a) Default constructor supported as per changes in the CDK b) VFMCS i…

…ndex error should point to -1 not null Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>
cdk · Aug 30, 2010 · 9c6c830 · 9c6c830
1 parent 1dae4f2
commit 9c6c830
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Showing 7 changed files with 31 additions and 8 deletions.
diff --git a/src/main/org/openscience/cdk/smsd/algorithm/mcsplus/GenerateCompatibilityGraph.java b/src/main/org/openscience/cdk/smsd/algorithm/mcsplus/GenerateCompatibilityGraph.java
@@ -59,6 +59,13 @@ public final class GenerateCompatibilityGraph {
     private IAtomContainer target = null;
     private boolean shouldMatchBonds = false;
 
+    /**
+    * Default constructor added 
+    */
+    public GenerateCompatibilityGraph(){
+
+    }
+
     /**
      * Generates a compatibility graph between two molecules
      * @param source

diff --git a/src/main/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlus.java b/src/main/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlus.java
@@ -45,6 +45,13 @@
 @TestClass("org.openscience.cdk.smsd.SMSDBondSensitiveTest")
 public class MCSPlus {
 
+    /**
+    * Default constructor added 
+    */
+    public MCSPlus(){
+
+    }
+
     private static TimeManager timeManager = null;
 
     /**

diff --git a/src/main/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java b/src/main/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java
@@ -52,6 +52,10 @@
 @TestClass("org.openscience.cdk.smsd.algorithm.cdk.CDKRMapHandlerTest")
 public class CDKRMapHandler {
 
+
+    public CDKRMapHandler(){
+
+    }
     /**
      * Returns source molecule
      * @return the source

diff --git a/src/main/org/openscience/cdk/smsd/algorithm/single/SingleMapping.java b/src/main/org/openscience/cdk/smsd/algorithm/single/SingleMapping.java
@@ -58,6 +58,12 @@ public class SingleMapping {
     private List<Map<IAtom, IAtom>> mappings = null;
     private Map<Integer, Double> connectedBondOrder = null;
 
+    /**
+     * Default
+     */
+    public SingleMapping() {
+    }
+
     /**
      * Returns single mapping solutions.
      * @param source
@@ -119,7 +125,7 @@ private void setSourceSingleAtomMap(IQueryAtomContainer source, boolean removeHy
         int counter = 0;
         BondEnergies be = BondEnergies.getInstance();
         for (IAtom sourceAtom : source.atoms()) {
-            IQueryAtom smartAtom=(IQueryAtom)sourceAtom;
+            IQueryAtom smartAtom = (IQueryAtom) sourceAtom;
             if ((removeHydrogen && !smartAtom.getSymbol().equals("H")) || (!removeHydrogen)) {
                 for (IAtom targetAtom : target.atoms()) {
                     Map<IAtom, IAtom> mapAtoms = new HashMap<IAtom, IAtom>();

diff --git a/src/main/org/openscience/cdk/smsd/algorithm/vflib/VFlibMCSHandler.java b/src/main/org/openscience/cdk/smsd/algorithm/vflib/VFlibMCSHandler.java
@@ -312,6 +312,7 @@ private void setVFMappings(boolean RONP, IQuery query) {
                 IAtom tAtom = null;
                 Integer qIndex = 0;
                 Integer tIndex = 0;
+
                 if (RONP) {
                     qAtom = query.getAtom(mapping.getKey());
                     tAtom = mapping.getValue();
@@ -323,13 +324,13 @@ private void setVFMappings(boolean RONP, IQuery query) {
                     qIndex = getReactantMol().getAtomNumber(qAtom);
                     tIndex = getProductMol().getAtomNumber(tAtom);
                 }
-
-                if (qIndex != null && tIndex != null) {
+                
+                if (qIndex != -1 && tIndex != -1) {
                     atomatomMapping.put(qAtom, tAtom);
                     indexindexMapping.put(qIndex, tIndex);
                 } else {
                     try {
-                        throw new CDKException("Atom index pointing to NULL");
+                        throw new CDKException("Atom index pointing to -1");
                     } catch (CDKException ex) {
                         Logger.error(Level.SEVERE, null, ex);
                     }

diff --git a/src/main/org/openscience/cdk/smsd/algorithm/vflib/builder/TargetProperties.java b/src/main/org/openscience/cdk/smsd/algorithm/vflib/builder/TargetProperties.java
@@ -95,8 +95,6 @@ public TargetProperties(IAtomContainer container) {
         map = new IBond[container.getAtomCount()][container.getAtomCount()];
         for (IAtom atom : container.atoms()) {
             int count = container.getConnectedAtomsCount(atom);
-//            int virtualHydrogenCount = atom.getImplicitHydrogenCount() == null ? 0 : atom.getImplicitHydrogenCount().intValue();
-//            count += virtualHydrogenCount;
             connectedTargetAtomCountMap.put(atom, count);
             List<IAtom> list = container.getConnectedAtomsList(atom);
             if (list != null) {

diff --git a/src/main/org/openscience/cdk/smsd/algorithm/vflib/map/VFMCSMapper.java b/src/main/org/openscience/cdk/smsd/algorithm/vflib/map/VFMCSMapper.java
@@ -75,8 +75,8 @@
 @TestClass("org.openscience.cdk.smsd.algorithm.vflib.VFLibTest")
 public class VFMCSMapper implements IMapper {
 
-    private IQuery query;
-    private List<Map<INode, IAtom>> maps;
+    private IQuery query = null;
+    private List<Map<INode, IAtom>> maps = null;
     private int currentMCSSize = -1;
     private static TimeManager timeManager = null;