Added topological Flexophore for testing

Actelion · Aug 21, 2024 · 94e467b · 94e467b
1 parent deeb2cd
commit 94e467b
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Showing 6 changed files with 41 additions and 14 deletions.
diff --git a/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java b/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java
@@ -772,7 +772,7 @@ public final static boolean atomAtomSubStrucMatch(StereoMolecule molecule, int a
 		return arr;
 	}
 
-	public final static int getMedianTopologicalDistance(int [][] topoDistMatrix, int [] at1, int [] at2) {
+	public final static int [] getTopologicalDistances(int [][] topoDistMatrix, int [] at1, int [] at2) {
 
 		int [] d = new int[at1.length*at2.length];
 		int cc=0;
@@ -781,6 +781,11 @@ public final static int getMedianTopologicalDistance(int [][] topoDistMatrix, in
 				d[cc++]=topoDistMatrix[at1[i]][at2[j]];
 			}
 		}
+
+		return d;
+	}
+	public final static int getMedianTopologicalDistance(int [][] topoDistMatrix, int [] at1, int [] at2) {
+		int [] d = getTopologicalDistances(topoDistMatrix, at1, at2);
 		int medTopoDist = MedianStatisticFunctions.getMedianForInteger(d).median;
 		return medTopoDist;
 	}

diff --git a/src/main/java/com/actelion/research/chem/descriptor/flexophore/SlidingWindowDistHist.java b/src/main/java/com/actelion/research/chem/descriptor/flexophore/SlidingWindowDistHist.java
@@ -53,4 +53,22 @@ public void apply(DistHist distHist){
 //        System.out.println("\n\n");
 //        System.out.println(StringFunctions.toStringShort(distHist.arrDistHists));
     }
+
+    public byte [] getBlurred(byte [] hist){
+
+        byte [] histBlurred = new byte[ConstantsFlexophoreGenerator.BINS_HISTOGRAM];
+
+        int n = ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
+        int end = n - lenFilHalf;
+
+        for (int k = lenFilHalf; k < end; k++) {
+            double v = 0;
+            for (int l = 0; l < arrFilter.length; l++) {
+                int ind = k - lenFilHalf + l;
+                v +=  hist[ind] * arrFilter[l];
+            }
+            histBlurred[k] = (byte)(v+0.5);
+        }
+        return histBlurred;
+    }
 }
diff --git a/...descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java b/...descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java
@@ -836,7 +836,7 @@ public void setBase(IMolDistHist iMolDistHistBase) {
 		}
 
 
-		if(!fragmentNodesMapping)
+		if((slidingWindowDistHist!=null) && !fragmentNodesMapping)
 			slidingWindowDistHist.apply(mdhvBaseBlurredHist);
 
 		nodesBase = iMolDistHistBase.getNumPPNodes();
@@ -851,7 +851,11 @@ public void setBase(IMolDistHist iMolDistHistBase) {
 
 		deltaNanoBaseBlur += System.nanoTime()-t0;
 	}
-
+
+	public void setSlidingWindowDistHistNull() {
+		this.slidingWindowDistHist = null;
+	}
+
 	public void setQuery(IMolDistHist iMolDistHistQuery) {
 
 		if(iMolDistHistQuery.getNumPPNodes()>=ConstantsFlexophore.MAX_NUM_NODES_FLEXOPHORE){
@@ -868,7 +872,7 @@ public void setQuery(IMolDistHist iMolDistHistQuery) {
 			mdhvQueryBlurredHist = new MolDistHistViz((MolDistHist) iMolDistHistQuery);
 		}
 
-		if(!fragmentNodesMapping)
+		if((slidingWindowDistHist!=null) && !fragmentNodesMapping)
 			slidingWindowDistHist.apply(mdhvQueryBlurredHist);
 
 		nodesQuery = iMolDistHistQuery.getNumPPNodes();
@@ -1153,10 +1157,13 @@ public float getSimilarityHistogram(int indexNode1Query, int indexNode2Query, in
 
 		if(arrSimilarityHistograms[indexHistogramQuery][indexHistogramBase] < 0){
 
-			float similarityHistogram =
+			float similarityHistogram = 0;
+
+			similarityHistogram =
 					(float)HistogramMatchCalculator.getSimilarity(
 							mdhvQueryBlurredHist, indexNode1Query, indexNode2Query, mdhvBaseBlurredHist, indexNode1Base, indexNode2Base);
 
+
 			arrSimilarityHistograms[indexHistogramQuery][indexHistogramBase]=similarityHistogram;
 		}
 

diff --git a/...ava/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java b/...ava/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java
@@ -515,11 +515,7 @@ public MolDistHistViz createFromGivenConformation(StereoMolecule molOrig) {
         InteractionAtomTypeCalculator.setInteractionTypes(molStart);
         Molecule3D molInPlace = new Molecule3D(molStart);
         molInPlace.ensureHelperArrays(Molecule.cHelperRings);
-
         List<SubGraphIndices> liSubGraphIndices = getSubGraphIndices(molInPlace);
-
-
-
         List<MultCoordFragIndex> liMultCoordFragIndex = new ArrayList<>();
         for (SubGraphIndices subGraphIndices : liSubGraphIndices) {
             liMultCoordFragIndex.add(new MultCoordFragIndex(subGraphIndices.getAtomIndices()));

diff --git a/src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java b/src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java
@@ -401,8 +401,9 @@ private boolean getNeighbourSolutions(SolutionCompleteGraph solution){
 						if(objectiveCompleteGraph.areNodesMapping(indexNodeQuery, indexNodeBase)){
 
 							SolutionCompleteGraph solutionNew = cm.getWithCopy(solution);
-
-							solutionNew.copyIntoThis(solution);
+
+							// to do: is this necessary?, no 21.08.2024
+							// solutionNew.copyIntoThis(solution);
 
 							solutionNew.setNodesQuery(nodesQuery);
 

diff --git a/src/main/java/com/actelion/research/util/graph/complete/SolutionCompleteGraph.java b/src/main/java/com/actelion/research/util/graph/complete/SolutionCompleteGraph.java
@@ -220,10 +220,10 @@ public String toString() {
 
 		if(sizeHeap>0) {
 
-			for (int i = 0; i < sizeHeap; i++) {
-				sb.append(arrSolution[i]);
-				if(i < sizeHeap -1)
+			for (int i = 0; i < maxIndexNodeQuery+1; i++) {
+				if(sb.length()>0)
 					sb.append(" ");
+				sb.append(arrSolution[i]);
 			}
 
 		} else {