Merge tag 'openchemlib-2024.1.3'

[maven-release-plugin]  copy for tag openchemlib-2024.1.3

Author: targos

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>2024.1.1</version>
+    <version>2024.1.3</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>
@@ -20,8 +20,7 @@
     <developers>
         <developer>
             <name>Thomas Sander</name>
-            <email>[email protected]</email>
-            <organization>Idorsia Pharmaceuticals Ltd.</organization>
+            <organization>Openmolecules.org</organization>
         </developer>
         <developer>
             <name>Christian Rufener</name>
@@ -33,8 +32,8 @@
         </developer>
         <developer>
             <name>Modest von Korff</name>
-            <email>modest.korff@idorsia.com</email>
-            <organization>Idorsia Pharmaceuticals Ltd.</organization>
+            <email>modest.korff@alipheron.com</email>
+            <organization>Alipheron AG</organization>
         </developer>
     </developers>
 
@@ -210,7 +209,7 @@
         <connection>scm:git:[email protected]:Actelion/openchemlib.git</connection>
         <developerConnection>scm:git:[email protected]:Actelion/openchemlib.git</developerConnection>
         <url>https://github.com/Actelion/openchemlib</url>
-      <tag>openchemlib-2024.1.1</tag>
+      <tag>openchemlib-2024.1.3</tag>
   </scm>
 
     <distributionManagement>

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

@@ -485,35 +485,36 @@ public static int getNumBytesEntry(){
 	 * @return
 	 */
 	public static List<PPNode> readNodes(String strMolDistHist){
-
 		int start = strMolDistHist.indexOf('(');
-		
 		boolean nodesProcessed = false;
-		
 		List<PPNode> liPPNode = new ArrayList<>();
 		while(!nodesProcessed){
-			
 			int end = StringFunctions.nextClosing(strMolDistHist, start, '(', ')');
-
 			if(end==-1){
 				throw new RuntimeException("Error for MolDistHist " + strMolDistHist);
 			}
-
 			String strNode = strMolDistHist.substring(start+1, end);
-
 			PPNode n = PPNode.read(strNode);
-
 			liPPNode.add(n);
-			
 			start = strMolDistHist.indexOf('(', end);
-			
 			if(start==-1){
 				nodesProcessed = true;
 			}
 		}
-
 		return liPPNode;
 	}
+	public static MolDistHist readNodes2MDH(String strMolDistHist){
+
+		List<PPNode> liPPNode = readNodes(strMolDistHist);
+		int size = liPPNode.size();
+		MolDistHist mdh = new MolDistHist(size);
+		for (PPNode ppNode : liPPNode) {
+			mdh.addNode(ppNode);
+		}
+		return  mdh;
+	}
+
+
 
 	public static MolDistHist read(String strMolDistHist){
 

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

@@ -4,7 +4,7 @@
 import com.actelion.research.util.ArrayUtils;
 import com.actelion.research.util.ByteArray;
 
-import java.util.Arrays;
+import java.util.*;
 
 public class MolDistHistHelper {
 
@@ -64,6 +64,29 @@ public static MolDistHist assemble (MolDistHist ... arr){
 
         return mdh;
     }
+    public static MolDistHist assembleNoDistHist (MolDistHist ... arr){
+
+        int nNodesSum = 0;
+        int maxNumNodes = 0;
+        for (MolDistHist mdhFrag : arr) {
+            int nNodes = mdhFrag.getNumPPNodes();
+            nNodesSum += nNodes;
+            if(nNodes>maxNumNodes)
+                maxNumNodes=nNodes;
+        }
+        MolDistHist mdh = new MolDistHist(nNodesSum);
+        int [] [] arrMapIndexNew = new int[arr.length][maxNumNodes];
+        int indexNew = 0;
+        for (int i = 0; i < arr.length; i++) {
+            int n = arr[i].getNumPPNodes();
+            for (int j = 0; j < n; j++) {
+                arrMapIndexNew[i][j]=indexNew;
+                indexNew++;
+                mdh.addNode(arr[i].getNode(j));
+            }
+        }
+        return mdh;
+    }
     public static boolean isZero(byte [] b){
         boolean z=true;
         for (byte v : b) {
@@ -163,7 +186,36 @@ public static MolDistHist getMostDistantPairOfNodesOneHeteroAtom (MolDistHist md
         return mdhSub;
     }
 
+    public static boolean areNodesEqual(MolDistHist mdh1, MolDistHist mdh2){
+        boolean eq = true;
+        if(mdh1.getNumPPNodes() != mdh2.getNumPPNodes()){
+            eq = false;
+        } else {
+            for (int i = 0; i < mdh1.getNumPPNodes(); i++) {
+                if(!mdh1.getNode(i).equals(mdh2.getNode(i))){
+                    eq = false;
+                    break;
+                }
+            }
+        }
+        return eq;
+    }
 
+    public static MolDistHist createFromNodes (Collection<PPNode> li){
+        MolDistHist mdh = new MolDistHist(li.size());
+        for (PPNode ppNode : li) {
+            mdh.addNode(ppNode);
+        }
+        mdh.realize();
+        return mdh;
+    }
 
+    public static MolDistHist [] toArray(List<MolDistHist> li){
+        MolDistHist [] a = new MolDistHist[li.size()];
+        for (int i = 0; i < li.size(); i++) {
+            a[i]=li.get(i);
+        }
+        return a;
+    }
 
 }

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

@@ -38,6 +38,7 @@
 import com.actelion.research.calc.ArrayUtilsCalc;
 import com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator;
 import com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator;
+import com.actelion.research.util.BurtleHasher;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -214,18 +215,19 @@ public boolean equals(Object o) {
 		PPNode n = (PPNode)o;
 		return equalAtoms(n);
 	}
-	
+
+	@Override
+	public int hashCode() {
+		return BurtleHasher.hashlittle(arrInteractionType, 13);
+	}
+
 	/**
 	 * May be called after finishing adding new interaction types. 
 	 */
 	public void realize(){
-		
 		int sizeBytes = size * getNumBytesEntry();
-		
 		arrInteractionType = ArrayUtilsCalc.resize(arrInteractionType, sizeBytes);
-		
 		sortInteractionTypes();
-
 		calcHasHeteroAtom();
 	}
 
@@ -611,10 +613,14 @@ public String toStringLongHardPPPoint(){
 	/**
 	 *
 	 * @param strNode i.e. 262,392,4358*2,8582,590088,598407
-	 * @return
+	 * @return the node with the atom types. If an empty string is given a node without atom types is returned.
 	 */
 	public static PPNode read(String strNode) {
 
+		if(strNode.length()==0){
+			return new PPNode();
+		}
+
 		String [] arr = strNode.split(SEPARATOR_ATOMS);
 
 		PPNode n = new PPNode();