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

Actelion · Sep 4, 2024 · 3c8e195 · 3c8e195
2 parents 9f1c588 + f60b78d
commit 3c8e195
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Showing 6 changed files with 84 additions and 6 deletions.
diff --git a/pom.xml b/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>2024.8.3-SNAPSHOT</version>
+    <version>2024.8.5-SNAPSHOT</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>

diff --git a/src/main/java/com/actelion/research/calc/ArrayUtilsCalc.java b/src/main/java/com/actelion/research/calc/ArrayUtilsCalc.java
@@ -57,15 +57,12 @@ public class ArrayUtilsCalc {
 
 	public final static int [] cat(int [] a, int [] b) {
 		int [] c = new int [a.length + b.length];
-
 		for (int i = 0; i < a.length; i++) {
 			c[i]=a[i];
 		}
-
 		for (int i = 0; i < b.length; i++) {
 			c[a.length+i]=b[i];
 		}
-
 		return c;
 	}
 
@@ -80,6 +77,16 @@ public final static boolean contains(int [] a, int b) {
 		}
 		return bFound;
 	}
+	public final static boolean containsAll(int [] a, int [] b) {
+		boolean bFound = true;
+		for (int i = 0; i < b.length; i++) {
+			if(!contains(a, b[i])){
+				bFound=false;
+				break;
+			}
+		}
+		return bFound;
+	}
 
 	public final static int [] copy(int [] a) {
 		int [] b = new int [a.length];

diff --git a/src/main/java/com/actelion/research/calc/histogram/Histogram.java b/src/main/java/com/actelion/research/calc/histogram/Histogram.java
@@ -38,6 +38,7 @@
 import java.text.DecimalFormat;
 import java.text.DecimalFormatSymbols;
 import java.text.NumberFormat;
+import java.util.Collection;
 import java.util.Locale;
 import java.util.Random;
 
@@ -83,6 +84,15 @@ public Histogram(double [] arrRaw, double min, double max, int bins) {
 		initialize(arrRaw,min,max,bins);
 	}
 
+	public Histogram(Collection<Double> values, double min, double max, int bins) {
+		double [] v = new double[values.size()];
+		int c=0;
+		for (Double value : values) {
+			v[c++]=value;
+		}
+		initialize(v,min,max,bins);
+	}
+
 	public Histogram(double [] arrRaw, int bins) {
 
 		double max = -Double.MAX_VALUE;
@@ -96,7 +106,6 @@ public Histogram(double [] arrRaw, int bins) {
 				min=v;
 			}
 		}
-
 		initialize(arrRaw,min,max,bins);
 	}
 

diff --git a/src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistViz.java b/src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistViz.java
@@ -176,6 +176,14 @@ public void setNodeWeight(int indexNode, double weight){
 		}
 		arrWeight[indexNode]=weight;
 	}
+	public void resetNodeWeights(){
+		if(!finalized){
+			throw new RuntimeException("MolDistHistViz not finalized!");
+		}
+		for (int i = 0; i < liPPNodeViz.size(); i++) {
+			arrWeight[i]=1;
+		}
+	}
 
 	public void removeInevitablePharmacophorePoint(int indexPPNode){
 		hsIndexMandatoryPPPoints.remove(indexPPNode);

diff --git a/...descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java b/...descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java
@@ -43,7 +43,10 @@ public class ObjectiveBlurFlexophoreHardMatchUncovered implements IObjectiveComp
 	// 03.03.2016 Top result so far for 0.9
 	// 13.04.2020 Maybe obsolete
 	// ToDo
-	final static double THRESH_NODE_SIMILARITY_START = 0.5;
+	// final static double THRESH_NODE_SIMILARITY_START = 0.5;
+
+	// Changed to 0.9 21.08.2024 MvK
+	final static double THRESH_NODE_SIMILARITY_START = 0.9;
 
 	private static final float INIT_VAL = -1;
 

diff --git a/...ava/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java b/...ava/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java
@@ -34,13 +34,15 @@
 
 package com.actelion.research.chem.descriptor.flexophore.generator;
 
+import com.actelion.research.calc.ArrayUtilsCalc;
 import com.actelion.research.calc.ThreadMaster;
 import com.actelion.research.chem.*;
 import com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore;
 import com.actelion.research.chem.descriptor.flexophore.*;
 import com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor;
 import com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices;
 import com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator;
+import com.actelion.research.util.StringFunctions;
 
 import java.util.*;
 
@@ -422,12 +424,61 @@ public static MolDistHistViz create(List<MultCoordFragIndex> liMultCoordFragInde
 
         return molDistHistViz;
 
+    }
+
+    public void addFlexophoreDistanceHistograms(MolDistHistViz mdhv){
+        Molecule3D molecule = mdhv.getMolecule();
+
+        List<MultCoordFragIndex> liMultCoordFragIndex = new ArrayList<>();
+        for (PPNodeViz node : mdhv.getNodes()) {
+            liMultCoordFragIndex.add(new MultCoordFragIndex(node.getArrayIndexOriginalAtoms()));
+        }
+        conformerGeneratorStageTries.setMolecule(molecule);
+        int ccConformationsGenerated=0;
+        for (int i = 0; i < DescriptorHandlerFlexophore.NUM_CONFORMATIONS; i++) {
+            boolean conformerGenerated = false;
+            try {
+                conformerGenerated = conformerGeneratorStageTries.generateConformerAndSetCoordinates(molecule.getAtoms(), molecule);
+            } catch (ExceptionTimeOutConformerGeneration e) {
+                System.err.println(
+                        "CreatorMolDistHistViz: ExceptionTimeOutConformerGeneration for idcode " + molecule.getIDCode( )+ ", hence generated " + ccConformationsGenerated + " conformers.");
+                // e.printStackTrace();
+                break;
+            }
+
+            if(!conformerGenerated){
+                break;
+            }
+            ccConformationsGenerated++;
+            calcFragmentCenter(molecule, liMultCoordFragIndex);
+
+        }
+
+        for (int i = 0; i < liMultCoordFragIndex.size(); i++) {
+            for (int j = i+1; j < liMultCoordFragIndex.size(); j++) {
+                byte [] arrDistHist = MultCoordFragIndex.getDistHist(liMultCoordFragIndex.get(i), liMultCoordFragIndex.get(j));
+                // System.out.println(StringFunctions.toString(arrDistHist));
+                mdhv.setDistHist(i,j,arrDistHist);
+            }
+        }
+
     }
     public MolDistHistViz createWithoutCoordinates(Molecule3D molecule3D){
         InteractionAtomTypeCalculator.setInteractionTypes(molecule3D);
         List<SubGraphIndices> sgis = getSubGraphIndices(molecule3D);
         return  createWithoutCoordinates(sgis, molecule3D);
     }
+    public MolDistHistViz createWithoutCoordinates(Molecule3D molecule3D, int [] indices2consider){
+        InteractionAtomTypeCalculator.setInteractionTypes(molecule3D);
+        List<SubGraphIndices> sgis = getSubGraphIndices(molecule3D);
+        List<SubGraphIndices> sgis2consider = new ArrayList<>();
+        for (SubGraphIndices sgi : sgis) {
+            if(ArrayUtilsCalc.containsAll(indices2consider, sgi.getAtomIndices()))    {
+                sgis2consider.add(sgi);
+            }
+        }
+        return  createWithoutCoordinates(sgis2consider, molecule3D);
+    }
 
 
     public static MolDistHistViz createWithoutCoordinates(List<SubGraphIndices> liMultCoordFragIndex, Molecule3D molecule3D){