From 2ceef95e7487920db56a0b4f59337adf588c602a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Wed, 24 Feb 2010 21:22:29 +0100 Subject: [PATCH 1/5] Synchronized behavior with the MDLV2000Reader (addressing bug #2942196) Signed-off-by: Rajarshi Guha --- src/main/org/openscience/cdk/io/MDLReader.java | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/src/main/org/openscience/cdk/io/MDLReader.java b/src/main/org/openscience/cdk/io/MDLReader.java index a847d2f0075..fb9246a475e 100644 --- a/src/main/org/openscience/cdk/io/MDLReader.java +++ b/src/main/org/openscience/cdk/io/MDLReader.java @@ -318,6 +318,8 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException { double x = 0.0; double y = 0.0; double z = 0.0; + double totalX = 0.0; + double totalY = 0.0; double totalZ = 0.0; //int[][] conMat = new int[0][0]; //String help; @@ -372,7 +374,10 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException { x = new Double(line.substring( 0,10).trim()).doubleValue(); y = new Double(line.substring(10,20).trim()).doubleValue(); z = new Double(line.substring(20,30).trim()).doubleValue(); - totalZ += Math.abs(z); // *all* values should be zero, not just the sum + // *all* values should be zero, not just the sum + totalX += Math.abs(x); + totalY += Math.abs(y); + totalZ += Math.abs(z); logger.debug("Coordinates: " + x + "; " + y + "; " + z); String element = line.substring(31,34).trim(); @@ -484,7 +489,12 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException { } // convert to 2D, if totalZ == 0 - if (totalZ == 0.0 && !forceReadAs3DCoords.isSet()) { + if (totalX == 0.0 && totalY == 0.0 && totalZ == 0.0) { + logger.info("All coordinates are 0.0"); + for (IAtom atomToUpdate : molecule.atoms()) { + atomToUpdate.setPoint3d(null); + } + } else if (totalZ == 0.0 && !forceReadAs3DCoords.isSet()) { logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure"); Iterator atomsToUpdate = molecule.atoms().iterator(); while (atomsToUpdate.hasNext()) { From 677b3f63361c70dc6805b78c99897322c91b5f6c Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Wed, 24 Feb 2010 22:00:01 +0100 Subject: [PATCH 2/5] Fixed some spelling errors and added JavaDoc links Signed-off-by: Rajarshi Guha --- .../UniversalIsomorphismTester.java | 168 +++++++++--------- 1 file changed, 86 insertions(+), 82 deletions(-) diff --git a/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java b/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java index 09a9b797e87..b9ca48a1f61 100644 --- a/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java +++ b/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java @@ -36,6 +36,7 @@ import org.openscience.cdk.isomorphism.matchers.IQueryAtom; import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer; import org.openscience.cdk.isomorphism.matchers.IQueryBond; +import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; import org.openscience.cdk.isomorphism.mcss.RGraph; import org.openscience.cdk.isomorphism.mcss.RMap; import org.openscience.cdk.isomorphism.mcss.RNode; @@ -59,15 +60,17 @@ * The constraint flexibility allows a number of interesting queries. * The substructure analysis relies on the RGraph generic class (see: RGraph) * This class implements the link between the RGraph model and the - * the CDK model in this way the RGraph remains independent and may be used + * the CDK model in this way the {@link RGraph} remains independent and may be used * in other contexts. * *

This algorithm derives from the algorithm described in * {@cdk.cite HAN90} and modified in the thesis of T. Hanser {@cdk.cite HAN93}. * - *

With the isSubgraph() method, the second, and only the second - * argument may be a IQueryAtomContainer, which allows one to do MQL like queries. - * The first IAtomContainer must never be an IQueryAtomContainer. An example:

