feat: update OCL to v2024.10.1 (#233)

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

@@ -4118,24 +4118,32 @@ public void validateBondQueryFeatures() {
 		ensureHelperArrays(cHelperRings);
 
 		for (int bond=0; bond<mBonds; bond++) {
-			if (isDelocalizedBond(bond))
-				mBondQueryFeatures[bond] &= ~cBondQFDelocalized;
+			int bondTypeQFCount = Integer.bitCount(mBondQueryFeatures[bond] & (Molecule.cBondQFBondTypes | Molecule.cBondQFRareBondTypes));
 
-			int bondType = mBondType[bond] & cBondTypeMaskSimple;
-			if (bondType == cBondTypeSingle)
-				mBondQueryFeatures[bond] &= ~cBondQFSingle;
-			else if (bondType == cBondTypeDouble)
-				mBondQueryFeatures[bond] &= ~cBondQFDouble;
-			else if (bondType == cBondTypeTriple)
-				mBondQueryFeatures[bond] &= ~cBondQFTriple;
-			else if (bondType == cBondTypeQuadruple)
-				mBondQueryFeatures[bond] &= ~cBondQFQuadruple;
-			else if (bondType == cBondTypeQuintuple)
-				mBondQueryFeatures[bond] &= ~cBondQFQuintuple;
-			else if (bondType == cBondTypeMetalLigand)
-				mBondQueryFeatures[bond] &= ~cBondQFMetalLigand;
-			else if (bondType == cBondTypeDelocalized)
+			if (isDelocalizedBond(bond) & (mBondQueryFeatures[bond] & cBondQFDelocalized) != 0) {
 				mBondQueryFeatures[bond] &= ~cBondQFDelocalized;
+				bondTypeQFCount--;
+				}
+
+			// if we have allowed bond types defined, then make sure,
+			// that the explicit bond type is one of them.
+			if (bondTypeQFCount != 0) {
+				int bondType = mBondType[bond] & cBondTypeMaskSimple;
+				if (bondType == cBondTypeSingle)
+					mBondQueryFeatures[bond] |= cBondQFSingle;
+				else if (bondType == cBondTypeDouble)
+					mBondQueryFeatures[bond] |= cBondQFDouble;
+				else if (bondType == cBondTypeTriple)
+					mBondQueryFeatures[bond] |= cBondQFTriple;
+				else if (bondType == cBondTypeQuadruple)
+					mBondQueryFeatures[bond] |= cBondQFQuadruple;
+				else if (bondType == cBondTypeQuintuple)
+					mBondQueryFeatures[bond] |= cBondQFQuintuple;
+				else if (bondType == cBondTypeMetalLigand)
+					mBondQueryFeatures[bond] |= cBondQFMetalLigand;
+				else if (bondType == cBondTypeDelocalized)
+					mBondQueryFeatures[bond] |= cBondQFDelocalized;
+				}
 			}
 		}
 

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

@@ -3475,8 +3475,9 @@ public void setBondQueryFeature(int bond, int feature, boolean value) {
 			mBondQueryFeatures[bond] |= feature;
 		else
 			mBondQueryFeatures[bond] &= ~feature;
-		mValidHelperArrays = cHelperNone;	// there is an influence on occipied valence, bond order, etc.
-		mIsFragment = true;
+		mValidHelperArrays = cHelperNone;	// there is an influence on occupied valence, bond order, etc.
+		if (value && feature != 0)
+			mIsFragment = true;
 		}
 
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/forcefield/mmff/ForceFieldMMFF94.java

@@ -33,16 +33,12 @@
 
 package com.actelion.research.chem.forcefield.mmff;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-import java.util.HashMap;
-
 import com.actelion.research.chem.StereoMolecule;
 import com.actelion.research.chem.forcefield.AbstractForceField;
 
