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fixed makeAtomsMapOfBondsMap with test
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Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
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@asad @rajarshi
asad authored and rajarshi committed May 22, 2010
1 parent 5193626 commit 5bd8d64
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Showing 2 changed files with 192 additions and 79 deletions.
230 changes: 154 additions & 76 deletions src/main/org/openscience/cdk/smsd/algorithm/cdk/CDKRMapHandler.java
View file
Expand Up @@ -24,6 +24,7 @@

import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Stack;
Expand All @@ -33,6 +34,8 @@
import org.openscience.cdk.smsd.helper.FinalMappings;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.tools.manipulator.BondManipulator;

/**
* This algorithm derives from the algorithm described in
Expand Down Expand Up @@ -80,7 +83,6 @@ public static IAtomContainer getTarget() {
public static void setTarget(IAtomContainer aTarget) {
target = aTarget;
}

private List<Map<Integer, Integer>> mappings;
private static IAtomContainer source;
private static IAtomContainer target;
Expand Down Expand Up @@ -119,7 +121,7 @@ public void calculateOverlapsAndReduce(IAtomContainer Molecule1, IAtomContainer
Stack<List<CDKRMap>> allMaxOverlaps = getAllMaximum(reducedList);
while (!allMaxOverlaps.empty()) {
// System.out.println("source: " + source.getAtomCount() + ", target: " + target.getAtomCount() + ", overl: " + allMaxOverlaps.peek().size());
List<CDKRMap> maxOverlapsAtoms = CDKMCS.makeAtomsMapOfBondsMap(allMaxOverlaps.peek(), getSource(), getTarget());
List<List<CDKRMap>> maxOverlapsAtoms = makeAtomsMapOfBondsMap(allMaxOverlaps.peek(), getSource(), getTarget());
// System.out.println("size of maxOverlaps: " + maxOverlapsAtoms.size());
identifyMatchedParts(maxOverlapsAtoms, getSource(), getTarget());
// identifyMatchedParts(allMaxOverlaps.peek(), source, target);
Expand Down Expand Up @@ -166,9 +168,8 @@ public void calculateOverlapsAndReduceExactMatch(IAtomContainer Molecule1, IAtom
Stack<List<CDKRMap>> allMaxOverlaps = getAllMaximum(reducedList);

while (!allMaxOverlaps.empty()) {
List<CDKRMap> maxOverlapsAtoms = CDKMCS.makeAtomsMapOfBondsMap(allMaxOverlaps.peek(), getSource(), getTarget());
List<List<CDKRMap>> maxOverlapsAtoms = makeAtomsMapOfBondsMap(allMaxOverlaps.peek(), getSource(), getTarget());
identifyMatchedParts(maxOverlapsAtoms, getSource(), getTarget());

allMaxOverlaps.pop();
}
}
Expand Down Expand Up @@ -219,64 +220,142 @@ protected List<CDKRMap> removeRedundantMappingsForSingleAtomCase(List<CDKRMap> o