+ *  
With the {@link #isSubgraph(IAtomContainer, IAtomContainer)} method,
+ *  the second, and only the second argument may be a {@link IQueryAtomContainer},
+ *  which allows one to do SMARTS or MQL like queries.
+ *  The first {@link IAtomContainer} must never be an {@link IQueryAtomContainer}.
+ *  An example:
  *  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  *  IAtomContainer atomContainer = sp.parseSmiles("CC(=O)OC(=O)C"); // acetic acid anhydride
  *  IAtomContainer SMILESquery = sp.parseSmiles("CC"); // acetic acid anhydride
@@ -77,11 +80,11 @@
  *
  *  
WARNING:
  *    As a result of the adjacency perception used in this algorithm
- *    there is a single limitation : cyclopropane and isobutane are seen as isomorph
+ *    there is a single limitation: cyclopropane and isobutane are seen as isomorph.
  *    This is due to the fact that these two compounds are the only ones where
- *    each bond is connected two each other bond (bonds are fully conected)
+ *    each bond is connected two each other bond (bonds are fully connected)
  *    with the same number of bonds and still they have different structures
- *    The algotihm could be easily enhanced with a simple atom mapping manager
+ *    The algorithm could be easily enhanced with a simple atom mapping manager
  *    to provide an atom level overlap definition that would reveal this case.
  *    We decided not to penalize the whole procedure because of one single
  *    exception query. Furthermore isomorphism may be discarded since  the number of atoms are
@@ -127,11 +130,10 @@ public class UniversalIsomorphismTester {
   /**
    * Tests if g1 and g2 are isomorph.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     true if the 2 molecule are isomorph
-   * @throws org.openscience.cdk.exception.CDKException if the first molecule is an instance
-   * of IQueryAtomContainer
+   * @throws     CDKException if the first molecule is an instance of IQueryAtomContainer
    */
   public static boolean isIsomorph(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
 	  if (g1 instanceof IQueryAtomContainer)
@@ -162,8 +164,8 @@ public static boolean isIsomorph(IAtomContainer g1, IAtomContainer g2)  throws C
   /**
    * Returns the first isomorph mapping found or null.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     the first isomorph mapping found projected of g1. This is a List of RMap objects containing Ids of matching bonds.
    */
   public static List getIsomorphMap(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
@@ -187,12 +189,11 @@ public static List getIsomorphMap(IAtomContainer g1, IAtomContainer g2)  t
   /**
    * Returns the first isomorph 'atom mapping' found for g2 in g1.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     the first isomorph atom mapping found projected on g1.
    * This is a List of RMap objects containing Ids of matching atoms.
-   * @throws org.openscience.cdk.exception.CDKException if the first molecules is not an instance of
-   *  {@link org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer}
+   * @throws CDKException if the first molecules is not an instance of {@link IQueryAtomContainer}
    */
   public static List getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g2)  throws CDKException {
 	  if (g1 instanceof IQueryAtomContainer)
@@ -215,8 +216,8 @@ public static List getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g
    * Returns all the isomorph 'mappings' found between two
    * atom containers.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     the list of all the 'mappings'
    */
   public static List> getIsomorphMaps(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
@@ -229,20 +230,22 @@ public static List> getIsomorphMaps(IAtomContainer g1, IAtomContainer
 
   /**
    * Returns all the subgraph 'bond mappings' found for g2 in g1.
-   * This is an ArrayList of ArrayLists of RMap objects.
+   * This is an {@link List} of {@link List}s of {@link RMap} objects.
    *
    * Note that if the query molecule is a single atom, then bond mappings
-   * cannot be defined. In such a case, the RMap object refers directly to
+   * cannot be defined. In such a case, the {@link RMap} object refers directly to
    * atom - atom mappings. Thus RMap.id1 is the index of the target atom
    * and RMap.id2 is the index of the matching query atom (in this case,
    * it will always be 0). Note that in such a case, there is no need
-   * to call makeAtomsMapsofBondsMaps, though if it is called, then the
+   * to call {@link #makeAtomsMapsOfBondsMaps(List, IAtomContainer, IAtomContainer)},
+   * though if it is called, then the
    * return value is simply the same as the return value of this method.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     the list of all the 'mappings' found projected of g1
-   * @see #makeAtomsMapsOfBondsMaps(java.util.List, org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IAtomContainer)
+   *
+   * @see #makeAtomsMapsOfBondsMaps(List, IAtomContainer, IAtomContainer)
    */
   public static List> getSubgraphMaps(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
     return search(g1, g2, new BitSet(), getBitSet(g2), true, true);
@@ -252,9 +255,10 @@ public static List> getSubgraphMaps(IAtomContainer g1, IAtomContainer
   /**
    * Returns the first subgraph 'bond mapping' found for g2 in g1.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
-   * @return     the first subgraph bond mapping found projected on g1. This is a List of RMap objects containing Ids of matching bonds.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
+   * @return     the first subgraph bond mapping found projected on g1. This is a {@link List} of
+   *             {@link RMap} objects containing Ids of matching bonds.
    */
   public static List getSubgraphMap(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
     List result = null;
@@ -270,12 +274,12 @@ public static List getSubgraphMap(IAtomContainer g1, IAtomContainer g2)  t
 
