcall> <antcall target="compile-module"><param name="module" value="test-valencycheck"/></antcall> Deleted: trunk/cdk/src/META-INF/test-libioweka.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-libioweka.cdkdepends 2006-10-24 16:57:46 UTC (rev 7171) +++ trunk/cdk/src/META-INF/test-libioweka.cdkdepends 2006-10-24 17:08:45 UTC (rev 7172) @@ -1,4 +0,0 @@ -cdk-core.jar -cdk-data.jar -cdk-libioweka.jar -cdk-test-core.jar Deleted: trunk/cdk/src/META-INF/test-libioweka.datafiles =================================================================== --- trunk/cdk/src/META-INF/test-libioweka.datafiles 2006-10-24 16:57:46 UTC (rev 7171) +++ trunk/cdk/src/META-INF/test-libioweka.datafiles 2006-10-24 17:08:45 UTC (rev 7172) @@ -1 +0,0 @@ -data/arff/** Deleted: trunk/cdk/src/META-INF/test-libioweka.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-libioweka.devellibdepends 2006-10-24 16:57:46 UTC (rev 7171) +++ trunk/cdk/src/META-INF/test-libioweka.devellibdepends 2006-10-24 17:08:45 UTC (rev 7172) @@ -1,2 +0,0 @@ -junit.jar - Deleted: trunk/cdk/src/META-INF/test-libioweka.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-libioweka.libdepends 2006-10-24 16:57:46 UTC (rev 7171) +++ trunk/cdk/src/META-INF/test-libioweka.libdepends 2006-10-24 17:08:45 UTC (rev 7172) @@ -1,3 +0,0 @@ -weka.jar -vecmath1.2-1.14.jar -log4j.jar Copied: trunk/cdk/src/META-INF/test-weka.cdkdepends (from rev 7161, trunk/cdk/src/META-INF/test-libioweka.cdkdepends) =================================================================== --- trunk/cdk/src/META-INF/test-weka.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/test-weka.cdkdepends 2006-10-24 17:08:45 UTC (rev 7172) @@ -0,0 +1,4 @@ +cdk-core.jar +cdk-data.jar +cdk-qsar-weka.jar +cdk-test-core.jar Copied: trunk/cdk/src/META-INF/test-weka.datafiles (from rev 7161, trunk/cdk/src/META-INF/test-libioweka.datafiles) =================================================================== --- trunk/cdk/src/META-INF/test-weka.datafiles (rev 0) +++ trunk/cdk/src/META-INF/test-weka.datafiles 2006-10-24 17:08:45 UTC (rev 7172) @@ -0,0 +1 @@ +data/arff/** Copied: trunk/cdk/src/META-INF/test-weka.devellibdepends (from rev 7161, trunk/cdk/src/META-INF/test-libioweka.devellibdepends) =================================================================== --- trunk/cdk/src/META-INF/test-weka.devellibdepends (rev 0) +++ trunk/cdk/src/META-INF/test-weka.devellibdepends 2006-10-24 17:08:45 UTC (rev 7172) @@ -0,0 +1,2 @@ +junit.jar + Copied: trunk/cdk/src/META-INF/test-weka.libdepends (from rev 7161, trunk/cdk/src/META-INF/test-libioweka.libdepends) =================================================================== --- trunk/cdk/src/META-INF/test-weka.libdepends (rev 0) +++ trunk/cdk/src/META-INF/test-weka.libdepends 2006-10-24 17:08:45 UTC (rev 7172) @@ -0,0 +1,3 @@ +weka.jar +vecmath1.2-1.14.jar +log4j.jar Deleted: trunk/cdk/src/org/openscience/cdk/test/MlibiowekaTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MlibiowekaTests.java 2006-10-24 16:57:46 UTC (rev 7171) +++ trunk/cdk/src/org/openscience/cdk/test/MlibiowekaTests.java 2006-10-24 17:08:45 UTC (rev 7172) @@ -1,27 +0,0 @@ -package org.openscience.cdk.test; - -import junit.framework.Test; -import junit.framework.TestSuite; - -import org.openscience.cdk.test.libio.weka.WekaTest; - -/** - * TestSuite that runs all the tests for the CDK reaction module. - * - * @cdk.module test-libioweka - * @cdk.depends weka.jar - * @cdk.depends junit.jar - */ -public class MlibiowekaTests { - - public static Test suite() { - TestSuite suite= new TestSuite("CDK weka Tests"); - - // Individual Tests - - suite.addTest(WekaTest.suite()); - - return suite; - } - -} Copied: trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java (from rev 7161, trunk/cdk/src/org/openscience/cdk/test/MlibiowekaTests.java) =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java (rev 0) +++ trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java 2006-10-24 17:08:45 UTC (rev 7172) @@ -0,0 +1,27 @@ +package org.openscience.cdk.test; + +import junit.framework.Test; +import junit.framework.TestSuite; + +import org.openscience.cdk.test.libio.weka.WekaTest; + +/** + * TestSuite that runs all the tests for the CDK reaction module. + * + * @cdk.module test-libioweka + * @cdk.depends weka.jar + * @cdk.depends junit.jar + */ +public class MwekaTests { + + public static Test suite() { + TestSuite suite= new TestSuite("CDK weka Tests"); + + // Individual Tests + + suite.addTest(WekaTest.suite()); + + return suite; + } + +} Modified: trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java 2006-10-24 16:57:46 UTC (rev 7171) +++ trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java 2006-10-24 17:08:45 UTC (rev 7172) @@ -40,8 +40,7 @@ /** * TestCase for Weka class. * - * @cdk.module test-libioweka - * + * @cdk.module test-weka */ public class WekaTest extends CDKTestCase { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2006-10-25 15:08:35
|
Revision: 7187 http://svn.sourceforge.net/cdk/?rev=7187&view=rev Author: shk3 Date: 2006-10-25 08:08:17 -0700 (Wed, 25 Oct 2006) Log Message: ----------- added a separate changelog for jcp; since releases are independent from cdk, the changelog should be as well. Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintViewerOnlyApplet.java trunk/cdk/src/org/openscience/cdk/io/MDLReader.java Added Paths: ----------- trunk/cdk/changelog-jcp.xml Added: trunk/cdk/changelog-jcp.xml =================================================================== --- trunk/cdk/changelog-jcp.xml (rev 0) +++ trunk/cdk/changelog-jcp.xml 2006-10-25 15:08:17 UTC (rev 7187) @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="utf-8"?> +<changelog xmlns="http://cdk.sf.net/schema/changelog" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://cdk.sf.net/schema/changelog changelog.xsd"> + + <release id="2.4.0"> + <addition contributor="shk3"> + Changed the system for handling Hs. JCP now traces implicit Hs by default and shows them along element symbols. This means you get OH, CH3 etc, which was often asked for. + </addition> + </release> +</changelog> Modified: trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintViewerOnlyApplet.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintViewerOnlyApplet.java 2006-10-25 14:50:02 UTC (rev 7186) +++ trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintViewerOnlyApplet.java 2006-10-25 15:08:17 UTC (rev 7187) @@ -31,7 +31,7 @@ import java.awt.event.MouseMotionListener; import java.lang.reflect.Method; -//import netscape.javascript.JSObject; +import netscape.javascript.JSObject; import org.openscience.cdk.applications.jchempaint.JChemPaintViewerOnlyPanel; import org.openscience.cdk.controller.Controller2D; @@ -138,7 +138,7 @@ public void highlightPeakInTable(int atomNumber){ if(getParameter("highlightTable")==null || getParameter("highlightTable").equals("false")) return; - /*JSObject win = JSObject.getWindow(this); + JSObject win = JSObject.getWindow(this); if(oldnumber!=-1){ JSObject tr = (JSObject) win.eval("document.getElementById(\"tableid"+oldnumber+"\")"); if((oldnumber+1)%2==0) @@ -152,7 +152,7 @@ }else{ tr.setMember("bgColor","red"); oldnumber=atomNumber; - }*/ + } } private Applet getSpectrumApplet() { Modified: trunk/cdk/src/org/openscience/cdk/io/MDLReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLReader.java 2006-10-25 14:50:02 UTC (rev 7186) +++ trunk/cdk/src/org/openscience/cdk/io/MDLReader.java 2006-10-25 15:08:17 UTC (rev 7187) @@ -435,6 +435,16 @@ logger.warn("A few fields are missing. Older MDL MOL file?"); } + //shk3: This reads shifts from after the molecule. I don't think this is an official format, but I saw it frequently 80=>78 for alk + if(line.length()>=78){ + double shift=Double.parseDouble(line.substring(69,80).trim()); + atom.setProperty("first shift",new Double(shift)); + } + if(line.length()>=87){ + double shift=Double.parseDouble(line.substring(79,87).trim()); + atom.setProperty("second shift",new Double(shift)); + } + molecule.addAtom(atom); } @@ -626,6 +636,7 @@ logger.debug(exception); throw exception; } catch (Exception exception) { + exception.printStackTrace(); String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.getMessage(); logger.error(error); logger.debug(exception); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2006-10-29 20:55:46
|
Revision: 7204 http://svn.sourceforge.net/cdk/?rev=7204&view=rev Author: egonw Date: 2006-10-29 12:55:13 -0800 (Sun, 29 Oct 2006) Log Message: ----------- Fixed weka and qsar test modules Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/test/MqsarTests.java trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/IPBondDescriptorTest.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/IPMolecularDescriptorTest.java Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2006-10-28 18:44:34 UTC (rev 7203) +++ trunk/cdk/build.xml 2006-10-29 20:55:13 UTC (rev 7204) @@ -707,10 +707,10 @@ <antcall target="test-module"><param name="module" value="extra"/></antcall> <antcall target="test-module"><param name="module" value="valencycheck"/></antcall> <antcall target="test-module"><param name="module" value="reaction"/></antcall> - <antcall target="test-module"><param name="module" value="libioweka"/></antcall> <antcall target="test-module"><param name="module" value="smiles"/></antcall> <antcall target="test-module"><param name="module" value="experimental"/></antcall> <antcall target="test-module"><param name="module" value="qsar"/></antcall> + <antcall target="test-module"><param name="module" value="weka"/></antcall> <antcall target="test-module"><param name="module" value="pdb"/></antcall> <antcall target="test-module"><param name="module" value="inchi"/></antcall> </target> Modified: trunk/cdk/src/org/openscience/cdk/test/MqsarTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MqsarTests.java 2006-10-28 18:44:34 UTC (rev 7203) +++ trunk/cdk/src/org/openscience/cdk/test/MqsarTests.java 2006-10-29 20:55:13 UTC (rev 7204) @@ -53,7 +53,7 @@ suite.addTest(DescriptorEngineTest.suite()); - // from cdk.test.qsar.atomic +// from cdk.test.qsar.atomic suite.addTest(AtomDegreeDescriptorTest.suite()); suite.addTest(AtomHybridizationDescriptorTest.suite()); suite.addTest(AtomHybridizationVSEPRDescriptorTest.suite()); @@ -64,7 +64,6 @@ suite.addTest(EffectiveAtomPolarizabilityDescriptorTest.suite()); suite.addTest(InductiveAtomicHardnessDescriptorTest.suite()); suite.addTest(InductiveAtomicSoftnessDescriptorTest.suite()); - suite.addTest(IPAtomicDescriptorTest.suite()); suite.addTest(IsProtonInAromaticSystemDescriptorTest.suite()); suite.addTest(IsProtonInConjugatedPiSystemDescriptorTest.suite()); suite.addTest(PartialPiChargeDescriptorTest.suite()); @@ -84,13 +83,12 @@ suite.addTest(BondPartialSigmaChargeDescriptorTest.suite()); suite.addTest(BondPartialTChargeDescriptorTest.suite()); suite.addTest(BondSigmaElectronegativityDescriptorTest.suite()); - suite.addTest(IPBondDescriptorTest.suite()); suite.addTest(ResonancePositiveChargeDescriptorTest.suite()); - // from cdk.test.qsar.molecular +// from cdk.test.qsar.molecular suite.addTest(AminoAcidCountDescriptorTest.suite()); suite.addTest(APolDescriptorTest.suite()); suite.addTest(AromaticAtomsCountDescriptorTest.suite()); @@ -108,7 +106,6 @@ suite.addTest(GravitationalIndexDescriptorTest.suite()); suite.addTest(HBondAcceptorCountDescriptorTest.suite()); suite.addTest(HBondDonorCountDescriptorTest.suite()); - suite.addTest(IPMolecularDescriptorTest.suite()); suite.addTest(KappaShapeIndicesDescriptorTest.suite()); suite.addTest(LargestChainDescriptorTest.suite()); suite.addTest(LargestPiSystemDescriptorTest.suite()); @@ -134,7 +131,7 @@ suite.addTest(ZagrebIndexDescriptorTest.suite()); - // from cdk.test.qsar.model.R +// from cdk.test.qsar.model.R suite.addTest(CNNClassificationModelTest.suite()); suite.addTest(org.openscience.cdk.test.qsar.model.R.CNNRegressionModelTest.suite()); suite.addTest(org.openscience.cdk.test.qsar.model.R.LinearRegressionModelTest.suite()); Modified: trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java 2006-10-28 18:44:34 UTC (rev 7203) +++ trunk/cdk/src/org/openscience/cdk/test/MwekaTests.java 2006-10-29 20:55:13 UTC (rev 7204) @@ -4,11 +4,13 @@ import junit.framework.TestSuite; import org.openscience.cdk.test.libio.weka.WekaTest; +import org.openscience.cdk.test.qsar.descriptors.atomic.IPAtomicDescriptorTest; +import org.openscience.cdk.test.qsar.descriptors.molecular.IPMolecularDescriptorTest; /** * TestSuite that runs all the tests for the CDK reaction module. * - * @cdk.module test-libioweka + * @cdk.module test-weka * @cdk.depends weka.jar * @cdk.depends junit.jar */ @@ -20,7 +22,11 @@ // Individual Tests suite.addTest(WekaTest.suite()); - + + suite.addTest(IPAtomicDescriptorTest.suite()); + suite.addTest(IPMolecularDescriptorTest.suite()); + suite.addTest(IPAtomicDescriptorTest.suite()); + return suite; } Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-10-28 18:44:34 UTC (rev 7203) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-10-29 20:55:13 UTC (rev 7204) @@ -41,7 +41,7 @@ /** * TestSuite that runs all QSAR tests. * - * @cdk.module test-qsar + * @cdk.module test-weka */ public class IPAtomicDescriptorTest extends CDKTestCase { Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/IPBondDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/IPBondDescriptorTest.java 2006-10-28 18:44:34 UTC (rev 7203) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/bond/IPBondDescriptorTest.java 2006-10-29 20:55:13 UTC (rev 7204) @@ -40,7 +40,7 @@ /** * TestSuite that runs all QSAR tests. * - * @cdk.module test-qsar + * @cdk.module test-weka */ public class IPBondDescriptorTest extends CDKTestCase { Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/IPMolecularDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/IPMolecularDescriptorTest.java 2006-10-28 18:44:34 UTC (rev 7203) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/IPMolecularDescriptorTest.java 2006-10-29 20:55:13 UTC (rev 7204) @@ -41,7 +41,7 @@ /** * TestSuite that runs all QSAR tests. * - * @cdk.module test-qsar + * @cdk.module test-weka */ public class IPMolecularDescriptorTest extends CDKTestCase { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2006-11-01 14:29:05
|
Revision: 7208 http://svn.sourceforge.net/cdk/?rev=7208&view=rev Author: egonw Date: 2006-11-01 06:28:26 -0800 (Wed, 01 Nov 2006) Log Message: ----------- More work: pending is an import clean up to fix failing imports Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/test/MqsarAtomicTests.java trunk/cdk/src/org/openscience/cdk/test/MqsarBondTests.java trunk/cdk/src/org/openscience/cdk/test/MqsarMolecularTests.java Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2006-11-01 13:53:12 UTC (rev 7207) +++ trunk/cdk/build.xml 2006-11-01 14:28:26 UTC (rev 7208) @@ -474,6 +474,9 @@ <antcall target="compile-module"><param name="module" value="test-valencycheck"/></antcall> <antcall target="compile-module"><param name="module" value="test-experimental"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsar"/></antcall> + <antcall target="compile-module"><param name="module" value="test-qsarAtomic"/></antcall> + <antcall target="compile-module"><param name="module" value="test-qsarBond"/></antcall> + <antcall target="compile-module"><param name="module" value="test-qsarMolecular"/></antcall> <antcall target="compile-module"><param name="module" value="test-pdb"/></antcall> <antcall target="compile-module"><param name="module" value="test-osjvmts"/></antcall> <antcall target="compile-module"><param name="module" value="test-inchi"/></antcall> @@ -710,7 +713,10 @@ <antcall target="test-module"><param name="module" value="smiles"/></antcall> <antcall target="test-module"><param name="module" value="experimental"/></antcall> <antcall target="test-module"><param name="module" value="qsar"/></antcall> - <antcall target="test-module"><param name="module" value="weka"/></antcall> + <antcall target="test-module"><param name="module" value="qsarAtomic"/></antcall> + <antcall target="test-module"><param name="module" value="qsarBond"/></antcall> + <antcall target="test-module"><param name="module" value="qsarMolecular"/></antcall> + <antcall target="test-module"><param name="module" value="weka"/></antcall> <antcall target="test-module"><param name="module" value="pdb"/></antcall> <antcall target="test-module"><param name="module" value="inchi"/></antcall> </target> Modified: trunk/cdk/src/org/openscience/cdk/test/MqsarAtomicTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MqsarAtomicTests.java 2006-11-01 13:53:12 UTC (rev 7207) +++ trunk/cdk/src/org/openscience/cdk/test/MqsarAtomicTests.java 2006-11-01 14:28:26 UTC (rev 7208) @@ -38,7 +38,7 @@ /** * TestSuite that runs all the sample tests. * - * @cdk.module test-qsar + * @cdk.module test-qsarAtomic * @cdk.depends log4j.jar * @cdk.depends junit.jar */ Modified: trunk/cdk/src/org/openscience/cdk/test/MqsarBondTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MqsarBondTests.java 2006-11-01 13:53:12 UTC (rev 7207) +++ trunk/cdk/src/org/openscience/cdk/test/MqsarBondTests.java 2006-11-01 14:28:26 UTC (rev 7208) @@ -37,7 +37,7 @@ /** * TestSuite that runs all the sample tests. * - * @cdk.module test-qsar + * @cdk.module test-qsarBond * @cdk.depends log4j.jar * @cdk.depends junit.jar */ Modified: trunk/cdk/src/org/openscience/cdk/test/MqsarMolecularTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MqsarMolecularTests.java 2006-11-01 13:53:12 UTC (rev 7207) +++ trunk/cdk/src/org/openscience/cdk/test/MqsarMolecularTests.java 2006-11-01 14:28:26 UTC (rev 7208) @@ -72,7 +72,7 @@ /** * TestSuite that runs all the sample tests. * - * @cdk.module test-qsar + * @cdk.module test-qsarMolecular * @cdk.depends log4j.jar * @cdk.depends junit.jar */ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2006-11-02 12:19:31
|
Revision: 7222 http://svn.sourceforge.net/cdk/?rev=7222&view=rev Author: shk3 Date: 2006-11-02 04:19:03 -0800 (Thu, 02 Nov 2006) Log Message: ----------- Added a function to enter functional groups directly Modified Paths: -------------- trunk/cdk/changelog-jcp.xml trunk/cdk/src/org/openscience/cdk/applications/jchempaint/JChemPaintEditorPanel.java trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/userhelp_jcp/contain/otherButtons.html trunk/cdk/src/org/openscience/cdk/controller/AbstractController2D.java trunk/cdk/src/org/openscience/cdk/controller/PopupController2D.java trunk/cdk/src/org/openscience/cdk/layout/AtomPlacer.java trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java Added Paths: ----------- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/text/funcgroups.txt Modified: trunk/cdk/changelog-jcp.xml =================================================================== --- trunk/cdk/changelog-jcp.xml 2006-11-02 12:13:54 UTC (rev 7221) +++ trunk/cdk/changelog-jcp.xml 2006-11-02 12:19:03 UTC (rev 7222) @@ -3,8 +3,13 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://cdk.sf.net/schema/changelog changelog.xsd"> - <release id="2.4.0"> + <release id="next"> <addition contributor="shk3"> + Added a function to enter functional groups directly + </addition> + </release> + <release id="2.3.1"> + <addition contributor="shk3"> Changed the system for handling Hs. JCP now traces implicit Hs by default and shows them along element symbols. This means you get OH, CH3 etc, which was often asked for. </addition> </release> Modified: trunk/cdk/src/org/openscience/cdk/applications/jchempaint/JChemPaintEditorPanel.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/JChemPaintEditorPanel.java 2006-11-02 12:13:54 UTC (rev 7221) +++ trunk/cdk/src/org/openscience/cdk/applications/jchempaint/JChemPaintEditorPanel.java 2006-11-02 12:19:03 UTC (rev 7222) @@ -27,42 +27,63 @@ */ package org.openscience.cdk.applications.jchempaint; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Container; +import java.awt.Dimension; +import java.awt.Graphics2D; +import java.awt.Image; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +import java.io.File; +import java.io.FileReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.Calendar; +import java.util.Enumeration; +import java.util.EventObject; +import java.util.HashMap; +import java.util.Iterator; +import java.util.StringTokenizer; + +import javax.swing.JFrame; +import javax.swing.JScrollPane; +import javax.swing.JToolBar; +import javax.swing.JViewport; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; +import javax.swing.event.EventListenerList; + import org.openscience.cdk.Atom; import org.openscience.cdk.Bond; +import org.openscience.cdk.CDKConstants; import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.Reaction; import org.openscience.cdk.applications.jchempaint.dnd.JCPTransferHandler; import org.openscience.cdk.applications.undoredo.JCPUndoRedoHandler; import org.openscience.cdk.controller.PopupController2D; import org.openscience.cdk.dict.DictionaryDatabase; -import org.openscience.cdk.event.ChemObjectChangeEvent; import org.openscience.cdk.event.ICDKChangeListener; import org.openscience.cdk.geometry.GeometryTools; +import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.renderer.Renderer2D; import org.openscience.cdk.renderer.Renderer2DModel; +import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; import org.openscience.cdk.tools.manipulator.MoleculeSetManipulator; import org.openscience.cdk.tools.manipulator.ReactionManipulator; -import org.openscience.cdk.validate.*; +import org.openscience.cdk.validate.BasicValidator; +import org.openscience.cdk.validate.CDKValidator; +import org.openscience.cdk.validate.DictionaryValidator; +import org.openscience.cdk.validate.PDBValidator; +import org.openscience.cdk.validate.ValencyValidator; +import org.openscience.cdk.validate.ValidatorEngine; -import javax.swing.*; -import javax.swing.event.ChangeEvent; -import javax.swing.event.ChangeListener; -import javax.swing.event.EventListenerList; -import java.awt.