}

// /**
// * This makes sourceAtom map of matching atoms out of sourceAtom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
// *
// * @param rMapList The list produced by the getMap method.
// * @param graph1 first molecule. Must not be an IQueryAtomContainer.
// * @param graph2 second molecule. May be an IQueryAtomContainer.
// * @return The mapping found projected on graph1. This is sourceAtom List of CDKRMap objects containing Ids of matching atoms.
// */
// public static List<CDKRMap> makeAtomsMapOfBondsMap(List<CDKRMap> rMapList, IAtomContainer graph1, IAtomContainer graph2) {
// if (rMapList == null) {
// return (rMapList);
// }
// List<CDKRMap> result = new ArrayList<CDKRMap>();
// for (int i = 0; i < rMapList.size(); i++) {
// IBond bond1 = graph1.getBond(rMapList.get(i).getId1());
// IBond bond2 = graph2.getBond(rMapList.get(i).getId2());
// IAtom[] atom1 = BondManipulator.getAtomArray(bond1);
// IAtom[] atom2 = BondManipulator.getAtomArray(bond2);
// for (int j = 0; j < 2; j++) {
// List<IBond> bondsConnectedToAtom1j = graph1.getConnectedBondsList(atom1[j]);
// for (int k = 0; k < bondsConnectedToAtom1j.size(); k++) {
// if (bondsConnectedToAtom1j.get(k) != bond1) {
// IBond testBond = bondsConnectedToAtom1j.get(k);
// for (int m = 0; m < rMapList.size(); m++) {
// IBond testBond2;
// if ((rMapList.get(m)).getId1() == graph1.getBondNumber(testBond)) {
// testBond2 = graph2.getBond((rMapList.get(m)).getId2());
// for (int n = 0; n < 2; n++) {
// List<IBond> bondsToTest = graph2.getConnectedBondsList(atom2[n]);
// if (bondsToTest.contains(testBond2)) {
// CDKRMap map;
// if (j == n) {
// map = new CDKRMap(graph1.getAtomNumber(atom1[0]), graph2.getAtomNumber(atom2[0]));
// } else {
// map = new CDKRMap(graph1.getAtomNumber(atom1[1]), graph2.getAtomNumber(atom2[0]));
// }
// if (!result.contains(map)) {
// result.add(map);
// }
// CDKRMap map2;
// if (j == n) {
// map2 = new CDKRMap(graph1.getAtomNumber(atom1[1]), graph2.getAtomNumber(atom2[1]));
// } else {
// map2 = new CDKRMap(graph1.getAtomNumber(atom1[0]), graph2.getAtomNumber(atom2[1]));
// }
// if (!result.contains(map2)) {
// result.add(map2);
// }
// }
// }
// }
// }
// }
// }
// }
// }
// return result;
// }
/**
* This makes sourceAtom map of matching atoms out of sourceAtom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
*
* @param rMapList The list produced by the getMap method.
* @param graph1 first molecule. Must not be an IQueryAtomContainer.
* @param graph2 second molecule. May be an IQueryAtomContainer.
* @return The mapping found projected on graph1. This is sourceAtom List of CDKRMap objects containing Ids of matching atoms.
*/
public static List<List<CDKRMap>> makeAtomsMapOfBondsMap(List<CDKRMap> rMapList, IAtomContainer graph1, IAtomContainer graph2) {
if (rMapList == null) {
return (null);
}
List<List<CDKRMap>> result = null;
if (rMapList.size() == 1) {
result = makeAtomsMapOfBondsMapSingleBond(rMapList, graph1, graph2);
} else {
List<CDKRMap> resultLocal = new ArrayList<CDKRMap>();
for (int i = 0; i < rMapList.size(); i++) {
IBond qBond = graph1.getBond(rMapList.get(i).getId1());
IBond tBond = graph2.getBond(rMapList.get(i).getId2());
IAtom[] qAtoms = BondManipulator.getAtomArray(qBond);
IAtom[] tAtoms = BondManipulator.getAtomArray(tBond);
for (int j = 0; j < 2; j++) {
List<IBond> bondsConnectedToAtom1j = graph1.getConnectedBondsList(qAtoms[j]);
for (int k = 0; k < bondsConnectedToAtom1j.size(); k++) {
if (bondsConnectedToAtom1j.get(k) != qBond) {
IBond testBond = bondsConnectedToAtom1j.get(k);
for (int m = 0; m < rMapList.size(); m++) {
IBond testBond2;
if ((rMapList.get(m)).getId1() == graph1.getBondNumber(testBond)) {
testBond2 = graph2.getBond((rMapList.get(m)).getId2());
for (int n = 0; n < 2; n++) {
List<IBond> bondsToTest = graph2.getConnectedBondsList(tAtoms[n]);
if (bondsToTest.contains(testBond2)) {
CDKRMap map;
if (j == n) {
map = new CDKRMap(graph1.getAtomNumber(qAtoms[0]), graph2.getAtomNumber(tAtoms[0]));
} else {
map = new CDKRMap(graph1.getAtomNumber(qAtoms[1]), graph2.getAtomNumber(tAtoms[0]));
}
if (!resultLocal.contains(map)) {
resultLocal.add(map);
}
CDKRMap map2;
if (j == n) {
map2 = new CDKRMap(graph1.getAtomNumber(qAtoms[1]), graph2.getAtomNumber(tAtoms[1]));
} else {
map2 = new CDKRMap(graph1.getAtomNumber(qAtoms[0]), graph2.getAtomNumber(tAtoms[1]));
}
if (!resultLocal.contains(map2)) {
resultLocal.add(map2);
}
}
}
}
}
}
}
}
}
result = new ArrayList<List<CDKRMap>>();
result.add(resultLocal);
}
return result;
}