   /**
    * Returns all subgraph 'atom mappings' found for g2 in g1.
-   * This is an ArrayList of ArrayLists of RMap objects.
+   * This is an {@link List} of {@link List}s of {@link RMap} objects.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     all subgraph atom mappings found projected on g1. This is a
-   *             List of RMap objects containing Ids of matching atoms.
+   *             {@link List} of {@link RMap} objects containing Ids of matching atoms.
    */
   public static List> getSubgraphAtomsMaps(IAtomContainer g1,
 		                                              IAtomContainer g2)
@@ -295,10 +299,10 @@ public static List> getSubgraphAtomsMaps(IAtomContainer g1,
   /**
    * Returns the first subgraph 'atom mapping' found for g2 in g1.
    *
-   * @param  g1 first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2 second molecule. May be an IQueryAtomContainer.
+   * @param  g1 first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2 second molecule. May be an {@link IQueryAtomContainer}.
    * @return    the first subgraph atom mapping found projected on g1.
-   *            This is a List of RMap objects containing Ids of matching atoms.
+   *            This is a {@link List} of {@link RMap} objects containing Ids of matching atoms.
    */
   public static List getSubgraphAtomsMap(IAtomContainer g1,
                                                IAtomContainer g2)
@@ -316,8 +320,8 @@ public static List getSubgraphAtomsMap(IAtomContainer g1,
   /**
    * Tests if g2 a subgraph of g1.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     true if g2 a subgraph on g1
    */
   public static boolean isSubgraph(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
@@ -353,10 +357,10 @@ public static boolean isSubgraph(IAtomContainer g1, IAtomContainer g2)  throws C
   // Maximum common substructure search
 
   /**
-   * Returns all the maximal common substructure between 2 atom containers.
+   * Returns all the maximal common substructure between twp atom containers.
    *
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
    * @return     the list of all the maximal common substructure
    *             found projected of g1 (list of AtomContainer )
    */
@@ -375,10 +379,10 @@ public static List getOverlaps(IAtomContainer g1, IAtomContainer
 
 
   /**
-   * Transforms an AtomContainer into a BitSet (which's size = number of bond
+   * Transforms an AtomContainer into a {@link BitSet} (which's size = number of bond
    * in the atomContainer, all the bit are set to true).
    *
-   * @param  ac  AtomContainer to transform
+   * @param  ac  {@link IAtomContainer} to transform
    * @return     The bitSet
    */
   public static BitSet getBitSet(IAtomContainer ac) {
@@ -400,7 +404,7 @@ public static BitSet getBitSet(IAtomContainer ac) {
   //          Internal methods
 
   /**
-   * Builds the RGraph ( resolution graph ), from two atomContainer
+   * Builds the {@link RGraph} ( resolution graph ), from two atomContainer
    * (description of the two molecules to compare)
    * This is the interface point between the CDK model and
    * the generic MCSS algorithm based on the RGRaph.
@@ -418,12 +422,12 @@ public static RGraph buildRGraph(IAtomContainer g1, IAtomContainer g2)  throws C
 
 
   /**
-   * General Rgraph parsing method (usually not used directly)
+   * General {@link RGraph} parsing method (usually not used directly)
    * This method is the entry point for the recursive search
    * adapted to the atom container input.
    *
-   * @param  g1                first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2                second molecule. May be an IQueryAtomContainer.
+   * @param  g1                first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2                second molecule. May be an {@link IQueryAtomContainer}.
    * @param  c1                initial condition ( bonds from g1 that
    *                           must be contains in the solution )
    * @param  c2                initial condition ( bonds from g2 that
@@ -431,7 +435,7 @@ public static RGraph buildRGraph(IAtomContainer g1, IAtomContainer g2)  throws C
    * @param  findAllStructure  if false stop at the first structure found
    * @param  findAllMap        if true search all the 'mappings' for one same
    *                           structure
-   * @return                   a List of Lists of RMap objects that represent the search solutions
+   * @return                   a List of Lists of {@link RMap} objects that represent the search solutions
    */
   public static List> search(IAtomContainer g1, IAtomContainer g2, BitSet c1,
 		  BitSet c2, boolean findAllStructure, boolean findAllMap)  throws CDKException{
@@ -484,11 +488,11 @@ public static List> search(IAtomContainer g1, IAtomContainer g2, BitS
   //    Manipulation tools
 
