Removed unused local variables (PMD report).

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Aug 29, 2014 · f6656e0 · f6656e0
1 parent d54f38e
commit f6656e0
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Showing 5 changed files with 0 additions and 9 deletions.
diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerSet.java b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerSet.java
@@ -131,7 +131,6 @@ public void removeAtomContainer(int pos) {
 	 * @param container  the replacement AtomContainer
 	 */
 	public void replaceAtomContainer(int position, IAtomContainer container) {
-		IAtomContainer old = atomContainers[position];
 		atomContainers[position] = container;
 	}
 

diff --git a/base/standard/src/main/java/org/openscience/cdk/ringsearch/AllRingsFinder.java b/base/standard/src/main/java/org/openscience/cdk/ringsearch/AllRingsFinder.java
@@ -130,7 +130,6 @@ public IRingSet findAllRings(IAtomContainer container) throws CDKException {
     public IRingSet findAllRings(IAtomContainer container,
                                  int maxRingSize) throws CDKException {
 
-        final int m = container.getBondCount();
         final EdgeToBondMap edges = EdgeToBondMap.withSpaceFor(container);
         final int[][]       graph = GraphUtil.toAdjList(container, edges);
 
@@ -199,7 +198,6 @@ public IRingSet findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer,
                                                      int maxRingSize) throws
                                                                       CDKException {
 
-        final int m = atomContainer.getBondCount();
         final EdgeToBondMap edges = EdgeToBondMap.withSpaceFor(atomContainer);
         final int[][]       graph = GraphUtil.toAdjList(atomContainer, edges);
 

diff --git a/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -410,7 +410,6 @@ public static int countExplicitHydrogens(IAtomContainer atomContainer, IAtom ato
     public static void convertImplicitToExplicitHydrogens(IAtomContainer atomContainer) {
         List<IAtom> hydrogens = new ArrayList<IAtom>();
         List<IBond> newBonds = new ArrayList<IBond>();
-        List<Integer> atomIndex = new ArrayList<Integer>();
 
         // store a single explicit hydrogen of each original neighbor
         Map<IAtom,IAtom> hNeighbor = Maps.newHashMapWithExpectedSize(atomContainer.getAtomCount());

diff --git a/descriptor/ionpot/src/main/java/org/openscience/cdk/tools/IonizationPotentialTool.java b/descriptor/ionpot/src/main/java/org/openscience/cdk/tools/IonizationPotentialTool.java
@@ -371,7 +371,6 @@ public static double[] getQSARs(IAtomContainer container,  IBond bond) throws CD
 	private static double getDTHalogenF(double[] resultsH) {
 		double result = 0.0;
 		double SE = resultsH[0];
-		double PE = resultsH[1];
 		double PSC = resultsH[2];
 		double PIC  = resultsH[3];
 		double ETP  = resultsH[4];
@@ -452,7 +451,6 @@ private static double getDTBondF(double[] resultsH) {
 		double PSC = resultsH[2];
 		double PIC  = resultsH[3];
 		double ETP  = resultsH[4];
-		double SPC  = resultsH[5];
 		double COUNTR  = resultsH[6];
 
 //		System.out.println("SE : "+SE+", PE : "+PE+", PSC : "+PSC+", PIC : "+PIC+", ETP : "+ETP+", SPC : "+SPC+", COUNTR : "+COUNTR);

diff --git a/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java b/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
@@ -402,7 +402,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 		smooth = -1.15;
 		int goodPosition = 0;
 		IBond goodBond;
-		int counter = 0;
 		for(double ghd = limitInf; ghd < limitSup; ghd = ghd + step) {
 			sum = 0;
 			for( int dou = 0; dou < doubles.size(); dou++ ) {
@@ -436,7 +435,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 			//gDr_function.add(new Double(sum));
 			rdfProtonCalculatedValues.add(sum);
 			logger.debug("GDR prob dist.: " + sum + " at distance " + ghd);
-			counter++;
 		}
 	}
 	else {
@@ -543,7 +541,6 @@ private int getNearestBondtoAGivenAtom(IAtomContainer mol, IAtom atom, IBond bon
         double[] values;
         double distance = 0;
         IAtom atom0 = bond.getAtom(0);
-        IAtom atom1 = bond.getAtom(1);
         List<IBond> bondsAtLeft = mol.getConnectedBondsList(atom0);
         int partial;
         for (int i = 0; i < bondsAtLeft.size(); i++) {