-/**
+import java.util.*;
+
+/*
  * The MMFF ForceField class is the top level class used to perform
  * energy calculations/minimisation on a molecule. It accepts an
  * ExtendedMolecule and the string name of the parameter tables to use.
@@ -68,17 +64,17 @@
  *      (default: 1.0)
  *  - "dielectric model": A string for the dielectric model. "distance"
  *      selects a distance-dependent dielectric model, everything else
-*       selects the constant dielectric model (default: "constant")
+ *      selects the constant dielectric model (default: "constant")
  *  - "angle bend": A boolean, default True, for whether to include angle
  *      bending energy terms.
  *  - "bond stretch": A boolean, default True, for whether to include bond
  *      stretching energy terms.
  *  - "electrostatic": A boolean, default True, for whether to include the
  *      nonbonded electrostatic energy terms.
  *  - "out of plane": A boolean, default True, for whether to include out
-        of plane energy terms.
+ *      of plane energy terms.
  *  - "stretch bend": A boolean, default True, for whether to include
-        stretch bending energy terms.
+ *      stretch bending energy terms.
  *  - "torsion angle": A boolean, default True, for whether to include
  *      torsional angle energy terms.
  *  - "van der waals": A boolean, default True, for whether to include the
@@ -88,20 +84,15 @@
  * @author joel
  *
  */
-/**
- * @author joel
- *
- */
 public final class ForceFieldMMFF94 extends AbstractForceField {
 	public static final String MMFF94 = "MMFF94";
 	public static final String MMFF94S = "MMFF94s";
     public static final String MMFF94SPLUS = "MMFF94s+";
 
 
-    //protected final ExtendedMolecule mol;
     private final MMFFMolecule mMMFFMol;
-    public static Map<String, Tables> mTables = new HashMap<String, Tables>();
-    private List<EnergyTerm> mEnergies = new ArrayList<EnergyTerm>();
+    public static Map<String, Tables> mTables = new HashMap<>();
+    private final List<EnergyTerm> mEnergies = new ArrayList<>();
 
 
     /**
@@ -114,25 +105,21 @@ public final class ForceFieldMMFF94 extends AbstractForceField {
      *      See class description of a list of options.
      */
 
-    public ForceFieldMMFF94(StereoMolecule m, String tablename,
-            Map<String, Object> options) {
+    public ForceFieldMMFF94(StereoMolecule m, String tablename, Map<String, Object> options)
+			throws BadAtomTypeException,BadRingAromException {
     	super(m);
     	mMMFFMol = new com.actelion.research.chem.forcefield.mmff.MMFFMolecule(m);
     	mMol.ensureHelperArrays(StereoMolecule.cHelperRings);
         Tables table = mTables.get(tablename);
 
         double nonBondedThresh = options.containsKey("nonbonded cutoff")
-            ? ((Double)options.get("nonbonded cutoff")).doubleValue()
+            ? (Double)options.get("nonbonded cutoff")
             : 100.0;
 
         double dielConst = options.containsKey("dielectric constant")
-            ? ((Double)options.get("dielectric constant")).doubleValue() : 1.0;
-
-        boolean dielModel = options.containsKey("dielectric model")
-            ? ((String)options.get("dielectric model")).equals("distance")
-            : false;
-
+            ? (Double)options.get("dielectric constant") : 1.0;
 
+        boolean dielModel = options.containsKey("dielectric model") && (options.get("dielectric model")).equals("distance");
 
         Separation sep = new Separation(mMMFFMol);
 
@@ -174,8 +161,8 @@ public ForceFieldMMFF94(StereoMolecule m, String tablename,
      *      must be a table with this name that has been loaded with
      *      "loadTable()".
      */
-    public ForceFieldMMFF94(StereoMolecule mol, String tablename) {
-        this(mol, tablename, new HashMap<String, Object>());
+    public ForceFieldMMFF94(StereoMolecule mol, String tablename) throws BadAtomTypeException,BadRingAromException {
+        this(mol, tablename, new HashMap<>());
     }
 
     /**

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/forcefield/mmff/MMFFMolecule.java

@@ -36,25 +36,24 @@
 import com.actelion.research.chem.StereoMolecule;
 import com.actelion.research.chem.RingCollection;
 
+import java.util.Arrays;
+
 /**
  * MMFF molecule is a wrapper class for the ExtendedMolecule. It holds some
  * additional data such as a cache of the atom types, whether the molecule is
  * valid for MMFF and the ring mmff aromaticity property.
  */
 public final class MMFFMolecule extends StereoMolecule  {
-    private RingBoolean[] mRingArom;
-    private int[] mAtomTypes;
-    private int[] mHydrogenMap;
+    private final RingBoolean[] mRingArom;
+    private final int[] mAtomTypes;
+    private final int[] mHydrogenMap;
 
-    public MMFFMolecule(StereoMolecule mol) throws BadAtomTypeException,
-                                                 BadRingAromException
-    {
+    public MMFFMolecule(StereoMolecule mol) throws BadAtomTypeException,BadRingAromException {
     	super(mol);
         mHydrogenMap = getHandleHydrogenMap();
         RingCollection rings = getRingSet();
         mRingArom = new RingBoolean[rings.getSize()];
-        for (int i=0; i<mRingArom.length; i++)
-            mRingArom[i] = RingBoolean.NOT_SET;
+		Arrays.fill(mRingArom, RingBoolean.NOT_SET);
 
         boolean allset = false, changed = true;
         while (!allset && changed) {
@@ -109,7 +108,7 @@ public int[] getHydrogenMap() {
      *  @return True if the ring is aromatic, false otherwise.
      */
     public boolean ringIsMMFFAromatic(int r) {
-        return mRingArom[r] == RingBoolean.TRUE ? true : false;
+        return mRingArom[r] == RingBoolean.TRUE;
     }
 
     /**
@@ -118,7 +117,7 @@ public boolean ringIsMMFFAromatic(int r) {
      *  @return True if the ring has had its flag set, false otherwise.
      */
     public boolean isSetRingMMFFAromaticity(int r) {
-        return mRingArom[r] == RingBoolean.NOT_SET ? false : true;
+        return mRingArom[r] != RingBoolean.NOT_SET;
     }
 
 

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

@@ -144,12 +144,13 @@ public double[][] alignRootAndExitAtoms(FragmentGeometry3D geometry, int permuta
 		return Coordinates.getRmsd(mAlignmentCoords, coords) > maxRMSD ? null : matrix;
 	}
 
-	public boolean hasMatchingExitVectors(FragmentGeometry3D geometry, Coordinates[] coords, int permutation, double maxDiversion) {
+	public boolean hasMatchingExitVectors(FragmentGeometry3D geometry, Coordinates[] coords, int permutation, double maxAngleDivergence) {
+		maxAngleDivergence *= Math.PI / 180;
 		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) > maxDiversion)
+			if (v1.getAngle(v2) > maxAngleDivergence)
 				return false;
 		}
 		return true;

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

@@ -291,49 +291,54 @@ private void setQueryFeatures(int bond) {
             queryFeatures |= (minAtoms << Molecule.cBondQFBridgeMinShift);
             queryFeatures |= (atomSpan << Molecule.cBondQFBridgeSpanShift);
             queryFeatures &= ~Molecule.cBondQFBondTypes;
+			mMol.setBondType(bond, Molecule.cBondTypeSingle);
             }
         else {
-        	// priority in order of bond orders
-            int bondOrder = -1;
-            if (mCBSingle.isSelected()) {
-                mMol.setBondType(bond, Molecule.cBondTypeSingle);
-				bondOrder = 1;
-                }
-            else if (mCBDelocalized.isSelected() && !mMol.isDelocalizedBond(bond)) {
-	            mMol.setBondType(bond, Molecule.cBondTypeDelocalized);
-	            bondOrder = 4;
-	            }
-            else if (mCBDouble.isSelected()) {
-                mMol.setBondType(bond, Molecule.cBondTypeDouble);
-				bondOrder = 2;
-                }
-            else if (mCBTriple.isSelected()) {
-                mMol.setBondType(bond, Molecule.cBondTypeTriple);
-				bondOrder = 3;
-                }
- 			else if (mCBMetalLigand.isSelected()) {
-				mMol.setBondType(bond, Molecule.cBondTypeMetalLigand);
-				bondOrder = 0;
-				}
+        	// priority in order of bond orders (except 0)
+            int bondType = -1;
+			int selectionCount = 0;
 
-            if (mCBSingle.isSelected() && bondOrder != 1)
-    			queryFeatures |= Molecule.cBondQFSingle;
-    		if (mCBDouble.isSelected() && bondOrder != 2)
-    			queryFeatures |= Molecule.cBondQFDouble;
-    		if (mCBTriple.isSelected() && bondOrder != 3)
-    			queryFeatures |= Molecule.cBondQFTriple;
-	        if (mCBQuadruple.isSelected() && bondOrder != 4)
-		        queryFeatures |= Molecule.cBondQFQuadruple;
-	        if (mCBQuintuple.isSelected() && bondOrder != 5)
-		        queryFeatures |= Molecule.cBondQFQuintuple;
-    		if (mCBDelocalized.isSelected() && !mMol.isDelocalizedBond(bond) && bondOrder != 4)
-    			queryFeatures |= Molecule.cBondQFDelocalized;
-			if (mCBMetalLigand.isSelected() && bondOrder != 0)
+			if (mCBMetalLigand.isSelected()) {
+				bondType = Molecule.cBondTypeMetalLigand;
 				queryFeatures |= Molecule.cBondQFMetalLigand;
-    		if (mCBMatchFormalOrder.isSelected())
-    			queryFeatures |= Molecule.cBondQFMatchFormalOrder;
-	        if (mCBMatchStereo.isSelected())
-		        queryFeatures |= Molecule.cBondQFMatchStereo;
+				selectionCount++;
+				}
+			if (mCBQuintuple.isSelected()) {
+				bondType = Molecule.cBondTypeQuintuple;
+				queryFeatures |= Molecule.cBondQFQuintuple;
+				selectionCount++;
+				}
+			if (mCBQuadruple.isSelected()) {
+				bondType = Molecule.cBondTypeQuadruple;
+				queryFeatures |= Molecule.cBondQFQuadruple;
+				selectionCount++;
+				}
+			if (mCBTriple.isSelected()) {
+				bondType = Molecule.cBondTypeTriple;
+				queryFeatures |= Molecule.cBondQFTriple;
+				selectionCount++;
+				}
+			if (mCBDouble.isSelected()) {
+				bondType = Molecule.cBondTypeDouble;
+				queryFeatures |= Molecule.cBondQFDouble;
+				selectionCount++;
+				}
+			if (mCBDelocalized.isSelected()) {
+				bondType = Molecule.cBondTypeDelocalized;
+				queryFeatures |= Molecule.cBondQFDelocalized;
+				selectionCount++;
+				}
+			if (mCBSingle.isSelected()) {
+				bondType = Molecule.cBondTypeSingle;
+				queryFeatures |= Molecule.cBondQFSingle;
+				selectionCount++;
+				}
+
+			if (bondType != -1)
+				mMol.setBondType(bond, bondType);	// set to the lowest bond order of query options
+
+			if (selectionCount < 2)
+				queryFeatures = 0;
 
 			if (mComboBoxRing.getSelectedIndex() != 0) {
 				if (mComboBoxRing.getSelectedIndex() == 1) {

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

@@ -943,15 +943,19 @@ private void eventHappened(GenericMouseEvent e) {
 				return;
 			}
 
+			if (e.getButton() == 1) {
+				mMouseIsDown = false;
+				updateCursor();
+				mouseReleasedButton1();
+			}
+		}
+
+		if (e.getWhat() == GenericMouseEvent.MOUSE_CLICKED) {
 			if (e.getButton() == 1) {
 				if (e.getClickCount() == 2) {
 					handleDoubleClick(e.getX(), e.getY());
 					return;
 				}
-
-				mMouseIsDown = false;
-				updateCursor();
-				mouseReleasedButton1();
 			}
 		}
 

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

@@ -135,8 +135,8 @@ public void setCurrentTool(int tool) {
 	public void paintContent(GenericDrawContext context) {
 		int background = mToolbarCanvas.getBackgroundRGB();
 		boolean isDark = (ColorHelper.perceivedBrightness(background) < 0.5);
-		int highlightBackground = isDark ? ColorHelper.brighter(background, 0.6f) : ColorHelper.darker(background, 0.6f);
-		int selectedBackground = isDark ? ColorHelper.brighter(background, 0.8f) : ColorHelper.darker(background, 0.8f);
+		int highlightBackground = isDark ? ColorHelper.brighter(background, 0.3f) : ColorHelper.darker(background, 0.6f);
+		int selectedBackground = isDark ? ColorHelper.brighter(background, 0.5f) : ColorHelper.darker(background, 0.8f);
 
 		int sw = mImageNormal.getWidth();
 		int sh = mImageNormal.getHeight();