   /**
-   * Projects a list of RMap on a molecule.
+   * Projects a list of {@link RMap} on a molecule.
    *
    * @param  rMapList  the list to project
    * @param  g         the molecule on which project
-   * @param  id        the id in the RMap of the molecule g
+   * @param  id        the id in the {@link RMap} of the molecule g
    * @return           an AtomContainer
    */
   public static IAtomContainer project(List rMapList, IAtomContainer g, int id) {
@@ -567,8 +571,7 @@ public static ArrayList projectList(List> rMapsList,
    *
    * @param  graphList  the list of structure to clean
    * @return            the list cleaned
-   * @throws org.openscience.cdk.exception.CDKException if there is a problem in obtaining
-   * subgraphs
+   * @throws CDKException if there is a problem in obtaining subgraphs
    */
   private static List getMaximum(ArrayList graphList) throws CDKException {
     List reducedGraphList = (List) graphList.clone();
@@ -592,13 +595,12 @@ private static List getMaximum(ArrayList graphLi
   }
 
   /**
-   *  Checks for single atom cases before doing subgraph/isomorphism search
+   *  Checks for single atom cases before doing subgraph/isomorphism search.
    *
-   * @param  g1  AtomContainer to match on. Must not be an IQueryAtomContainer.
-   * @param  g2  AtomContainer as query. May be an IQueryAtomContainer.
-   * @return     List of List of RMap objects for the Atoms (not Bonds!), null if no single atom case
-   * @throws org.openscience.cdk.exception.CDKException if the first molecule is an instance
-   * of IQueryAtomContainer
+   * @param  g1  AtomContainer to match on. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  AtomContainer as query. May be an {@link IQueryAtomContainer}.
+   * @return     {@link List} of {@link List} of {@link RMap} objects for the Atoms (not Bonds!), null if no single atom case
+   * @throws     CDKException if the first molecule is an instance of IQueryAtomContainer
   */
   public static List checkSingleAtomCases(IAtomContainer g1, IAtomContainer g2) throws CDKException {
 	  if (g1 instanceof IQueryAtomContainer)
@@ -644,12 +646,13 @@ public static List checkSingleAtomCases(IAtomContainer g1, IAtomContainer
   }
 
   /**
-   *  This makes maps of matching atoms out of a maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
+   *  This makes maps of matching atoms out of a maps of matching bonds as produced by the
+   *  get(Subgraph|Ismorphism)Maps methods.
    *
    * @param  l   The list produced by the getMap method.
-   * @param  g1  The first atom container. Must not be a IQueryAtomContainer.
-   * @param  g2  The second one (first and second as in getMap). May be an QueryAtomContaienr.
-   * @return     A Vector of Vectors of RMap objects of matching Atoms.
+   * @param  g1  The first atom container. Must not be a {@link IQueryAtomContainer}.
+   * @param  g2  The second one (first and second as in getMap). May be an {@link QueryAtomContainer}.
+   * @return     A List of {@link List}s of {@link RMap} objects of matching Atoms.
    */
   public static List> makeAtomsMapsOfBondsMaps(List> l, IAtomContainer g1, IAtomContainer g2) {
       if (l == null) {
@@ -664,12 +667,14 @@ public static List> makeAtomsMapsOfBondsMaps(List> l, IAto
   }
 
   /**
-   *  This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
+   *  This makes a map of matching atoms out of a map of matching bonds as produced by the
+   *  get(Subgraph|Ismorphism)Map methods.
    *
    * @param  l   The list produced by the getMap method.
-   * @param  g1  first molecule. Must not be an IQueryAtomContainer.
-   * @param  g2  second molecule. May be an IQueryAtomContainer.
-   * @return     The mapping found projected on g1. This is a List of RMap objects containing Ids of matching atoms.
+   * @param  g1  first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  g2  second molecule. May be an {@link IQueryAtomContainer}.
+   * @return     The mapping found projected on g1. This is a {@link List} of {@link RMap} objects
+   *             containing Ids of matching atoms.
    */
   public static List makeAtomsMapOfBondsMap(List l, IAtomContainer g1, IAtomContainer g2) {
     if(l==null)
@@ -723,13 +728,13 @@ public static List makeAtomsMapOfBondsMap(List l, IAtomContainer g1,
 
