Merge tag 'openchemlib-2024.7.1'

[maven-release-plugin]  copy for tag openchemlib-2024.7.1

buildOpenChemLib

@@ -9,3 +9,4 @@ find . -name "*.java" > sources.txt
 javac -target 8 -d ./build @sources.txt
 rm sources.txt
 jar -cf build/OpenChemLib.jar -C ./build .
+ls -al build/OpenChemLib.jar

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>2024.5.1</version>
+    <version>2024.7.1</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>
@@ -209,7 +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-2024.5.1</tag>
+      <tag>openchemlib-2024.7.1</tag>
   </scm>
 
     <distributionManagement>

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

@@ -45,10 +45,9 @@ public DrawingObjectList() {
 	public DrawingObjectList(DrawingObjectList l) {
 		super();
 		try {
-			if (l != null) {
-				for (int i = 0; i < l.size(); i++)
-					add((AbstractDrawingObject) l.get(i).clone());
-			}
+			if (l != null)
+				for (AbstractDrawingObject abstractDrawingObject : l)
+					add(abstractDrawingObject.clone());
 		} catch (Exception e) {
 		} finally {
 
@@ -57,7 +56,7 @@ public DrawingObjectList(DrawingObjectList l) {
 
 	public DrawingObjectList(String objectString) {
 		super();
-		if (objectString == null || objectString.length() == 0)
+		if (objectString == null || objectString.isEmpty())
 			return;
 
 		int index1 = 0;
@@ -72,9 +71,9 @@ public DrawingObjectList(String objectString) {
 		}
 
 	public String toString() {
-		StringBuffer objectString = new StringBuffer();
-		for (int i=0; i<size(); i++)
-			objectString.append(get(i).getDescriptor()+"\n");
+		StringBuilder objectString = new StringBuilder();
+		for (AbstractDrawingObject abstractDrawingObject : this)
+			objectString.append(abstractDrawingObject.getDescriptor()).append("\n");
 		return objectString.toString();
 		}
 	}

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

@@ -538,21 +538,37 @@ public int getConnAtom(int atom, int i) {
 
 	/**
 	 * The neighbours (connected atoms) of any atom are sorted by their relevance:<br>
-	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non natural abundance isotops, custom labelled hydrogen, etc.)<br>
+	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non-natural abundance isotops, custom labelled hydrogen, etc.)<br>
+	 * 2. plain-hydrogen atoms (natural abundance, bond order 1)<br>
+	 * 3. loosely connected atoms (bond order 0, i.e. metall ligand bond)<br>
+	 * Only valid after calling ensureHelperArrays(cHelperNeighbours or higher);
+	 * Note: This method includes neighbours marked as being part of an exclude group!
+	 * @param atom
+	 * @return count of category 1 neighbour atoms (excludes plain H and bond zero orders)
+	 */
+	public int getNotExcludedConnAtoms(int atom) {
+		return mConnAtoms[atom] - getExcludedNeighbourCount(atom);
+		}
+
+
+	/**
+	 * The neighbours (connected atoms) of any atom are sorted by their relevance:<br>
+	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non-natural abundance isotops, custom labelled hydrogen, etc.)<br>
 	 * 2. plain-hydrogen atoms (natural abundance, bond order 1)<br>
 	 * 3. loosely connected atoms (bond order 0, i.e. metall ligand bond)<br>
 	 * Only valid after calling ensureHelperArrays(cHelperNeighbours or higher);
+	 * Note: This method includes neighbours marked as being part of an exclude group!
 	 * @param atom
 	 * @return count of category 1 neighbour atoms (excludes plain H and bond zero orders)
 	 */
 	public int getConnAtoms(int atom) {
 		return mConnAtoms[atom];
-		}
+	}
 