*; -import java.awt.event.ComponentAdapter; -import java.awt.event.ComponentEvent; -import java.io.File; -import java.io.FileReader; -import java.io.IOException; -import java.util.Calendar; -import java.util.Enumeration; -import java.util.EventObject; - /** * This class implements an editing JChemPaintPanel. * @@ -254,7 +275,39 @@ public void registerModel(JChemPaintModel model) { - PopupController2D inputAdapter = new PopupController2D(model.getChemModel(), model.getRendererModel(),model.getControllerModel(), lastAction, this.moveButton); + String filename = "org/openscience/cdk/applications/jchempaint/resources/text/funcgroups.txt"; + InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); + + HashMap funcgroups=new HashMap(); + SmilesParser sp=new SmilesParser(); + StringBuffer sb=new StringBuffer(); + InputStreamReader isr = new InputStreamReader(ins); + try{ + while(true){ + int i=isr.read(); + if(i==-1){ + break; + }else if(((char)i)=='\n' || ((char)i)=='\r'){ + if(!sb.toString().equals("")){ + StringTokenizer st=new StringTokenizer(sb.toString()); + funcgroups.put(st.nextElement(), sp.parseSmiles((String)st.nextElement())); + sb=new StringBuffer(); + } + }else{ + sb.append((char)i); + } + } + if(!sb.toString().equals("")){ + StringTokenizer st=new StringTokenizer(sb.toString()); + funcgroups.put(st.nextElement(), sp.parseSmiles((String)st.nextElement())); + } + }catch(Exception ex){ + ex.printStackTrace(); + logger.error("cannot instantiate funcgroupsmap",ex.getMessage()); + } + + + PopupController2D inputAdapter = new PopupController2D(model.getChemModel(), model.getRendererModel(),model.getControllerModel(), lastAction, this.moveButton, funcgroups); JCPUndoRedoHandler undoRedoHandler=new JCPUndoRedoHandler(model.getControllerModel()); inputAdapter.setUndoRedoHandler(undoRedoHandler); setupPopupMenus(inputAdapter); Added: trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/text/funcgroups.txt =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/text/funcgroups.txt (rev 0) +++ trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/text/funcgroups.txt 2006-11-02 12:19:03 UTC (rev 7222) @@ -0,0 +1,3 @@ +cooh C(=O)-O +co C=O +cocl C(=O)-[Cl] \ No newline at end of file Modified: trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/userhelp_jcp/contain/otherButtons.html =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/userhelp_jcp/contain/otherButtons.html 2006-11-02 12:13:54 UTC (rev 7221) +++ trunk/cdk/src/org/openscience/cdk/applications/jchempaint/resources/userhelp_jcp/contain/otherButtons.html 2006-11-02 12:19:03 UTC (rev 7222) @@ -39,7 +39,9 @@ <li>The Text Symbol Button <img src="../../small-bin/enterelement.gif"></li> </ul> <p>This button allows entering of element symbols via keyboard. Click on an - atom and enter the element name. Capitalisation does not matter</p><br> + atom and enter the element name. Capitalisation does not matter. You can also + enter functional groups here which will be "expanded". For the possible groups + see <a href="../../text/funcgroups.txt">here</a>.</p><br> <ul type="circle"> <li> The Eraser Button <img src="../../small-bin/eraser.gif"></li> Modified: trunk/cdk/src/org/openscience/cdk/controller/AbstractController2D.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/controller/AbstractController2D.java 2006-11-02 12:13:54 UTC (rev 7221) +++ trunk/cdk/src/org/openscience/cdk/controller/AbstractController2D.java 2006-11-02 12:19:03 UTC (rev 7222) @@ -45,6 +45,7 @@ import java.util.EventObject; import java.util.HashMap; import java.util.Iterator; +import java.util.List; import java.util.Vector; import javax.swing.JButton; @@ -76,17 +77,17 @@ import org.openscience.cdk.interfaces.IIsotope; import org.openscience.cdk.interfaces.IMapping; import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IRing; -import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.layout.AtomPlacer; import org.openscience.cdk.layout.RingPlacer; import org.openscience.cdk.renderer.Renderer2DModel; import org.openscience.cdk.tools.HydrogenAdder; import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; import org.openscience.cdk.tools.manipulator.MoleculeSetManipulator; -import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** * Class that acts on MouseEvents and KeyEvents. @@ -139,6 +140,8 @@ double moveoldY; private IUndoRedoHandler undoRedoHandler; + private HashMap funcgroupsmap=new HashMap(); + // Helper classes HydrogenAdder hydrogenAdder = new HydrogenAdder("org.openscience.cdk.tools.ValencyChecker"); @@ -165,6 +168,7 @@ AbstractController2D(Renderer2DModel r2dm, Controller2DModel c2dm) { + this(c2dm); this.r2dm = r2dm; } @@ -1298,16 +1302,63 @@ { String x=JOptionPane.showInputDialog(null,"Enter new element symbol"); try{ - if(Character.isLowerCase(x.toCharArray()[0])) - x=Character.toUpperCase(x.charAt(0))+x.substring(1); - IsotopeFactory ifa=IsotopeFactory.getInstance(r2dm.getHighlightedAtom().getBuilder()); - IIsotope iso=ifa.getMajorIsotope(x); - String formerSymbol=r2dm.getHighlightedAtom().getSymbol(); - if(iso!=null) - r2dm.getHighlightedAtom().setSymbol(x); - // update atom - IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange); - updateAtom(container, atomInRange); + IAtomContainer ac=(IAtomContainer)funcgroupsmap.get(x); + String formerSymbol=""; + //this means a functional group was entered + //TODO undo-redo + if(ac!=null){ + ac=(IAtomContainer)((IAtomContainer)funcgroupsmap.get(x)).clone(); + IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange); + container.add(ac); + List connbonds=container.getConnectedBondsList(atomInRange); + IAtom lastplaced=null; + for(int i=0;i<connbonds.size();i++){ + IBond bond=(IBond)connbonds.get(i); + if(bond.getAtom(0)==atomInRange){ + bond.setAtom(ac.getAtom(0), 0); + lastplaced=bond.getAtom(1); + }else{ + bond.setAtom(ac.getAtom(0), 1); + lastplaced=bond.getAtom(0); + } + } + container.removeAtomAndConnectedElectronContainers(atomInRange); + AtomPlacer ap=new AtomPlacer(); + int counter=0; + while(lastplaced!=null){ + IAtomContainer placedNeighbours=container.getBuilder().newAtomContainer(); + IAtomContainer unplacedNeighbours=container.getBuilder().newAtomContainer(); + List l=container.getConnectedAtomsList(lastplaced); + for(int i=0;i<l.size();i++){ + if(r2dm.getRenderingCoordinate((IAtom)l.get(i))!=null) + placedNeighbours.addAtom((IAtom)l.get(i)); + else + unplacedNeighbours.addAtom((IAtom)l.get(i)); + } + ap.distributePartners(lastplaced, placedNeighbours, GeometryTools.get2DCenter(placedNeighbours,r2dm.getRenderingCoordinates()), unplacedNeighbours, r2dm.getBondLength(), r2dm.getRenderingCoordinates()); + lastplaced=ac.getAtom(counter); + counter++; + if(counter==ac.getAtomCount()) + lastplaced=null; + } + Iterator it=container.atoms(); + while(it.hasNext()){ + IAtom atom=(IAtom)it.next(); + if(r2dm.getRenderingCoordinate(atom)==null) + r2dm.setRenderingCoordinate(atom, atom.getPoint2d()); + } + }else{ + if(Character.isLowerCase(x.toCharArray()[0])) + x=Character.toUpperCase(x.charAt(0))+x.substring(1); + IsotopeFactory ifa=IsotopeFactory.getInstance(r2dm.getHighlightedAtom().getBuilder()); + IIsotope iso=ifa.getMajorIsotope(x); + formerSymbol=r2dm.getHighlightedAtom().getSymbol(); + if(iso!=null) + r2dm.getHighlightedAtom().setSymbol(x); + // update atom + IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange); + updateAtom(container, atomInRange); + } /* * PRESERVE THIS. This notifies the @@ -1325,6 +1376,7 @@ r2dm.fireChange(); fireChange(); }catch(Exception ex){ + ex.printStackTrace(); logger.debug(ex.getMessage()+" in SELECTELEMENT"); } } @@ -2229,5 +2281,13 @@ public void setUndoRedoHandler(IUndoRedoHandler undoRedoHandler) { this.undoRedoHandler = undoRedoHandler; } + + public HashMap getFuncgroupsmap() { + return funcgroupsmap; + } + + public void setFuncgroupsmap(HashMap funcgroupsmap) { + this.funcgroupsmap = funcgroupsmap; + } } Modified: trunk/cdk/src/org/openscience/cdk/controller/PopupController2D.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/controller/PopupController2D.java 2006-11-02 12:13:54 UTC (rev 7221) +++ trunk/cdk/src/org/openscience/cdk/controller/PopupController2D.java 2006-11-02 12:19:03 UTC (rev 7222) @@ -30,6 +30,7 @@ package org.openscience.cdk.controller; import java.awt.event.MouseEvent; +import java.util.HashMap; import java.util.Hashtable; import java.util.Vector; @@ -57,10 +58,11 @@ private static Hashtable popupMenus = null; - public PopupController2D(IChemModel chemModel, Renderer2DModel r2dm, Controller2DModel c2dm, Vector lastAction, JButton moveButton) { + public PopupController2D(IChemModel chemModel, Renderer2DModel r2dm, Controller2DModel c2dm, Vector lastAction, JButton moveButton, HashMap funcgroups) { this(chemModel,r2dm,c2dm); this.lastAction=lastAction; this.moveButton=moveButton; + this.setFuncgroupsmap(funcgroups); } public PopupController2D(IChemModel chemModel, Renderer2DModel r2dm, Controller2DModel c2dm) { Modified: trunk/cdk/src/org/openscience/cdk/layout/AtomPlacer.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/layout/AtomPlacer.java 2006-11-02 12:13:54 UTC (rev 7221) +++ trunk/cdk/src/org/openscience/cdk/layout/AtomPlacer.java 2006-11-02 12:19:03 UTC (rev 7222) @@ -191,7 +191,7 @@ * one placed neigbor, the chain placement methods * should be used. */ - if (placedNeighbours.getAtomCount() == 1) + if (placedNeighbours.getAtomCount() >= 1) { logger.debug("Only one neighbour..."); for (int f = 0; f < unplacedNeighbours.getAtomCount(); f++) @@ -235,11 +235,11 @@ addAngle = Math.PI * 2.0 / unplacedNeighbours.getAtomCount(); /* - * IMPORTANT: At this point we need a calculation of the + * IMPORTANT: At this point we need a calculation of the * start angle. Not done yet. */ startAngle = 0.0; - populatePolygonCorners(atomsToDraw, new Point2d(renderingCoordinates==null ? atom.getPoint2d() : ((Point2d)renderingCoordinates.get(atom))), startAngle, addAngle, bondLength); + populatePolygonCorners(atomsToDraw, new Point2d(renderingCoordinates==null ? atom.getPoint2d() : ((Point2d)renderingCoordinates.get(atom))), startAngle, addAngle, bondLength,renderingCoordinates); return; } @@ -531,6 +531,76 @@ /** + * Populates the corners of a polygon with atoms. Used to place atoms in a + * geometrically regular way around a ring center or another atom. If this is + * used to place the bonding partner of an atom (and not to draw a ring) we + * want to place the atoms such that those with highest "weight" are placed + * farmost away from the rest of the molecules. The "weight" mentioned here is + * calculated by a modified morgan number algorithm. + * + *@param atomsToDraw All the atoms to draw + *@param startAngle A start angle, giving the angle of the most clockwise + * atom which has already been placed + *@param addAngle An angle to be added to startAngle for each atom from + * atomsToDraw + *@param rotationCenter The center of a ring, or an atom for which the + * partners are to be placed + *@param radius The radius of the polygon to be populated: bond + * length or ring radius + */ + public void populatePolygonCorners(Vector atomsToDraw, Point2d rotationCenter, double startAngle, double addAngle, double radius, HashMap renderingCoordinates) + { + IAtom connectAtom = null; + double angle = startAngle; + double newX; + double newY; + double x; + double y; + logger.debug("populatePolygonCorners->startAngle: ", Math.toDegrees(angle)); + Vector points = new Vector(); + //IAtom atom = null; + + logger.debug(" centerX:", rotationCenter.x); + logger.debug(" centerY:", rotationCenter.y); + logger.debug(" radius :", radius); + + for (int i = 0; i < atomsToDraw.size(); i++) + { + angle = angle + addAngle; + if (angle >= 2.0 * Math.PI) + { + angle -= 2.0 * Math.PI; + } + logger.debug("populatePolygonCorners->angle: ", Math.toDegrees(angle)); + x = Math.cos(angle) * radius; + y = Math.sin(angle) * radius; + newX = x + rotationCenter.x; + newY = y + rotationCenter.y; + logger.debug(" newX:", newX); + logger.debug(" newY:", newY); + points.addElement(new Point2d(newX, newY)); + + if (logger.isDebugEnabled()) + try + { + logger.debug("populatePolygonCorners->connectAtom: " + (molecule.getAtomNumber(connectAtom) + 1) + " placed at " + connectAtom.getPoint2d()); + } catch (Exception exc) + { + //nothing to catch here. This is just for logging + } + } + + for (int i = 0; i < atomsToDraw.size(); i++) + { + connectAtom = (IAtom) atomsToDraw.elementAt(i); + renderingCoordinates.put(connectAtom, points.elementAt(i)); + connectAtom.setFlag(CDKConstants.ISPLACED, true); + } + + } + + + /** * Partition the bonding partners of a given atom into placed (coordinates * assinged) and not placed. * Modified: trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java 2006-11-02 12:13:54 UTC (rev 7221) +++ trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java 2006-11-02 12:19:03 UTC (rev 7222) @@ -1066,4 +1066,8 @@ public void setNotification(boolean notification) { this.notification = notification; } + + public void setRenderingCoordinates(HashMap renderingCoordinates) { + this.renderingCoordinates = renderingCoordinates; + } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2006-12-19 16:58:23
|
Revision: 7510 http://svn.sourceforge.net/cdk/?rev=7510&view=rev Author: egonw Date: 2006-12-19 08:58:04 -0800 (Tue, 19 Dec 2006) Log Message: ----------- New module: test-builder3d Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java trunk/cdk/src/org/openscience/cdk/test/MextraTests.java trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java Added Paths: ----------- trunk/cdk/src/META-INF/test-builder3d.cdkdepends trunk/cdk/src/META-INF/test-builder3d.libdepends trunk/cdk/src/org/openscience/cdk/test/Mbuilder3dTests.java Removed Paths: ------------- trunk/cdk/src/META-INF/test-builder.cdkdepends trunk/cdk/src/META-INF/test-builder.libdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2006-12-19 15:47:54 UTC (rev 7509) +++ trunk/cdk/build.xml 2006-12-19 16:58:04 UTC (rev 7510) @@ -470,6 +470,7 @@ <antcall target="compile-module"><param name="module" value="test-smiles"/></antcall> <antcall target="compile-module"><param name="module" value="test-weka"/></antcall> <antcall target="compile-module"><param name="module" value="test-reaction"/></antcall> + <antcall target="compile-module"><param name="module" value="test-builder3d"/></antcall> <antcall target="compile-module"><param name="module" value="test-forcefield"/></antcall> <antcall target="compile-module"><param name="module" value="test-valencycheck"/></antcall> <antcall target="compile-module"><param name="module" value="test-experimental"/></antcall> @@ -586,6 +587,7 @@ <includesfile name="${metainf}/test-datadebug.libdepends"/> <includesfile name="${metainf}/test-experimental.libdepends"/> <includesfile name="${metainf}/test-extra.libdepends"/> + <includesfile name="${metainf}/test-builder3d.libdepends"/> <includesfile name="${metainf}/test-forcefield.libdepends"/> <includesfile name="${metainf}/test-inchi.libdepends"/> <includesfile name="${metainf}/test-io.libdepends"/> @@ -607,6 +609,7 @@ <include name="cdk-test-datadebug.jar"/> <include name="cdk-test-experimental.jar"/> <include name="cdk-test-extra.jar"/> + <include name="cdk-test-builder3d.jar"/> <include name="cdk-test-forcefield.jar"/> <include name="cdk-test-inchi.jar"/> <include name="cdk-test-io.jar"/> @@ -777,8 +780,9 @@ <antcall target="test-module"><param name="module" value="nonotify"/></antcall> <antcall target="test-module"><param name="module" value="standard"/></antcall> <antcall target="test-module"><param name="module" value="io"/></antcall> + <antcall target="test-module"><param name="module" value="extra"/></antcall> + <antcall target="test-module"><param name="module" value="builder3d"/></antcall> <antcall target="test-module"><param name="module" value="forcefield"/></antcall> - <antcall target="test-module"><param name="module" value="extra"/></antcall> <antcall target="test-module"><param name="module" value="valencycheck"/></antcall> <antcall target="test-module"><param name="module" value="reaction"/></antcall> <antcall target="test-module"><param name="module" value="smiles"/></antcall> Deleted: trunk/cdk/src/META-INF/test-builder.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-builder.cdkdepends 2006-12-19 15:47:54 UTC (rev 7509) +++ trunk/cdk/src/META-INF/test-builder.cdkdepends 2006-12-19 16:58:04 UTC (rev 7510) @@ -1,7 +0,0 @@ -cdk-core.jar -cdk-data.jar -cdk-interfaces.jar -cdk-qsar.jar -cdk-io.jar -cdk-standard.jar -cdk-charges.jar Deleted: trunk/cdk/src/META-INF/test-builder.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-builder.libdepends 2006-12-19 15:47:54 UTC (rev 7509) +++ trunk/cdk/src/META-INF/test-builder.libdepends 2006-12-19 16:58:04 UTC (rev 7510) @@ -1,3 +0,0 @@ -Jama-1.0.1.jar -vecmath1.2-1.14.jar - Copied: trunk/cdk/src/META-INF/test-builder3d.cdkdepends (from rev 7509, trunk/cdk/src/META-INF/test-builder.cdkdepends) =================================================================== --- trunk/cdk/src/META-INF/test-builder3d.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/test-builder3d.cdkdepends 2006-12-19 16:58:04 UTC (rev 7510) @@ -0,0 +1,14 @@ +cdk-core.jar +cdk-data.jar +cdk-interfaces.jar +cdk-qsar.jar +cdk-io.jar +cdk-standard.jar +cdk-charges.jar +cdk-smiles.jar +cdk-builder3d.jar +cdk-sdg.jar +cdk-extra.jar +cdk-forcefield.jar +cdk-valencycheck.jar +cdk-test-core.jar Copied: trunk/cdk/src/META-INF/test-builder3d.libdepends (from rev 7509, trunk/cdk/src/META-INF/test-builder.libdepends) =================================================================== --- trunk/cdk/src/META-INF/test-builder3d.libdepends (rev 0) +++ trunk/cdk/src/META-INF/test-builder3d.libdepends 2006-12-19 16:58:04 UTC (rev 7510) @@ -0,0 +1,4 @@ +Jama-1.0.1.jar +vecmath1.2-1.14.jar +log4j.jar +jgrapht-0.6.0.jar Modified: trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java 2006-12-19 15:47:54 UTC (rev 7509) +++ trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java 2006-12-19 16:58:04 UTC (rev 7510) @@ -30,6 +30,7 @@ import java.io.IOException; import java.util.Hashtable; +import java.util.Iterator; import java.util.Vector; import javax.vecmath.Point3d; @@ -223,14 +224,15 @@ if (ringSetMolecule.getAtomContainerCount() > 0) { ringSystems = RingPartitioner.partitionRings(ringSetMolecule); largestRingSet = getLargestRingSet(ringSystems); - NumberOfRingAtoms = (double) ((IAtomContainer) RingSetManipulator.getAllInOneContainer(largestRingSet)).getAtomCount(); - templateHandler.mapTemplates(RingSetManipulator.getAllInOneContainer(largestRingSet), NumberOfRingAtoms); - if (!checkAllRingAtomsHasCoordinates(RingSetManipulator.getAllInOneContainer(largestRingSet))) { + IAtomContainer largestRingSetContainer = getAllInOneContainer(largestRingSet); + NumberOfRingAtoms = (double)largestRingSetContainer.getAtomCount(); + templateHandler.mapTemplates(largestRingSetContainer, NumberOfRingAtoms); + if (!checkAllRingAtomsHasCoordinates(largestRingSetContainer)) { throw new IOException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout.Sorry"); } - setAtomsToPlace(RingSetManipulator.getAllInOneContainer(largestRingSet)); - searchAndPlaceBranches(RingSetManipulator.getAllInOneContainer(largestRingSet)); + setAtomsToPlace(largestRingSetContainer); + searchAndPlaceBranches(largestRingSetContainer); largestRingSet = null; } else { //System.out.println("****** Start of handling aliphatic molecule ******"); @@ -297,9 +299,10 @@ //System.out.println("layout RingSystem..."); IAtom unplacedAtom = ap3d.getUnplacedRingHeavyAtom(molecule, atom); IRingSet ringSetA = getRingSetOfAtom(ringSetMolecule, unplacedAtom); - templateHandler.mapTemplates(RingSetManipulator.getAllInOneContainer(ringSetA), (double) ((IAtomContainer) RingSetManipulator.getAllInOneContainer(ringSetA)).getAtomCount()); + IAtomContainer ringSetAContainer = getAllInOneContainer(ringSetA); + templateHandler.mapTemplates(ringSetAContainer, (double)ringSetAContainer.getAtomCount()); - if (checkAllRingAtomsHasCoordinates(RingSetManipulator.getAllInOneContainer(ringSetA))) { + if (checkAllRingAtomsHasCoordinates(ringSetAContainer)) { } else { throw new IOException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout.Sorry"); } @@ -309,7 +312,7 @@ setBranchAtom(unplacedAtom, atom, ap3d.getPlacedHeavyAtoms(molecule, atom)); layoutRingSystem(firstAtomOriginalCoord, unplacedAtom, ringSetA, centerPlacedMolecule, atom); - searchAndPlaceBranches(RingSetManipulator.getAllInOneContainer(ringSetA)); + searchAndPlaceBranches(ringSetAContainer); //System.out.println("Ready layout Ring System"); ringSetA = null; unplacedAtom = null; @@ -341,7 +344,7 @@ */ private void layoutRingSystem(Point3d originalCoord, IAtom placedRingAtom, IRingSet ringSet, Point3d centerPlacedMolecule, IAtom atomB) { //System.out.print("****** Layout ring System ******");System.out.println(">around atom:"+molecule.getAtomNumber(placedRingAtom)); - IAtomContainer ac = RingSetManipulator.getAllInOneContainer(ringSet); + IAtomContainer ac = getAllInOneContainer(ringSet); Point3d newCoord = placedRingAtom.getPoint3d(); Vector3d axis = new Vector3d(atomB.getPoint3d().x - newCoord.x, atomB.getPoint3d().y - newCoord.y, atomB.getPoint3d().z - newCoord.z); translateStructure(originalCoord, newCoord, ac); @@ -408,6 +411,16 @@ } + private IAtomContainer getAllInOneContainer(IRingSet ringSet) { + IAtomContainer resultContainer = ringSet.getBuilder().newAtomContainer(); + Iterator containers = RingSetManipulator.getAllAtomContainers(ringSet).iterator(); + while (containers.hasNext()) { + resultContainer.add((IAtomContainer) containers.next()); + } + return resultContainer; + } + + /** * Sets a branch atom to a ring or aliphatic chain * @@ -586,7 +599,7 @@ int atomNumber = 0; IAtomContainer container = null; for (int i = 0; i < ringSystems.size(); i++) { - container = RingSetManipulator.getAllInOneContainer((IRingSet) ringSystems.get(i)); + container = getAllInOneContainer((IRingSet) ringSystems.get(i)); if (atomNumber < container.getAtomCount()) { atomNumber = container.getAtomCount(); largestRingSet = (IRingSet) ringSystems.get(i); Added: trunk/cdk/src/org/openscience/cdk/test/Mbuilder3dTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/Mbuilder3dTests.java (rev 0) +++ trunk/cdk/src/org/openscience/cdk/test/Mbuilder3dTests.java 2006-12-19 16:58:04 UTC (rev 7510) @@ -0,0 +1,47 @@ +/* $RCSfile$ + * $Author: egonw $ + * $Date: 2006-03-30 00:42:34 +0200 (Thu, 30 Mar 2006) $ + * $Revision: 5865 $ + * + * Copyright (C) 1997-2006 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ + +package org.openscience.cdk.test; + +import junit.framework.Test; +import junit.framework.TestSuite; + +import org.openscience.cdk.test.modeling.builder3d.ModelBuilder3dTest; + +/** + * TestSuite that runs all the sample tests. + * + * @cdk.module test-builder3d + */ +public class Mbuilder3dTests { + + public static Test suite () { + TestSuite suite= new TestSuite("The CDK force field module Tests"); + + suite.addTest(ModelBuilder3dTest.suite()); + + return suite; + } + +} Modified: trunk/cdk/src/org/openscience/cdk/test/MextraTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MextraTests.java 2006-12-19 15:47:54 UTC (rev 7509) +++ trunk/cdk/src/org/openscience/cdk/test/MextraTests.java 2006-12-19 16:58:04 UTC (rev 7510) @@ -28,7 +28,6 @@ import junit.framework.TestSuite; import org.openscience.cdk.applications.swing.MoleculeListViewer; -import org.openscience.cdk.structgen.deterministic.GENMDeterministicGenerator; import org.openscience.cdk.test.applications.undoredo.AddAtomsAndBondsEditTest; import org.openscience.cdk.test.applications.undoredo.AddHydrogenEditTest; import org.openscience.cdk.test.applications.undoredo.AdjustBondOrdersEditTest; @@ -55,7 +54,6 @@ import org.openscience.cdk.test.layout.StructureDiagramGeneratorTest; import org.openscience.cdk.test.layout.TemplateHandlerTest; import org.openscience.cdk.test.libio.openbabel.OpenBabelConvertTest; -import org.openscience.cdk.test.modeling.builder3d.ModelBuilder3dTest; import org.openscience.cdk.test.ringsearch.RingSearchTest; import org.openscience.cdk.test.similarity.TanimotoTest; import org.openscience.cdk.test.structgen.RandomStructureGeneratorTest; @@ -109,8 +107,6 @@ // from cdk.test.libio.openbabel suite.addTest(OpenBabelConvertTest.suite()); // from cdk.test.math - // from cdk.test.modeling - suite.addTest(ModelBuilder3dTest.suite()); // from cdk.test.ringsearch suite.addTest(RingSearchTest.suite()); // from cdk.test.similarity Modified: trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java 2006-12-19 15:47:54 UTC (rev 7509) +++ trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java 2006-12-19 16:58:04 UTC (rev 7510) @@ -50,7 +50,7 @@ /** * Description of the Class * - * @cdk.module test-extra + * @cdk.module test-builder3d * *@author chhoppe *@cdk.created 2004-11-04 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2006-12-21 17:54:27