 
   /**
-   *  Builds  the nodes of the RGraph ( resolution graph ), from
+   *  Builds  the nodes of the {@link RGraph} ( resolution graph ), from
    *  two atom containers (description of the two molecules to compare)
    *
    * @param  gr   the target RGraph
-   * @param  ac1   first molecule. Must not be an IQueryAtomContainer.
-   * @param  ac2   second molecule. May be an IQueryAtomContainer.
-   * @throws org.openscience.cdk.exception.CDKException if it takes too long to identify overlaps
+   * @param  ac1   first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  ac2   second molecule. May be an {@link IQueryAtomContainer}.
+   * @throws CDKException if it takes too long to identify overlaps
    */
   private static void nodeConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2) throws CDKException {
 	  if (ac1 instanceof IQueryAtomContainer)
@@ -797,15 +802,15 @@ private static void nodeConstructor(RGraph gr, IAtomContainer ac1, IAtomContaine
 
 
   /**
-   *  Build edges of the RGraphs
+   *  Build edges of the {@link RGraph}s.
    *  This method create the edge of the RGraph and
-   *  calculates the incompatibility and neighbourhood
+   *  calculates the incompatibility and neighborhood
    *  relationships between RGraph nodes.
    *
    * @param  gr   the rGraph
-   * @param  ac1   first molecule. Must not be an IQueryAtomContainer.
-   * @param  ac2   second molecule. May be an IQueryAtomContainer.
-   * @throws org.openscience.cdk.exception.CDKException if it takes too long to get the overlaps
+   * @param  ac1   first molecule. Must not be an {@link IQueryAtomContainer}.
+   * @param  ac2   second molecule. May be an {@link IQueryAtomContainer}.
+   * @throws CDKException if it takes too long to get the overlaps
    */
   private static void arcConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2) throws CDKException{
     // each node is incompatible with himself
@@ -825,7 +830,7 @@ private static void arcConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer
     for (int i = 0; i < gr.getGraph().size(); i++) {
       RNode x = gr.getGraph().get(i);
 
-      // two nodes are neighbours if their adjacency
+      // two nodes are neighbors if their adjacency
       // relationship in are equivalent in G1 and G2
       // else they are incompatible.
       for (int j = i + 1; j < gr.getGraph().size(); j++) {
@@ -875,7 +880,7 @@ private static boolean hasCommonAtom(IBond a, IBond b) {
   }
 
   /**
-   *  Determines if 2 bond have 1 atom in common and returns the common symbol
+   *  Determines if 2 bond have 1 atom in common and returns the common symbol.
    *
    * @param  a  first bond
    * @param  b  second bond
@@ -895,7 +900,7 @@ private static String getCommonSymbol(IBond a, IBond b) {
   }
 
     /**
-   *  Determines if 2 bond have 1 atom in common if second is a query AtomContainer
+   *  Determines if 2 bond have 1 atom in common if second is a query AtomContainer.
    *
    * @param  a1  first bond
    * @param  b1  second bond
@@ -928,7 +933,7 @@ private static boolean queryAdjacency(IBond a1, IBond b1, IBond a2, IBond b2) {
   
   /**
    *  Determines if 2 bond have 1 atom in common if second is a query AtomContainer
-   *  and wheter the order of the atoms is correct (atoms match).
+   *  and whether the order of the atoms is correct (atoms match).
    *
    * @param  bond1  first bond
    * @param  bond2  second bond
@@ -973,11 +978,10 @@ private static boolean queryAdjacencyAndOrder(IBond bond1, IBond bond2, IBond qu
    *  number of nitrogen atoms in the query is larger than that of the supergraph
    *  it cannot be part of it.
    *
-   * @param  ac1  the supergraph to be checked. Must not be an IQueryAtomContainer.
-   * @param  ac2  the subgraph to be tested for. May be an IQueryAtomContainer.
+   * @param  ac1  the supergraph to be checked. Must not be an {@link IQueryAtomContainer}.
+   * @param  ac2  the subgraph to be tested for. May be an {@link IQueryAtomContainer}.
    * @return    true if the subgraph ac2 has a chance to be a subgraph of ac1
-   * @throws org.openscience.cdk.exception.CDKException if the first molecule is an instance
-   * of IQueryAtomContainer
+   * @throws CDKException if the first molecule is an instance of {@link IQueryAtomContainer}
    */
   private static boolean testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
   	throws CDKException {

From 14e1d12d71f63ccc8243237b706e0ffdea9e42c0 Mon Sep 17 00:00:00 2001
From: Egon Willighagen 
Date: Wed, 24 Feb 2010 22:00:49 +0100
Subject: [PATCH 3/5] Removed output to STDOUT

