Merge branch 'master' of https://github.com/Actelion/openchemlib

pom.xml

@@ -8,7 +8,7 @@
     Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH
     (eg. 2016.4.1 for second release in Apr 2016)
     -->
-    <version>2024.7.1-SNAPSHOT</version>
+    <version>2024.7.2-SNAPSHOT</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>

src/main/java/com/actelion/research/chem/descriptor/flexophore/IMolDistHist.java

@@ -45,7 +45,9 @@ public interface IMolDistHist extends ICompleteGraph {
 	byte [] getDistHist(int indexAt1, int indexAt2, byte[] arr);
 
 	boolean isInevitablePharmacophorePoint(int indexNode);
-
+
+	double getWeightPharmacophorePoint(int indexNode);
+
 	int getNumInevitablePharmacophorePoints();
 
 

src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHist.java

@@ -459,9 +459,12 @@ public int getNumInevitablePharmacophorePoints() {
 
 	@Override
 	public boolean isInevitablePharmacophorePoint(int indexNode) {
-		// TODO Auto-generated method stub
 		return false;
 	}
+	@Override
+	public double getWeightPharmacophorePoint(int indexNode) {
+		return 1.0;
+	}
 
 	public static int getNumBytesEntry(){
 		return PPNode.getNumBytesEntry()+1;

src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistViz.java

@@ -104,7 +104,8 @@ public class MolDistHistViz extends DistHist implements Serializable, IMolDistHi
 	private boolean finalized;
 
 	private HashSet<Integer> hsIndexInevitablePPPoints;
-
+	private double [] arrWeight;
+
 	// List of the original distance table generated by the conformations.
 	private List<float[][]> liDistanceTable;
 
@@ -167,19 +168,14 @@ public MolDistHistViz(MolDistHist mdh) {
 		if(mdh.getNumPPNodes()==0){
 			throw new RuntimeException("Empty object given into constructor.");
 		}
-
 		mdh.copy(this);
-
 		modeFlexophore = mdh.getModeFlexophore();
-
-		liPPNodeViz=new ArrayList<PPNodeViz>(mdh.getNumPPNodes());
+		liPPNodeViz=new ArrayList<>(mdh.getNumPPNodes());
 		for (int i = 0; i < mdh.getNumPPNodes(); i++) {
 			PPNodeViz node = new PPNodeViz(mdh.getNode(i));
 			liPPNodeViz.add(node);
 		}
-
-		hsIndexInevitablePPPoints = new HashSet<Integer>();
-
+		hsIndexInevitablePPPoints = new HashSet<>();
 		realize();
 	}
 
@@ -191,6 +187,13 @@ public void addInevitablePharmacophorePoint(int indexPPNode){
 		hsIndexInevitablePPPoints.add(indexPPNode);
 	}
 
+	public void setNodeWeight(int indexNode, double weight){
+		if(!finalized){
+			throw new RuntimeException("MolDistHistViz not finalized!");
+		}
+		arrWeight[indexNode]=weight;
+	}
+
 	public void removeInevitablePharmacophorePoint(int indexPPNode){
 		hsIndexInevitablePPPoints.remove(indexPPNode);
 	}
@@ -301,6 +304,10 @@ public void copy(MolDistHistViz copy){
 		copy.hsIndexInevitablePPPoints.clear();
 
 		copy.hsIndexInevitablePPPoints.addAll(hsIndexInevitablePPPoints);
+
+		copy.arrWeight = new double[this.arrWeight.length];
+
+		System.arraycopy(this.arrWeight, 0, copy.arrWeight, 0, this.arrWeight.length);
 
 	}
 
@@ -571,6 +578,12 @@ public void swapNodes(int n1, int n2){
 				setDistHist(n2,i, histTmp);
 			}
 		}
+
+		double w1 = arrWeight[n1];
+
+		arrWeight[n1]=arrWeight[n2];
+		arrWeight[n2]=w1;
+
 	}
 
 	private int compare(byte [] arr1, byte [] arr2) {
@@ -616,7 +629,10 @@ public boolean isInevitablePharmacophorePoint(int indexNode){
 
 		return hsIndexInevitablePPPoints.contains(indexNode);
 	}
-
+	@Override
+	public double getWeightPharmacophorePoint(int indexNode) {
+		return arrWeight[indexNode];
+	}
 	public boolean isAliphatic(int indexNode) {
 
 		boolean aliphatic = true;
@@ -757,6 +773,10 @@ private int calcNumCExclusiveNodes(){
 	 * Must be called after changes in the nodes or distance histograms.
 	 */
 	public void realize() {
+
+		arrWeight = new double[liPPNodeViz.size()];
+		Arrays.fill(arrWeight, 1.0);
+
 		for(PPNodeViz node : liPPNodeViz){
 			node.realize();
 		}

src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java

@@ -1,5 +1,6 @@
 package com.actelion.research.chem.descriptor.flexophore.completegraphmatcher;
 