|
Revision: 7564 http://svn.sourceforge.net/cdk/?rev=7564&view=rev Author: egonw Date: 2006-12-21 09:54:23 -0800 (Thu, 21 Dec 2006) Log Message: ----------- Added some developers tools to test things. Should be removed again later. Added Paths: ----------- trunk/cdk/perf/ trunk/cdk/perf/PerfDetermStructGen.java trunk/cdk/perf/ShowRandomGenerator.java Added: trunk/cdk/perf/PerfDetermStructGen.java =================================================================== --- trunk/cdk/perf/PerfDetermStructGen.java (rev 0) +++ trunk/cdk/perf/PerfDetermStructGen.java 2006-12-21 17:54:23 UTC (rev 7564) @@ -0,0 +1,69 @@ +import java.util.ArrayList; +import java.util.List; + +import org.openscience.cdk.structgen.IStructureGenerationListener; +import org.openscience.cdk.structgen.deterministic.GENMDeterministicGenerator; + + +public class PerfDetermStructGen { + + GENMDeterministicGenerator gdg; + StructureGenerationCounterListener myListener; + + public PerfDetermStructGen(String formula) throws Exception { + gdg = new GENMDeterministicGenerator("" + formula,""); + System.out.println("MF: " + formula); + // myListener = new StructureGenerationCounterListener(); + // gdg.addListener(myListener); + } + + public void run() throws Exception { + long startTime = System.currentTimeMillis(); + gdg.generate(); + long endTime = System.currentTimeMillis(); + System.out.println("Time consumed (ms): " + (endTime - startTime)); + System.out.println("Structures found: " + gdg.getNumberOfStructures()); + } + + public static void main(String[] args) throws Exception { + PerfDetermStructGen test = new PerfDetermStructGen(args[0]); + test.run(); +// System.in.read(); + } + + class MyStructureGenerationListener implements IStructureGenerationListener { + + private List structures; + + public MyStructureGenerationListener() { + structures = new ArrayList(); + } + + public void stateChanged(List list) throws Exception { + structures.addAll(list); + } + + public List getStructures() { + return structures; + } + + } + + class StructureGenerationCounterListener implements IStructureGenerationListener { + + private int count; + + public StructureGenerationCounterListener() { + count = 0; + } + + public void stateChanged(List list) throws Exception { + count += list.size(); + } + + public int getCount() { + return count; + } + + } +} Added: trunk/cdk/perf/ShowRandomGenerator.java =================================================================== --- trunk/cdk/perf/ShowRandomGenerator.java (rev 0) +++ trunk/cdk/perf/ShowRandomGenerator.java 2006-12-21 17:54:23 UTC (rev 7564) @@ -0,0 +1,44 @@ +import java.util.Iterator; + +import javax.swing.JFrame; + +import org.openscience.cdk.applications.swing.MoleculeListViewer; +import org.openscience.cdk.graph.ConnectivityChecker; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; +import org.openscience.cdk.smiles.SmilesParser; +import org.openscience.cdk.structgen.RandomGenerator; +import org.openscience.cdk.structgen.VicinitySampler; +import org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine; + + +public class ShowRandomGenerator { + + private MoleculeListViewer listViewer; + + public ShowRandomGenerator() throws Exception { + listViewer = new MoleculeListViewer(); + listViewer.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); + + SmilesParser parser = new SmilesParser(NoNotificationChemObjectBuilder.getInstance()); + + IMolecule mol = parser.parseSmiles("CNC(C(=O)(C)C"); + listViewer.addStructure(mol, true, true, "parent"); + + int i = 0; + RandomGenerator machine = new RandomGenerator(mol); + while (i < 5) { + machine.mutate(mol); + if (ConnectivityChecker.isConnected(mol)) { + i++; + listViewer.addStructure(mol, true, true, "gen " + i); + } + } + } + + public static void main(String[] args) throws Exception { + new ShowRandomGenerator(); + } + +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2006-12-27 17:00:30
|
Revision: 7575 http://svn.sourceforge.net/cdk/?rev=7575&view=rev Author: egonw Date: 2006-12-27 09:00:27 -0800 (Wed, 27 Dec 2006) Log Message: ----------- Updated for new PMD version Modified Paths: -------------- trunk/cdk/pmd-unused.xml trunk/cdk/pmd.xml Modified: trunk/cdk/pmd-unused.xml =================================================================== --- trunk/cdk/pmd-unused.xml 2006-12-27 16:53:42 UTC (rev 7574) +++ trunk/cdk/pmd-unused.xml 2006-12-27 17:00:27 UTC (rev 7575) @@ -9,9 +9,10 @@ <path id="pmd.classpath"> <pathelement location="${build}"/> <fileset dir="${lib}"> - <include name="jakarta-oro-2.0.8.jar"/> - <include name="pmd-3.6.jar"/> - <include name="jaxen-1.1-beta-7.jar"/> + <include name="asm-3.0.jar"/> + <include name="backport-util-concurrent.jar"/> + <include name="pmd-3.9.jar"/> + <include name="jaxen-1.1-beta-10.jar"/> </fileset> </path> Modified: trunk/cdk/pmd.xml =================================================================== --- trunk/cdk/pmd.xml 2006-12-27 16:53:42 UTC (rev 7574) +++ trunk/cdk/pmd.xml 2006-12-27 17:00:27 UTC (rev 7575) @@ -9,9 +9,10 @@ <path id="pmd.classpath"> <pathelement location="${build}"/> <fileset dir="${lib}"> - <include name="jakarta-oro-2.0.8.jar"/> - <include name="pmd-3.6.jar"/> - <include name="jaxen-1.1-beta-7.jar"/> + <include name="asm-3.0.jar"/> + <include name="backport-util-concurrent.jar"/> + <include name="pmd-3.9.jar"/> + <include name="jaxen-1.1-beta-10.jar"/> </fileset> </path> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-01-11 11:48:30
|
Revision: 7691 http://svn.sourceforge.net/cdk/?rev=7691&view=rev Author: egonw Date: 2007-01-11 03:47:48 -0800 (Thu, 11 Jan 2007) Log Message: ----------- Set up a 'structgen' module Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/structgen/IStructureGenerationListener.java trunk/cdk/src/org/openscience/cdk/structgen/RandomGenerator.java trunk/cdk/src/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java trunk/cdk/src/org/openscience/cdk/structgen/VicinitySampler.java trunk/cdk/src/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java trunk/cdk/src/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java trunk/cdk/src/org/openscience/cdk/structgen/deterministic/Graph.java trunk/cdk/src/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/ChemGraph.java trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachine.java trunk/cdk/src/org/openscience/cdk/test/MextraTests.java trunk/cdk/src/org/openscience/cdk/test/structgen/RandomStructureGeneratorTest.java trunk/cdk/src/org/openscience/cdk/test/structgen/SingleStructureRandomGeneratorTest.java trunk/cdk/src/org/openscience/cdk/test/structgen/VicinitySamplerTest.java trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/EquivalentClassesDeterministicGeneratorTest.java trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java Added Paths: ----------- trunk/cdk/src/META-INF/structgen.cdkdepends trunk/cdk/src/META-INF/test-structgen.cdkdepends trunk/cdk/src/META-INF/test-structgen.devellibdepends trunk/cdk/src/META-INF/test-structgen.libdepends trunk/cdk/src/org/openscience/cdk/test/MstructgenTests.java trunk/cdk/src/org/openscience/cdk/test/StructgenCoverageTest.java Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/build.xml 2007-01-11 11:47:48 UTC (rev 7691) @@ -438,6 +438,7 @@ <antcall target="compile-module"><param name="module" value="control"/></antcall> <antcall target="compile-module"><param name="module" value="datadebug"/></antcall> <antcall target="compile-module"><param name="module" value="nonotify"/></antcall> + <antcall target="compile-module"><param name="module" value="structgen"/></antcall> <antcall target="compile-module"><param name="module" value="pdb"/></antcall> <antcall target="compile-module"><param name="module" value="extra"/></antcall> <antcall target="compile-module"><param name="module" value="smiles"/></antcall> @@ -466,6 +467,7 @@ <antcall target="compile-module"><param name="module" value="test-datadebug"/></antcall> <antcall target="compile-module"><param name="module" value="test-nonotify"/></antcall> <antcall target="compile-module"><param name="module" value="test-io"/></antcall> + <antcall target="compile-module"><param name="module" value="test-structgen"/></antcall> <antcall target="compile-module"><param name="module" value="test-extra"/></antcall> <antcall target="compile-module"><param name="module" value="test-smiles"/></antcall> <antcall target="compile-module"><param name="module" value="test-weka"/></antcall> @@ -784,8 +786,8 @@ <antcall target="test-module"><param name="module" value="builder3d"/></antcall> <antcall target="test-module"><param name="module" value="forcefield"/></antcall> <antcall target="test-module"><param name="module" value="valencycheck"/></antcall> - <antcall target="test-module"><param name="module" value="reaction"/></antcall> - <antcall target="test-module"><param name="module" value="smiles"/></antcall> + <antcall target="test-module"><param name="module" value="reaction"/></antcall> + <antcall target="test-module"><param name="module" value="smiles"/></antcall> <antcall target="test-module"><param name="module" value="experimental"/></antcall> <antcall target="test-module"><param name="module" value="qsar"/></antcall> <antcall target="test-module"><param name="module" value="qsarAtomic"/></antcall> @@ -794,6 +796,7 @@ <antcall target="test-module"><param name="module" value="weka"/></antcall> <antcall target="test-module"><param name="module" value="pdb"/></antcall> <antcall target="test-module"><param name="module" value="inchi"/></antcall> + <antcall target="test-module"><param name="module" value="structgen"/></antcall> </target> <target id="limitations" name="limitations" depends="noJunit, dist-all" Added: trunk/cdk/src/META-INF/structgen.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/structgen.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/structgen.cdkdepends 2007-01-11 11:47:48 UTC (rev 7691) @@ -0,0 +1,4 @@ +cdk-interfaces.jar +cdk-core.jar +cdk-standard.jar +cdk-nonotify.jar Added: trunk/cdk/src/META-INF/test-structgen.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-structgen.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/test-structgen.cdkdepends 2007-01-11 11:47:48 UTC (rev 7691) @@ -0,0 +1,9 @@ +cdk-interfaces.jar +cdk-core.jar +cdk-data.jar +cdk-nonotify.jar +cdk-standard.jar +cdk-structgen.jar +cdk-smiles.jar +cdk-extra.jar +cdk-test-core.jar Added: trunk/cdk/src/META-INF/test-structgen.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-structgen.devellibdepends (rev 0) +++ trunk/cdk/src/META-INF/test-structgen.devellibdepends 2007-01-11 11:47:48 UTC (rev 7691) @@ -0,0 +1,2 @@ +junit.jar + Added: trunk/cdk/src/META-INF/test-structgen.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-structgen.libdepends (rev 0) +++ trunk/cdk/src/META-INF/test-structgen.libdepends 2007-01-11 11:47:48 UTC (rev 7691) @@ -0,0 +1,3 @@ +log4j.jar +jgrapht-0.6.0.jar +vecmath1.2-1.14.jar Modified: trunk/cdk/src/org/openscience/cdk/structgen/IStructureGenerationListener.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/IStructureGenerationListener.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/IStructureGenerationListener.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -1,3 +1,27 @@ +/* $Revision: 7636 $ $Author: egonw $ $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $ + * + * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ package org.openscience.cdk.structgen; import java.util.List; @@ -2,5 +26,9 @@ -public interface IStructureGenerationListener -{ +/** + * @cdk.module structgen + */ +public interface IStructureGenerationListener{ + public void stateChanged(List list) throws Exception; + } Modified: trunk/cdk/src/org/openscience/cdk/structgen/RandomGenerator.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/RandomGenerator.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/RandomGenerator.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -27,6 +27,7 @@ import org.openscience.cdk.graph.ConnectivityChecker; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.math.MinMax; import org.openscience.cdk.tools.LoggingTool; /** @@ -35,6 +36,11 @@ * constitutional space from there. * This generator was first suggested by J.-L. Faulon {@cdk.cite FAU96}. * + * <p>Unlike the VicinitySampler, this methods does not sample + * the full Faulon vicinity. + * + * @see org.openscience.cdk.structgen.VicinitySampler + * * @cdk.keyword structure generator */ public class RandomGenerator { @@ -197,8 +203,8 @@ /* Compute the range for b11 (see Faulons formulae for details) */ double[] cmax = {0, a11 - a22, a11 + a12 - 3, a11 + a21 - 3}; double[] cmin = {3, a11 + a12, a11 + a21, a11 - a22 + 3}; - lowerborder = max(cmax); - upperborder = min(cmin); + lowerborder = MinMax.max(cmax); + upperborder = MinMax.min(cmin); /* Randomly choose b11 != a11 in the range max > r > min */ logger.debug("*** New Try ***"); logger.debug("a11 = ", a11); @@ -299,45 +305,6 @@ logger.debug("b11 b12 b21 b22: " + b11 + " " + b12 + " " + b21 + " " + b22); } - - /** - * Analog of <code>Math.max</code> that returns the largest int value in an array of ints. - * - * @param values the values to be searched for the largest value among them - * @return the largest value among a set of given values - */ - protected double max(double[] values) - { - double max = values[0]; - for (int f = 0; f < values.length; f++) - { - if (values[f] > max) - { - max = values[f]; - } - } - return max; - } - - /** - * Analog of <code>Math.min</code> that returns the largest int value in an array of ints. - * - * @param values the values to be searched for the smallest value among them - * @return the smallest value among a set of given values - */ - protected double min(double[] values) - { - double min = values[0]; - for (int f = 0; f < values.length; f++) - { - if (values[f] < min) - { - min = values[f]; - } - } - return min; - } - /** * Assigns a starting structure to this generator. Modified: trunk/cdk/src/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -63,6 +63,7 @@ * * @author steinbeck * @cdk.created 2001-09-04 + * @cdk.module structgen */ public class SingleStructureRandomGenerator { Modified: trunk/cdk/src/org/openscience/cdk/structgen/VicinitySampler.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/VicinitySampler.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/VicinitySampler.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -41,7 +41,8 @@ * constitutional space from there. This generator was first suggested by * Faulon {@cdk.cite FAU96}. * - * @cdk.keyword structure generator + * @cdk.keyword structure generator + * @cdk.module structgen */ public class VicinitySampler { Modified: trunk/cdk/src/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -32,6 +32,7 @@ * * @author steinbeck * @cdk.created 2000-10-02 + * @cdk.module structgen */ public class EquivalentClassesDeterministicGenerator { Modified: trunk/cdk/src/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -71,6 +71,7 @@ * @author Junfeng Hao * @author Christoph Steinbeck * @cdk.created 2004-02-16 + * @cdk.module structgen */ public class GENMDeterministicGenerator { @@ -136,7 +137,7 @@ { numberOfStructures = 0; generateBasicUnits(); - logger.debug("numberofstructure is="+numberOfStructures); + logger.debug("numberofstructure is=", numberOfStructures); fireChange(); } @@ -417,12 +418,12 @@ /* for F,Cl,Br,I */ for(i=19;i<=22;i++) if(molecularFormula[i-11]!=0)numberOfBasicUnit[i]=molecularFormula[i-11]; - for(i=0;i<=22;i++) - { - if(numberOfBasicUnit[i]!=0) - { - // logger.debug("numberOfBasicUnit["+i+"]="+numberOfBasicUnit[i]); - //logger.debug("numberOfBasicUnit["+i+"]="+numberOfBasicUnit[i]); + if (logger.isDebugEnabled()) { + for(i=0;i<=22;i++) { + if(numberOfBasicUnit[i]!=0) { + logger.debug("numberOfBasicUnit["+i+"]="+numberOfBasicUnit[i]); + logger.debug("numberOfBasicUnit["+i+"]="+numberOfBasicUnit[i]); + } } } @@ -575,8 +576,7 @@ boolean flag; int[] maxNumberOfBasicFragment=new int[34]; /*initialization for the variables*/ - for(i=0;i<=22;i++) - if(numberOfBasicUnit[i]!=0)logger.debug("numberOfBasicUnit["+i+"]="+numberOfBasicUnit[i]); + if (logger.isDebugEnabled()) for(i=0;i<=22;i++) if(numberOfBasicUnit[i]!=0)logger.debug("numberOfBasicUnit["+i+"]=", numberOfBasicUnit[i]); for(i=1;i<34;i++)numberOfBasicFragment[i]=0; /* maximum number of basic fragments*/ @@ -655,10 +655,11 @@ if(flag) { numberOfSetFragment+=1; - logger.debug("Fragment Set "+numberOfSetFragment); - for(i=1;i<34;i++) - { - if(numberOfBasicFragment[i]!=0)logger.debug(((BasicFragment)(basicFragment.get(i-1))).getBasicFragment()+" "+numberOfBasicFragment[i]); + logger.debug("Fragment Set ", numberOfSetFragment); + if (logger.isDebugEnabled()) { + for(i=1;i<34;i++) { + if(numberOfBasicFragment[i]!=0)logger.debug(((BasicFragment)(basicFragment.get(i-1))).getBasicFragment()+" "+numberOfBasicFragment[i]); + } } generateIsomers(); } @@ -679,62 +680,62 @@ if(k>numberOfBasicUnit[6])continue; else break; } - if(iter1==3) + else if(iter1==3) { k=numberOfBasicFragment[1]+numberOfBasicFragment[2]+numberOfBasicFragment[3]; if(k>numberOfBasicUnit[6])continue; else break; } - if(iter1==4) + else if(iter1==4) { k=numberOfBasicFragment[1]+numberOfBasicFragment[2]+numberOfBasicFragment[3]+numberOfBasicFragment[4]; if(k>numberOfBasicUnit[6])continue; else break; } - if(iter1==6) + else if(iter1==6) { k=numberOfBasicFragment[5]+numberOfBasicFragment[6]; if(k>numberOfBasicUnit[18])continue; else break; } - if(iter1==7) + else if(iter1==7) { k=numberOfBasicFragment[5]+numberOfBasicFragment[6]+numberOfBasicFragment[7]; if(k>numberOfBasicUnit[18])continue; else break; } - if(iter1==9) + else if(iter1==9) { k=numberOfBasicFragment[8]+numberOfBasicFragment[9]; if(k>numberOfBasicUnit[4])continue; else break; } - if(iter1==10) + else if(iter1==10) { k=numberOfBasicFragment[8]+numberOfBasicFragment[9]+numberOfBasicFragment[10]; if(k>numberOfBasicUnit[4])continue; else break; } - if(iter1==12) + else if(iter1==12) { k=numberOfBasicFragment[11]+numberOfBasicFragment[12]; if(k>numberOfBasicUnit[17])continue; else break; } - if(iter1==14) + else if(iter1==14) { k=numberOfBasicFragment[13]+numberOfBasicFragment[14]; if(k>numberOfBasicUnit[14])continue; else break; } - if(iter1==16) + else if(iter1==16) { k=numberOfBasicFragment[15]+numberOfBasicFragment[16]; if(k>numberOfBasicUnit[5])continue; else break; } - if(iter1==18) + else if(iter1==18) { k=numberOfBasicFragment[17]+numberOfBasicFragment[18]; if(k>numberOfBasicUnit[3])continue; Modified: trunk/cdk/src/org/openscience/cdk/structgen/deterministic/Graph.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/deterministic/Graph.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/deterministic/Graph.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -31,6 +31,8 @@ * * @author steinbeck * @cdk.created 2000-10-02 + * + * @cdk.module structgen */ public class Graph extends ArrayList { Modified: trunk/cdk/src/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -57,6 +57,7 @@ * * @author steinbeck * @cdk.created 2001-09-04 + * @cdk.module structgen */ public class PartialFilledStructureMerger { Modified: trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/ChemGraph.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/ChemGraph.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/ChemGraph.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -31,6 +31,9 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.math.RandomNumbersTool; +/** + * @cdk.module structgen + */ public class ChemGraph { /*Number of atoms in this structure*/ Modified: trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachine.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachine.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachine.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -33,7 +33,9 @@ /** * Modified molecular structures by applying crossover operator on a pair of parent structures * and generate a pair of offspring structures. Each of the two offspring structures inherits - * a certain fragments from both of its parents. + * a certain fragments from both of its parents. + * + * @cdk.module structgen */ public class CrossoverMachine { Modified: trunk/cdk/src/org/openscience/cdk/test/MextraTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MextraTests.