/**
* This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
* @see Added by Asad since CDK one doesn't pick up the correct changes
* @param list The list produced by the getMap method.
* @param sourceGraph first molecule. Must not be an IQueryAtomContainer.
* @param targetGraph second molecule. May be an IQueryAtomContainer.
* @return The mapping found projected on sourceGraph. This is atom List of CDKRMap objects containing Ids of matching atoms.
*/
public static List<List<CDKRMap>> makeAtomsMapOfBondsMapSingleBond(List<CDKRMap> list, IAtomContainer sourceGraph, IAtomContainer targetGraph) {
if (list == null) {
return null;
}
Map<IBond, IBond> bondMap = new HashMap<IBond, IBond>(list.size());
for (CDKRMap solBondMap : list) {
int id1 = solBondMap.getId1();
int id2 = solBondMap.getId2();
IBond qBond = sourceGraph.getBond(id1);
IBond tBond = targetGraph.getBond(id2);
bondMap.put(qBond, tBond);
}
List<CDKRMap> result1 = new ArrayList<CDKRMap>();
List<CDKRMap> result2 = new ArrayList<CDKRMap>();
for (IBond qbond : sourceGraph.bonds()) {
if (bondMap.containsKey(qbond)) {
IBond tbond = bondMap.get(qbond);
CDKRMap map00 = null;
CDKRMap map01 = null;
CDKRMap map10 = null;
CDKRMap map11 = null;

if ((qbond.getAtom(0).getSymbol().equals(tbond.getAtom(0).getSymbol()))
&& (qbond.getAtom(1).getSymbol().equals(tbond.getAtom(1).getSymbol()))) {
map00 = new CDKRMap(sourceGraph.getAtomNumber(qbond.getAtom(0)),
targetGraph.getAtomNumber(tbond.getAtom(0)));
map11 = new CDKRMap(sourceGraph.getAtomNumber(qbond.getAtom(1)),
targetGraph.getAtomNumber(tbond.getAtom(1)));
if (!result1.contains(map00)) {
result1.add(map00);
}
if (!result1.contains(map11)) {
result1.add(map11);
}
}
if ((qbond.getAtom(0).getSymbol().equals(tbond.getAtom(1).getSymbol()))
&& (qbond.getAtom(1).getSymbol().equals(tbond.getAtom(0).getSymbol()))) {
map01 = new CDKRMap(sourceGraph.getAtomNumber(qbond.getAtom(0)),
targetGraph.getAtomNumber(tbond.getAtom(1)));
map10 = new CDKRMap(sourceGraph.getAtomNumber(qbond.getAtom(1)),
targetGraph.getAtomNumber(tbond.getAtom(0)));
if (!result2.contains(map01)) {
result2.add(map01);
}
if (!result2.contains(map10)) {
result2.add(map10);
}
}
}
}
List<List<CDKRMap>> result = new ArrayList<List<CDKRMap>>();
if (result1.size() == result2.size()) {
result.add(result1);
result.add(result2);
} else if (result1.size() > result2.size()) {
result.add(result1);
} else {
result.add(result2);
}
return result;
}

/**
*
* @param overlaps
Expand Down Expand Up @@ -338,33 +417,32 @@ protected Stack<List<CDKRMap>> getAllMaximum(List<List<CDKRMap>> overlaps) {
* @param source
* @param target
*/
protected void identifyMatchedParts(List<CDKRMap> list, IAtomContainer source, IAtomContainer target) {
protected void identifyMatchedParts(List<List<CDKRMap>> list, IAtomContainer source, IAtomContainer target) {

List<IAtom> array1 = new ArrayList<IAtom>();
List<IAtom> array2 = new ArrayList<IAtom>();

TreeMap<Integer, Integer> atomNumbersFromContainer = new TreeMap<Integer, Integer>();

