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[Cdk-commits] SF.net SVN: cdk:[11971] cdk/trunk/src/main/org/openscience/cdk/isomorphism/ UniversalIsomorphismTester.java
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From: <raj...@us...> - 2008-08-10 04:47:37
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Revision: 11971
http://cdk.svn.sourceforge.net/cdk/?rev=11971&view=rev
Author: rajarshi
Date: 2008-08-10 04:47:34 +0000 (Sun, 10 Aug 2008)
Log Message:
-----------
Cleaned up some code and javadocs
Modified Paths:
--------------
cdk/trunk/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
Modified: cdk/trunk/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java 2008-08-10 04:09:40 UTC (rev 11970)
+++ cdk/trunk/src/main/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java 2008-08-10 04:47:34 UTC (rev 11971)
@@ -28,26 +28,21 @@
*/
package org.openscience.cdk.isomorphism;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
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.IQueryAtomContainer;
import org.openscience.cdk.isomorphism.mcss.RGraph;
import org.openscience.cdk.isomorphism.mcss.RMap;
import org.openscience.cdk.isomorphism.mcss.RNode;
import org.openscience.cdk.tools.manipulator.BondManipulator;
+import java.util.*;
+
/**
* This class implements a multipurpose structure comparison tool.
* It allows to find maximal common substructure, find the
@@ -122,6 +117,8 @@
* @param g1 first molecule. Must not be an IQueryAtomContainer.
* @param g2 second molecule. May be an IQueryAtomContainer.
* @return true if the 2 molecule are isomorph
+ * @throws org.openscience.cdk.exception.CDKException if the first molecule is an instance
+ * of IQueryAtomContainer
*/
public static boolean isIsomorph(IAtomContainer g1, IAtomContainer g2) throws CDKException{
if (g1 instanceof IQueryAtomContainer)
@@ -179,7 +176,8 @@
*
* @param g1 first molecule. Must not be an IQueryAtomContainer.
* @param g2 second molecule. May be an IQueryAtomContainer.
- * @return the first isomorph atom mapping found projected on g1. This is a List of RMap objects containing Ids of matching atoms.
+ * @return the first isomorph atom mapping found projected on g1.
+ * This is a List of RMap objects containing Ids of matching atoms.
*/
public static List<RMap> getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g2) throws CDKException {
if (g1 instanceof IQueryAtomContainer)
@@ -417,10 +415,9 @@
List<BitSet> solutionList = rGraph.getSolutions();
// conversions of RGraph's internal solutions to G1/G2 mappings
- for (Iterator<BitSet> i = solutionList.iterator(); i.hasNext(); ) {
- BitSet set = i.next();
- rMapsList.add(rGraph.bitSetToRMap(set));
- }
+ for (BitSet set : solutionList) {
+ rMapsList.add(rGraph.bitSetToRMap(set));
+ }
return rMapsList;
}
@@ -467,7 +464,7 @@
}
a = bond.getAtom(1);
- a2 = (IAtom) table.get(a);
+ a2 = table.get(a);
if (a2 == null) {
try {
@@ -500,11 +497,10 @@
public static ArrayList<IAtomContainer> projectList(List<List<RMap>> rMapsList, IAtomContainer g, int id) {
ArrayList<IAtomContainer> graphList = new ArrayList<IAtomContainer>();
- for (Iterator<List<RMap>> i = rMapsList.iterator(); i.hasNext(); ) {
- List<RMap> rMapList = i.next();
- IAtomContainer ac = project(rMapList, g, id);
- graphList.add(ac);
- }
+ for (List<RMap> rMapList : rMapsList) {
+ IAtomContainer ac = project(rMapList, g, id);
+ graphList.add(ac);
+ }
return graphList;
}
@@ -513,9 +509,11 @@
*
* @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
*/
- private static List<IAtomContainer> getMaximum(ArrayList<IAtomContainer> graphList) throws CDKException{
- List<IAtomContainer> reducedGraphList = (List) graphList.clone();
+ private static List<IAtomContainer> getMaximum(ArrayList<IAtomContainer> graphList) throws CDKException {
+ List<IAtomContainer> reducedGraphList = (List<IAtomContainer>) graphList.clone();
for (int i = 0; i < graphList.size(); i++) {
IAtomContainer gi = graphList.get(i);
@@ -541,6 +539,8 @@
* @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
*/
public static List<RMap> checkSingleAtomCases(IAtomContainer g1, IAtomContainer g2) throws CDKException {
if (g1 instanceof IQueryAtomContainer)
@@ -598,10 +598,9 @@
return l;
}
List<List<RMap>> result = new ArrayList<List<RMap>>();
- for (int i = 0; i < l.size(); i++) {
- List<RMap> l2 = l.get(i);
- result.add(makeAtomsMapOfBondsMap(l2, g1, g2));
- }
+ for (List<RMap> l2 : l) {
+ result.add(makeAtomsMapOfBondsMap(l2, g1, g2));
+ }
return result;
}
@@ -669,8 +668,9 @@
* two atom containers (description of the two molecules to compare)
*
* @param gr the target RGraph
- * @param g1 first molecule. Must not be an IQueryAtomContainer.
