From: <eg...@us...> - 2006-04-20 21:59:35
|
Revision: 6064 Author: egonw Date: 2006-04-20 14:59:04 -0700 (Thu, 20 Apr 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6064&view=rev Log Message: ----------- Created the smiles module Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/META-INF/applications.cdkdepends trunk/cdk/src/META-INF/experimental.cdkdepends trunk/cdk/src/META-INF/test-experimental.cdkdepends trunk/cdk/src/META-INF/test-extra.cdkdepends trunk/cdk/src/META-INF/test-forcefield.cdkdepends trunk/cdk/src/META-INF/test-io.cdkdepends trunk/cdk/src/META-INF/test-reaction.cdkdepends trunk/cdk/src/META-INF/test-standard.cdkdepends trunk/cdk/src/META-INF/test-valencycheck.cdkdepends trunk/cdk/src/org/openscience/cdk/fingerprint/StandardSubstructureSets.java trunk/cdk/src/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java trunk/cdk/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java trunk/cdk/src/org/openscience/cdk/smiles/SmilesGenerator.java trunk/cdk/src/org/openscience/cdk/smiles/SmilesParser.java trunk/cdk/src/org/openscience/cdk/tools/Normalizer.java Added Paths: ----------- trunk/cdk/src/META-INF/smiles.cdkdepends trunk/cdk/src/META-INF/smiles.libdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/build.xml 2006-04-20 21:59:04 UTC (rev 6064) @@ -596,13 +596,14 @@ <antcall target="compile-module"><param name="module" value="pdb"/></antcall> <antcall target="compile-module"><param name="module" value="valencycheck"/></antcall> <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="pdb-cml"/></antcall> <antcall target="compile-module"><param name="module" value="experimental"/></antcall> <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="forcefield"/></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="reaction"/></antcall> <antcall target="compile-module"><param name="module" value="svg"/></antcall> @@ -680,7 +681,8 @@ <include name="cdk-standard.jar"/> <include name="cdk-svg.jar"/> <include name="cdk-valencycheck.jar"/> - <include name="cdk-forcefield.jar"/> + <include name="cdk-forcefield.jar"/> + <include name="cdk-smiles.jar"/> </fileset> </unjar> Modified: trunk/cdk/src/META-INF/applications.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/applications.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/applications.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -11,4 +11,4 @@ cdk-render.jar cdk-standard.jar cdk-svg.jar - +cdk-smiles.jar Modified: trunk/cdk/src/META-INF/experimental.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/experimental.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/experimental.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -6,4 +6,4 @@ cdk-pdb.jar cdk-standard.jar cdk-valencycheck.jar - +cdk-smiles.jar Added: trunk/cdk/src/META-INF/smiles.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/smiles.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/smiles.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -0,0 +1,8 @@ +cdk-data.jar +cdk-core.jar +cdk-interfaces.jar +cdk-io.jar +cdk-render.jar +cdk-standard.jar +cdk-valencycheck.jar +cdk-extra.jar Added: trunk/cdk/src/META-INF/smiles.libdepends =================================================================== --- trunk/cdk/src/META-INF/smiles.libdepends (rev 0) +++ trunk/cdk/src/META-INF/smiles.libdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -0,0 +1 @@ +vecmath1.2-1.14.jar Modified: trunk/cdk/src/META-INF/test-experimental.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-experimental.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/test-experimental.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -14,4 +14,5 @@ cdk-qsar-pdb.jar cdk-applications.jar cdk-valencycheck.jar +cdk-smiles.jar cdk-test-core.jar \ No newline at end of file Modified: trunk/cdk/src/META-INF/test-extra.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-extra.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/test-extra.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -14,4 +14,6 @@ cdk-qsar-pdb.jar cdk-applications.jar cdk-valencycheck.jar +cdk-forcefield.jar +cdk-smiles.jar cdk-test-core.jar Modified: trunk/cdk/src/META-INF/test-forcefield.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-forcefield.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/test-forcefield.