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/test/MextraTests.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -109,11 +109,6 @@ suite.addTest(RingSearchTest.suite()); // from cdk.test.similarity suite.addTest(TanimotoTest.suite()); - // from cdk.test.structgen - suite.addTest(RandomStructureGeneratorTest.suite()); - suite.addTest(VicinitySamplerTest.suite()); - // from cdk.test.structgen.deterministic - suite.addTest(GENMDeterministicGeneratorTest.suite()); // Below are the tests that are not always possible to execute, because // the class might not be compiled (depeding on Ant and Java VM versions). Added: trunk/cdk/src/org/openscience/cdk/test/MstructgenTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MstructgenTests.java (rev 0) +++ trunk/cdk/src/org/openscience/cdk/test/MstructgenTests.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -0,0 +1,51 @@ +/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ + * + * Copyright (C) 2007 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.test; + +import junit.framework.Test; +import junit.framework.TestSuite; + +import org.openscience.cdk.test.structgen.RandomStructureGeneratorTest; +import org.openscience.cdk.test.structgen.VicinitySamplerTest; +import org.openscience.cdk.test.structgen.deterministic.EquivalentClassesDeterministicGeneratorTest; +import org.openscience.cdk.test.structgen.deterministic.GENMDeterministicGeneratorTest; + +/** + * TestSuite that runs all the sample tests for the structgen module. + * + * @cdk.module test-structgen + */ +public class MstructgenTests { + + public static Test suite() { + TestSuite suite= new TestSuite("JUnit tests for the structgen module"); + + suite.addTest(StructgenCoverageTest.suite()); + + suite.addTest(RandomStructureGeneratorTest.suite()); + suite.addTest(VicinitySamplerTest.suite()); + suite.addTest(GENMDeterministicGeneratorTest.suite()); + suite.addTest(EquivalentClassesDeterministicGeneratorTest.suite()); + + return suite; + } + +} Added: trunk/cdk/src/org/openscience/cdk/test/StructgenCoverageTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/StructgenCoverageTest.java (rev 0) +++ trunk/cdk/src/org/openscience/cdk/test/StructgenCoverageTest.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -0,0 +1,55 @@ +/* $Revision: 7635 $ $Author: egonw $ $Date: 2007-01-04 18:32:54 +0100 (Thu, 04 Jan 2007) $ + * + * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.test; + +import junit.framework.Test; +import junit.framework.TestSuite; + +/** + * TestSuite that performs a simple coverage test of the structgen module. + * + * @cdk.module test-structgen + */ +public class StructgenCoverageTest extends CoverageTest { + + private final static String CLASS_LIST = "structgen.javafiles"; + + public StructgenCoverageTest(String name){ + super(name); + } + + public void setUp() { + super.setUp(); + try { + super.loadClassList(CLASS_LIST); + } catch (Exception exception) { + fail("Could not load classes to test: " + exception.getMessage()); + } + } + + public static Test suite() { + return new TestSuite(StructgenCoverageTest.class); + } + + public void testCoverage() { + super.runCoverageTest(); + } +} Modified: trunk/cdk/src/org/openscience/cdk/test/structgen/RandomStructureGeneratorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/structgen/RandomStructureGeneratorTest.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/test/structgen/RandomStructureGeneratorTest.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -42,7 +42,7 @@ import org.openscience.cdk.test.CDKTestCase; /** - * @cdk.module test-extra + * @cdk.module test-structgen */ public class RandomStructureGeneratorTest extends CDKTestCase { Modified: trunk/cdk/src/org/openscience/cdk/test/structgen/SingleStructureRandomGeneratorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/structgen/SingleStructureRandomGeneratorTest.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/test/structgen/SingleStructureRandomGeneratorTest.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -42,7 +42,7 @@ import org.openscience.cdk.tools.MFAnalyser; /** - * @cdk.module test-extra + * @cdk.module test-structgen */ public class SingleStructureRandomGeneratorTest { Modified: trunk/cdk/src/org/openscience/cdk/test/structgen/VicinitySamplerTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/structgen/VicinitySamplerTest.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/test/structgen/VicinitySamplerTest.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -46,7 +46,7 @@ import org.openscience.cdk.tools.HydrogenAdder; /** - * @cdk.module test-extra + * @cdk.module test-structgen */ public class VicinitySamplerTest extends CDKTestCase { Modified: trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/EquivalentClassesDeterministicGeneratorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/EquivalentClassesDeterministicGeneratorTest.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/EquivalentClassesDeterministicGeneratorTest.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -32,7 +32,7 @@ import org.openscience.cdk.test.CDKTestCase; /** - * @cdk.module test-extra + * @cdk.module test-structgen */ public class EquivalentClassesDeterministicGeneratorTest extends CDKTestCase { Modified: trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java 2007-01-11 11:46:09 UTC (rev 7690) +++ trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java 2007-01-11 11:47:48 UTC (rev 7691) @@ -45,7 +45,7 @@ import org.openscience.cdk.test.CDKTestCase; /** - * @cdk.module test-extra + * @cdk.module test-structgen */ public class GENMDeterministicGeneratorTest extends CDKTestCase { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2007-01-19 09:51:53
|
Revision: 7734 http://svn.sourceforge.net/cdk/?rev=7734&view=rev Author: shk3 Date: 2007-01-19 01:46:10 -0800 (Fri, 19 Jan 2007) Log Message: ----------- Added a method to the applet to import a structure and leave the old one via js Modified Paths: -------------- trunk/cdk/EditorApplet.html trunk/cdk/src/org/openscience/cdk/applications/jchempaint/InsertTextPanel.java trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java Modified: trunk/cdk/EditorApplet.html =================================================================== --- trunk/cdk/EditorApplet.html 2007-01-18 13:26:09 UTC (rev 7733) +++ trunk/cdk/EditorApplet.html 2007-01-19 09:46:10 UTC (rev 7734) @@ -11,13 +11,14 @@ <applet code="org.openscience.cdk.applications.jchempaint.applet.JChemPaintEditorApplet" archive="dist/jar/jchempaint-applet-core.jar" name="Editor" width="600" height="500"> -<param name="load" value="src/data/mdl/a-pinene.mol"> +<param name="load" value="src/data/mdl/withcharges.mol"> <param name="impliciths" value="true"> </applet> <a href="javascript:alert(document.Editor.getMolFile())">show mol file</a> <a href="javascript:alert(document.Editor.getSmiles())">show smiles</a> <a href="javascript:alert(document.Editor.getSmilesChiral())">show stereo smiles</a> <a href="javascript:document.Editor.clear()">clear</a> +<a href="javascript:document.Editor.addMolFileWithReplace('\n CDK 1/19/07,10:3\n\n 2 1 0 0 0 0 0 0 0 0999 V2000 \n 252.0000 1022.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 227.0000 1047.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 1 0 0 0 0 \nM END')">insert CC</a> <blockquote> <hr> Modified: trunk/cdk/src/org/openscience/cdk/applications/jchempaint/InsertTextPanel.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/InsertTextPanel.java 2007-01-18 13:26:09 UTC (rev 7733) +++ trunk/cdk/src/org/openscience/cdk/applications/jchempaint/InsertTextPanel.java 2007-01-19 09:46:10 UTC (rev 7734) @@ -259,7 +259,7 @@ return data; } - private void generateModel(IMolecule molecule) { + public void generateModel(IMolecule molecule) { if (molecule == null) return; // ok, get relevent bits from active model Modified: trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java 2007-01-18 13:26:09 UTC (rev 7733) +++ trunk/cdk/src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java 2007-01-19 09:46:10 UTC (rev 7734) @@ -41,8 +41,10 @@ import org.openscience.cdk.AtomContainer; import org.openscience.cdk.ChemModel; +import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.Molecule; import org.openscience.cdk.MoleculeSet; +import org.openscience.cdk.applications.jchempaint.InsertTextPanel; import org.openscience.cdk.applications.jchempaint.JCPPropertyHandler; import org.openscience.cdk.applications.jchempaint.JChemPaintModel; import org.openscience.cdk.applications.jchempaint.JChemPaintPanel; @@ -52,13 +54,14 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.IChemObjectReader; +import org.openscience.cdk.io.MDLV2000Reader; import org.openscience.cdk.io.MDLWriter; import org.openscience.cdk.io.ReaderFactory; import org.openscience.cdk.layout.HydrogenPlacer; import org.openscience.cdk.smiles.SmilesGenerator; import org.openscience.cdk.tools.HydrogenAdder; +import org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; -import org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator; import org.openscience.cdk.tools.manipulator.MoleculeSetManipulator; /** @@ -356,10 +359,37 @@ return generator.createChiralSMILES(moleculewithh,bool); } + /** + * This method sets a structure in the editor and leaves the old one. * This method replaces all \n characters with the system line separator. This can be used when setting a mol file in an applet * without knowing which platform the applet is running on. * + * @param mol The mol file to set (V2000) + * @throws Exception + */ + public void addMolFileWithReplace(String mol) throws Exception{ + StringBuffer newmol=new StringBuffer(); + int s = 0; + int e = 0; + while ((e = mol.indexOf("\\n", s)) >= 0) { + newmol.append(mol.substring(s, e)); + newmol.append(System.getProperty("file.separator")); + s = e + 1; + } + newmol.append(mol.substring(s)); + MDLV2000Reader reader=new MDLV2000Reader(new StringReader(newmol.toString())); + IMolecule cdkmol=(IMolecule)reader.read(DefaultChemObjectBuilder.getInstance().newMolecule()); + new InsertTextPanel(theJcpp,null).generateModel(cdkmol); + repaint(); + } + + + /** + * This method sets a new structure in the editor and removes the old one. + * This method replaces all \n characters with the system line separator. This can be used when setting a mol file in an applet + * without knowing which platform the applet is running on. + * * @param mol The mol file to set * @throws Exception */ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-01-31 15:35:57
|
Revision: 7799 http://svn.sourceforge.net/cdk/?rev=7799&view=rev Author: egonw Date: 2007-01-31 07:35:46 -0800 (Wed, 31 Jan 2007) Log Message: ----------- Removed traces of Xerces which is not needed because Java1.4 has a XML parser itself. Modified Paths: -------------- trunk/cdk/src/META-INF/standard.libdepends trunk/cdk/src/META-INF/test-experimental.libdepends trunk/cdk/src/META-INF/test-extra.libdepends trunk/cdk/src/META-INF/test-osjvmts.libdepends Removed Paths: ------------- trunk/cdk/jar/xercesImpl.jar trunk/cdk/jar/xercesSamples.jar Deleted: trunk/cdk/jar/xercesImpl.jar =================================================================== (Binary files differ) Deleted: trunk/cdk/jar/xercesSamples.jar =================================================================== (Binary files differ) Modified: trunk/cdk/src/META-INF/standard.libdepends =================================================================== --- trunk/cdk/src/META-INF/standard.libdepends 2007-01-31 15:15:47 UTC (rev 7798) +++ trunk/cdk/src/META-INF/standard.libdepends 2007-01-31 15:35:46 UTC (rev 7799) @@ -1,4 +1,3 @@ vecmath1.2-1.14.jar log4j.jar -xerces-2.5.0.jar jgrapht-0.6.0.jar Modified: trunk/cdk/src/META-INF/test-experimental.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-experimental.libdepends 2007-01-31 15:15:47 UTC (rev 7798) +++ trunk/cdk/src/META-INF/test-experimental.libdepends 2007-01-31 15:35:46 UTC (rev 7799) @@ -7,7 +7,6 @@ printf.jar sjava-0.68.jar vecmath1.2-1.14.jar -xerces-2.5.0.jar xindice.jar xmldb.jar -xom-1.1.jar \ No newline at end of file +xom-1.1.jar Modified: trunk/cdk/src/META-INF/test-extra.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-extra.libdepends 2007-01-31 15:15:47 UTC (rev 7798) +++ trunk/cdk/src/META-INF/test-extra.libdepends 2007-01-31 15:35:46 UTC (rev 7799) @@ -7,7 +7,6 @@ printf.jar sjava-0.68.jar vecmath1.2-1.14.jar -xerces-2.5.0.jar xindice.jar xmldb.jar -xom-1.1.jar \ No newline at end of file +xom-1.1.jar Modified: trunk/cdk/src/META-INF/test-osjvmts.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-osjvmts.libdepends 2007-01-31 15:15:47 UTC (rev 7798) +++ trunk/cdk/src/META-INF/test-osjvmts.libdepends 2007-01-31 15:35:46 UTC (rev 7799) @@ -7,7 +7,6 @@ printf.jar sjava-0.68.jar vecmath1.2-1.14.jar -xerces-2.5.0.jar xindice.jar xmldb.jar -xom-1.1.jar \ No newline at end of file +xom-1.1.jar This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-02-01 10:39:09
|
Revision: 7819 http://svn.sourceforge.net/cdk/?rev=7819&view=rev Author: egonw Date: 2007-02-01 02:39:07 -0800 (Thu, 01 Feb 2007) Log Message: ----------- Added reaction and structgen for auto testing. Modified Paths: -------------- trunk/cdk/pmd-unused.xml trunk/cdk/pmd.xml Modified: trunk/cdk/pmd-unused.xml =================================================================== --- trunk/cdk/pmd-unused.xml 2007-02-01 10:37:22 UTC (rev 7818) +++ trunk/cdk/pmd-unused.xml 2007-02-01 10:39:07 UTC (rev 7819) @@ -38,6 +38,7 @@ <antcall target="test-module"><param name="module" value="io-jmol"/></antcall> <antcall target="test-module"><param name="module" value="extra"/></antcall> <antcall target="test-module"><param name="module" value="render"/></antcall> + <antcall target="test-module"><param name="module" value="reaction"/></antcall> <antcall target="test-module"><param name="module" value="libio-cml"/></antcall> <antcall target="test-module"><param name="module" value="libio-joelib"/></antcall> <antcall target="test-module"><param name="module" value="libio-biojava"/></antcall> @@ -47,6 +48,7 @@ <antcall target="test-module"><param name="module" value="qsar"/></antcall> <antcall target="test-module"><param name="module" value="experimental"/></antcall> <antcall target="test-module"><param name="module" value="svg"/></antcall> + <antcall target="test-module"><param name="module" value="structgen"/></antcall> <antcall target="test-module"><param name="module" value="valencycheck"/></antcall> <!-- the test modules --> <antcall target="test-module"><param name="module" value="test-core"/></antcall> Modified: trunk/cdk/pmd.xml =================================================================== --- trunk/cdk/pmd.xml 2007-02-01 10:37:22 UTC (rev 7818) +++ trunk/cdk/pmd.xml 2007-02-01 10:39:07 UTC (rev 7819) @@ -38,6 +38,7 @@ <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="io-jmol"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="extra"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="render"/></antcall> + <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="reaction"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-cml"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-joelib"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-biojava"/></antcall> @@ -47,6 +48,7 @@ <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsar"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="experimental"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="svg"/></antcall> + <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="structgen"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="valencycheck"/></antcall> <!-- the test modules --> <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-core"/></antcall> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-02-01 23:46:39
|
Revision: 7855 http://svn.sourceforge.net/cdk/?rev=7855&view=rev Author: egonw Date: 2007-02-01 15:46:36 -0800 (Thu, 01 Feb 2007) Log Message: ----------- Fixed mol2 reader: flag atoms as aromatic, instead of use of 1.5 bond order; single bonds are not longer read as aromatic. Modified Paths: -------------- trunk/cdk/.classpath trunk/cdk/.externalToolBuilders/EclipsePreBuild.launch trunk/cdk/.project trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java Modified: trunk/cdk/.classpath =================================================================== --- trunk/cdk/.classpath 2007-02-01 23:34:55 UTC (rev 7854) +++ trunk/cdk/.classpath 2007-02-01 23:46:36 UTC (rev 7855) @@ -1,13 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <classpath> <classpathentry excluding="org/openscience/cdk/libio/joelib/Convertor.java|org/openscience/cdk/test/libio/joelib/JOELibIOTest.java" kind="src" path="src"/> + <classpathentry kind="src" path="perf"/> <classpathentry kind="lib" path="develjar/ant_doxygen.jar"/> <classpathentry kind="lib" path="develjar/dbdoclet.jar"/> - <classpathentry kind="lib" path="develjar/jakarta-oro-2.0.8.jar"/> - <classpathentry kind="lib" path="develjar/jaxen-1.1-beta-7.jar"/> <classpathentry kind="lib" path="develjar/junit.jar"/> - <classpathentry kind="lib" path="develjar/pmd-3.6.jar"/> - <classpathentry kind="lib" path="develjar/saxpath-1.0-fcs.jar"/> <classpathentry kind="lib" path="doc/jar/jabref.jar"/> <classpathentry kind="lib" path="jar/antlr.jar"/> <classpathentry kind="lib" path="jar/batik-awt-util.jar"/> @@ -37,8 +34,6 @@ <classpathentry kind="lib" path="jar/sjava-0.68.jar"/> <classpathentry kind="lib" path="jar/vecmath1.2-1.14.jar"/> <classpathentry kind="lib" path="jar/weka.jar"/> - <classpathentry kind="lib" path="jar/xercesImpl.jar"/> - <classpathentry kind="lib" path="jar/xercesSamples.jar"/> <classpathentry kind="lib" path="jar/xindice.jar"/> <classpathentry kind="lib" path="jar/xml-apis.jar"/> <classpathentry kind="lib" path="jar/xmldb.jar"/> Modified: trunk/cdk/.externalToolBuilders/EclipsePreBuild.launch =================================================================== --- trunk/cdk/.externalToolBuilders/EclipsePreBuild.launch 2007-02-01 23:34:55 UTC (rev 7854) +++ trunk/cdk/.externalToolBuilders/EclipsePreBuild.launch 2007-02-01 23:46:36 UTC (rev 7855) @@ -1,16 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType"> <booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/> +<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="true"/> <booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="false"/> -<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="true"/> +<stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="incremental,auto,"/> +<booleanAttribute key="org.eclipse.ant.ui.ATTR_TARGETS_UPDATED" value="true"/> +<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/> +<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/> +<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/> +<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="false"/> <stringAttribute key="org.eclipse.ant.ui.ATTR_ANT_MANUAL_TARGETS" value="preBuild,"/> <stringAttribute key="org.eclipse.ant.ui.ATTR_ANT_AUTO_TARGETS" value="preBuild,"/> -<stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="incremental,auto,"/> -<booleanAttribute key="org.eclipse.ant.ui.ATTR_TARGETS_UPDATED" value="true"/> <stringAttribute key="org.eclipse.debug.core.ATTR_REFRESH_SCOPE" value="${project}"/> <stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${workspace_loc:/cdk/build-eclipse.xml}"/> -<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/> -<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/> -<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/> </launchConfiguration> - Modified: trunk/cdk/.project =================================================================== --- trunk/cdk/.project 2007-02-01 23:34:55 UTC (rev 7854) +++ trunk/cdk/.project 2007-02-01 23:46:36 UTC (rev 7855) @@ -4,23 +4,23 @@ <comment></comment> <projects> </projects> - <buildSpec> - <buildCommand> - <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name> - <triggers>auto,incremental,</triggers> - <arguments> - <dictionary> - <key>LaunchConfigHandle</key> - <value><project>/.externalToolBuilders/EclipsePreBuild.launch</value> - </dictionary> - </arguments> - </buildCommand> - <buildCommand> - <name>org.eclipse.jdt.core.javabuilder</name> - <arguments> - </arguments> - </buildCommand> - </buildSpec> + <buildSpec> + <buildCommand> + <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name> + <triggers>auto,incremental,</triggers> + <arguments> + <dictionary> + <key>LaunchConfigHandle</key> + <value><project>/.externalToolBuilders/EclipsePreBuild.launch</value> + </dictionary> + </arguments> + </buildCommand> + <buildCommand> + <name>org.eclipse.jdt.core.javabuilder</name> + <arguments> + </arguments> + </buildCommand> + </buildSpec> <natures> <nature>org.eclipse.jdt.core.javanature</nature> </natures> Modified: trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java 2007-02-01 23:34:55 UTC (rev 7854) +++ trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java 2007-02-01 23:46:36 UTC (rev 7855) @@ -37,17 +37,18 @@ import javax.vecmath.Point3d; +import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomType; -import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.config.AtomTypeFactory; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.Mol2Format; import org.openscience.cdk.tools.LoggingTool; @@ -254,28 +255,31 @@ try { int atom1 = Integer.parseInt(atom1Str); int atom2 = Integer.parseInt(atom2Str); - double order = 0; - if ("1".equals(orderStr)) { - order = CDKConstants.BONDORDER_AROMATIC; - } else if ("2".equals(orderStr)) { - order = CDKConstants.BONDORDER_DOUBLE; - } else if ("3".equals(orderStr)) { - order = CDKConstants.BONDORDER_TRIPLE; - } else if ("am".equals(orderStr)) { - order = CDKConstants.BONDORDER_SINGLE; - } else if ("ar".equals(orderStr)) { - order = CDKConstants.BONDORDER_AROMATIC; - } else if ("du".equals(orderStr)) { - order = CDKConstants.BONDORDER_SINGLE; - } else if ("un".equals(orderStr)) { - order = CDKConstants.BONDORDER_SINGLE; - } else if ("nc".equals(orderStr)) { - // not connected - order = 0; + if ("nc".equals(orderStr)) { + // do not connect the atoms + } else { + IBond bond = molecule.getBuilder().newBond( + molecule.getAtom(atom1-1), + molecule.getAtom(atom2-1) + ); + if ("1".equals(orderStr)) { + bond.setOrder(CDKConstants.BONDORDER_SINGLE); + } else if ("2".equals(orderStr)) { + bond.setOrder(CDKConstants.BONDORDER_DOUBLE); + } else if ("3".equals(orderStr)) { + bond.setOrder(CDKConstants.BONDORDER_TRIPLE); + } else if ("am".equals(orderStr) || "ar".equals(orderStr)) { + bond.setOrder(CDKConstants.BONDORDER_SINGLE); + bond.setFlag(CDKConstants.ISAROMATIC, true); + bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true); + bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true); + } else if ("du".equals(orderStr)) { + bond.setOrder(CDKConstants.BONDORDER_SINGLE); + } else if ("un".equals(orderStr)) { + bond.setOrder(CDKConstants.BONDORDER_SINGLE); + } + molecule.addBond(bond); } - if (order != 0) { - molecule.addBond(atom1-1, atom2-1, order); - } } catch (NumberFormatException nfExc) { String error = "Error while reading bond information"; logger.error(error); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-02-02 12:17:19
