Merge remote-tracking branch 'origin/master'

Author: thsa

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>2026.1.5-SNAPSHOT</version>
+    <version>2026.2.1-SNAPSHOT</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>

src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java

@@ -1547,10 +1547,32 @@ public static float getSimilarity(StereoMolecule m1, StereoMolecule m2, Descript
 	public static StereoMolecule getSphere(StereoMolecule mol, int rootAtom, int depth){
 		mol.ensureHelperArrays(Molecule.cHelperRings);
 		StereoMolecule fragment = new StereoMolecule(mol.getAtoms(), mol.getBonds());
+
 		boolean[] atomMask = getSphereAtomMask(mol, rootAtom, depth);
-		mol.copyMoleculeByAtoms(fragment, atomMask, true, null);
+
+		int [] atomMap = new int[atomMask.length];
+		mol.copyMoleculeByAtoms(fragment, atomMask, true, atomMap);
+		fragment.ensureHelperArrays(Molecule.cHelperRings);
+		fragment.setFragment(true);
+		for (int i = 0; i < atomMap.length; i++) {
+			int indAtFrag = atomMap[i];
+			if(indAtFrag==-1) continue;
+			long queryFeatures = 0;
+			if(mol.isRingAtom(i))
+				queryFeatures |= Molecule.cAtomQFNotChain;
+			else
+				queryFeatures |= Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds ;
+			if(mol.isAromaticAtom(i))
+				queryFeatures |= Molecule.cAtomQFAromatic;
+			else
+				queryFeatures |= Molecule.cAtomQFNotAromatic;
+
+			fragment.setAtomQueryFeature(indAtFrag, queryFeatures, true);
+		}
 		return fragment;
 	}
+
+
 	public static StereoMolecule getSphereWithDummyAtom(StereoMolecule mol, int rootAtom, int depth, int atNoDummy){
 
 		mol.ensureHelperArrays(Molecule.cHelperRings);

src/main/java/com/actelion/research/chem/descriptor/DescriptorWeightsHelper.java

@@ -8,24 +8,35 @@
 import java.util.List;
 
 /*
- 
- Copyright (c) 2024 Alipheron AG. All rights reserved.
- 
- This file is part of the Alipheron AG software suite.
- 
- Licensed under the Alipheron AG Software License Agreement (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at the company's official website or upon request.
- 
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License. 
- 
- Created by Modest von Korff 
- 26/07/2024
- 
+ * Copyright (c) 1997 - 2016
+ * Actelion Pharmaceuticals Ltd.
+ * Gewerbestrasse 16
+ * CH-4123 Allschwil, Switzerland
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 3. Neither the name of the the copyright holder nor the
+ *    names of its contributors may be used to endorse or promote products
+ *    derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 public class DescriptorWeightsHelper {
 

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

@@ -6,7 +6,40 @@
 import com.actelion.research.util.ByteArray;
 
 import java.util.*;
-
+/**
+ * Copyright (c) 2026
+ * Alipheron AG
+ * Hochbergerstrasse 60C
+ * CH-4057 Basel
+ * Switzerland
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 3. Neither the name of the copyright holder nor the
+ *    names of its contributors may be used to endorse or promote products
+ *    derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * @author Modest v. Korff
+ */
 public class MolDistHistHelper {
 
 
@@ -287,4 +320,30 @@ public static void reNormalizeDistHist(MolDistHist mdh, int margin){
         }
     }
 
+    public static Comparator<MolDistHist> getComparator() {
+
+        return new Comparator<MolDistHist>() {
+            @Override
+            public int compare(MolDistHist o1, MolDistHist o2) {
+                int cmp = 0;
+
+                if(o1.getNumPPNodes()>o2.getNumPPNodes()){
+                    cmp=1;
+                } else if(o1.getNumPPNodes()<o2.getNumPPNodes()){
+                    cmp=-1;
+                } else {
+                    for (int i = 0; i < o1.getNumPPNodes(); i++) {
+                        PPNode n1 = o1.getNode(i);
+                        PPNode n2 = o2.getNode(i);
+                        cmp = n1.compareTo(n2);
+                        if(cmp!=0){
+                            break;
+                        }
+                    }
+                }
+                return cmp;
+            }
+        };
+    }
+
 }