- * @param g2 second molecule. May be an IQueryAtomContainer.
+ * @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
*/
private static void nodeConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2) throws CDKException {
if (ac1 instanceof IQueryAtomContainer)
@@ -744,8 +744,9 @@
* relationships between RGraph nodes.
*
* @param gr the rGraph
- * @param g1 first molecule. Must not be an IQueryAtomContainer.
- * @param g2 second molecule. May be an IQueryAtomContainer.
+ * @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
*/
private static void arcConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2) throws CDKException{
// each node is incompatible with himself
@@ -763,7 +764,7 @@
gr.setSecondGraphSize(ac2.getBondCount());
for (int i = 0; i < gr.getGraph().size(); i++) {
- RNode x = (RNode) gr.getGraph().get(i);
+ RNode x = gr.getGraph().get(i);
// two nodes are neighbours if their adjacency
// relationship in are equivalent in G1 and G2
@@ -771,12 +772,12 @@
for (int j = i + 1; j < gr.getGraph().size(); j++) {
if(timeout>-1 && (System.currentTimeMillis()-start)>timeout)
throw new CDKException("Timeout exceeded in getOverlaps");
- RNode y = (RNode) gr.getGraph().get(j);
+ RNode y = gr.getGraph().get(j);
- a1 = ac1.getBond(((RNode) gr.getGraph().get(i)).getRMap().getId1());
- a2 = ac2.getBond(((RNode) gr.getGraph().get(i)).getRMap().getId2());
- b1 = ac1.getBond(((RNode) gr.getGraph().get(j)).getRMap().getId1());
- b2 = ac2.getBond(((RNode) gr.getGraph().get(j)).getRMap().getId2());
+ a1 = ac1.getBond(gr.getGraph().get(i).getRMap().getId1());
+ a2 = ac2.getBond(gr.getGraph().get(i).getRMap().getId2());
+ b1 = ac1.getBond(gr.getGraph().get(j).getRMap().getId1());
+ b2 = ac2.getBond(gr.getGraph().get(j).getRMap().getId2());
if (a2 instanceof IQueryBond) {
if (a1.equals(b1) || a2.equals(b2) ||
@@ -870,10 +871,11 @@
* 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).
*
- * @param a1 first bond
- * @param b1 second bond
- * @return the symbol of the common atom or "" if
- * the 2 bonds have no common atom
+ * @param bond1 first bond
+ * @param bond2 second bond
+ * @param queryBond1 first query bond
+ * @param queryBond2 second query bond
+ * @return the symbol of the common atom or "" if the 2 bonds have no common atom
*/
private static boolean queryAdjacencyAndOrder(IBond bond1, IBond bond2, IBond queryBond1, IBond queryBond2) {
@@ -915,6 +917,8 @@
* @param ac1 the supergraph to be checked. Must not be an IQueryAtomContainer.
* @param ac2 the subgraph to be tested for. May be an 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
*/
private static boolean testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
throws CDKException {
@@ -1007,10 +1011,9 @@
if (ac1ClCount < ac2ClCount) return false;
if (ac1BrCount < ac2BrCount) return false;
if (ac1ICount < ac2ICount) return false;
- if (ac1CCount < ac2CCount) return false;
+ return ac1CCount >= ac2CCount;
- return true;
}
}
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