feat: update OCL to v2024.10.2 (#237)

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

@@ -170,12 +170,12 @@ public class Canonizer {
 	private boolean[] mNitrogenQualifiesForParity;
 	private ArrayList<CanonizerFragment> mFragmentList;
 	private ArrayList<int[]> mTHParityNormalizationGroupList;
-	private int mMode,mNoOfRanks,mNoOfPseudoGroups;
+	private final int mMode;
+	private int mNoOfRanks,mNoOfPseudoGroups;
 	private boolean mIsOddParityRound;
-	private boolean mZCoordinatesAvailable,mAllHydrogensAreExplicit;
+	private final boolean mZCoordinatesAvailable,mAllHydrogensAreExplicit;
 	private boolean mCIPParityNoDistinctionProblem;
 	private boolean mEncodeAvoid127;
-
 	private boolean mGraphGenerated;
 	private int mGraphRings,mFeatureBlock;
 	private int[] mGraphAtom;
@@ -184,9 +184,10 @@ public class Canonizer {
 	private int[] mGraphFrom;
 	private int[] mGraphClosure;
 
-	private String		    mIDCode, mEncodedCoords,mMapping;
-	private StringBuilder	mEncodingBuffer;
-	private	int				mEncodingBitsAvail,mEncodingTempData,mAtomBits,mMaxConnAtoms;
+	private String mIDCode, mEncodedCoords,mMapping;
+	private StringBuilder mEncodingBuffer;
+	private	int mEncodingBitsAvail,mEncodingTempData,mMaxConnAtoms;
+	private final int mAtomBits;
 
 	/**
 	 * Runs a canonicalization procedure for the given molecule that creates unique atom ranks,
@@ -204,7 +205,7 @@ public Canonizer(StereoMolecule mol) {
 	 * If mode includes ENCODE_ATOM_CUSTOM_LABELS, than custom atom labels are
 	 * considered for the atom ranking and are encoded into the idcode.<br>
 	 * If mode includes COORDS_ARE_3D, then getEncodedCoordinates() always returns
-	 * a 3D-encoding even if all z-coordinates are 0.0. Otherwise coordinates are
+	 * a 3D-encoding even if all z-coordinates are 0.0. Otherwise, coordinates are
 	 * encoded in 3D only, if at least one of the z-coords is not 0.0.
 	 * @param mol
 	 * @param mode 0 or one or more of CONSIDER...TOPICITY, CREATE..., ENCODE_ATOM_CUSTOM_LABELS, ASSIGN_PARITIES_TO_TETRAHEDRAL_N, COORDS_ARE_3D
@@ -226,17 +227,7 @@ public Canonizer(StereoMolecule mol, int mode) {
 
 		mZCoordinatesAvailable = ((mode & COORDS_ARE_3D) != 0) || mMol.is3D();
 
-		mAllHydrogensAreExplicit = false;
-		if (mMol.getAllAtoms() > mMol.getAtoms()
-		 && !mMol.isFragment()) {
-			mAllHydrogensAreExplicit = true;
-			for (int i=0; i<mMol.getAtoms(); i++) {
-				if (mMol.getImplicitHydrogens(i) != 0) {
-					mAllHydrogensAreExplicit = false;
-					break;
-					}
-				}
-			}
+		mAllHydrogensAreExplicit = (mMol.getImplicitHydrogens() == 0);
 
 		if ((mMode & NEGLECT_ANY_STEREO_INFORMATION) == 0) {
 			mTHParity = new byte[mMol.getAtoms()];
@@ -639,7 +630,7 @@ private boolean canInnerBreakTiesByHeteroTopicity() {
 	private void canBreakTiesRandomly() {
 		for (int atom=0; atom<mMol.getAtoms(); atom++) {
 			mCanBase[atom].init(atom);
-			mCanBase[atom].add(mAtomBits+1, 2*mCanRank[atom]);
+			mCanBase[atom].add(mAtomBits+1, (long)2*mCanRank[atom]);
 			}
 
 		// promote randomly one atom of lowest shared rank.
@@ -895,7 +886,7 @@ private void canRecursivelyFindAllParities() {
 					thParityInfo |= mTHESRGroup[atom];
 					}
 
-				mCanBase[atom].add(2 * parityInfoBits, thParityInfo << parityInfoBits); // generate space for bond parity
+				mCanBase[atom].add(2 * parityInfoBits, (long)thParityInfo << parityInfoBits); // generate space for bond parity
 				}
 
 			for (int bond=0; bond<mMol.getBonds(); bond++) {
@@ -3371,7 +3362,7 @@ public String getEncodedCoordinates() {
 	 * original molecule including coordinates.<br>
 	 * If keepPositionAndScale==false, then coordinate encoding will be relative,
 	 * i.e. scale and absolute positions get lost during the encoding.
-	 * Otherwise the encoding retains scale and absolute positions.<br>
+	 * Otherwise, the encoding retains scale and absolute positions.<br>
 	 * If the molecule has 3D-coordinates and if there are no implicit hydrogen atoms,
 	 * i.e. all hydrogen atoms are explicitly available with their coordinates, then
 	 * hydrogen 3D-coordinates are also encoded despite the fact that the idcode itself does

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

@@ -1445,7 +1445,28 @@ public boolean supportsImplicitHydrogen(int atom) {
 		}
 
 	/**
-	 * Calculates and return the number of implicit hydrogens at atom.
+	 * Calculates and returns the number of implicit hydrogens of the molecule.
+	 * For hydrogens atoms, metals except Al, or a noble gases, 0 is assumed.
+	 * For all other atom kinds the number of implicit hydrogens is basically
+	 * the lowest typical valence that is compatible with the occupied valence,
+	 * minus the occupied valence corrected by atom charge and radical state.
+	 * If this molecule is a fragment, then 0 is returned.
+	 * @return number of implicit hydrogens of the molecule
+	 */
+	public int getImplicitHydrogens() {
+		if (mIsFragment)
+			return 0;
+
+		ensureHelperArrays(cHelperNeighbours);
+		int implicitHydrogens = 0;
+		for (int atom=0; atom<mAtoms; atom++)
+			implicitHydrogens += getImplicitHydrogens(atom);
+
+		return implicitHydrogens;
+		}
+
+	/**
+	 * Calculates and returns the number of implicit hydrogens at atom.
 	 * If atom is itself a hydrogen atom, a metal except Al, or a noble gas,
 	 * then 0 is returned. For all other atom kinds the number of
 	 * implicit hydrogens is basically the lowest typical valence that is compatible
@@ -1463,8 +1484,9 @@ public int getImplicitHydrogens(int atom) {
 		if (!supportsImplicitHydrogen(atom))
 			return 0;
 
-		if ("*".equals(getAtomCustomLabel(atom)))
-			return 0;
+		// attachment points have at least a valence of 1, i.e. they must be connected to something
+		if (mAtomicNo[atom] == 0 || "*".equals(getAtomCustomLabel(atom)))
+			return mAllConnAtoms[atom] == 0 ? 1 : 0;
 
 		ensureHelperArrays(cHelperNeighbours);
 

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

@@ -820,7 +820,7 @@ private void appendBondOrderSymbol(int bond, int parentAtom, StringBuilder build
 		if (mEZHalfParity[bond] != 0)
 			builder.append(mEZHalfParity[bond] == 1 ? '/' : '\\');
 		if (mMode == MODE_CREATE_SMARTS) {
-			int bondTypes = mMol.getBondQueryFeatures(Molecule.cBondQFBondTypes | Molecule.cBondQFRareBondTypes);
+			int bondTypes = mMol.getBondQueryFeatures(bond) & (Molecule.cBondQFBondTypes | Molecule.cBondQFRareBondTypes);
 			if (bondTypes != 0) {
 				if ((bondTypes & Molecule.cBondTypeSingle) != 0 && mEZHalfParity[bond] == 0) {
 					builder.append('-');

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

@@ -1322,6 +1322,14 @@ public boolean areBondsSimilar(int moleculeBond, int fragmentBond) {
 			 && ringSize == (mMolecule.getBondQueryFeatures(fragmentBond) & Molecule.cBondQFRingSize) >> Molecule.cBondQFRingSizeShift)
 				return true;
 
+			if (ringSize <= 2) {    // ring size 8-11 is encoded as 1; ring size >=12 is encoded as 2
+				int moleculeRingSize = mMolecule.getBondRingSize(moleculeBond);
+				if (ringSize == 1)
+					return (moleculeRingSize >= 8) && (moleculeRingSize <= 12);
+				else
+					return moleculeRingSize >= 12;
+				}
+
 			boolean found = false;
 			RingCollection ringSet = mMolecule.getRingSet();
 			for (int i=0; i<ringSet.getSize(); i++) {

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/descriptor/DescriptorWeightsHelper.java

@@ -71,7 +71,7 @@ public DescriptorWeightsHelper() {
      * - Charged pp points are set mandatory.
      * @param liSubGraphIndices
      * @param molecule3D
-     * @return
+     * @return array with dimension molecule3D.getAtoms().
      */
     public static int [] calcWeightLabels(List<SubGraphIndices> liSubGraphIndices, Molecule3D molecule3D){
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/shredder/FragmentGeometry3D.java

@@ -74,7 +74,7 @@ private Coordinates[] determineAlignmentCoords() {
 			coords[i] = mMol.getCoordinates(mExitVector[i].rootAtom);
 			coords[mExitVector.length + i] = mMol.getCoordinates(mExitVector[i].exitAtom);
 
-			// for lonely hydrogens (selected H connects to other exit atom)
+			// for lonely hydrogens (single selected H connecting to non-selected exit atom)
 			// we need to place the root coord (hydrogen) further away from the exit atom,
 			// to reflect the longer bond length of a C-C compared to H-C
 			if (mMol.getAtomicNo(mExitVector[i].rootAtom) == 1)
@@ -123,9 +123,10 @@ public boolean equals(FragmentGeometry3D geometry) {
 	 * is returned.
 	 * @param geometry the geometry to be aligned with this
 	 * @param permutation permutation index for equivalent root atoms of the passed geometry
+	 * @param rmsdHolder null or double[1] to receive RMSD value
 	 * @return rotation matrix or null, depending on whether alignment is acceptable
 	 */
-	public double[][] alignRootAndExitAtoms(FragmentGeometry3D geometry, int permutation, double maxRMSD) {
+	public double[][] alignRootAndExitAtoms(FragmentGeometry3D geometry, int permutation, double[] rmsdHolder, double maxRMSD) {
 		ExitVector[] geomEV = geometry.mExitVector;
 		Coordinates[] coords = new Coordinates[2*geomEV.length];
 		for (int i=0; i<geomEV.length; i++)
@@ -141,19 +142,27 @@ public double[][] alignRootAndExitAtoms(FragmentGeometry3D geometry, int permuta
 			c.add(mAlignmentCOG);
 		}
 
-		return Coordinates.getRmsd(mAlignmentCoords, coords) > maxRMSD ? null : matrix;
+		double rmsd = Coordinates.getRmsd(mAlignmentCoords, coords);
+		if (rmsdHolder != null)
+			rmsdHolder[0] = rmsd;
+
+		return rmsd > maxRMSD ? null : matrix;
 	}
 
-	public boolean hasMatchingExitVectors(FragmentGeometry3D geometry, Coordinates[] coords, int permutation, double maxAngleDivergence) {
-		maxAngleDivergence *= Math.PI / 180;
-		for (int i = 0; i<mExitVector.length; i++) {
+	public boolean hasMatchingExitVectors(FragmentGeometry3D geometry, Coordinates[] coords, int permutation, double[][] angleHolder, double maxAngleDivergence) {
+		double[] angleDif = new double[mExitVector.length];
+		boolean qualifies = true;
+		for (int i=0; i<mExitVector.length; i++) {
 			Coordinates v1 = mAlignmentCoords[mExitVector.length+i].subC(mAlignmentCoords[i]);
 			ExitVector ev2 = geometry.mExitVector[mPermutation[permutation][i]];
 			Coordinates v2 = coords[ev2.exitAtom].subC(coords[ev2.rootAtom]);
-			if (v1.getAngle(v2) > maxAngleDivergence)
-				return false;
+			angleDif[i] = v1.getAngle(v2) * 180 / Math.PI;
+			if (angleDif[i] > maxAngleDivergence)
+				qualifies = false;
 		}
-		return true;
+		if (angleHolder != null)
+			angleHolder[0] = angleDif;
+		return qualifies;
 	}
 
 	public int getPermutationCount() {

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/shredder/Fragmenter3D.java

@@ -55,7 +55,7 @@ public ArrayList<Fragment3D> buildFragments(StereoMolecule mol, boolean withHydr
 		int fragmentCount = mol.getFragmentNumbers(fragmentNo, isRotatableBond, true);
 
 		int[] atomCount = new int[fragmentCount];
-		for (int atom=0; atom<mol.getAllAtoms(); atom++)
+		for (int atom=0; atom<mol.getAtoms(); atom++)
 			atomCount[fragmentNo[atom]]++;
 
 		BaseFragmentInfo[] fragmentData = new BaseFragmentInfo[fragmentCount];

src/com/actelion/research/gwt/chemlib/com/actelion/research/gui/editor/BondQueryFeatureDialogBuilder.java

@@ -116,6 +116,8 @@ private void build(ExtendedMolecule mol, int bond) {
 		mComboBoxRingSize.addItem("is in 5-membered ring");
 		mComboBoxRingSize.addItem("is in 6-membered ring");
 		mComboBoxRingSize.addItem("is in 7-membered ring");
+		mComboBoxRingSize.addItem("smallest ring 8 to 11");
+		mComboBoxRingSize.addItem("smallest ring >= 12");
 		mDialog.add(mComboBoxRingSize, 1,13,3,13);
 
 		mCBMatchFormalOrder = mDialog.createCheckBox("Match formal bond order");
@@ -223,7 +225,7 @@ else if (aromState == Molecule.cBondQFNotAromatic)
 			mComboBoxRing.setSelectedIndex(0);
 
 		int ringSize = (queryFeatures & Molecule.cBondQFRingSize) >> Molecule.cBondQFRingSizeShift;
-		mComboBoxRingSize.setSelectedIndex((ringSize == 0) ? 0 : ringSize-2);
+		mComboBoxRingSize.setSelectedIndex((ringSize == 0) ? 0 : (ringSize <= 2) ? ringSize+5 : ringSize-2);
 
         if ((queryFeatures & Molecule.cBondQFBridge) != 0) {
             mCBIsBridge.setSelected(true);
@@ -361,9 +363,12 @@ else if (mComboBoxRing.getSelectedIndex() == 4) {
 
 			if (mComboBoxRingSize.getSelectedIndex() != 0) {
 				int ringSize = mComboBoxRingSize.getSelectedIndex() + 2;
+				if (ringSize > 7)	// ringsize 8-11 is encoded as 1; ringsize >12 is encoded as 2
+					ringSize -= 7;
 				int implicitSize = mMol.getBondRingSize(bond);
-				if (ringSize != implicitSize)
+				if (ringSize <= 2 || ringSize != implicitSize) {	// options 1 and 2 cover spans and cannot be implicit
 					queryFeatures |= (ringSize << Molecule.cBondQFRingSizeShift);
+					}
 				}
             }