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

@@ -47,9 +47,7 @@
 import java.io.Serializable;
 import java.util.*;
 
-/**
- * Class for Flexophore visualization and atom tracking. Information about corresponding atoms is stored in PPNodeViz.
- */
+
 public class MolDistHistViz extends DistHist implements Serializable, IMolDistHist, ICompleteGraph {
 
 	private static final long serialVersionUID = 15052013;
@@ -289,7 +287,48 @@ public void copy(MolDistHistViz copy){
 		copy.arrWeight = new double[this.arrWeight.length];
 		System.arraycopy(this.arrWeight, 0, copy.arrWeight, 0, this.arrWeight.length);
 	}
-	
+	public MolDistHistViz copy(boolean [] nodes){
+
+		int n = 0;
+		for (boolean node : nodes) {
+			if(node)n++;
+		}
+
+		MolDistHistViz copy = new MolDistHistViz(n);
+
+		copy.liPPNodeViz = new ArrayList<PPNodeViz>();
+		for (int i = 0; i < liPPNodeViz.size(); i++) {
+			if(nodes[i]) {
+				copy.liPPNodeViz.add(new PPNodeViz(liPPNodeViz.get(i)));
+			}
+		}
+
+		int ind1=0;
+		for (int i = 0; i < liPPNodeViz.size(); i++) {
+			if(!nodes[i])
+				continue;
+			int ind2=ind1+1;
+			for (int j = i+1; j < liPPNodeViz.size(); j++) {
+				if(!nodes[j])
+					continue;
+				byte [] distHist = getDistHist(i,j);
+				copy.setDistHist(ind1,ind2,distHist);
+				ind2++;
+			}
+			ind1++;
+		}
+
+		copy.flagsDescribe = flagsDescribe;
+		if(molecule3D !=null) {
+			copy.molecule3D = new Molecule3D(molecule3D);
+			copy.molecule3D.ensureHelperArrays(Molecule.cHelperRings);
+		}
+
+		copy.realize();
+
+		return copy;
+	}
+
 	/**
 	 * Recalculates the coordinates off the pharmacophore nodes. 
 	 * Has to be called after changing the coordinates for the Molecule3D.
@@ -403,7 +442,10 @@ public void set(Molecule3D ff ){
 		if(ff!=null)
 			molecule3D = new Molecule3D(ff);
 	}
-	
+	public void setMoleculeNull(){
+		molecule3D = null;
+	}
+
 	public void setMappingIndex(int index, int info) {
 		getNode(index).setMappingIndex(info);
 	}
@@ -454,7 +496,6 @@ public void canonize(){
 			fin=true;
 			for (int i = 1; i < liPPNodeViz.size(); i++) {
 				int cmp = compareNodes(i, i-1);
-				
 				if(cmp<0){
 					fin=false;
 					swapNodes(i, i-1);
@@ -997,18 +1038,20 @@ public String toStringNodesText(){
 	public String toStringNodesShort(){
 		if(!finalized)
 			realize();
-		StringBuffer b = new StringBuffer();
-		b.append("[");
-		for (int i = 0; i < getNumPPNodes(); i++) {
-			PPNodeViz ppNodeViz = getNode(i);
-			b.append(ppNodeViz.toStringShort());
-			if(i<getNumPPNodes()-1){
-				b.append(" ");
-			} else {
-				b.append("]");
+		StringBuilder sb = new StringBuilder();
+		sb.append("[");
+		if(getNumPPNodes()==0){
+			sb.append("()");
+		} else {
+			for (int i = 0; i < getNumPPNodes(); i++) {
+				sb.append(getNode(i).toStringShort());
+				if(i<getNumPPNodes()-1){
+					sb.append(" ");
+				}
 			}
 		}
-		return b.toString();
+		sb.append("]");
+		return sb.toString();
 	}
 	public String toStringPPNodesText(){
 

