Updated Flexophore similarity calculations for synthon similarity.

Actelion · Sep 30, 2024 · ef65f43 · ef65f43
1 parent 52b9bab
commit ef65f43
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Showing 4 changed files with 14 additions and 31 deletions.
diff --git a/...on/research/chem/descriptor/flexophore/completegraphmatcher/HistogramMatchCalculator.java b/...on/research/chem/descriptor/flexophore/completegraphmatcher/HistogramMatchCalculator.java
@@ -40,21 +40,27 @@
  * 
  * HistogramMatchCalculator
  * @author Modest von Korff
- * @version 1.0
  * Oct 2, 2012 MvK: Start implementation
  * May 15 2013 MvK: Heavy bug detected. Wrong similarity results. reset() added.
  * Mar 01 2016 MvK sliding filter added.
  * 2020 March, re-written
  */
 public class HistogramMatchCalculator {
 
+	/**
+	 *
+	 * @param dh1
+	 * @param indexDistHist1At1
+	 * @param indexDistHist1At2
+	 * @param dh2
+	 * @param indexDistHist2At1
+	 * @param indexDistHist2At2
+	 * @return integral of overlap
+	 */
 	public static double getSimilarity(DistHist dh1, int indexDistHist1At1, int indexDistHist1At2, DistHist dh2, int indexDistHist2At1, int indexDistHist2At2){
-
 		int indexPostStartDistHist1 = dh1.getIndexPosStartForDistHist(indexDistHist1At1, indexDistHist1At2);
 		int indexPostStartDistHist2 = dh2.getIndexPosStartForDistHist(indexDistHist2At1, indexDistHist2At2);
-
 		int n = ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
-
 		double sumMin = 0;
 		double sumMax = 0;
 
@@ -64,24 +70,17 @@ public static double getSimilarity(DistHist dh1, int indexDistHist1At1, int inde
 			sumMin += Math.min(v1, v2);
 			sumMax += Math.max(v1, v2);
 		}
-
 		double score = sumMin / sumMax;
-
 		return score;
-
 	}
 
 	public static double getPercentageOverlap(DistHist dh1, int indexDistHist1At1, int indexDistHist1At2, DistHist dh2, int indexDistHist2At1, int indexDistHist2At2){
-
 		int indexPostStartDistHist1 = dh1.getIndexPosStartForDistHist(indexDistHist1At1, indexDistHist1At2);
 		int indexPostStartDistHist2 = dh2.getIndexPosStartForDistHist(indexDistHist2At1, indexDistHist2At2);
-
 		int n = ConstantsFlexophoreGenerator.BINS_HISTOGRAM;
-
 		double sumMin = 0;
 		double sum1 = 0;
 		double sum2 = 0;
-
 		for (int i = 0; i < n; i++) {
 			int v1 = dh1.getValueAtAbsolutePosition(indexPostStartDistHist1+i);
 			int v2 = dh2.getValueAtAbsolutePosition(indexPostStartDistHist2+i);
@@ -90,11 +89,8 @@ public static double getPercentageOverlap(DistHist dh1, int indexDistHist1At1, i
 			sum1 += v1;
 			sum2 += v2;
 		}
-
 		double score = sumMin / Math.max(sum1, sum2);;
-
 		return score;
-
 	}
 
 

diff --git a/...descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java b/...descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java
@@ -47,6 +47,7 @@ public class ObjectiveBlurFlexophoreHardMatchUncovered implements IObjectiveComp
 
 	// Changed to 0.9 21.08.2024 MvK
 	final static double THRESH_NODE_SIMILARITY_START = 0.9;
+	final static double OPTIMISTIC_HISTOGRAM_THRESH = 0.0;
 
 	private static final float INIT_VAL = -1;
 
@@ -1128,50 +1129,35 @@ private double getScorePairwiseMapping(int indexNode1Query, int indexNode2Query,
 		double simHists = getSimilarityHistogram(indexNode1Query, indexNode2Query, indexNode1Base, indexNode2Base);
 
 		if(optimisticHistogramSimilarity) {
-			if (simHists > 0) {
+			if (simHists >= OPTIMISTIC_HISTOGRAM_THRESH) {
 				simHists = 1.0;
 			}
 		}
 
 		if(verbose){
 			System.out.println("simHists " + Formatter.format2(simHists));
 		}
-
-		// score = simNodePair1 * simNodePair1 * simNodePair2 * simNodePair2 * simHists * simHists * simHists;
-
 		score = simNodePair1 * simNodePair1 * simNodePair2 * simNodePair2 * simHists * simHists;
-
-
 		return score;
 	}
 
 	public double getSimilarityNodes(int indexNodeQuery, int indexNodeBase) {
-
 		if(arrSimilarityNodes[indexNodeQuery][indexNodeBase] < 0 || verbose){
-
 			float similarity = (float)nodeSimilarity.getSimilarity(mdhvQueryBlurredHist.getNode(indexNodeQuery), mdhvBaseBlurredHist.getNode(indexNodeBase));
-
 			arrSimilarityNodes[indexNodeQuery][indexNodeBase]=similarity;
 		} 
-
 		return arrSimilarityNodes[indexNodeQuery][indexNodeBase];
 	}
 
 	public float getSimilarityHistogram(int indexNode1Query, int indexNode2Query, int indexNode1Base, int indexNode2Base) {
 
 		int indexHistogramQuery = DistHist.getIndex(indexNode1Query, indexNode2Query, nodesQuery);
-
 		int indexHistogramBase = DistHist.getIndex(indexNode1Base, indexNode2Base, nodesBase);
-
 		if(arrSimilarityHistograms[indexHistogramQuery][indexHistogramBase] < 0){
-
 			float similarityHistogram = 0;
-
 			similarityHistogram =
 					(float)HistogramMatchCalculator.getSimilarity(
 							mdhvQueryBlurredHist, indexNode1Query, indexNode2Query, mdhvBaseBlurredHist, indexNode1Base, indexNode2Base);
-
-
 			arrSimilarityHistograms[indexHistogramQuery][indexHistogramBase]=similarityHistogram;
 		}
 

diff --git a/.../actelion/research/chem/descriptor/flexophore/generator/ConstantsFlexophoreGenerator.java b/.../actelion/research/chem/descriptor/flexophore/generator/ConstantsFlexophoreGenerator.java
@@ -30,6 +30,7 @@ public class ConstantsFlexophoreGenerator {
      */
     // public static final double [] FILTER = FILTER05;
     public static final double [] FILTER07_ = {0.125, 0.125, 0.125,0.25,0.125, 0.125, 0.125};
+    public static final double [] FILTER05_ = {0.125, 0.25,0.25,0.25, 0.125};
 
     public static final double [] FILTER = FILTER07_;
 

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
@@ -62,7 +62,7 @@ public class SolutionCompleteGraph extends AMemorizedObject implements Comparabl
 	private byte maxIndexNodeQuery;
 
 	/**
-	 * The index is the index of the node in the query molecule.
+	 * The index is the index of the node in the query molecule. Not matched query nodes contain a -1.
 	 * The value at 'index' is the index of the node in the base molecule.
 	 * Contains the same information as heapIndexBase and heapIndexQuery. Used for fast lookup.
 	 */