 
 	/**
 	 * The neighbours (connected atoms) of any atom are sorted by their relevance:<br>
-	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non natural abundance isotops, custom labelled hydrogen, etc.)<br>
+	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non-natural abundance isotops, custom labelled hydrogen, etc.)<br>
 	 * 2. plain-hydrogen atoms (natural abundance, bond order 1)<br>
 	 * 3. loosely connected atoms (bond order 0, i.e. metall ligand bond)<br>
 	 * Only valid after calling ensureHelperArrays(cHelperNeighbours or higher);
@@ -566,7 +582,7 @@ public int getAllConnAtomsPlusMetalBonds(int atom) {
 
 	/**
 	 * The neighbours (connected atoms) of any atom are sorted by their relevance:<br>
-	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non natural abundance isotops, custom labelled hydrogen, etc.)<br>
+	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non-natural abundance isotops, custom labelled hydrogen, etc.)<br>
 	 * 2. plain-hydrogen atoms (natural abundance, bond order 1)<br>
 	 * 3. loosely connected atoms (bond order 0, i.e. metall ligand bond)<br>
 	 * Only valid after calling ensureHelperArrays(cHelperNeighbours or higher);
@@ -581,7 +597,7 @@ public int getConnBond(int atom, int i) {
 
 	/**
 	 * The neighbours (connected atoms) of any atom are sorted by their relevance:<br>
-	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non natural abundance isotops, custom labelled hydrogen, etc.)<br>
+	 * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non-natural abundance isotops, custom labelled hydrogen, etc.)<br>
 	 * 2. plain-hydrogen atoms (natural abundance, bond order 1)<br>
 	 * 3. loosely connected atoms (bond order 0, i.e. metall ligand bond)<br>
 	 * Only valid after calling ensureHelperArrays(cHelperNeighbours or higher);
@@ -616,13 +632,14 @@ public int getNonHydrogenNeighbourCount(int atom) {
 	/**
 	 * This method returns the count of atom neighbours which are marked as being an exclude group.
 	 * @param atom
-	 * @return the number of non-hydrogen neighbor atoms
+	 * @return the number of non-hydrogen neighbor atoms marked as being part of an exclude group
 	 */
 	public int getExcludedNeighbourCount(int atom) {
 		int count = 0;
-		for (int i=0; i<mConnAtoms[atom]; i++)
-			if ((mAtomQueryFeatures[mConnAtom[atom][i]] & Molecule.cAtomQFExcludeGroup) != 0)
-				count++;
+		if (mIsFragment)
+			for (int i=0; i<mConnAtoms[atom]; i++)
+				if ((mAtomQueryFeatures[mConnAtom[atom][i]] & Molecule.cAtomQFExcludeGroup) != 0)
+					count++;
 		return count;
 		}
 
@@ -1736,17 +1753,17 @@ public boolean isHeteroAromaticAtom(int atom) {
 	 * @return whether the atom is a member of a delocalized ring (subset of aromatic rings)
 	 */
 	public boolean isDelocalizedAtom(int atom) {
-		return (atom < mAtoms) ? mRingSet.isDelocalizedAtom(atom) : false;
+		return atom<mAtoms && mRingSet.isDelocalizedAtom(atom);
 	}
 
 
 	public boolean isAromaticBond(int bond) {
-		return (bond < mBonds) ? mRingSet.isAromaticBond(bond) : false;
+		return bond<mBonds && mRingSet.isAromaticBond(bond);
 	}
 
 
 	public boolean isHeteroAromaticBond(int bond) {
-		return (bond < mBonds) ? mRingSet.isHeteroAromaticBond(bond) : false;
+		return bond<mBonds && mRingSet.isHeteroAromaticBond(bond);
 	}
 
 
@@ -3482,12 +3499,12 @@ public void ensureHelperArrays(int required) {
 		if ((mValidHelperArrays & cHelperBitNeighbours) == 0) {
 			handleHydrogens();
 			calculateNeighbours();
-
 			mValidHelperArrays |= cHelperBitNeighbours;
 
 			if (convertHydrogenToQueryFeatures()) {
 				handleHydrogens();
 				calculateNeighbours();
+				mValidHelperArrays |= cHelperBitNeighbours;
 				}
 			}
 