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

@@ -105,4 +105,59 @@ public static void setWeightsFromCategory(MolDistHistViz mdhv, int [] arrWeightC
             }
         }
     }
+
+    public static MolDistHistViz mergeDistHists(List<MolDistHistViz> mdhvs){
+
+        MolDistHistViz mdhvMerged = null;
+
+        if(mdhvs.size()==0) return mdhvMerged;
+        MolDistHistViz mdhv0 = mdhvs.get(0);
+        if(mdhvs.size()==1) {
+            mdhvMerged = new MolDistHistViz(mdhv0);
+            return mdhvMerged;
+        }
+
+        String strNodes0 = mdhv0.toStringNodesShort();
+        List<PPNodeViz> nodes = mdhv0.getNodes();
+        int nNodes = nodes.size();
+
+        mdhvMerged = new MolDistHistViz(nodes.size());
+        for (PPNodeViz node : nodes) {
+            mdhvMerged.addNode(node);
+        }
+        mdhvMerged.set(mdhv0.getMolecule());
+
+        for (MolDistHistViz mdhv : mdhvs) {
+            String strNodes = mdhv.toStringNodesShort();
+            if(!strNodes0.equals(strNodes)){
+                throw new RuntimeException("Nodes in Flexophore differ! " + strNodes0 + " vs " + strNodes);
+            }
+        }
+
+        for (int i = 0; i < nNodes; i++) {
+            for (int j = i + 1; j < nNodes; j++) {
+                byte[][] arrDistHist = new byte[mdhvs.size()][];
+                for (int k = 0; k < mdhvs.size(); k++) {
+                    MolDistHistViz mdh = mdhvs.get(k);
+                    byte[] distHist = mdh.getDistHist(i, j);
+                    arrDistHist[k] = distHist;
+                }
+                byte[] distHistMax = new byte[arrDistHist[0].length];
+                for (int k = 0; k < distHistMax.length; k++) {
+                    byte max = 0;
+                    for (int l = 0; l < mdhvs.size(); l++) {
+                        if (arrDistHist[l][k] > max) {
+                            max = arrDistHist[l][k];
+                        }
+                    }
+                    distHistMax[k] = max;
+                }
+                byte[] distHistMaxNormalized = DistHistHelper.normalize(distHistMax);
+
+                mdhvMerged.setDistHist(i, j, distHistMaxNormalized);
+            }
+        }
+        mdhvMerged.realize();
+        return mdhvMerged;
+    }
 }

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

@@ -128,16 +128,10 @@ public void addAtoms(PPNode node){
 
 	public int compareTo(PPNode o) {
 		int cmp=0;
-		
-		
 		int size1 = getInteractionTypeCount();
-		
 		int size2 = o.getInteractionTypeCount();
-		
 		int max1 = getMaximumInteractionType(this);
-		
 		int max2 = getMaximumInteractionType(o);
-		
 		if(max1 > max2)
 			cmp=1;
 		else if(max1 < max2)
@@ -148,19 +142,17 @@ else if(max1 < max2)
 			else if(size1 < size2)
 				cmp=-1;
 			else {
-				
 				for (int i = 0; i < size1; i++) {
-					
-					int id1 = getInteractionType(i);
-					
-					int id2 = o.getInteractionType(i);
-					
-					if(id1 > id2){
+					InterActionTypeFreq iaf1 = getInteraction(i);
+					InterActionTypeFreq iaf2 = o.getInteraction(i);
+					int p1 = iaf1.frequency*iaf1.interactionType;
+					int p2 = iaf2.frequency*iaf2.interactionType;
+					if(p1 > p2){
 						cmp=1;
-						
-					} else if(id1 < id2){
-						
+						break;
+					} else if(p1 < p2){
 						cmp=-1;
+						break;
 					}
 				}
 			}