/*
* We have serial numbers of the bonds/Atoms to delete
* Now we will collect the actual bond/Atoms rather than
* serial number for deletion. RonP flag check whether Reactant is
* mapped on Product or Vise Versa
*
*
*/
for (List<CDKRMap> rMap : list) {
Map<Integer, Integer> atomNumbersFromContainer = new TreeMap<Integer, Integer>();
for (CDKRMap rmap : rMap) {
IAtom sourceAtom = source.getAtom(rmap.getId1());
IAtom targetAtom = target.getAtom(rmap.getId2());

for (CDKRMap rmap : list) {
IAtom sourceAtom = source.getAtom(rmap.getId1());
IAtom targetAtom = target.getAtom(rmap.getId2());
array1.add(sourceAtom);
array2.add(targetAtom);

array1.add(sourceAtom);
array2.add(targetAtom);

int IndexI = source.getAtomNumber(sourceAtom);
int IndexJ = target.getAtomNumber(targetAtom);

atomNumbersFromContainer.put(IndexI, IndexJ);
int IndexI = source.getAtomNumber(sourceAtom);
int IndexJ = target.getAtomNumber(targetAtom);

atomNumbersFromContainer.put(IndexI, IndexJ);
}
/*Added the Mapping Numbers to the FinalMapping*
*/
getMappings().add(atomNumbersFromContainer);
Expand Down
41 changes: 38 additions & 3 deletions src/test/org/openscience/cdk/smsd/SMSDTest.java
View file
Expand Up @@ -125,11 +125,12 @@ public void testSearchMCS() throws CDKException {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer target = null;
target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
IAtomContainer queryac = null;
queryac = sp.parseSmiles("Nc1ccccc1");
IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");
SMSD smsd1 = new SMSD(Algorithm.DEFAULT, true);
smsd1.init(queryac, target, true);
smsd1.setChemFilters(true, true, true);
Assert.assertEquals(7, smsd1.getFirstAtomMapping().size());
Assert.assertEquals(2, smsd1.getAllAtomMapping().size());
assertNotNull(smsd1.getFirstMapping());
} catch (InvalidSmilesException ex) {
Logger.getLogger(MCSPlusHandlerTest.class.getName()).log(Level.SEVERE, null, ex);
Expand Down Expand Up @@ -529,7 +530,23 @@ public void testQueryAtomContainerSubstructure() throws CDKException {
Assert.assertTrue(foundMatches);
}

@Test
public void testQueryAtomCount() throws CDKException {
SMSD smsd = new SMSD(Algorithm.DEFAULT, true);
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer query = sp.parseSmiles("CC");
IAtomContainer target = sp.parseSmiles("C1CCC12CCCC2");

smsd.init(query, target, false);
boolean foundMatches = smsd.isSubgraph();
Assert.assertEquals(18, smsd.getAllAtomMapping().size());
Assert.assertTrue(foundMatches);

IQueryAtomContainer queryContainer = QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(query);
smsd.init(queryContainer, target, false);
foundMatches = smsd.isSubgraph();
Assert.assertTrue(foundMatches);
}

public void testMatchCount() throws CDKException {
SMSD smsd = new SMSD(Algorithm.DEFAULT, true);
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
Expand All @@ -547,6 +564,24 @@ public void testMatchCount() throws CDKException {
Assert.assertTrue(foundMatches);
}

@Test
public void testMatchCountCDKMCS() throws CDKException {
SMSD smsd = new SMSD(Algorithm.DEFAULT, true);
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer query = sp.parseSmiles("CC");
IAtomContainer target = sp.parseSmiles("C1CCC12CCCC2");

smsd.init(query, target, false);
boolean foundMatches = smsd.isSubgraph();
Assert.assertEquals(18, smsd.getAllAtomMapping().size());
Assert.assertTrue(foundMatches);

IQueryAtomContainer queryContainer = QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(query);
smsd.init(queryContainer, target, false);
foundMatches = smsd.isSubgraph();
Assert.assertTrue(foundMatches);
}

@Test
public void testImpossibleQuery() throws CDKException {
SMSD smsd = new SMSD(Algorithm.DEFAULT, true);
Expand Down

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