+import com.actelion.research.calc.ArrayUtilsCalc;
 import com.actelion.research.calc.Matrix;
 import com.actelion.research.calc.graph.MinimumSpanningTree;
 import com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore;
@@ -93,6 +94,8 @@ public class ObjectiveBlurFlexophoreHardMatchUncovered implements IObjectiveComp
 
 	private double [][] arrRelativeDistanceMatrixBase;
 
+	private double [] arrSimilarityTmp;
+
 	private Matrix maHelperAdjacencyQuery;
 
 	private Matrix maHelperAdjacencyBase;
@@ -192,6 +195,8 @@ private void initSimilarityMatrices(){
 			arrSimilarityHistograms[i] = new float [maxNumHistograms];
 			Arrays.fill(arrSimilarityHistograms[i], INIT_VAL);
 		}
+
+		arrSimilarityTmp=new double[ConstantsFlexophore.MAX_NUM_NODES_FLEXOPHORE];
 	}
 
 	/**
@@ -320,11 +325,8 @@ public boolean isValidSolution(SolutionCompleteGraph solution) {
 		//
 		if(mapping){
 			for (int i = 0; i < heap; i++) {
-
 				int indexNodeQuery = solution.getIndexQueryFromHeap(i);
-
 				int indexNodeBase = solution.getIndexCorrespondingBaseNode(indexNodeQuery);
-
 				if(!areNodesMapping(indexNodeQuery, indexNodeBase)) {
 					mapping = false;
 					break;
@@ -467,10 +469,17 @@ public float getSimilarity(SolutionCompleteGraph solution) {
 		}
 
 
-		double sumPairwiseMapping = 0;
+		// double sumPairwiseMapping = 0;
 
 		// double productPairwiseMapping = 0;
 
+		int cc=0;
+
+		int nMappings = ((heap * heap)-heap) / 2;
+
+		double [] arrMappingWeights = new double[nMappings];
+		double [] arrSimilarityWeighted = new double[nMappings];
+
 		for (int i = 0; i < heap; i++) {
 
 			int indexNode1Query = solution.getIndexQueryFromHeap(i);
@@ -484,17 +493,25 @@ public float getSimilarity(SolutionCompleteGraph solution) {
 
 				double scorePairwiseMapping = getScorePairwiseMapping(indexNode1Query, indexNode2Query, indexNode1Base, indexNode2Base);
 
-				sumPairwiseMapping += scorePairwiseMapping;
+				double w =
+						mdhvQuery.getWeightPharmacophorePoint(indexNode1Query)
+								* mdhvQuery.getWeightPharmacophorePoint(indexNode2Query);
+
+				arrMappingWeights[cc]=w;
+
+				arrSimilarityWeighted[cc++]=scorePairwiseMapping * w;
 
 				if(verbose) {
 					System.out.println("scorePairwiseMapping " + Formatter.format2(scorePairwiseMapping));
 				}
 			}
 		}
-
-		double mappings = ((heap * heap)-heap) / 2.0;
-
-		avrPairwiseMappingScaled = sumPairwiseMapping/mappings;
+		// double mappings = ((heap * heap)-heap) / 2.0;
+
+		double sumMappingWeights = ArrayUtilsCalc.sum(arrMappingWeights);
+		double sumSimilarityWeighted = ArrayUtilsCalc.sum(arrSimilarityWeighted);
+
+		avrPairwiseMappingScaled = sumSimilarityWeighted/sumMappingWeights;
 
 		coverageQuery = getRatioMinimumSpanningTreeQuery(solution);
 
@@ -633,16 +650,19 @@ public float getSimilarityNodes(SolutionCompleteGraph solution) {
 			return (float)similarity;
 		}
 
-		double sumSimilarityNodes = 0;
+		double sumSimilarityNodesWeighted = 0;
+
+		double sumWeights = 0;
 		for (int i = 0; i < heap; i++) {
 			int indexNodeQuery = solution.getIndexQueryFromHeap(i);
+			double w = mdhvQuery.getWeightPharmacophorePoint(indexNodeQuery);
 			int indexNodeBase = solution.getIndexCorrespondingBaseNode(indexNodeQuery);
-			double similarityNodePair = getSimilarityNodes(indexNodeQuery, indexNodeBase);
-			sumSimilarityNodes += similarityNodePair;
+			double similarityNodePairWeighted = getSimilarityNodes(indexNodeQuery, indexNodeBase)*w;
+			sumSimilarityNodesWeighted += similarityNodePairWeighted;
+			sumWeights+=w;
 		}
 
-		double mappings = heap;
-		avrPairwiseMappingScaled = sumSimilarityNodes/mappings;
+		avrPairwiseMappingScaled = sumSimilarityNodesWeighted / sumWeights;
 		coverageQuery = 0;
 		coverageBase = 0;
 		double ratioNodesMatchQuery = Math.min(nodesQuery, heap) / (double)Math.max(nodesQuery, heap);