|
Revision: 7865 http://svn.sourceforge.net/cdk/?rev=7865&view=rev Author: egonw Date: 2007-02-02 04:17:17 -0800 (Fri, 02 Feb 2007) Log Message: ----------- Put the helper tool into a separate module, to solve dependency issues. Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java Added Paths: ----------- trunk/cdk/src/META-INF/builder3dtools.cdkdepends trunk/cdk/src/META-INF/builder3dtools.libdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2007-02-02 12:11:49 UTC (rev 7864) +++ trunk/cdk/build.xml 2007-02-02 12:17:17 UTC (rev 7865) @@ -453,6 +453,7 @@ <antcall target="compile-module"><param name="module" value="qsar-weka"/></antcall> <antcall target="compile-module"><param name="module" value="forcefield"/></antcall> <antcall target="compile-module"><param name="module" value="builder3d"/></antcall> + <antcall target="compile-module"><param name="module" value="builder3dtools"/></antcall> <antcall target="compile-module"><param name="module" value="svg"/></antcall> <antcall target="compile-module"><param name="module" value="experimental"/></antcall> <antcall target="compile-module"><param name="module" value="applications"/></antcall> @@ -494,6 +495,7 @@ <fileset dir="${lib}"> <includesfile name="${metainf}/applications.libdepends"/> <includesfile name="${metainf}/builder3d.libdepends"/> + <includesfile name="${metainf}/builder3dtools.libdepends"/> <includesfile name="${metainf}/charges.libdepends"/> <includesfile name="${metainf}/core.libdepends"/> <includesfile name="${metainf}/control.libdepends"/> @@ -524,6 +526,7 @@ <fileset dir="${dist}/jar"> <include name="cdk-applications.jar"/> <include name="cdk-builder3d.jar"/> + <include name="cdk-builder3dtools.jar"/> <include name="cdk-charges.jar"/> <include name="cdk-core.jar"/> <include name="cdk-control.jar"/> Added: trunk/cdk/src/META-INF/builder3dtools.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/builder3dtools.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/builder3dtools.cdkdepends 2007-02-02 12:17:17 UTC (rev 7865) @@ -0,0 +1,12 @@ +cdk-core.jar +cdk-data.jar +cdk-extra.jar +cdk-interfaces.jar +cdk-io.jar +cdk-qsar.jar +cdk-standard.jar +cdk-charges.jar +cdk-forcefield.jar +cdk-valencycheck.jar +cdk-sdg.jar +cdk-smiles.jar Added: trunk/cdk/src/META-INF/builder3dtools.libdepends =================================================================== --- trunk/cdk/src/META-INF/builder3dtools.libdepends (rev 0) +++ trunk/cdk/src/META-INF/builder3dtools.libdepends 2007-02-02 12:17:17 UTC (rev 7865) @@ -0,0 +1,2 @@ +vecmath1.2-1.14.jar + Modified: trunk/cdk/src/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java 2007-02-02 12:11:49 UTC (rev 7864) +++ trunk/cdk/src/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java 2007-02-02 12:17:17 UTC (rev 7865) @@ -58,7 +58,12 @@ import org.openscience.cdk.smiles.SmilesGenerator; import org.openscience.cdk.tools.manipulator.RingSetManipulator; - +/** + * Helper class that help setup a template library of CDK's Builder3D. + * + * @author egonw + * @cdk.module builder3dtools + */ public class TemplateExtractor{ static final String usage = "Usage: TemplateExtractor SDFinfile outfile anyAtom=true/false anyBondAnyAtom=true/false"; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-02-09 15:37:10
|
Revision: 7928 http://svn.sourceforge.net/cdk/?rev=7928&view=rev Author: egonw Date: 2007-02-09 07:37:02 -0800 (Fri, 09 Feb 2007) Log Message: ----------- Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bug reporting! Modified Paths: -------------- trunk/cdk/build.props trunk/cdk/build.xml Modified: trunk/cdk/build.props =================================================================== --- trunk/cdk/build.props 2007-02-09 13:07:20 UTC (rev 7927) +++ trunk/cdk/build.props 2007-02-09 15:37:02 UTC (rev 7928) @@ -1,2 +1,2 @@ -version=20060925 -jcp.version=2.3.1 +version=0.99.1 +jcp.version=2.3.2 Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2007-02-09 13:07:20 UTC (rev 7927) +++ trunk/cdk/build.xml 2007-02-09 15:37:02 UTC (rev 7928) @@ -726,8 +726,9 @@ <tstamp> <format property="TODAY_SVN" pattern="yyyyMMdd" locale="en" /> </tstamp> - <property name="package" value="cdk-source-${TODAY_SVN}"/> + <property name="package" value="cdk-src+libs-${version}"/> <property name="sourcedist.dir" value="${sourcedist}/${package}"/> + <delete dir="${sourcedist.dir}"/> <copy todir="${sourcedist.dir}/${src}"> <fileset dir="${build}" includes="*.javafiles" /> <fileset dir="${build}" includes="*.classes" /> @@ -735,6 +736,7 @@ <fileset dir="${src}" includes="**/*.java" /> <fileset dir="${src}" includes="**/*.jj" /> <fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" /> + <fileset dir="${src}" excludes="org/openscience/cdk/test/**" /> </copy> <copy todir="${sourcedist.dir}"> <fileset dir="." includes="build.props" /> @@ -755,9 +757,6 @@ <exclude name="dbdoclet*.*"/> </fileset> </copy> - <copy todir="${sourcedist.dir}/src/data"> - <fileset dir="src/data" /> - </copy> <copy todir="${sourcedist.dir}/src/META-INF"> <fileset dir="src/META-INF" /> </copy> @@ -791,6 +790,12 @@ <fileset dir="doc/" includes="lgpl.license" /> </copy> <mkdir dir="${sourcedist.dir}/doc/javadoc" /> + <!-- the below deteles are a workaround, because the above should not have copied + in the src/data and src/org/openscience/cdk/test dirs --> + <delete dir="${sourcedist.dir}/src/data"/> + <delete dir="${sourcedist.dir}/src/org/openscience/cdk/test"/> + + <!-- now package things up --> <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" /> <gzip zipfile="${package}.tar.gz" src="${package}.tar" /> <delete file="${package}.tar" /> @@ -802,8 +807,9 @@ <tstamp> <format property="TODAY_SVN" pattern="yyyyMMdd" locale="en" /> </tstamp> - <property name="package" value="cdk-pure-source-${TODAY_SVN}"/> + <property name="package" value="cdk-${version}"/> <property name="sourcedist.dir" value="${sourcedist}/${package}"/> + <delete dir="${sourcedist.dir}"/> <copy todir="${sourcedist.dir}/${src}"> <fileset dir="${build}" includes="*.javafiles" /> <fileset dir="${build}" includes="*.classes" /> @@ -855,6 +861,12 @@ <fileset dir="doc/" includes="lgpl.license" /> </copy> <mkdir dir="${sourcedist.dir}/doc/javadoc" /> + <!-- the below deteles are a workaround, because the above should not have copied + in the src/data and src/org/openscience/cdk/test dirs --> + <delete dir="${sourcedist.dir}/src/data"/> + <delete dir="${sourcedist.dir}/src/org/openscience/cdk/test"/> + + <!-- now package things up --> <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" /> <gzip zipfile="${package}.tar.gz" src="${package}.tar" /> <delete file="${package}.tar" /> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-02-16 09:20:02
|
Revision: 7945 http://svn.sourceforge.net/cdk/?rev=7945&view=rev Author: egonw Date: 2007-02-16 01:19:59 -0800 (Fri, 16 Feb 2007) Log Message: ----------- Forgot to move the CDK wrappers around two Jmol IO classes to the new cdk-libio module. Added Paths: ----------- trunk/cdk-libio/src/org/openscience/cdk/io/ trunk/cdk-libio/src/org/openscience/cdk/io/JMEReader.java trunk/cdk-libio/src/org/openscience/cdk/io/MOPAC97Reader.java Removed Paths: ------------- trunk/cdk/src/org/openscience/cdk/io/JMEReader.java trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java Deleted: trunk/cdk/src/org/openscience/cdk/io/JMEReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/JMEReader.java 2007-02-16 09:02:28 UTC (rev 7944) +++ trunk/cdk/src/org/openscience/cdk/io/JMEReader.java 2007-02-16 09:19:59 UTC (rev 7945) @@ -1,131 +0,0 @@ -/* $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project - * - * Contact: cdk...@li... - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * All we ask is that proper credit is given for our work, which includes - * - but is not limited to - adding the above copyright notice to the beginning - * of your source code files, and to any copyright notice that you may distribute - * with programs based on this work. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. - * - */ -package org.openscience.cdk.io; - -import org.jmol.adapter.smarter.SmarterJmolAdapter; -import org.jmol.api.JmolAdapter; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.IChemObject; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.io.formats.JMEFormat; -import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.libio.jmol.Convertor; - -import java.io.*; - -/** - * Reads a molecule from an JME file using Jmol's JME reader. - * - * @author Egon Willighagen - * @author Miguel Howard - * @cdk.module io-jmol - * @cdk.created 2004-05-18 - * @cdk.keyword file format, JME - * @cdk.builddepends jmolIO.jar - * @cdk.builddepends jmolApis.jar - * @cdk.depends jmolIO.jar - * @cdk.depends jmolApis.jar - */ -public class JMEReader extends DefaultChemObjectReader { - - BufferedReader input = null; - - public JMEReader() { - this(new StringReader("")); - } - - public JMEReader(InputStream inputStream) { - this(new InputStreamReader(inputStream)); - } - - public JMEReader(Reader input) { - if (input instanceof BufferedReader) { - this.input = (BufferedReader) input; - } else { - this.input = new BufferedReader(input); - } - } - - public IResourceFormat getFormat() { - return JMEFormat.getInstance(); - } - - public void setReader(Reader input) throws CDKException { - if (input instanceof BufferedReader) { - this.input = (BufferedReader) input; - } else { - this.input = new BufferedReader(input); - } - } - - public void setReader(InputStream input) throws CDKException { - setReader(new InputStreamReader(input)); - } - - public boolean accepts(Class classObject) { - Class[] interfaces = classObject.getInterfaces(); - for (int i = 0; i < interfaces.length; i++) { - if (IMolecule.class.equals(interfaces[i])) return true; - } - return false; - } - - public IChemObject read(IChemObject object) throws CDKException { - if (object instanceof IMolecule) { - return readMolecule((IMolecule) object); - } else { - throw new CDKException("Only supported are Molecule."); - } - } - - /** - * Read a Molecule from a JME file. - * - * @return The Molecule that was read from the MDL file. - */ - private IMolecule readMolecule(IMolecule molecule) throws CDKException { - JmolAdapter adapter = new SmarterJmolAdapter(null); - // note that it actually let's the adapter detect the format! - Object model = adapter.openBufferedReader("", input); - molecule.add(new Convertor(molecule.getBuilder()).convert(model)); - return molecule; - } - - public void close() throws IOException { - input.close(); - } - - public IOSetting[] getIOSettings() { - return new IOSetting[0]; - } - - -} - Deleted: trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java 2007-02-16 09:02:28 UTC (rev 7944) +++ trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java 2007-02-16 09:19:59 UTC (rev 7945) @@ -1,112 +0,0 @@ -/* $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project - * - * Contact: cdk...@li... - * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public - * License as published by the Free Software Foundation; either - * version 2.1 of the License, or (at your option) any later version. - * - * This library is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this library; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. - */ -package org.openscience.cdk.io; - -import org.jmol.adapter.smarter.SmarterJmolAdapter; -import org.jmol.api.JmolAdapter; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.IChemObject; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.io.formats.MOPAC97Format; -import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.libio.jmol.Convertor; - -import java.io.*; - -/** - * Reader for MOPAC 93, 97 and 2002 files. Only tested for MOPAC 93 files. - * It uses Jmol IO classes. - * - * @cdk.module io-jmol - * @cdk.keyword file format, MOPAC - * @cdk.builddepends jmolIO.jar - * @cdk.builddepends jmolApis.jar - * @cdk.depends jmolIO.jar - * @cdk.depends jmolApis.jar - */ -public class MOPAC97Reader extends DefaultChemObjectReader { - - BufferedReader input = null; - - public MOPAC97Reader(InputStream inputStream) { - this(new BufferedReader(new InputStreamReader(inputStream))); - } - - public MOPAC97Reader(Reader input) { - if (input instanceof BufferedReader) { - this.input = (BufferedReader) input; - } else { - this.input = new BufferedReader(input); - } - } - - public IResourceFormat getFormat() { - return MOPAC97Format.getInstance(); - } - - public void setReader(Reader input) throws CDKException { - if (input instanceof BufferedReader) { - this.input = (BufferedReader) input; - } else { - this.input = new BufferedReader(input); - } - } - - public void setReader(InputStream input) throws CDKException { - setReader(new InputStreamReader(input)); - } - - public boolean accepts(Class classObject) { - Class[] interfaces = classObject.getInterfaces(); - for (int i = 0; i < interfaces.length; i++) { - if (IMolecule.class.equals(interfaces[i])) return true; - } - return false; - } - - public IChemObject read(IChemObject object) throws CDKException { - if (object instanceof IMolecule) { - return readMolecule((IMolecule) object); - } else { - throw new CDKException("Only supported are Molecule."); - } - } - - private IMolecule readMolecule(IMolecule molecule) throws CDKException { - JmolAdapter adapter = new SmarterJmolAdapter(null); - // note that it actually let's the adapter detect the format! - Object model = adapter.openBufferedReader("", input); - molecule.add(new Convertor(molecule.getBuilder()).convert(model)); - return molecule; - } - - public void close() throws IOException { - input.close(); - } - - public IOSetting[] getIOSettings() { - return new IOSetting[0]; - } -} Copied: trunk/cdk-libio/src/org/openscience/cdk/io/JMEReader.java (from rev 7942, trunk/cdk/src/org/openscience/cdk/io/JMEReader.java) =================================================================== --- trunk/cdk-libio/src/org/openscience/cdk/io/JMEReader.java (rev 0) +++ trunk/cdk-libio/src/org/openscience/cdk/io/JMEReader.java 2007-02-16 09:19:59 UTC (rev 7945) @@ -0,0 +1,131 @@ +/* $RCSfile$ + * $Author$ + * $Date$ + * $Revision$ + * + * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + * + */ +package org.openscience.cdk.io; + +import org.jmol.adapter.smarter.SmarterJmolAdapter; +import org.jmol.api.JmolAdapter; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.io.formats.IResourceFormat; +import org.openscience.cdk.io.formats.JMEFormat; +import org.openscience.cdk.io.setting.IOSetting; +import org.openscience.cdk.libio.jmol.Convertor; + +import java.io.*; + +/** + * Reads a molecule from an JME file using Jmol's JME reader. + * + * @author Egon Willighagen + * @author Miguel Howard + * @cdk.module io-jmol + * @cdk.created 2004-05-18 + * @cdk.keyword file format, JME + * @cdk.builddepends jmolIO.jar + * @cdk.builddepends jmolApis.jar + * @cdk.depends jmolIO.jar + * @cdk.depends jmolApis.jar + */ +public class JMEReader extends DefaultChemObjectReader { + + BufferedReader input = null; + + public JMEReader() { + this(new StringReader("")); + } + + public JMEReader(InputStream inputStream) { + this(new InputStreamReader(inputStream)); + } + + public JMEReader(Reader input) { + if (input instanceof BufferedReader) { + this.input = (BufferedReader) input; + } else { + this.input = new BufferedReader(input); + } + } + + public IResourceFormat getFormat() { + return JMEFormat.getInstance(); + } + + public void setReader(Reader input) throws CDKException { + if (input instanceof BufferedReader) { + this.input = (BufferedReader) input; + } else { + this.input = new BufferedReader(input); + } + } + + public void setReader(InputStream input) throws CDKException { + setReader(new InputStreamReader(input)); + } + + public boolean accepts(Class classObject) { + Class[] interfaces = classObject.getInterfaces(); + for (int i = 0; i < interfaces.length; i++) { + if (IMolecule.class.equals(interfaces[i])) return true; + } + return false; + } + + public IChemObject read(IChemObject object) throws CDKException { + if (object instanceof IMolecule) { + return readMolecule((IMolecule) object); + } else { + throw new CDKException("Only supported are Molecule."); + } + } + + /** + * Read a Molecule from a JME file. + * + * @return The Molecule that was read from the MDL file. + */ + private IMolecule readMolecule(IMolecule molecule) throws CDKException { + JmolAdapter adapter = new SmarterJmolAdapter(null); + // note that it actually let's the adapter detect the format! + Object model = adapter.openBufferedReader("", input); + molecule.add(new Convertor(molecule.getBuilder()).convert(model)); + return molecule; + } + + public void close() throws IOException { + input.close(); + } + + public IOSetting[] getIOSettings() { + return new IOSetting[0]; + } + + +} + Copied: trunk/cdk-libio/src/org/openscience/cdk/io/MOPAC97Reader.java (from rev 7942, trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java) =================================================================== --- trunk/cdk-libio/src/org/openscience/cdk/io/MOPAC97Reader.java (rev 0) +++ trunk/cdk-libio/src/org/openscience/cdk/io/MOPAC97Reader.java 2007-02-16 09:19:59 UTC (rev 7945) @@ -0,0 +1,112 @@ +/* $RCSfile$ + * $Author$ + * $Date$ + * $Revision$ + * + * Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.io; + +import org.jmol.adapter.smarter.SmarterJmolAdapter; +import org.jmol.api.JmolAdapter; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.io.formats.IResourceFormat; +import org.openscience.cdk.io.formats.MOPAC97Format; +import org.openscience.cdk.io.setting.IOSetting; +import org.openscience.cdk.libio.jmol.Convertor; + +import java.io.*; + +/** + * Reader for MOPAC 93, 97 and 2002 files. Only tested for MOPAC 93 files. + * It uses Jmol IO classes. + * + * @cdk.module io-jmol + * @cdk.keyword file format, MOPAC + * @cdk.builddepends jmolIO.jar + * @cdk.builddepends jmolApis.jar + * @cdk.depends jmolIO.jar + * @cdk.depends jmolApis.jar + */ +public class MOPAC97Reader extends DefaultChemObjectReader { + + BufferedReader input = null; + + public MOPAC97Reader(InputStream inputStream) { + this(new BufferedReader(new InputStreamReader(inputStream))); + } + + public MOPAC97Reader(Reader input) { + if (input instanceof BufferedReader) { + this.input = (BufferedReader) input; + } else { + this.input = new BufferedReader(input); + } + } + + public IResourceFormat getFormat() { + return MOPAC97Format.getInstance(); + } + + public void setReader(Reader input) throws CDKException { + if (input instanceof BufferedReader) { + this.input = (BufferedReader) input; + } else { + this.input = new BufferedReader(input); + } + } + + public void setReader(InputStream input) throws CDKException { + setReader(new InputStreamReader(input)); + } + + public boolean accepts(Class classObject) { + Class[] interfaces = classObject.getInterfaces(); + for (int i = 0; i < interfaces.length; i++) { + if (IMolecule.class.equals(interfaces[i])) return true; + } + return false; + } + + public IChemObject read(IChemObject object) throws CDKException { + if (object instanceof IMolecule) { + return readMolecule((IMolecule) object); + } else { + throw new CDKException("Only supported are Molecule."); + } + } + + private IMolecule readMolecule(IMolecule molecule) throws CDKException { + JmolAdapter adapter = new SmarterJmolAdapter(null); + // note that it actually let's the adapter detect the format! + Object model = adapter.openBufferedReader("", input); + molecule.add(new Convertor(molecule.getBuilder()).convert(model)); + return molecule; + } + + public void close() throws IOException { + input.close(); + } + + public IOSetting[] getIOSettings() { + return new IOSetting[0]; + } +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-02-16 09:29:35
|