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -9,4 +9,5 @@ cdk-qsar-pdb.jar cdk-valencycheck.jar cdk-forcefield.jar +cdk-smiles.jar cdk-test-core.jar Modified: trunk/cdk/src/META-INF/test-io.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-io.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/test-io.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -10,6 +10,7 @@ cdk-pdb.jar cdk-qsar.jar cdk-qsar-pdb.jar +cdk-smiles.jar cdk-test-core.jar cdk-test-data.jar Modified: trunk/cdk/src/META-INF/test-reaction.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-reaction.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/test-reaction.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -6,4 +6,5 @@ cdk-reaction.jar cdk-io.jar cdk-valencycheck.jar +cdk-smiles.jar cdk-test-core.jar \ No newline at end of file Modified: trunk/cdk/src/META-INF/test-standard.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-standard.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/test-standard.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -5,4 +5,5 @@ cdk-extra.jar cdk-valencycheck.jar cdk-standard.jar +cdk-smiles.jar cdk-test-core.jar Modified: trunk/cdk/src/META-INF/test-valencycheck.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-valencycheck.cdkdepends 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/META-INF/test-valencycheck.cdkdepends 2006-04-20 21:59:04 UTC (rev 6064) @@ -5,4 +5,5 @@ cdk-io.jar cdk-extra.jar cdk-valencycheck.jar +cdk-smiles.jar cdk-test-core.jar Modified: trunk/cdk/src/org/openscience/cdk/fingerprint/StandardSubstructureSets.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/fingerprint/StandardSubstructureSets.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/fingerprint/StandardSubstructureSets.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -7,6 +7,8 @@ * Default sets of atom containers aimed for use with the substructure * * @author egonw + * + * @cdk.module experimental */ public class StandardSubstructureSets { Modified: trunk/cdk/src/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -44,6 +44,8 @@ * * @cdk.keyword fingerprint * @cdk.keyword similarity + * + * @cdk.module experimental */ public class SubstructureFingerprinter implements IFingerprinter { Modified: trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -64,7 +64,7 @@ * <p>For each line a molecule is generated, and multiple Molecules are * read as SetOfMolecules. * - * @cdk.module extra + * @cdk.module smiles * @cdk.keyword file format, SMILES * * @see org.openscience.cdk.io.iterator.IteratingSMILESReader Modified: trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -56,7 +56,7 @@ /** * Writes the SMILES strings to a plain text file. * - * @cdk.module extra + * @cdk.module smiles * * @cdk.keyword file format */ Modified: trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -48,7 +48,7 @@ * * <p>For parsing each SMILES it still uses the normal SMILESReader. * - * @cdk.module extra + * @cdk.module smiles * * @see org.openscience.cdk.io.SMILESReader * Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -27,17 +27,20 @@ import java.util.Vector; import org._3pq.jgrapht.graph.SimpleGraph; +import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.graph.BFSShortestPath; +import org.openscience.cdk.graph.MoleculeGraphs; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; +import org.openscience.cdk.isomorphism.matchers.IQueryAtom; import org.openscience.cdk.isomorphism.matchers.OrderQueryBond; -import org.openscience.cdk.isomorphism.matchers.IQueryAtom; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator; import org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom; @@ -45,16 +48,13 @@ import org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom; import org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond; import org.openscience.cdk.isomorphism.mcss.RMap; -import org.openscience.cdk.qsar.result.DoubleResult; -import org.openscience.cdk.qsar.IDescriptor; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; +import org.openscience.cdk.qsar.IDescriptor; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.ringsearch.SSSRFinder; -import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.manipulator.RingSetManipulator; -import org.openscience.cdk.graph.BFSShortestPath; -import org.openscience.cdk.graph.MoleculeGraphs; /** * Prediction of logP based on the atom-type method called XLogP. For @@ -198,7 +198,7 @@ HueckelAromaticityDetector.detectAromaticity(ac, rs, true); } double xlogP = 0; - SmilesParser sp = new SmilesParser(); +// SmilesParser sp = new SmilesParser(); org.openscience.cdk.interfaces.IAtom[] atoms = ac.getAtoms(); String symbol = ""; int bondCount = 0; @@ -825,7 +825,10 @@ if (checkAminoAcid>1){ // alpha amino acid - QueryAtomContainer aminoAcid=QueryAtomContainerCreator.createBasicQueryContainer(sp.parseSmiles("NCC(=O)O")); + QueryAtomContainer aminoAcid = + QueryAtomContainerCreator.createBasicQueryContainer( + createAminoAcid(ac.getBuilder()) + ); IBond [] bonds=aminoAcid.getBonds(); IAtom[] bondAtoms=null; for (int i=0;i<bonds.length;i++){ @@ -857,7 +860,7 @@ } } - IAtomContainer paba = sp.parseSmiles("CS(=O)(=O)c1ccc(N)cc1"); + IAtomContainer paba = createPaba(ac.getBuilder()); // p-amino sulphonic acid if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ac, paba)) { xlogP -= 0.501; @@ -867,7 +870,7 @@ // salicylic acid if (salicylFlag){ - IAtomContainer salicilic = sp.parseSmiles("O=C(O)c1ccccc1O"); + IAtomContainer salicilic = createSalicylicAcid(ac.getBuilder()); if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ac, salicilic)) { xlogP += 0.554; //System.out.println("XLOGP: salicylic acid 0.554"); @@ -1403,5 +1406,135 @@ public Object getParameterType(String name) { return new Boolean(true); } + + private IAtomContainer createPaba(IChemObjectBuilder builder) { + // SMILES CS(=O)(=O)c1ccc(N)cc1 + IAtomContainer container = builder.newAtomContainer(); + IAtom atom1 = builder.newAtom("C"); + container.addAtom(atom1); + IAtom atom2 = builder.newAtom("S"); + container.addAtom(atom2); + IAtom atom3 = builder.newAtom("O"); + container.addAtom(atom3); + IAtom atom4 = builder.newAtom("O"); + container.addAtom(atom4); + IAtom atom5 = builder.newAtom("C"); atom5.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom5); + IAtom atom6 = builder.newAtom("C"); atom6.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom6); + IAtom atom7 = builder.newAtom("C"); atom7.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom7); + IAtom atom8 = builder.newAtom("C"); atom8.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom8); + IAtom atom9 = builder.newAtom("N"); + container.addAtom(atom9); + IAtom atom10 = builder.newAtom("C"); atom10.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom10); + IAtom atom11 = builder.newAtom("C"); atom11.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom11); + IBond bond1 = builder.newBond(atom1, atom2, CDKConstants.BONDORDER_SINGLE); + container.addBond(bond1); + IBond bond2 = builder.newBond(atom2, atom3, CDKConstants.BONDORDER_DOUBLE); + container.addBond(bond2); + IBond bond3 = builder.newBond(atom2, atom4, CDKConstants.BONDORDER_DOUBLE); + container.addBond(bond3); + IBond bond4 = builder.newBond(atom2, atom5, CDKConstants.BONDORDER_SINGLE); + container.addBond(bond4); + IBond bond5 = builder.newBond(atom5, atom6, CDKConstants.BONDORDER_DOUBLE); + bond5.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond5); + IBond bond6 = builder.newBond(atom6, atom7, CDKConstants.BONDORDER_SINGLE); + bond6.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond6); + IBond bond7 = builder.newBond(atom7, atom8, CDKConstants.BONDORDER_DOUBLE); + bond7.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond7); + IBond bond8 = builder.newBond(atom8, atom9, CDKConstants.BONDORDER_SINGLE); + container.addBond(bond8); + IBond bond9 = builder.newBond(atom8, atom10, CDKConstants.BONDORDER_SINGLE); + bond9.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond9); + IBond bond10 = builder.newBond(atom10, atom11, CDKConstants.BONDORDER_DOUBLE); + bond10.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond10); + IBond bond11 = builder.newBond(atom5, atom11, CDKConstants.BONDORDER_SINGLE); + bond11.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond11); + + return container; + } + + private IAtomContainer createAminoAcid(IChemObjectBuilder builder) { + // SMILES NCC(=O)O + IAtomContainer container = builder.newAtomContainer(); + IAtom atom1 = builder.newAtom("N"); + container.addAtom(atom1); + IAtom atom2 = builder.newAtom("C"); + container.addAtom(atom2); + IAtom atom3 = builder.newAtom("C"); // carbonyl + container.addAtom(atom3); + IAtom atom4 = builder.newAtom("O"); // carbonyl + container.addAtom(atom4); + IAtom atom5 = builder.newAtom("O"); + container.addAtom(atom5); + container.addBond(builder.newBond(atom1, atom2, CDKConstants.BONDORDER_SINGLE)); + container.addBond(builder.newBond(atom2, atom3, CDKConstants.BONDORDER_SINGLE)); + container.addBond(builder.newBond(atom3, atom4, CDKConstants.BONDORDER_DOUBLE)); + container.addBond(builder.newBond(atom3, atom5, CDKConstants.BONDORDER_SINGLE)); + return container; + } + + private IAtomContainer createSalicylicAcid(IChemObjectBuilder builder) { + // SMILES O=C(O)c1ccccc1O + IAtomContainer container = builder.newAtomContainer(); + IAtom atom1 = builder.newAtom("C"); + container.addAtom(atom1); + IAtom atom2 = builder.newAtom("O"); + container.addAtom(atom2); + IAtom atom3 = builder.newAtom("O"); + container.addAtom(atom3); + IAtom atom4 = builder.newAtom("C"); atom4.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom4); + IAtom atom5 = builder.newAtom("C"); atom5.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom5); + IAtom atom6 = builder.newAtom("C"); atom6.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom6); + IAtom atom7 = builder.newAtom("C"); atom7.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom7); + IAtom atom8 = builder.newAtom("C"); atom8.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom8); + IAtom atom9 = builder.newAtom("C"); atom9.setHybridization(CDKConstants.HYBRIDIZATION_SP2); + container.addAtom(atom9); + IAtom atom10 = builder.newAtom("O"); + container.addAtom(atom10); + IBond bond1 = builder.newBond(atom1, atom2, CDKConstants.BONDORDER_DOUBLE); + container.addBond(bond1); + IBond bond2 = builder.newBond(atom1, atom3, CDKConstants.BONDORDER_SINGLE); + container.addBond(bond2); + IBond bond3 = builder.newBond(atom1, atom4, CDKConstants.BONDORDER_SINGLE); + container.addBond(bond3); + IBond bond4 = builder.newBond(atom4, atom5, CDKConstants.BONDORDER_DOUBLE); + bond4.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond4); + IBond bond5 = builder.newBond(atom5, atom6, CDKConstants.BONDORDER_SINGLE); + bond5.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond5); + IBond bond6 = builder.newBond(atom6, atom7, CDKConstants.BONDORDER_DOUBLE); + bond6.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond6); + IBond bond7 = builder.newBond(atom7, atom8, CDKConstants.BONDORDER_SINGLE); + bond7.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond7); + IBond bond8 = builder.newBond(atom8, atom9, CDKConstants.BONDORDER_DOUBLE); + bond8.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond8); + IBond bond9 = builder.newBond(atom9, atom4, CDKConstants.BONDORDER_SINGLE); + bond9.setFlag(CDKConstants.ISAROMATIC, true); + container.addBond(bond9); + IBond bond10 = builder.newBond(atom9, atom10, CDKConstants.BONDORDER_SINGLE); + container.addBond(bond10); + + return container; + } } Modified: trunk/cdk/src/org/openscience/cdk/smiles/SmilesGenerator.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/smiles/SmilesGenerator.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/smiles/SmilesGenerator.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -74,6 +74,8 @@ *@author Stefan Kuhn (chiral smiles) *@cdk.created 2002-02-26 *@cdk.keyword SMILES, generator + * + * @cdk.module smiles */ public class SmilesGenerator { Modified: trunk/cdk/src/org/openscience/cdk/smiles/SmilesParser.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/smiles/SmilesParser.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/smiles/SmilesParser.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -66,7 +66,7 @@ * *@author Christoph Steinbeck *@author Egon Willighagen - *@cdk.module extra + *@cdk.module smiles *@cdk.created 2002-04-29 *@cdk.keyword SMILES, parser *@cdk.bug 1095696 Modified: trunk/cdk/src/org/openscience/cdk/tools/Normalizer.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/tools/Normalizer.java 2006-04-20 20:19:27 UTC (rev 6063) +++ trunk/cdk/src/org/openscience/cdk/tools/Normalizer.java 2006-04-20 21:59:04 UTC (rev 6064) @@ -46,7 +46,7 @@ * * @author shk3 * @cdk.created 2004-03-04 - * @cdk.module extra + * @cdk.module smiles */ public class Normalizer { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |