fix: update OCL to 2024.7.1

src/com/actelion/research/gwt/chemlib/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/com/actelion/research/gwt/chemlib/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/com/actelion/research/gwt/chemlib/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java

@@ -75,7 +75,7 @@ public void neglectSpaceDelimitedCoordinates() {
 	 * @return
 	 */
 	public StereoMolecule getCompactMolecule(String idcode) {
-		return (idcode == null || idcode.length() == 0) ? null : getCompactMolecule(idcode.getBytes(StandardCharsets.UTF_8), null);
+		return (idcode == null || idcode.isEmpty()) ? null : getCompactMolecule(idcode.getBytes(StandardCharsets.UTF_8), null);
 		}
 
 	/**
@@ -151,7 +151,7 @@ public StereoMolecule getCompactMolecule(byte[] idcode, byte[] coordinates, int
 	 * @param idcode null or idcode, which may contain coordinates separated by a space character
 	 */
 	public void parse(StereoMolecule mol, String idcode) {
-		if (idcode == null || idcode.length() == 0) {
+		if (idcode == null || idcode.isEmpty()) {
 			parse(mol, (byte[])null, (byte[])null);
 			return;
 			}
@@ -437,9 +437,10 @@ public void parse(StereoMolecule mol, byte[] idcode, byte[] coordinates, int idc
 		int offset = 0;
 		while (decodeBits(1) == 1) {
 			int dataType = offset + decodeBits(4);
+			int no;
 			switch (dataType) {
 			case 0:	//	datatype 'AtomQFNoMoreNeighbours'
-				int no = decodeBits(abits);
+				no = decodeBits(abits);
 				for (int i=0; i<no; i++) {
 					int atom = decodeBits(abits);
 					mMol.setAtomQueryFeature(atom, Molecule.cAtomQFNoMoreNeighbours, true);
@@ -762,10 +763,10 @@ public void parse(StereoMolecule mol, byte[] idcode, byte[] coordinates, int idc
 							from = 0;
 							factor = 8.0;
 							}
-						mMol.setAtomX(atom, mMol.getAtomX(from) + factor * (decodeBits(resolutionBits) - binCount / 2));
-						mMol.setAtomY(atom, mMol.getAtomY(from) + factor * (decodeBits(resolutionBits) - binCount / 2));
+						mMol.setAtomX(atom, mMol.getAtomX(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
+						mMol.setAtomY(atom, mMol.getAtomY(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
 						if (coordsAre3D)
-							mMol.setAtomZ(atom, mMol.getAtomZ(from) + factor * (decodeBits(resolutionBits) - binCount / 2));
+							mMol.setAtomZ(atom, mMol.getAtomZ(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
 						}
 
 					if (coordinates[coordsStart] == '#') {    // we have 3D-coordinates that include implicit hydrogen coordinates
@@ -781,10 +782,10 @@ public void parse(StereoMolecule mol, byte[] idcode, byte[] coordinates, int idc
 								int hydrogen = mMol.addAtom(1);
 								mMol.addBond(atom, hydrogen, Molecule.cBondTypeSingle);
 
-								mMol.setAtomX(hydrogen, mMol.getAtomX(atom) + (decodeBits(resolutionBits) - binCount / 2));
-								mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) - binCount / 2));
+								mMol.setAtomX(hydrogen, mMol.getAtomX(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
+								mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
 								if (coordsAre3D)
-									mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) - binCount / 2));
+									mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
 								}
 							}
 
@@ -935,10 +936,10 @@ public void parseCoordinates(byte[] encodedCoords, int coordsStart, StereoMolecu
 				from = 0;
 				factor = 8.0;
 				}
-			coords[atom].x = coords[from].x + factor * (decodeBits(resolutionBits) - binCount / 2);
-			coords[atom].y = coords[from].y + factor * (decodeBits(resolutionBits) - binCount / 2);
+			coords[atom].x = coords[from].x + factor * (decodeBits(resolutionBits) - binCount / 2.0);
+			coords[atom].y = coords[from].y + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 			if (coordsAre3D)
-				coords[atom].z = coords[from].z + factor * (decodeBits(resolutionBits) - binCount / 2);
+				coords[atom].z = coords[from].z + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 			}
 
 		double avbl = coordsAre3D ? 1.5 : Molecule.getDefaultAverageBondLength();
@@ -954,10 +955,10 @@ public void parseCoordinates(byte[] encodedCoords, int coordsStart, StereoMolecu
 			for (int atom = 0; atom < atomCount; atom++) {
 				int hCount = mol.getAllConnAtoms(atom) - mol.getConnAtoms(atom);
 				for (int i = 0; i < hCount; i++) {
-					coords[hydrogen].x = coords[atom].x + (decodeBits(resolutionBits) - binCount / 2);
-					coords[hydrogen].y = coords[atom].y + (decodeBits(resolutionBits) - binCount / 2);
+					coords[hydrogen].x = coords[atom].x + (decodeBits(resolutionBits) - binCount / 2.0);
+					coords[hydrogen].y = coords[atom].y + (decodeBits(resolutionBits) - binCount / 2.0);
 					if (coordsAre3D)
-						coords[hydrogen].z = coords[atom].z + (decodeBits(resolutionBits) - binCount / 2);
+						coords[hydrogen].z = coords[atom].z + (decodeBits(resolutionBits) - binCount / 2.0);
 
 					hydrogen++;
 					}
@@ -1072,7 +1073,7 @@ else if (coordinates[coordStart] == '!' || coordinates[coordStart] == '#') {
 		}
 
 	public int getIDCodeVersion(String idcode) {
-		if (idcode == null || idcode.length() == 0)
+		if (idcode == null || idcode.isEmpty())
 			return -1;
 
 		return getIDCodeVersion(idcode.getBytes(StandardCharsets.UTF_8));
@@ -1090,7 +1091,7 @@ public int getIDCodeVersion(byte[] idcode) {
 		}
 
 	public int getAtomCount(String idcode) {
-		if (idcode == null || idcode.length() == 0)
+		if (idcode == null || idcode.isEmpty())
 			return 0;
 
 		return getAtomCount(idcode.getBytes(StandardCharsets.UTF_8), 0);
@@ -1120,7 +1121,7 @@ public int getAtomCount(byte[] idcode, int offset) {
 	 * @return int[] with atom and bond count as first and second values
 	 */
 	public int[] getAtomAndBondCounts(String idcode, int[] count) {
-		if (idcode == null || idcode.length() == 0)
+		if (idcode == null || idcode.isEmpty())
 			return null;
 
 		return getAtomAndBondCounts(idcode.getBytes(StandardCharsets.UTF_8), 0, count);
@@ -1192,7 +1193,7 @@ private double decodeShift(int value, int binCount) {
 		boolean isNegative = (value >= halfBinCount);
 		if (isNegative)
 			value -= halfBinCount;
-		double steepness = binCount/32;
+		double steepness = binCount/32.0;
 		double doubleValue = steepness * value / (halfBinCount - value);
 		return isNegative ? -doubleValue : doubleValue;
 		}
@@ -1366,9 +1367,10 @@ public void printContent(byte[] idcode, byte[] coordinates) {
 			int offset = 0;
 			while (decodeBits(1) == 1) {
 				int dataType = offset + decodeBits(4);
+				int no;
 				switch (dataType) {
 					case 0: //  datatype 'AtomQFNoMoreNeighbours'
-						int no = decodeBits(abits);
+						no = decodeBits(abits);
 						System.out.print("noMoreNeighbours:");
 						for (int i = 0; i < no; i++)
 							System.out.print(" " + decodeBits(abits));
@@ -1675,12 +1677,12 @@ public void printContent(byte[] idcode, byte[] coordinates) {
 							factor = 8.0;
 						}
 						System.out.print(atom + " (");
-						coords[0][atom] = coords[0][from] + factor * (decodeBits(resolutionBits) - binCount / 2);
+						coords[0][atom] = coords[0][from] + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 						System.out.print((int) coords[0][atom] + ",");
-						coords[1][atom] = coords[1][from] + factor * (decodeBits(resolutionBits) - binCount / 2);
+						coords[1][atom] = coords[1][from] + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 						System.out.print((int) coords[1][atom]);
 						if (coordsAre3D) {
-							coords[2][atom] = coords[2][from] + factor * (decodeBits(resolutionBits) - binCount / 2);
+							coords[2][atom] = coords[2][from] + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 							System.out.print("," + (int) coords[0][atom]);
 						}
 						System.out.print("), ");
@@ -1719,12 +1721,12 @@ public void printContent(byte[] idcode, byte[] coordinates) {
 								System.out.print(atom);
 							for (int i = 0; i < hCount[atom]; i++) {
 								System.out.print(" (");
-								coords[0][hydrogen] = coords[0][atom] + (decodeBits(resolutionBits) - binCount / 2);
+								coords[0][hydrogen] = coords[0][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
 								System.out.print((int) coords[0][hydrogen] + ",");
-								coords[1][hydrogen] = coords[1][atom] + (decodeBits(resolutionBits) - binCount / 2);
+								coords[1][hydrogen] = coords[1][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
 								System.out.print((int) coords[1][hydrogen]);
 								if (coordsAre3D) {
-									coords[2][hydrogen] = coords[2][atom] + (decodeBits(resolutionBits) - binCount / 2);
+									coords[2][hydrogen] = coords[2][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
 									System.out.print("," + (int) coords[2][hydrogen]);
 								}
 								System.out.print("), ");

src/com/actelion/research/gwt/chemlib/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)