Revision: 7948 http://svn.sourceforge.net/cdk/?rev=7948&view=rev Author: egonw Date: 2007-02-16 01:29:33 -0800 (Fri, 16 Feb 2007) Log Message: ----------- Removed referals to libio Jmol and libio JOElib (now in the cdk-libio module). Modified Paths: -------------- trunk/cdk/javadoc.xml trunk/cdk/pmd-unused.xml trunk/cdk/pmd.xml Modified: trunk/cdk/javadoc.xml =================================================================== --- trunk/cdk/javadoc.xml 2007-02-16 09:28:43 UTC (rev 7947) +++ trunk/cdk/javadoc.xml 2007-02-16 09:29:33 UTC (rev 7948) @@ -110,12 +110,10 @@ <antcall target="doccheck-module"><param name="module" value="nonotify"/></antcall> <antcall target="doccheck-module"><param name="module" value="standard"/></antcall> <antcall target="doccheck-module"><param name="module" value="io"/></antcall> - <antcall target="doccheck-module"><param name="module" value="io-jmol"/></antcall> <antcall target="doccheck-module"><param name="module" value="extra"/></antcall> <antcall target="doccheck-module"><param name="module" value="render"/></antcall> <antcall target="doccheck-module"><param name="module" value="reaction"/></antcall> <antcall target="doccheck-module"><param name="module" value="libio-cml"/></antcall> - <antcall target="doccheck-module"><param name="module" value="libio-joelib"/></antcall> <antcall target="doccheck-module"><param name="module" value="libio-biojava"/></antcall> <antcall target="doccheck-module"><param name="module" value="builder3d"/></antcall> <antcall target="doccheck-module"><param name="module" value="smiles"/></antcall> Modified: trunk/cdk/pmd-unused.xml =================================================================== --- trunk/cdk/pmd-unused.xml 2007-02-16 09:28:43 UTC (rev 7947) +++ trunk/cdk/pmd-unused.xml 2007-02-16 09:29:33 UTC (rev 7948) @@ -35,12 +35,10 @@ <antcall target="test-module"><param name="module" value="core"/></antcall> <antcall target="test-module"><param name="module" value="standard"/></antcall> <antcall target="test-module"><param name="module" value="io"/></antcall> - <antcall target="test-module"><param name="module" value="io-jmol"/></antcall> <antcall target="test-module"><param name="module" value="extra"/></antcall> <antcall target="test-module"><param name="module" value="render"/></antcall> <antcall target="test-module"><param name="module" value="reaction"/></antcall> <antcall target="test-module"><param name="module" value="libio-cml"/></antcall> - <antcall target="test-module"><param name="module" value="libio-joelib"/></antcall> <antcall target="test-module"><param name="module" value="libio-biojava"/></antcall> <antcall target="test-module"><param name="module" value="builder3d"/></antcall> <antcall target="test-module"><param name="module" value="smiles"/></antcall> Modified: trunk/cdk/pmd.xml =================================================================== --- trunk/cdk/pmd.xml 2007-02-16 09:28:43 UTC (rev 7947) +++ trunk/cdk/pmd.xml 2007-02-16 09:29:33 UTC (rev 7948) @@ -35,12 +35,10 @@ <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="core"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="standard"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="io"/></antcall> - <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="io-jmol"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="extra"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="render"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="reaction"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-cml"/></antcall> - <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-joelib"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-biojava"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="builder3d"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smiles"/></antcall> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-02-19 12:16:07
|
Revision: 7973 http://svn.sourceforge.net/cdk/?rev=7973&view=rev Author: egonw Date: 2007-02-19 04:16:03 -0800 (Mon, 19 Feb 2007) Log Message: ----------- Added taglet to put citations inline, to increase JavaDoc information content. See http://chem-bla-ics.blogspot.com/2007/02/pimp-my-javadoc.html. Modified Paths: -------------- trunk/cdk/javadoc.xml Added Paths: ----------- trunk/cdk/src/net/sf/cdk/tools/bibtex/ trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLEntry.java trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLFile.java trunk/cdk/src/net/sf/cdk/tools/doclets/ trunk/cdk/src/net/sf/cdk/tools/doclets/CDKBugTaglet.java trunk/cdk/src/net/sf/cdk/tools/doclets/CDKCiteTaglet.java trunk/cdk/src/net/sf/cdk/tools/doclets/CDKDictRefTaglet.java trunk/cdk/src/net/sf/cdk/tools/doclets/CDKModuleTaglet.java Removed Paths: ------------- trunk/cdk/doc/javadoc/source/CDKBugTaglet.java trunk/cdk/doc/javadoc/source/CDKCiteTaglet.java trunk/cdk/doc/javadoc/source/CDKDictRefTaglet.java trunk/cdk/doc/javadoc/source/CDKModuleTaglet.java Deleted: trunk/cdk/doc/javadoc/source/CDKBugTaglet.java =================================================================== --- trunk/cdk/doc/javadoc/source/CDKBugTaglet.java 2007-02-19 12:13:48 UTC (rev 7972) +++ trunk/cdk/doc/javadoc/source/CDKBugTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -1,100 +0,0 @@ -/* $Revision$ $Author$ $Date$ - * - * Copyright (C) 2004-2006 Egon Willighagen <eg...@us...> - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ -package net.sf.cdk.tools; - -import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.*; -import java.util.Map; - -/** - * Taglet that expands @cdk.bug tag into a weblink to CDK's - * SourceForge bug track system. It's typically used as: - * <pre> - * @cdk.bug 1095690 - * </pre> - */ -public class CDKBugTaglet implements Taglet { - - private static final String NAME = "cdk.bug"; - - public String getName() { - return NAME; - } - - public boolean inField() { - return false; - } - - public boolean inConstructor() { - return false; - } - - public boolean inMethod() { - return false; - } - - public boolean inOverview() { - return false; - } - - public boolean inPackage() { - return false; - } - - public boolean inType() { - return true; - } - - public boolean isInlineTag() { - return false; - } - - public static void register(Map tagletMap) { - CDKBugTaglet tag = new CDKBugTaglet(); - Taglet t = (Taglet) tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } - - public String toString(Tag tag) { - return "<DT><B>This class is affected by these bug(s): </B><DD>" - + expand(tag) + "</DD>\n"; - } - - public String toString(Tag[] tags) { - if (tags.length == 0) { - return null; - } else { - StringBuffer list = new StringBuffer(); - list.append("<DT><B>This class is affected by these bug(s): </B><DD>"); - for (int i=0; i<tags.length; i++) { - list.append(expand(tags[i])).append(" "); - } - list.append("</DD>\n"); - return list.toString(); - } - } - - private String expand(Tag tag) { - return "<a href=\"http://sourceforge.net/tracker/index.php?func=detail&group_id=20024&atid=120024&aid=" - + tag.text() + "\">" + tag.text() + "</a>"; - } -} Deleted: trunk/cdk/doc/javadoc/source/CDKCiteTaglet.java =================================================================== --- trunk/cdk/doc/javadoc/source/CDKCiteTaglet.java 2007-02-19 12:13:48 UTC (rev 7972) +++ trunk/cdk/doc/javadoc/source/CDKCiteTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -1,131 +0,0 @@ -/* $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2004-2006 The Chemistry Development Kit (CDK) project - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ -package net.sf.cdk.tools; - -import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.*; -import java.util.Map; -import java.util.StringTokenizer; - -/** - * Taglet that expands inline cdk.cite tags into a weblink to the CDK - * bibliography webpage. Like all inline tags it's used in the JavaDoc - * text as: - * <pre> - * This class does nothing {@cdk.cite NULL}. - * </pre> - * For this code a reference is created like this: - * <pre> - * <a href="http://cdk.sf.net/biblio.html#NULL">NULL</a> - * </pre> - * - * <p>Citations can be singular, like <code>{@cdk.cite BLA}</code>, - * and multiple, like <code>{@cdk.cite BLA,BLA2,FOO}</code>. - */ -public class CDKCiteTaglet implements Taglet { - - private static final String NAME = "cdk.cite"; - - public String getName() { - return NAME; - } - - public boolean inField() { - return true; - } - - public boolean inConstructor() { - return true; - } - - public boolean inMethod() { - return true; - } - - public boolean inOverview() { - return true; - } - - public boolean inPackage() { - return true; - } - - public boolean inType() { - return true; - } - - public boolean isInlineTag() { - return true; - } - - public static void register(Map tagletMap) { - CDKCiteTaglet tag = new CDKCiteTaglet(); - Taglet t = (Taglet) tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } - - public String toString(Tag tag) { - return "[" + expandCitation(tag.text()) + "]"; - } - - public String toString(Tag[] tags) { - String result = null; - if (tags.length > 0) { - result = "["; - for (int i=0; i<tags.length; i++) { - result += expandCitation(tags[i].text()); - if ((i+1)<tags.length) result += ", "; - } - result += "]"; - } - return result; - } - - /** - * Expands a citation into HTML code. - */ - private String expandCitation(String citation) { - String result = ""; - final String separator = ","; - result += "<!-- indexOf" + citation.indexOf(separator) + " -->"; - if (citation.indexOf(separator) != -1) { - StringTokenizer tokenizer = new StringTokenizer(citation, separator); - while (tokenizer.hasMoreTokens()) { - String token = tokenizer.nextToken().trim(); - result += "<a href=\"http://almost.cubic.uni-koeln.de/cdk/cdk_top/bib/" - + token + "\">" + token + "</a>"; - if (tokenizer.hasMoreTokens()) { - result += ", "; - } - } - } else { - citation = citation.trim(); - result += "<a href=\"http://almost.cubic.uni-koeln.de/cdk/cdk_top/bib/" - + citation + "\">" + citation + "</a>"; - } - return result; - } - -} Deleted: trunk/cdk/doc/javadoc/source/CDKDictRefTaglet.java =================================================================== --- trunk/cdk/doc/javadoc/source/CDKDictRefTaglet.java 2007-02-19 12:13:48 UTC (rev 7972) +++ trunk/cdk/doc/javadoc/source/CDKDictRefTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -1,137 +0,0 @@ -/* $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2004 The Chemistry Development Kit (CDK) project - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ -package net.sf.cdk.tools; - -import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.*; -import java.util.Map; -import java.util.StringTokenizer; -import java.util.Hashtable; - -/** - * Taglet that expands inline cdk.dictref tags into a weblink to the appropriate - * dictionary. For example. - * <pre> - * @cdk.dictref blue-obelisk:graphPartitioning - * </pre> - * - * <p>The known dictionaries are: - * <ul> - * <li>blue-obelisk: <a href="http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml">Blue Obelisk Chemoinformatics Dictionary</a> - * <li>bodf: <a href="http://qsar.sourceforge.net/ontologies/data-features/index.xhtml">Blue Obelisk Data Features Dictionary</a> - * <li>qsar-descriptors: <a href="http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml">QSAR.sf.net Descriptors Dictionary</a> - * </ul> - */ -public class CDKDictRefTaglet implements Taglet { - - private static final String NAME = "cdk.dictref"; - - private static final Map dictURLs; - private static final Map dictNames; - - static { - dictURLs = new Hashtable(5); - dictNames = new Hashtable(5); - - dictURLs.put("bodf", "http://qsar.sourceforge.net/ontologies/data-features/index.xhtml"); - dictNames.put("bodf", "Blue Obelisk Data Features Dictionary"); - - dictURLs.put("blue-obelisk", "http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml"); - dictNames.put("blue-obelisk", "Blue Obelisk Chemoinformatics Dictionary"); - - dictURLs.put("qsar-descriptors", "http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml"); - dictNames.put("qsar-descriptors", "QSAR.sf.net Descriptors Dictionary"); - } - - public String getName() { - return NAME; - } - - public boolean inField() { - return true; - } - - public boolean inConstructor() { - return true; - } - - public boolean inMethod() { - return true; - } - - public boolean inOverview() { - return true; - } - - public boolean inPackage() { - return true; - } - - public boolean inType() { - return true; - } - - public boolean isInlineTag() { - return false; - } - - public static void register(Map tagletMap) { - CDKDictRefTaglet tag = new CDKDictRefTaglet(); - Taglet t = (Taglet) tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } - - public String toString(Tag tag) { - String tagText = tag.text(); - String separator = ":"; - if (tagText.indexOf(separator) != -1) { - StringTokenizer tokenizer = new StringTokenizer(tagText, separator); - String dictCode = tokenizer.nextToken(); - String dictRef = tokenizer.nextToken(); - String output = "<DT><B>Dictionary pointer(s): </B><DD>"; - if (dictURLs.containsKey(dictCode)) { - String url = dictURLs.get(dictCode) + "#" + dictRef; - output += "<a href=\"" + url + "\">" + dictRef + - "</a> in the <a href=\"" + dictURLs.get(dictCode) + - "\">" + dictNames.get(dictCode) + "</a> [" + - tagText + "]</DD>\n"; - } else { - output += "Unknown code: " + tagText + "</DD>\n"; - } - return output; - } else { - return "<DT><B>A pointer to a dictionary: </B><DD>Unknown code: " + tagText + "</DD>\n"; - } - } - - public String toString(Tag[] tags) { - if (tags.length == 0) { - return null; - } else { - return toString(tags[0]); - } - } - -} Deleted: trunk/cdk/doc/javadoc/source/CDKModuleTaglet.java =================================================================== --- trunk/cdk/doc/javadoc/source/CDKModuleTaglet.java 2007-02-19 12:13:48 UTC (rev 7972) +++ trunk/cdk/doc/javadoc/source/CDKModuleTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -1,91 +0,0 @@ -/* $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2004 The Chemistry Development Kit (CDK) project - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ -package net.sf.cdk.tools; - -import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.*; -import java.util.Map; - -/** - * Taglet that expands @cdk.module tag into a weblink to the CDK - * webpage. - */ -public class CDKModuleTaglet implements Taglet { - - private static final String NAME = "cdk.module"; - - public String getName() { - return NAME; - } - - public boolean inField() { - return true; - } - - public boolean inConstructor() { - return true; - } - - public boolean inMethod() { - return true; - } - - public boolean inOverview() { - return true; - } - - public boolean inPackage() { - return true; - } - - public boolean inType() { - return true; - } - - public boolean isInlineTag() { - return false; - } - - public static void register(Map tagletMap) { - CDKModuleTaglet tag = new CDKModuleTaglet(); - Taglet t = (Taglet) tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } - - public String toString(Tag tag) { - return "<DT><B>Belongs to CDK module: </B><DD>" - + "<a href=\"http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/modules/module-" - + tag.text() + "/\">" + tag.text() + "</a></DD>\n"; - } - - public String toString(Tag[] tags) { - if (tags.length == 0) { - return null; - } else { - return toString(tags[0]); - } - } - -} Modified: trunk/cdk/javadoc.xml =================================================================== --- trunk/cdk/javadoc.xml 2007-02-19 12:13:48 UTC (rev 7972) +++ trunk/cdk/javadoc.xml 2007-02-19 12:16:03 UTC (rev 7973) @@ -53,8 +53,17 @@ <javadoc destdir="${javadoc.dir}" author="true" version="true" use="true" public="true" - windowtitle="CDK API - version ${TODAY_SVN}"> - <classpath refid="project.class.path" /> + windowtitle="CDK API - version ${TODAY_SVN}" + verbose="true"> + <classpath> + <pathelement location="." /> + <fileset dir="jar"> + <include name="*.jar" /> + </fileset> + <dirset dir="src"> + <include name="net/**/*"/> + </dirset> + </classpath> <tag name="cdk.set" scope="all" description="Belongs to the set:" /> <tag name="cdk.keyword" scope="all" description="Keywords:" /> <tag name="cdk.created" scope="all" description="Created on:" /> @@ -63,12 +72,12 @@ <tag name="cdk.builddepends" scope="all" description="Required library to be able to compile this class:" /> <tag name="cdk.todo" scope="all" description="To do:" /> <tag name="cdk.license" scope="all" description="License:" /> - <taglet name="net.sf.cdk.tools.CDKModuleTaglet" path="doc/javadoc" /> - <taglet name="net.sf.cdk.tools.CDKCiteTaglet" path="doc/javadoc" /> - <taglet name="net.sf.cdk.tools.CDKBugTaglet" path="doc/javadoc" /> - <taglet name="net.sf.cdk.tools.CDKDictRefTaglet" path="doc/javadoc" /> + <taglet name="net.sf.cdk.tools.doclets.CDKCiteTaglet" path="jar/xom-1.1.jar:src" /> + <taglet name="net.sf.cdk.tools.doclets.CDKModuleTaglet" path="jar/xom-1.1.jar:src" /> + <taglet name="net.sf.cdk.tools.doclets.CDKBugTaglet" path="jar/xom-1.1.jar:src" /> + <taglet name="net.sf.cdk.tools.doclets.CDKDictRefTaglet" path="jar/xom-1.1.jar:src" /> <packageset dir="${src}" defaultexcludes="yes"> - <include name="org/openscience/cdk/**" /> + <include name="org/openscience/cdk/ringsearch/**" /> <exclude name="org/openscience/cdk/test/**"/> </packageset> </javadoc> @@ -157,6 +166,8 @@ <target name="compileTaglets.MacOSX" id="compileTaglets.MacOSX" if="isMacOsX"> <javac srcdir="doc/javadoc/source" destdir="doc/javadoc" includes="*Taglet.java" debug="on" optimize="off"/> + <javac srcdir="src" destdir="src" + includes="*Taglet.java" debug="on" optimize="off"/> </target> <target name="compileTaglets.Other" id="compileTaglets.Other" unless="isMacOsX"> @@ -171,6 +182,20 @@ </fileset> </classpath> </javac> + <javac srcdir="src" destdir="src" + includes="net/sf/cdk/tools/**/*.java" debug="on" optimize="off"> + <classpath> + <fileset dir="${java.ext.dirs}"> + <include name="tools.jar" /> + </fileset> + <fileset dir="${java.ext.dirs}/../../../lib"> + <include name="tools.jar" /> + </fileset> + <fileset dir="jar/"> + <include name="xom-1.1.jar" /> + </fileset> + </classpath> + </javac> </target> </project> Added: trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLEntry.java =================================================================== --- trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLEntry.java (rev 0) +++ trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLEntry.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -0,0 +1,106 @@ +/* $Revision: 6707 $ $Author: egonw $ $Date: 2006-07-30 16:38:18 -0400 (Sun, 30 Jul 2006) $ + * + * Copyright (C) 2007 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package net.sf.cdk.tools.bibtex; + +import nu.xom.Element; +import nu.xom.Node; +import nu.xom.Nodes; +import nu.xom.XPathContext; + +/** + * This is a tool that creates HTML for a subset of the entry types + * defined in BibTeXML. It expects the document to be valid according to + * the BibTeXML schema, or will fail horribly. + * + * @author egonw + */ +public class BibTeXMLEntry { + + private Node entry; + private XPathContext context; + + public BibTeXMLEntry(Node entry) { + this.entry = entry; + context = new XPathContext("bibtex", BibTeXMLFile.BIBTEXML_NAMESPACE); + context.addNamespace("b", BibTeXMLFile.BIBTEXML_NAMESPACE); + } + + /** + * The style is undefined and just made to look nice. + */ + public String toHTML() { + // b:article + Nodes results = entry.query("./b:article", context); + for (int i=0; i<results.size(); i++) { + Element article = (Element)results.get(i); + // the obligatory fields + return formatArticle( + getString(article, "author", "?Authors?"), + getString(article, "title", "?Title?"), + getString(article, "journal", "?Journal?"), + getString(article, "year", "19??"), + getString(article, "volume", "?"), + getString(article, "pages", "?-?") + ); + } + // b:article + results = entry.query("./b:misc", context); + for (int i=0; i<results.size(); i++) { + Element misc = (Element)results.get(i); + // the obligatory fields + return formatMisc( + getString(misc, "author", "?Authors?"), + getString(misc, "title", "?Title?") + ); + } + return "Unknown BibTeXML type: " + ((Element)entry).getAttributeValue("id"); + } + + protected String formatArticle(String authors, String title, String journal, String year, String volume, String pages) { + StringBuffer buffer = new StringBuffer(); + buffer.append(authors).append(", <i>").append(title).append("</i>, "); + buffer.append(journal).append(", <b>").append(year).append("</b>, "); + buffer.append(volume).append(":").append(pages); + return buffer.toString(); + } + + protected String formatMisc(String authors, String title) { + StringBuffer buffer = new StringBuffer(); + buffer.append(authors).append(", <i>").append(title).append("</i>"); + return buffer.toString(); + } + + /** + * @param node Parent for the child. + * @param childElement Localname of the child element. + * @param def String to default to if no child element is found. + * @return String value for the child node. + */ + private String getString(Node node, String childElement, String def) { + Nodes result = node.query("./b:" + childElement, context); + return result.size() > 0 ? ((Element)result.get(0)).getValue() : def; + } + +} Added: trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLFile.java =================================================================== --- trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLFile.java (rev 0) +++ trunk/cdk/src/net/sf/cdk/tools/bibtex/BibTeXMLFile.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -0,0 +1,73 @@ +/* $Revision: 6707 $ $Author: egonw $ $Date: 2006-07-30 16:38:18 -0400 (Sun, 30 Jul 2006) $ + * + * Copyright (C) 2007 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package net.sf.cdk.tools.bibtex; + +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import nu.xom.Node; +import nu.xom.Nodes; +import nu.xom.XPathContext; + +/** + * Wrapper for a BibTeXML file. + * + * @author egonw + */ +public class BibTeXMLFile { + + public final static String BIBTEXML_NAMESPACE = "http://bibtexml.sf.net/"; + + private Node root; + private XPathContext context; + + public BibTeXMLFile(Node root) { + this.root = root; + context = new XPathContext("bibtex", BIBTEXML_NAMESPACE); + context.addNamespace("b", BIBTEXML_NAMESPACE); + } + + /** + * Returns an Iterator<BibTeXMLEntry>. + */ + public Iterator getEntries() { + List entries = new ArrayList(); + Nodes results = root.query("//b:entry", context); + for (int i=0; i<results.size(); i++) { + entries.add(new BibTeXMLEntry(results.get(i))); + } + return entries.iterator(); + } + + public BibTeXMLEntry getEntry(String id) { + Nodes results = root.query("//b:entry[./@id='" + id+ "']", context); + if (results.size() > 0) { + return new BibTeXMLEntry(results.get(0)); + } + return null; + } + +} Copied: trunk/cdk/src/net/sf/cdk/tools/doclets/CDKBugTaglet.java (from rev 7968, trunk/cdk/doc/javadoc/source/CDKBugTaglet.java) =================================================================== --- trunk/cdk/src/net/sf/cdk/tools/doclets/CDKBugTaglet.java (rev 0) +++ trunk/cdk/src/net/sf/cdk/tools/doclets/CDKBugTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -0,0 +1,100 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + */ +package net.sf.cdk.tools.doclets; + +import com.sun.tools.doclets.Taglet; +import com.sun.javadoc.