Signed-off-by: Rajarshi  Guha 
---
 .../cdk/isomorphism/UniversalIsomorphismTesterTest.java    | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/src/test/org/openscience/cdk/isomorphism/UniversalIsomorphismTesterTest.java b/src/test/org/openscience/cdk/isomorphism/UniversalIsomorphismTesterTest.java
index 2f8bcd40fb8..923c522ab30 100644
--- a/src/test/org/openscience/cdk/isomorphism/UniversalIsomorphismTesterTest.java
+++ b/src/test/org/openscience/cdk/isomorphism/UniversalIsomorphismTesterTest.java
@@ -262,13 +262,6 @@ public class UniversalIsomorphismTesterTest extends CDKTestCase
 //		CDKHueckelAromaticityDetector.detectAromaticity(mol1);
 		Iterator atoms = mol1.atoms().iterator();
 		int i= 1;
-		while (atoms.hasNext()) {
-			IAtom nextAtom = atoms.next();
-			System.out.println(i + ": " + nextAtom.getSymbol() +
-				" T:" + nextAtom.getAtomTypeName() +
-				" A:" + nextAtom.getFlag(CDKConstants.ISAROMATIC));
-			i++;
-		}
 		AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
 		Assert.assertTrue(CDKHueckelAromaticityDetector.detectAromaticity(mol2));
         list = UniversalIsomorphismTester.getOverlaps(mol1, mol2);

From 7727b72d7f3a0b55a335fcd474e1bb26009e3236 Mon Sep 17 00:00:00 2001
From: Egon Willighagen 
Date: Wed, 24 Feb 2010 22:05:27 +0100
Subject: [PATCH 4/5] Removed last bits of implementation details from the API:
 now uses List<> instead of ArrayList<>

Signed-off-by: Rajarshi  Guha 
---
 .../cdk/isomorphism/UniversalIsomorphismTester.java   | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java b/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
index b9ca48a1f61..8a186ef5407 100644
--- a/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
+++ b/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
@@ -369,7 +369,7 @@ public static List getOverlaps(IAtomContainer g1, IAtomContainer
       List> rMapsList = search(g1, g2, new BitSet(), new BitSet(), true, false);
 
       // projection on G1
-      ArrayList graphList = projectList(rMapsList, g1, ID1);
+      List graphList = projectList(rMapsList, g1, ID1);
 
       // reduction of set of solution (isomorphism and substructure
       // with different 'mappings'
@@ -556,8 +556,8 @@ public static IAtomContainer project(List rMapList, IAtomContainer g, int
    * @param  id         the id in the RMap of the molecule g
    * @return            a list of AtomContainer
    */
-  public static ArrayList projectList(List> rMapsList, IAtomContainer g, int id) {
-    ArrayList graphList = new ArrayList();
+  public static List projectList(List> rMapsList, IAtomContainer g, int id) {
+    List graphList = new ArrayList();
 
       for (List rMapList : rMapsList) {
           IAtomContainer ac = project(rMapList, g, id);
@@ -573,8 +573,9 @@ public static ArrayList projectList(List> rMapsList,
    * @return            the list cleaned
    * @throws CDKException if there is a problem in obtaining subgraphs
    */
-  private static List getMaximum(ArrayList graphList) throws CDKException {
-    List reducedGraphList = (List) graphList.clone();
+  private static List getMaximum(List graphList) throws CDKException {
+    List reducedGraphList = new ArrayList();
+    reducedGraphList.addAll(graphList);
 
     for (int i = 0; i < graphList.size(); i++) {
       IAtomContainer gi = graphList.get(i);

From e1c03fbff0543113fb7b1d2be15dd32441592ada Mon Sep 17 00:00:00 2001
From: Egon Willighagen 
Date: Fri, 26 Feb 2010 09:01:10 +0100
Subject: [PATCH 5/5] Removed unused import

---
 .../openscience/cdk/isomorphism/UniversalIsomorphismTester.java  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java b/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
index 8a186ef5407..3f29cc5bba1 100644
--- a/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
+++ b/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
@@ -36,7 +36,6 @@
 import org.openscience.cdk.isomorphism.matchers.IQueryAtom;
 import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer;
 import org.openscience.cdk.isomorphism.matchers.IQueryBond;
-import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
 import org.openscience.cdk.isomorphism.mcss.RGraph;
 import org.openscience.cdk.isomorphism.mcss.RMap;
 import org.openscience.cdk.isomorphism.mcss.RNode;