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

@@ -1179,23 +1179,43 @@ public int[] addMolecule(Molecule mol) {
 	 * @return atom mapping from original mol to this molecule after incorporation of mol
 	 */
 	public int[] addMolecule(Molecule mol, int atoms, int bonds) {
+		return addMolecule(mol, 0, atoms, 0, bonds);
+		}
+
+
+	/**
+	 * Copies first atoms and first bonds of mol to the end of this Molecule's atom and bond
+	 * tables. If mol is a fragment then this Molecule's fragment flag is set to true
+	 * and all query features of mol are also copied. Typically, this is used to add a
+	 * molecule without explicit hydrogen atoms. If parities of copied molecules are valid,
+	 * then you may call setParitiesValid() on this molecule after adding molecules.
+	 * High level function for constructing a molecule. Does not require any helper arrays.
+	 * @param mol
+	 * @param atom1 first atom to be copied
+	 * @param atom2 1+last atom to be copied
+	 * @param bond1 first bond to be copied
+	 * @param bond2 one+last bond to be copied
+	 * @return atom mapping from original mol to this molecule after incorporation of mol
+	 */
+	public int[] addMolecule(Molecule mol, int atom1, int atom2, int bond1, int bond2) {
 		mIsFragment |= mol.mIsFragment;
 
 		int[] atomMap = new int[mol.mAllAtoms];
 		int esrGroupCountAND = renumberESRGroups(cESRTypeAnd);
 		int esrGroupCountOR = renumberESRGroups(cESRTypeOr);
-		for (int atom=0; atom<atoms; atom++) {
+		for (int atom=atom1; atom<atom2; atom++) {
 			atomMap[atom] = mol.copyAtom(this, atom, esrGroupCountAND, esrGroupCountOR);
-			}
-		for (int bond=0; bond<bonds; bond++) {
+		}
+		for (int bond=bond1; bond<bond2; bond++) {
 			mol.copyBond(this, bond, esrGroupCountAND, esrGroupCountOR, atomMap, false);
-			}
+		}
 
 		mIsRacemate = (mIsRacemate && mol.mIsRacemate);
 		mChirality = cChiralityUnknown;
 		mValidHelperArrays = cHelperNone;
 		return atomMap;
-		}
+	}
+
 
 	/**
 	 * Adds and connects the substituent molecule to the rootAtom of this molecule.
@@ -1655,24 +1675,11 @@ public void swapBonds(int bond1, int bond2) {
 	 * @param atom
 	 */
 	public void deleteAtom(int atom) {
-		for (int bnd=0; bnd<mAllBonds; bnd++) {
-			for (int i=0; i<2; i++) {
-				if (mBondAtom[i][bnd] == atom) {
+		for (int bnd=0; bnd<mAllBonds; bnd++)
+			for (int i=0; i<2; i++)
+				if (mBondAtom[i][bnd] == atom)
 					mBondType[bnd] = cBondTypeDeleted;	// mark for delete
-					int bonds = 0;
-					for (int j=0; j<mAllBonds; j++) {
-						if (j == bnd) continue;
-						if ((mBondAtom[0][j] == mBondAtom[1-i][bnd])
-						 || (mBondAtom[1][j] == mBondAtom[1-i][bnd]))
-							bonds++;
-						}
-					if (bonds == 0) {
-						removeMappingNo(mAtomMapNo[mBondAtom[1-i][bnd]]);
-						mAtomicNo[mBondAtom[1-i][bnd]] = -1;
-						}			// mark for delete
-					}
-				}
-			}
+
 		removeMappingNo(mAtomMapNo[atom]);
 		mAtomicNo[atom] = -1;		// mark for delete
 		if (mAtomList != null)