*; +import java.util.Map; + +/** + * Taglet that expands @cdk.bug tag into a weblink to CDK's + * SourceForge bug track system. It's typically used as: + * <pre> + * @cdk.bug 1095690 + * </pre> + */ +public class CDKBugTaglet implements Taglet { + + private static final String NAME = "cdk.bug"; + + public String getName() { + return NAME; + } + + public boolean inField() { + return false; + } + + public boolean inConstructor() { + return false; + } + + public boolean inMethod() { + return false; + } + + public boolean inOverview() { + return false; + } + + public boolean inPackage() { + return false; + } + + public boolean inType() { + return true; + } + + public boolean isInlineTag() { + return false; + } + + public static void register(Map tagletMap) { + CDKBugTaglet tag = new CDKBugTaglet(); + Taglet t = (Taglet) tagletMap.get(tag.getName()); + if (t != null) { + tagletMap.remove(tag.getName()); + } + tagletMap.put(tag.getName(), tag); + } + + public String toString(Tag tag) { + return "<DT><B>This class is affected by these bug(s): </B><DD>" + + expand(tag) + "</DD>\n"; + } + + public String toString(Tag[] tags) { + if (tags.length == 0) { + return null; + } else { + StringBuffer list = new StringBuffer(); + list.append("<DT><B>This class is affected by these bug(s): </B><DD>"); + for (int i=0; i<tags.length; i++) { + list.append(expand(tags[i])).append(" "); + } + list.append("</DD>\n"); + return list.toString(); + } + } + + private String expand(Tag tag) { + return "<a href=\"http://sourceforge.net/tracker/index.php?func=detail&group_id=20024&atid=120024&aid=" + + tag.text() + "\">" + tag.text() + "</a>"; + } +} Added: trunk/cdk/src/net/sf/cdk/tools/doclets/CDKCiteTaglet.java =================================================================== --- trunk/cdk/src/net/sf/cdk/tools/doclets/CDKCiteTaglet.java (rev 0) +++ trunk/cdk/src/net/sf/cdk/tools/doclets/CDKCiteTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -0,0 +1,156 @@ +/* $Revision: 7327 $ $Author: egonw $ $Date: 2006-11-20 20:22:51 +0100 (Mon, 20 Nov 2006) $ + * + * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + */ +package net.sf.cdk.tools.doclets; + +import java.io.File; +import java.util.Map; +import java.util.StringTokenizer; + +import net.sf.cdk.tools.bibtex.BibTeXMLEntry; +import net.sf.cdk.tools.bibtex.BibTeXMLFile; +import nu.xom.Builder; +import nu.xom.Document; + +import com.sun.javadoc.Tag; +import com.sun.tools.doclets.Taglet; + +/** + * Taglet that expands inline cdk.cite tags into a weblink to the CDK + * bibliography webpage. Like all inline tags it's used in the JavaDoc + * text as: + * <pre> + * This class does nothing {@cdk.cite NULL}. + * </pre> + * For this code a reference is created like this: + * <pre> + * <a href="http://cdk.sf.net/biblio.html#NULL">NULL</a> + * </pre> + * + * <p>Citations can be singular, like <code>{@cdk.cite BLA}</code>, + * and multiple, like <code>{@cdk.cite BLA,BLA2,FOO}</code>. + */ +public class CDKCiteTaglet implements Taglet { + + private static final String NAME = "cdk.cite"; + + private static BibTeXMLFile bibtex = null; + + static { + try { + Builder parser = new Builder(); + Document doc = parser.build(new File("doc/refs/cheminf.bibx")); + bibtex = new BibTeXMLFile(doc.getRootElement()); + } catch (Exception exc) { + System.out.println("Horrible problem: " + exc.getMessage()); + exc.printStackTrace(); + } + } + + public String getName() { + return NAME; + } + + public boolean inField() { + return true; + } + + public boolean inConstructor() { + return true; + } + + public boolean inMethod() { + return true; + } + + public boolean inOverview() { + return true; + } + + public boolean inPackage() { + return true; + } + + public boolean inType() { + return true; + } + + public boolean isInlineTag() { + return true; + } + + public static void register(Map tagletMap) { + CDKCiteTaglet tag = new CDKCiteTaglet(); + Taglet t = (Taglet) tagletMap.get(tag.getName()); + if (t != null) { + tagletMap.remove(tag.getName()); + } + tagletMap.put(tag.getName(), tag); + } + + public String toString(Tag tag) { + return "[" + expandCitation(tag.text()) + "]"; + } + + public String toString(Tag[] tags) { + String result = null; + if (tags.length > 0) { + result = "["; + for (int i=0; i<tags.length; i++) { + result += expandCitation(tags[i].text()); + if ((i+1)<tags.length) result += ", "; + } + result += "]"; + } + return result; + } + + /** + * Expands a citation into HTML code. + */ + private String expandCitation(String citation) { + String result = ""; + final String separator = ","; + result += "<!-- indexOf" + citation.indexOf(separator) + " -->"; + if (citation.indexOf(separator) != -1) { + StringTokenizer tokenizer = new StringTokenizer(citation, separator); + while (tokenizer.hasMoreTokens()) { + String token = tokenizer.nextToken().trim(); + BibTeXMLEntry entry = bibtex.getEntry(token); + if (entry != null) { + result += entry.toHTML(); + } else { + result += token + " (not found in db)"; + } + if (tokenizer.hasMoreTokens()) { + result += ", "; + } + } + } else { + citation = citation.trim(); + BibTeXMLEntry entry = bibtex.getEntry(citation); + if (entry != null) { + result += entry.toHTML(); + } else { + result += citation + " (not found in db)"; + } + } + return result; + } + +} Copied: trunk/cdk/src/net/sf/cdk/tools/doclets/CDKDictRefTaglet.java (from rev 7968, trunk/cdk/doc/javadoc/source/CDKDictRefTaglet.java) =================================================================== --- trunk/cdk/src/net/sf/cdk/tools/doclets/CDKDictRefTaglet.java (rev 0) +++ trunk/cdk/src/net/sf/cdk/tools/doclets/CDKDictRefTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -0,0 +1,134 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + */ +package net.sf.cdk.tools.doclets; + +import com.sun.tools.doclets.Taglet; +import com.sun.javadoc.*; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Hashtable; + +/** + * Taglet that expands inline cdk.dictref tags into a weblink to the appropriate + * dictionary. For example. + * <pre> + * @cdk.dictref blue-obelisk:graphPartitioning + * </pre> + * + * <p>The known dictionaries are: + * <ul> + * <li>blue-obelisk: <a href="http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml">Blue Obelisk Chemoinformatics Dictionary</a> + * <li>bodf: <a href="http://qsar.sourceforge.net/ontologies/data-features/index.xhtml">Blue Obelisk Data Features Dictionary</a> + * <li>qsar-descriptors: <a href="http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml">QSAR.sf.net Descriptors Dictionary</a> + * </ul> + */ +public class CDKDictRefTaglet implements Taglet { + + private static final String NAME = "cdk.dictref"; + + private static final Map dictURLs; + private static final Map dictNames; + + static { + dictURLs = new Hashtable(5); + dictNames = new Hashtable(5); + + dictURLs.put("bodf", "http://qsar.sourceforge.net/ontologies/data-features/index.xhtml"); + dictNames.put("bodf", "Blue Obelisk Data Features Dictionary"); + + dictURLs.put("blue-obelisk", "http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml"); + dictNames.put("blue-obelisk", "Blue Obelisk Chemoinformatics Dictionary"); + + dictURLs.put("qsar-descriptors", "http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml"); + dictNames.put("qsar-descriptors", "QSAR.sf.net Descriptors Dictionary"); + } + + public String getName() { + return NAME; + } + + public boolean inField() { + return true; + } + + public boolean inConstructor() { + return true; + } + + public boolean inMethod() { + return true; + } + + public boolean inOverview() { + return true; + } + + public boolean inPackage() { + return true; + } + + public boolean inType() { + return true; + } + + public boolean isInlineTag() { + return false; + } + + public static void register(Map tagletMap) { + CDKDictRefTaglet tag = new CDKDictRefTaglet(); + Taglet t = (Taglet) tagletMap.get(tag.getName()); + if (t != null) { + tagletMap.remove(tag.getName()); + } + tagletMap.put(tag.getName(), tag); + } + + public String toString(Tag tag) { + String tagText = tag.text(); + String separator = ":"; + if (tagText.indexOf(separator) != -1) { + StringTokenizer tokenizer = new StringTokenizer(tagText, separator); + String dictCode = tokenizer.nextToken(); + String dictRef = tokenizer.nextToken(); + String output = "<DT><B>Dictionary pointer(s): </B><DD>"; + if (dictURLs.containsKey(dictCode)) { + String url = dictURLs.get(dictCode) + "#" + dictRef; + output += "<a href=\"" + url + "\">" + dictRef + + "</a> in the <a href=\"" + dictURLs.get(dictCode) + + "\">" + dictNames.get(dictCode) + "</a> [" + + tagText + "]</DD>\n"; + } else { + output += "Unknown code: " + tagText + "</DD>\n"; + } + return output; + } else { + return "<DT><B>A pointer to a dictionary: </B><DD>Unknown code: " + tagText + "</DD>\n"; + } + } + + public String toString(Tag[] tags) { + if (tags.length == 0) { + return null; + } else { + return toString(tags[0]); + } + } + +} Copied: trunk/cdk/src/net/sf/cdk/tools/doclets/CDKModuleTaglet.java (from rev 7968, trunk/cdk/doc/javadoc/source/CDKModuleTaglet.java) =================================================================== --- trunk/cdk/src/net/sf/cdk/tools/doclets/CDKModuleTaglet.java (rev 0) +++ trunk/cdk/src/net/sf/cdk/tools/doclets/CDKModuleTaglet.java 2007-02-19 12:16:03 UTC (rev 7973) @@ -0,0 +1,88 @@ +/* $Revision$ $Author$ $Date$ + * + * Copyright (C) 2004 Egon Willighagen <eg...@us...> + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + */ +package net.sf.cdk.tools.doclets; + +import com.sun.tools.doclets.Taglet; +import com.sun.javadoc.*; +import java.util.Map; + +/** + * Taglet that expands @cdk.module tag into a weblink to the CDK + * webpage. + */ +public class CDKModuleTaglet implements Taglet { + + private static final String NAME = "cdk.module"; + + public String getName() { + return NAME; + } + + public boolean inField() { + return true; + } + + public boolean inConstructor() { + return true; + } + + public boolean inMethod() { + return true; + } + + public boolean inOverview() { + return true; + } + + public boolean inPackage() { + return true; + } + + public boolean inType() { + return true; + } + + public boolean isInlineTag() { + return false; + } + + public static void register(Map tagletMap) { + CDKModuleTaglet tag = new CDKModuleTaglet(); + Taglet t = (Taglet) tagletMap.get(tag.getName()); + if (t != null) { + tagletMap.remove(tag.getName()); + } + tagletMap.put(tag.getName(), tag); + } + + public String toString(Tag tag) { + return "<DT><B>Belongs to CDK module: </B><DD>" + + "<a href=\"http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/modules/module-" + + tag.text() + "/\">" + tag.text() + "</a></DD>\n"; + } + + public String toString(Tag[] tags) { + if (tags.length == 0) { + return null; + } else { + return toString(tags[0]); + } + } + +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <se...@us...> - 2007-02-22 16:01:59
|
Revision: 7988 http://svn.sourceforge.net/cdk/?rev=7988&view=rev Author: sea36 Date: 2007-02-22 08:01:40 -0800 (Thu, 22 Feb 2007) Log Message: ----------- Updated JNI InChI library to v0.4 Modified Paths: -------------- trunk/cdk/.classpath trunk/cdk/src/META-INF/inchi.libdepends trunk/cdk/src/META-INF/jchempaint.libdepends trunk/cdk/src/META-INF/test-inchi.libdepends Added Paths: ----------- trunk/cdk/jar/jniinchi-0.4.jar Removed Paths: ------------- trunk/cdk/jar/jniInChI-0.1.1.jar Modified: trunk/cdk/.classpath =================================================================== --- trunk/cdk/.classpath 2007-02-21 15:28:53 UTC (rev 7987) +++ trunk/cdk/.classpath 2007-02-22 16:01:40 UTC (rev 7988) @@ -1,46 +1,46 @@ -<?xml version="1.0" encoding="UTF-8"?> -<classpath> - <classpathentry excluding="org/openscience/cdk/libio/joelib/Convertor.java|org/openscience/cdk/test/libio/joelib/JOELibIOTest.java" kind="src" path="src"/> - <classpathentry kind="src" path="perf"/> - <classpathentry kind="lib" path="develjar/ant_doxygen.jar"/> - <classpathentry kind="lib" path="develjar/dbdoclet.jar"/> - <classpathentry kind="lib" path="develjar/junit.jar"/> - <classpathentry kind="lib" path="doc/jar/jabref.jar"/> - <classpathentry kind="lib" path="jar/antlr.jar"/> - <classpathentry kind="lib" path="jar/batik-awt-util.jar"/> - <classpathentry kind="lib" path="jar/batik-dom.jar"/> - <classpathentry kind="lib" path="jar/batik-svggen.jar"/> - <classpathentry kind="lib" path="jar/batik-util.jar"/> - <classpathentry kind="lib" path="jar/batik-xml.jar"/> - <classpathentry kind="lib" path="jar/baysmith-io.jar"/> - <classpathentry kind="lib" path="jar/bcel-5.1.jar"/> - <classpathentry kind="lib" path="jar/biojava-1.4.jar"/> - <classpathentry kind="lib" path="jar/commons-cli-1.0.jar"/> - <classpathentry kind="lib" path="jar/dadml.jar"/> - <classpathentry kind="lib" path="jar/jai_codec.jar"/> - <classpathentry kind="lib" path="jar/jai_core.jar"/> - <classpathentry kind="lib" path="jar/Jama-1.0.1.jar"/> - <classpathentry kind="lib" path="jar/javacc.jar"/> - <classpathentry kind="lib" path="jar/jfontchooser.jar"/> - <classpathentry kind="lib" path="jar/jgrapht-0.6.0.jar"/> - <classpathentry kind="lib" path="jar/jniInChI-0.1.1.jar"/> - <classpathentry kind="lib" path="jar/JRI.jar"/> - <classpathentry kind="lib" path="jar/jumbo52.jar"/> - <classpathentry kind="lib" path="jar/log4j.jar"/> - <classpathentry kind="lib" path="jar/mysql-2.0.4.jar"/> - <classpathentry kind="lib" path="jar/postgresql7.0-1.2.jar"/> - <classpathentry kind="lib" path="jar/sjava-0.68.jar"/> - <classpathentry kind="lib" path="jar/vecmath1.2-1.14.jar"/> - <classpathentry kind="lib" path="jar/weka.jar"/> - <classpathentry kind="lib" path="jar/xindice.jar"/> - <classpathentry kind="lib" path="jar/xml-apis.jar"/> - <classpathentry kind="lib" path="jar/xmldb.jar"/> - <classpathentry kind="lib" path="jar/xom-1.1.jar"/> - <classpathentry kind="lib" path="pluginjar/aminoacidtemplates.jar"/> - <classpathentry kind="lib" path="pluginjar/dadmlbrowser.jar"/> - <classpathentry kind="lib" path="pluginjar/dirbrowser.jar"/> - <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> - <classpathentry kind="lib" path="develjar/com-sun-javadoc.jar"/> - <classpathentry kind="lib" path="develjar/com-sun-tools-doclets-Taglet.jar"/> - <classpathentry kind="output" path="bin"/> -</classpath> +<?xml version="1.0" encoding="UTF-8"?> +<classpath> + <classpathentry excluding="org/openscience/cdk/libio/joelib/Convertor.java|org/openscience/cdk/test/libio/joelib/JOELibIOTest.java" kind="src" path="src"/> + <classpathentry kind="src" path="perf"/> + <classpathentry kind="lib" path="develjar/ant_doxygen.jar"/> + <classpathentry kind="lib" path="develjar/dbdoclet.jar"/> + <classpathentry kind="lib" path="develjar/junit.jar"/> + <classpathentry kind="lib" path="doc/jar/jabref.jar"/> + <classpathentry kind="lib" path="jar/antlr.jar"/> + <classpathentry kind="lib" path="jar/batik-awt-util.jar"/> + <classpathentry kind="lib" path="jar/batik-dom.jar"/> + <classpathentry kind="lib" path="jar/batik-svggen.jar"/> + <classpathentry kind="lib" path="jar/batik-util.jar"/> + <classpathentry kind="lib" path="jar/batik-xml.jar"/> + <classpathentry kind="lib" path="jar/baysmith-io.jar"/> + <classpathentry kind="lib" path="jar/bcel-5.1.jar"/> + <classpathentry kind="lib" path="jar/biojava-1.4.jar"/> + <classpathentry kind="lib" path="jar/commons-cli-1.0.jar"/> + <classpathentry kind="lib" path="jar/dadml.jar"/> + <classpathentry kind="lib" path="jar/jai_codec.jar"/> + <classpathentry kind="lib" path="jar/jai_core.jar"/> + <classpathentry kind="lib" path="jar/Jama-1.0.1.jar"/> + <classpathentry kind="lib" path="jar/javacc.jar"/> + <classpathentry kind="lib" path="jar/jfontchooser.jar"/> + <classpathentry kind="lib" path="jar/jgrapht-0.6.0.jar"/> + <classpathentry kind="lib" path="jar/jniinchi-0.4.jar"/> + <classpathentry kind="lib" path="jar/JRI.jar"/> + <classpathentry kind="lib" path="jar/jumbo52.jar"/> + <classpathentry kind="lib" path="jar/log4j.jar"/> + <classpathentry kind="lib" path="jar/mysql-2.0.4.jar"/> + <classpathentry kind="lib" path="jar/postgresql7.0-1.2.jar"/> + <classpathentry kind="lib" path="jar/sjava-0.68.jar"/> + <classpathentry kind="lib" path="jar/vecmath1.2-1.14.jar"/> + <classpathentry kind="lib" path="jar/weka.jar"/> + <classpathentry kind="lib" path="jar/xindice.jar"/> + <classpathentry kind="lib" path="jar/xml-apis.jar"/> + <classpathentry kind="lib" path="jar/xmldb.jar"/> + <classpathentry kind="lib" path="jar/xom-1.1.jar"/> + <classpathentry kind="lib" path="pluginjar/aminoacidtemplates.jar"/> + <classpathentry kind="lib" path="pluginjar/dadmlbrowser.jar"/> + <classpathentry kind="lib" path="pluginjar/dirbrowser.jar"/> + <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> + <classpathentry kind="lib" path="develjar/com-sun-javadoc.jar"/> + <classpathentry kind="lib" path="develjar/com-sun-tools-doclets-Taglet.jar"/> + <classpathentry kind="output" path="bin"/> +</classpath> Deleted: trunk/cdk/jar/jniInChI-0.1.1.jar =================================================================== (Binary files differ) Added: trunk/cdk/jar/jniinchi-0.4.jar =================================================================== (Binary files differ) Property changes on: trunk/cdk/jar/jniinchi-0.4.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Modified: trunk/cdk/src/META-INF/inchi.libdepends =================================================================== --- trunk/cdk/src/META-INF/inchi.libdepends 2007-02-21 15:28:53 UTC (rev 7987) +++ trunk/cdk/src/META-INF/inchi.libdepends 2007-02-22 16:01:40 UTC (rev 7988) @@ -1,4 +1,4 @@ vecmath1.2-1.14.jar xom-1.1.jar -jniInChI-0.1.1.jar +jniInChI-0.4.jar jumbo52.jar Modified: trunk/cdk/src/META-INF/jchempaint.libdepends =================================================================== --- trunk/cdk/src/META-INF/jchempaint.libdepends 2007-02-21 15:28:53 UTC (rev 7987) +++ trunk/cdk/src/META-INF/jchempaint.libdepends 2007-02-22 16:01:40 UTC (rev 7988) @@ -5,4 +5,4 @@ jh.jar xom-1.1.jar jumbo52.jar -jniInChI-0.1.1.jar +jniInChI-0.4.jar Modified: trunk/cdk/src/META-INF/test-inchi.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-inchi.libdepends 2007-02-21 15:28:53 UTC (rev 7987) +++ trunk/cdk/src/META-INF/test-inchi.libdepends 2007-02-22 16:01:40 UTC (rev 7988) @@ -1,5 +1,5 @@ vecmath1.2-1.14.jar xom-1.1.jar -jniInChI-0.1.1.jar +jniInChI-0.4.jar jumbo52.jar log4j.jar This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-04-10 08:14:06
|
Revision: 8179 http://svn.sourceforge.net/cdk/?rev=8179&view=rev Author: egonw Date: 2007-04-10 01:14:02 -0700 (Tue, 10 Apr 2007) Log Message: ----------- Created a 'smarts' module Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java Added Paths: ----------- trunk/cdk/src/META-INF/smarts.cdkdepends trunk/cdk/src/META-INF/smarts.libdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2007-04-09 00:10:31 UTC (rev 8178) +++ trunk/cdk/build.xml 2007-04-10 08:14:02 UTC (rev 8179) @@ -430,6 +430,7 @@ <antcall target="compile-module"><param name="module" value="builder3d"/></antcall> <antcall target="compile-module"><param name="module" value="builder3dtools"/></antcall> <antcall target="compile-module"><param name="module" value="svg"/></antcall> + <antcall target="compile-module"><param name="module" value="smarts"/></antcall> <antcall target="compile-module"><param name="module" value="experimental"/></antcall> <antcall target="compile-module"><param name="module" value="applications"/></antcall> <antcall target="compile-module"><param name="module" value="inchi"/></antcall> Added: trunk/cdk/src/META-INF/smarts.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/smarts.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/smarts.cdkdepends 2007-04-10 08:14:02 UTC (rev 8179) @@ -0,0 +1,8 @@ +cdk-data.jar +cdk-nonotify.jar +cdk-core.jar +cdk-interfaces.jar +cdk-io.jar +cdk-render.jar +cdk-standard.jar +cdk-valencycheck.jar Added: trunk/cdk/src/META-INF/smarts.libdepends =================================================================== --- trunk/cdk/src/META-INF/smarts.libdepends (rev 0) +++ trunk/cdk/src/META-INF/smarts.libdepends 2007-04-10 08:14:02 UTC (rev 8179) @@ -0,0 +1 @@ +vecmath1.2-1.14.jar Modified: trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj =================================================================== --- trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj 2007-04-09 00:10:31 UTC (rev 8178) +++ trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj 2007-04-10 08:14:02 UTC (rev 8179) @@ -8,6 +8,7 @@ /* $Revision: 7636 $ $Author: egonw $ $Date: 2007-01-04 12:46:10 -0500 (Thu, 04 Jan 2007) $ * * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> + * Copyright (C) 2007 Sushil Ronghe <ron...@gm...> * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public @@ -75,7 +76,7 @@ * @cdk.created 2004-03-29 * * @cdk.require ant1.6 - * @cdk.module experimental + * @cdk.module smarts * * @cdk.keyword SMARTS * @cdk.keyword substructure search Modified: trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java 2007-04-09 00:10:31 UTC (rev 8178) +++ trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java 2007-04-10 08:14:02 UTC (rev 8179) @@ -1,27 +1,23 @@ -/* $RCSfile$ - * $Author: rajarshi $ - * $Date: 2007-04-08 14:46:29 -0500 (Thu, 01 Feb 2007) $ - * $Revision: 7844 $ +/* $Revision: 7844 $ $Author: rajarshi $ $Date: 2007-04-08 14:46:29 -0500 (Thu, 01 Feb 2007) $ * - * Copyright (C) 2004-2007 Rajarshi Guha <raj...@us...> + * Copyright (C) 2007 Rajarshi Guha <raj...@us...> * - * Contact: cdk...@li... + * Contact: cdk...@li... * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */ - package org.openscience.cdk.smiles.smarts; import org.openscience.cdk.CDKConstants; @@ -61,9 +57,9 @@ * } * </pre> * - * @author Rajarshi Guha + * @author Rajarshi Guha * @cdk.created 2007-04-08 - * @cdk.module experimental + * @cdk.module smarts * @cdk.keyword SMARTS * @cdk.keyword substructure search */ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <raj...@us...> - 2007-04-10 18:00:44
|
Revision: 8183 http://svn.sourceforge.net/cdk/?rev=8183&view=rev Author: rajarshi Date: 2007-04-10 11:00:42 -0700 (Tue, 10 Apr 2007) Log Message: ----------- Updated PMD scripts to work with the new smarts module Modified Paths: -------------- trunk/cdk/pmd-unused.xml trunk/cdk/pmd.xml Modified: trunk/cdk/pmd-unused.xml =================================================================== --- trunk/cdk/pmd-unused.xml 2007-04-10 17:00:51 UTC (rev 8182) +++ trunk/cdk/pmd-unused.xml 2007-04-10 18:00:42 UTC (rev 8183) @@ -42,6 +42,7 @@ <antcall target="test-module"><param name="module" value="libio-biojava"/></antcall> <antcall target="test-module"><param name="module" value="builder3d"/></antcall> <antcall target="test-module"><param name="module" value="smiles"/></antcall> + <antcall target="test-module"><param name="module" value="smarts"/></antcall> <antcall target="test-module"><param name="module" value="forcefield"/></antcall> <antcall target="test-module"><param name="module" value="qsar"/></antcall> <antcall target="test-module"><param name="module" value="experimental"/></antcall> Modified: trunk/cdk/pmd.xml =================================================================== --- trunk/cdk/pmd.xml 2007-04-10 17:00:51 UTC (rev 8182) +++ trunk/cdk/pmd.xml 2007-04-10 18:00:42 UTC (rev 8183) @@ -42,6 +42,7 @@ <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-biojava"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="builder3d"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smiles"/></antcall> + <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smarts"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="forcefield"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsar"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="experimental"/></antcall> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-04-11 11:33:45
|
Revision: 8185 http://svn.sourceforge.net/cdk/?rev=8185&view=rev Author: egonw Date: 2007-04-11 04:33:42 -0700 (Wed, 11 Apr 2007) Log Message: ----------- Forgot to commit the additions for the smarts module Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/javadoc.xml Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2007-04-10 18:02:10 UTC (rev 8184) +++ trunk/cdk/build.xml 2007-04-11 11:33:42 UTC (rev 8185) @@ -462,6 +462,7 @@ <antcall target="compile-module"><param name="module" value="test-osjvmts"/></antcall> <antcall target="compile-module"><param name="module" value="test-inchi"/></antcall> <antcall target="compile-module"><param name="module" value="test-libiomd"/></antcall> + <antcall target="compile-module"><param name="module" value="test-smarts"/></antcall> </target> <target id="dist-large" name="dist-large" depends="dist-all" Modified: trunk/cdk/javadoc.xml =================================================================== --- trunk/cdk/javadoc.xml 2007-04-10 18:02:10 UTC (rev 8184) +++ trunk/cdk/javadoc.xml 2007-04-11 11:33:42 UTC (rev 8185) @@ -132,6 +132,7 @@ <antcall target="doccheck-module"><param name="module" value="qsar"/></antcall> <antcall target="doccheck-module"><param name="module" value="experimental"/></antcall> <antcall target="doccheck-module"><param name="module" value="svg"/></antcall> + <antcall target="doccheck-module"><param name="module" value="smarts"/></antcall> <antcall target="doccheck-module"><param name="module" value="structgen"/></antcall> <antcall target="doccheck-module"><param name="module" value="valencycheck"/></antcall> </target> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-05-31 10:26:44
|
Revision: 8345 http://svn.sourceforge.net/cdk/?rev=8345&view=rev Author: egonw Date: 2007-05-31 03:26:17 -0700 (Thu, 31 May 2007) Log Message: ----------- Java5 List<IAtom> like constructs in the interfaces. trunk/cdk/ now officially requires Java5. Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainer.java trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainerSet.java trunk/cdk/src/org/openscience/cdk/interfaces/IBioPolymer.java trunk/cdk/src/org/openscience/cdk/interfaces/IBond.java trunk/cdk/src/org/openscience/cdk/interfaces/IChemFile.java trunk/cdk/src/org/openscience/cdk/interfaces/IChemSequence.java trunk/cdk/src/org/openscience/cdk/interfaces/IMapping.java trunk/cdk/src/org/openscience/cdk/interfaces/IMoleculeSet.java trunk/cdk/src/org/openscience/cdk/interfaces/IPDBPolymer.java trunk/cdk/src/org/openscience/cdk/interfaces/IPolymer.java trunk/cdk/src/org/openscience/cdk/interfaces/IReaction.java trunk/cdk/src/org/openscience/cdk/interfaces/IReactionSet.java trunk/cdk/src/org/openscience/cdk/interfaces/IRingSet.java trunk/cdk/src/org/openscience/cdk/interfaces/IStrand.java Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/build.xml 2007-05-31 10:26:17 UTC (rev 8345) @@ -196,7 +196,7 @@ </or> </not> </condition> - + <fail if="isNotJava15+" message="This CDK release requires Java5 or better."/> </target> @@ -307,7 +307,7 @@ <!-- ok, now that we have a copy, compile this copy --> <javac srcdir="${build.src}" destdir="${build}" optimize="${optimization}" - debug="${debug}" deprecation="${deprecation}" target="1.3" source="1.3"> + debug="${debug}" deprecation="${deprecation}" target="1.5" source="1.5"> <classpath> <fileset dir="${lib}" > <exclude name="**/*" unless="module.libdepends.present" /> Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainer.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainer.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainer.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -127,35 +127,35 @@ * *@return An Iterator with the atoms in this container */ - public Iterator atoms(); + public Iterator<IAtom> atoms(); /** * Returns an Iterator for looping over all bonds in this container. * *@return An Iterator with the bonds in this container */ - public Iterator bonds(); + public Iterator<IBond> bonds(); /** * Returns an Iterator for looping over all lone pairs in this container. * *@return An Iterator with the lone pairs in this container */ - public Iterator lonePairs(); + public Iterator<ILonePair> lonePairs(); /** * Returns an Iterator for looping over all single electrons in this container. * *@return An Iterator with the single electrons in this container */ - public Iterator singleElectrons(); + public Iterator<ISingleElectron> singleElectrons(); /** * Returns an Iterator for looping over all electron containers in this container. * *@return An Iterator with the electron containers in this container */ - public Iterator electronContainers(); + public Iterator<IElectronContainer> electronContainers(); /** * Returns the atom at position 0 in the container. @@ -285,7 +285,7 @@ *@param atom The atom the bond partners are searched of. *@return The ArrayList with the connected atoms */ - public List getConnectedAtomsList(IAtom atom); + public List<IAtom> getConnectedAtomsList(IAtom atom); /** * Returns an ArrayList of all Bonds connected to the given atom. @@ -293,7 +293,7 @@ *@param atom The atom the connected bonds are searched of *@return The ArrayList with connected atoms */ - public List getConnectedBondsList(IAtom atom); + public List<IBond> getConnectedBondsList(IAtom atom); /** * Returns the array of lone pairs connected to an atom. @@ -301,7 +301,7 @@ *@param atom The atom for which to get lone pairs *@return The array of LonePairs of this AtomContainer */ - public List getConnectedLonePairsList(IAtom atom); + public List<ILonePair> getConnectedLonePairsList(IAtom atom); /** * Returns an array of all SingleElectron connected to the given atom. @@ -309,7 +309,7 @@ *@param atom The atom on which the single electron is located *@return The array of SingleElectron of this AtomContainer */ - public List getConnectedSingleElectronsList(IAtom atom); + public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom); /** * Returns an ArrayList of all electronContainers connected to the given atom. @@ -317,7 +317,7 @@ *@param atom The atom the connected electronContainers are searched of *@return The ArrayList with the connected atoms */ - public List getConnectedElectronContainersList(IAtom atom); + public List<IElectronContainer> getConnectedElectronContainersList(IAtom atom); /** Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainerSet.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainerSet.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IAtomContainerSet.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -24,6 +24,8 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + /** * A set of AtomContainers. * @@ -126,7 +128,7 @@ * * @return A new Iterator for this AtomContainerSet. */ - public java.util.Iterator atomContainers(); + public Iterator<IAtomContainer> atomContainers(); /** * Returns the AtomContainer at position <code>number</code> in the Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IBioPolymer.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IBioPolymer.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IBioPolymer.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -97,7 +97,7 @@ * * @return a <code>Collection</code> of all the monomer names. */ - public Collection getMonomerNames(); + public Collection<String> getMonomerNames(); /** * Return the number of strands present in the BioPolymer. @@ -120,7 +120,7 @@ * * @return a <code>Collection</code> of all the strand names. */ - public Collection getStrandNames(); + public Collection<String> getStrandNames(); /** * Removes a particular strand, specified by its name. @@ -134,6 +134,6 @@ * * @return hashtable containing the strands in the Polymer */ - public Map getStrands(); + public Map<String,IStrand> getStrands(); } Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IBond.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IBond.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IBond.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -23,6 +23,8 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + import javax.vecmath.Point2d; import javax.vecmath.Point3d; @@ -46,7 +48,7 @@ *@return An Iterator to atoms participating in this bond *@see #setAtoms */ - public java.util.Iterator atoms(); + public Iterator<IAtom> atoms(); /** * Sets the array of atoms making up this bond. Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IChemFile.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IChemFile.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IChemFile.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -23,6 +23,8 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + /** * A Object containing a number of ChemSequences. This is supposed to be the * top level container, which can contain all the concepts stored in a chemical @@ -55,7 +57,7 @@ *@return The Iterator to ChemSequences of this container *@see #addChemSequence */ - public java.util.Iterator chemSequences(); + public Iterator<IChemSequence> chemSequences(); /** * Returns the ChemSequence at position <code>number</code> in the container. Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IChemSequence.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IChemSequence.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IChemSequence.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -23,6 +23,8 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + /** * A sequence of ChemModels, which can, for example, be used to * store the course of a reaction. Each state of the reaction would be @@ -56,7 +58,7 @@ * @return The Iterator to ChemModels in this container * @see #addChemModel */ - public java.util.Iterator chemModels(); + public Iterator<IChemModel> chemModels(); /** * Returns the ChemModel at position <code>number</code> in the Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IMapping.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IMapping.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IMapping.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -23,6 +23,8 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + /** * Represents a set of Molecules. * @@ -37,7 +39,7 @@ * * @return An Iterator to two IChemObjects that define the mapping */ - public java.util.Iterator relatedChemObjects(); + public Iterator<IChemObject> relatedChemObjects(); /** * Retrieve the first or second of the related IChemObjects. Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IMoleculeSet.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IMoleculeSet.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IMoleculeSet.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -23,6 +23,8 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + /** * Represents a set of Molecules. * @@ -61,7 +63,7 @@ * @return The array of Molecules of this container * @see #setMolecules(IMolecule[]) */ - public java.util.Iterator molecules(); + public Iterator<IMolecule> molecules(); /** * Returns the Molecule at position <code>number</code> in the Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IPDBPolymer.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IPDBPolymer.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IPDBPolymer.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -73,6 +73,6 @@ * * @return Collection containing the PDBStructure in the PDBPolymer */ - public Collection getStructures(); + public Collection<IPDBStructure> getStructures(); } Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IPolymer.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IPolymer.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IPolymer.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -79,7 +79,7 @@ * * @return a <code>Collection</code> of all the monomer names. */ - public Collection getMonomerNames(); + public Collection<String> getMonomerNames(); /** * Removes a particular monomer, specified by its name. Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IReaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IReaction.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IReaction.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -28,6 +28,8 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + /** * Represents the idea of a chemical reaction. The reaction consists of * a set of reactants and a set of products. @@ -115,7 +117,7 @@ * @return An Iterator to the Mappings. * @see #addMapping */ - public java.util.Iterator mappings(); + public Iterator<IMapping> mappings(); /** * Adds a reactant to this reaction. Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IReactionSet.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IReactionSet.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IReactionSet.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -23,7 +23,9 @@ */ package org.openscience.cdk.interfaces; +import java.util.Iterator; + /** * A set of reactions, for example those taking part in a reaction. * @@ -61,7 +63,7 @@ * * @return The Iterator over Reactions of this container */ - public java.util.Iterator reactions(); + public Iterator<IReaction> reactions(); /** * Returns the number of Reactions in this Container. Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IRingSet.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IRingSet.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IRingSet.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -40,7 +40,7 @@ * @param bond The bond to be checked * @return A vector of all rings that this bond is part of */ - public List getRings(IBond bond); + public List<IRing> getRings(IBond bond); /** * Returns a vector of all rings that this atom is part of. @@ -57,7 +57,7 @@ * @param ring A ring with which all return rings must share one or more atoms * @return All the rings that share one or more atoms with a given ring. */ - public List getConnectedRings(IRing ring); + public List<IRing> getConnectedRings(IRing ring); /** * Adds all rings of another RingSet if they are not allready part of this ring set. Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IStrand.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IStrand.java 2007-05-31 08:43:49 UTC (rev 8344) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IStrand.java 2007-05-31 10:26:17 UTC (rev 8345) @@ -109,7 +109,7 @@ * * @return a <code>Collection</code> of all the monomer names. */ - public Collection getMonomerNames(); + public Collection<String> getMonomerNames(); /** * Removes a particular monomer, specified by its name. @@ -123,5 +123,5 @@ * * @return hashtable containing the monomers in the strand. */ - public Hashtable getMonomers(); + public Hashtable<String,IMonomer> getMonomers(); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2007-06-04 15:03:08
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Revision: 8356 http://svn.sourceforge.net/cdk/?rev=8356&view=rev Author: egonw Date: 2007-06-04 08:03:02 -0700 (Mon, 04 Jun 2007) Log Message: ----------- Installed the Java4 dependent JUnit 4.3.1 Modified Paths: -------------- trunk/cdk/src/META-INF/test-builder3d.devellibdepends trunk/cdk/src/META-INF/test-core.devellibdepends trunk/cdk/src/META-INF/test-data.devellibdepends trunk/cdk/src/META-INF/test-datadebug.devellibdepends trunk/cdk/src/META-INF/test-experimental.devellibdepends trunk/cdk/src/META-INF/test-extra.devellibdepends trunk/cdk/src/META-INF/test-forcefield.devellibdepends trunk/cdk/src/META-INF/test-inchi.devellibdepends trunk/cdk/src/META-INF/test-io.devellibdepends trunk/cdk/src/META-INF/test-libiomd.devellibdepends trunk/cdk/src/META-INF/test-nonotify.devellibdepends trunk/cdk/src/META-INF/test-osjvmts.devellibdepends trunk/cdk/src/META-INF/test-pdb.devellibdepends trunk/cdk/src/META-INF/test-qsar.devellibdepends trunk/cdk/src/META-INF/test-qsarAtomic.devellibdepends trunk/cdk/src/META-INF/test-qsarBond.devellibdepends trunk/cdk/src/META-INF/test-qsarMolecular.devellibdepends trunk/cdk/src/META-INF/test-reaction.devellibdepends trunk/cdk/src/META-INF/test-smarts.devellibdepends trunk/cdk/src/META-INF/test-smiles.devellibdepends trunk/cdk/src/META-INF/test-standard.devellibdepends trunk/cdk/src/META-INF/test-structgen.devellibdepends trunk/cdk/src/META-INF/test-valencycheck.devellibdepends trunk/cdk/src/META-INF/test-weka.devellibdepends trunk/cdk/src/META-INF/test.devellibdepends Added Paths: ----------- trunk/cdk/develjar/junit-4.3.1.jar Removed Paths: ------------- trunk/cdk/develjar/junit.jar Added: trunk/cdk/develjar/junit-4.3.1.jar =================================================================== (Binary files differ) Property changes on: trunk/cdk/develjar/junit-4.3.1.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Deleted: trunk/cdk/develjar/junit.jar =================================================================== (Binary files differ) Modified: trunk/cdk/src/META-INF/test-builder3d.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-builder3d.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-builder3d.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-core.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-core.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-core.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-data.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-data.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-data.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-datadebug.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-datadebug.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-datadebug.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-experimental.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-experimental.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-experimental.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-extra.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-extra.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-extra.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-forcefield.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-forcefield.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-forcefield.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-inchi.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-inchi.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-inchi.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-io.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-io.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-io.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-libiomd.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-libiomd.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-libiomd.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-nonotify.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-nonotify.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-nonotify.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-osjvmts.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-osjvmts.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-osjvmts.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-pdb.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-pdb.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-pdb.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-qsar.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-qsar.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-qsar.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-qsarAtomic.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-qsarAtomic.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-qsarAtomic.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-qsarBond.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-qsarBond.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-qsarBond.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-qsarMolecular.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-qsarMolecular.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-qsarMolecular.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-reaction.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-reaction.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-reaction.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-smarts.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-smarts.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-smarts.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-smiles.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-smiles.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-smiles.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-standard.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-standard.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-standard.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-structgen.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-structgen.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-structgen.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-valencycheck.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-valencycheck.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-valencycheck.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test-weka.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-weka.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test-weka.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar Modified: trunk/cdk/src/META-INF/test.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test.devellibdepends 2007-05-31 14:26:34 UTC (rev 8355) +++ trunk/cdk/src/META-INF/test.devellibdepends 2007-06-04 15:03:02 UTC (rev 8356) @@ -1,2 +1,2 @@ -junit.jar +junit-4.3.1.jar This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |