Added a method to generate tautomers

bioclipse · Aug 16, 2012 · 5c1c645 · 5c1c645
1 parent cfb29f6
commit 5c1c645
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Showing 3 changed files with 37 additions and 1 deletion.
diff --git a/plugins/net.bioclipse.cdk.business/META-INF/MANIFEST.MF b/plugins/net.bioclipse.cdk.business/META-INF/MANIFEST.MF
@@ -41,7 +41,8 @@ Require-Bundle: org.openscience.cdk.io,
  net.bioclipse.inchi,
  net.bioclipse.ui.business,
  net.sf.cglib,
- org.openscience.cdk.silent;bundle-version="1.4.10"
+ org.openscience.cdk.silent;bundle-version="1.4.10",
+ org.openscience.cdk.tautomer
 Bundle-ActivationPolicy: lazy
 Export-Package: net.bioclipse.cdk.business,
  net.bioclipse.cdk.domain,

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java
@@ -154,6 +154,7 @@
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
 import org.openscience.cdk.smiles.smarts.parser.TokenMgrError;
+import org.openscience.cdk.tautomers.InChITautomerGenerator;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
@@ -3160,6 +3161,33 @@ public List<ICDKMolecule> kabsch(List<IMolecule> molecules,
         return results;
     }
 
+    public List<ICDKMolecule> getTautomers(IMolecule molecule, IProgressMonitor monitor)
+    throws BioclipseException {
+    	if (monitor == null) monitor = new NullProgressMonitor();
+
+    	monitor.beginTask("Generating tautomers...", 100); // we won't get more than that, I guess
+    	InChITautomerGenerator tautomerGenerator = new InChITautomerGenerator();
+    	monitor.worked(1); // a bonus point for just starting
+
+    	ICDKMolecule cdkMol = asCDKMolecule(molecule);
+    	try {
+			List<IAtomContainer> tautomers = tautomerGenerator.getTautomers(cdkMol.getAtomContainer());
+	    	List<ICDKMolecule> tautomerList = new ArrayList<ICDKMolecule>();
+
+	    	for (IAtomContainer tautomer : tautomers) {
+	    		tautomerList.add(newMolecule(tautomer));
+	    		monitor.worked(1);
+	    	}
+	    	monitor.done();
+	    	return tautomerList;
+		} catch (Exception exception) {
+			throw new BioclipseException(
+				"Error while generating tautomers: " + exception.getMessage(),
+				exception
+			);
+		}
+    }
+
     /**
      * Split a list of mols in N equally sized parts by random sampling.
      * 

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java
@@ -1196,4 +1196,11 @@ public List<ICDKMolecule> loadSMILESFile( IFile file,
     public void appendToSDF( String sdFile, ICDKMolecule molecule ) throws BioclipseException;
 
     public void appendToSDF( IFile sdFile, ICDKMolecule molecule ) throws BioclipseException;
+
+    @Recorded
+    @PublishedMethod(
+         params="IMolecule molecule",
+         methodSummary="Generates a list of tautomers."
+    )
+    public List<ICDKMolecule> getTautomers(IMolecule molecule) throws BioclipseException;
 }