feat: update OCL to v2022.10.2

scripts/openchemlib/classes.js

@@ -38,9 +38,13 @@ const changed = [
   ['chem/MolfileCreator', changeLineSeparator],
   ['chem/MolfileV3Creator', changeLineSeparator],
   ['chem/Molecule3D', removeCloneInfos],
+  ['chem/TautomerHelper', changeTautomerHelper],
   ['chem/TextDrawingObject', changeTextDrawingObject],
+  ['gui/editor/GenericEditorArea', changeGenericEditorArea],
+  ['gui/editor/CustomAtomDialogBuilder', changeCustomAtomDialogBuilder],
   ['share/gui/editor/Model', removePrintf],
   ['util/ArrayUtils', changeArrayUtils],
+  ['util/datamodel/IntVec', changeIntVec],
 ];
 
 exports.changed = changed.map(([path, ...transformers]) => {
@@ -93,8 +97,6 @@ const removed = [
   'chem/descriptor/pharmacophoretree',
   'chem/dnd', // ui
   'chem/docking',
-  'chem/ExtendedDepictor.java',
-  'chem/ExtendedMoleculeFunctions.java',
   'chem/forcefield/mmff/Sdf.java', // needs access to disk
   'chem/hyperspace',
   'chem/interactionstatistics',
@@ -103,11 +105,9 @@ const removed = [
   'chem/io/DWARFileCreator.java',
   'chem/io/NativeMDLReactionReader.java',
   'chem/io/pdb',
-  'chem/mcs',
   'chem/mmp',
   'chem/Molecule3DFunctions.java',
   'chem/optimization/MCHelper.java',
-  'chem/PeriodicTable.java',
   'chem/phesa',
   'chem/phesaflex',
   'chem/potentialenergy',
@@ -117,32 +117,30 @@ const removed = [
   'chem/properties/complexity',
   'chem/properties/fractaldimension',
   'chem/reaction/ClassificationData.java',
-  'chem/reaction/CommonSubGraphHelper.java',
   'chem/reaction/FunctionalGroupClassifier.java',
   'chem/reaction/mapping',
-  'chem/reaction/MCSReactionMapper.java',
   'chem/reaction/ReactionClassifier.java',
   'chem/reaction/ReactionSearch.java',
   'chem/RingHelper.java',
   'chem/shredder/Fragment.java',
   'chem/StructureSearch.java',
   'jfx',
-  'gui/clipboard',
+  'gui/clipboard/ClipboardHandler.java',
+  'gui/clipboard/external',
+  'gui/clipboard/ImageClipboardHandler.java',
+  'gui/clipboard/NativeClipboardAccessor.java',
+  'gui/clipboard/TextClipboardHandler.java',
   'gui/CompoundCollectionPane.java',
   'gui/dnd',
   'gui/dock',
-  'gui/editor/CustomAtomDialogBuilder.java',
   'gui/editor/FXEditorArea.java',
   'gui/editor/FXEditorDialog.java',
   'gui/editor/FXEditorPane.java',
   'gui/editor/FXEditorToolbar.java',
-  'gui/editor/GenericEditorArea.java',
-  'gui/editor/GenericEditorToolbar.java',
   'gui/editor/SwingEditorArea.java',
   'gui/editor/SwingEditorDialog.java',
   'gui/editor/SwingEditorPanel.java',
   'gui/editor/SwingEditorToolbar.java',
-  'gui/FileHelper.java',
   'gui/fx',
   'gui/HeaderPaintHelper.java',
   'gui/hidpi',
@@ -168,11 +166,9 @@ const removed = [
   'gui/JScrollableMenu.java',
   'gui/JStructureView.java',
   'gui/JTextDrawingObjectDialog.java',
-  'gui/LookAndFeelHelper.java',
   'gui/MultiPanelDragListener.java',
   'gui/PopupItemProvider.java',
   'gui/ScrollPaneAutoScrollerWhenDragging.java',
-  'gui/swing',
   'gui/table',
   'gui/VerticalFlowLayout.java',
   'gui/wmf',
@@ -184,7 +180,6 @@ const removed = [
   'util/CommandLineParser.java',
   'util/concurrent',
   'util/convert/String2DoubleArray.java',
-  'util/datamodel',
   'util/Formatter.java',
   'util/graph',
   'util/IO.java',
@@ -213,6 +208,9 @@ exports.generated = generated.map((file) => [getFilename(file[0]), file[1]]);
 function getFilename(file) {
   if (file.startsWith('@org/')) {
     return `../org/${file.replace('@org/', '')}.java`;
+  }
+  if (file.startsWith('@gwt/')) {
+    return `../../${file.replace('@gwt/', '')}.java`;
   } else {
     return `actelion/research/${file}.java`;
   }
@@ -228,7 +226,10 @@ function getFolderName(file) {
 
 function methodRegExp(methodName, options = {}) {
   const { indent = '\t' } = options;
-  return new RegExp(`public.*? ${methodName}\\(.*\n(.*\n)*?${indent}}`, 'g');
+  return new RegExp(
+    `(?:public|private|protected).*? ${methodName}\\(.*\n(?:.*\n)*?${indent}}`,
+    'g',
+  );
 }
 
 function removePrintf(code) {
@@ -253,19 +254,62 @@ function removeCloneInfos(code) {
   );
 }
 
+function changeTautomerHelper(code) {
+  code = code.replace(
+    'import java.util',
+    'import java.util.Arrays;\nimport java.util',
+  );
+  code = code.replace(
+    'mRegionDCount.clone();',
+    'Arrays.copyOf(mRegionDCount, mRegionDCount.length);',
+  );
+  code = code.replace(
+    'mRegionTCount.clone();',
+    'Arrays.copyOf(mRegionTCount, mRegionTCount.length);',
+  );
+  return code;
+}
+
 function changeTextDrawingObject(code) {
   return code.replace(
     'detail.append(String.format(" size=\\"%.4f\\"", new Double(mSize)));',
     'detail.append(" size=\\""+mSize+"\\"");',
   );
 }
 
+function changeGenericEditorArea(code) {
+  // TODO: find replacements
+  code = code.replaceAll(
+    methodRegExp('showWarningMessage'),
+    'private void showWarningMessage(String msg) {}',
+  );
+  code = code.replaceAll(
+    methodRegExp('openReaction'),
+    'private void openReaction() {}',
+  );
+  code = code.replaceAll('System.getProperty("development") != null', 'false');
+  return code;
+}
+
+function changeCustomAtomDialogBuilder(code) {
+  code = code.replace('e.getSource() instanceof JTextField', 'false');
+  return code;
+}
+
 function changeArrayUtils(code) {
   code = removeSlice(code, '\n	/**\n	 * Resize an array', 'return newArray;\n	}');
   code = removeSlice(code, '\n	/**\n	 * Copy an array ', 'return newArray;\n	}');
   return code;
 }
 
+function changeIntVec(code) {
+  const options = { indent: '    ' };
+  code = code.replace(methodRegExp('convert', options), '');
+  code = code.replace(methodRegExp('read', options), '');
+  code = code.replace(methodRegExp('readBitStringDense', options), '');
+  return code;
+}
+
 function removeSlice(code, start, end) {
   const startIdx = code.indexOf(start);
   if (startIdx === -1) {

scripts/openchemlib/modified/com/actelion/research/gui/hidpi/HiDPIHelper.java

@@ -1,7 +1,21 @@
 package com.actelion.research.gui.hidpi;
 
+import com.actelion.research.gui.generic.GenericImage;
+
 public class HiDPIHelper {
 	public static int scale(float value) {
-		return value;
+		return Math.round(getUIScaleFactor() * value);
+	}
+
+	public static float getUIScaleFactor() {
+		return 1.0f;
+	}
+
+	public static void adaptForLookAndFeel(GenericImage image) {
+		return;
+	}
+
+	public static void disableImage(GenericImage image) {
+		return;
 	}
 }

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

@@ -134,7 +134,7 @@ public abstract class AbstractDepictor<T> {
 	public static final int	cDModeSuppressCIPParity = 0x0040;
 	public static final int	cDModeSuppressESR = 0x0080;
 
-	private static final int cDModeShowSymmetryAny = 0x0700;
+	private static final int cDModeShowSymmetryAny = 0x0300;
 	public static final int cDModeShowSymmetrySimple = 0x0100;
     public static final int cDModeShowSymmetryStereoHeterotopicity = 0x0200;
 	public static final int	cDModeNoImplicitAtomLabelColors = 0x0400;
@@ -1782,30 +1782,36 @@ else if (neighbours == Molecule.cAtomQFNot0Neighbours+Molecule.cAtomQFNot1Neighb
                 else if (neighbours == (Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot4Neighbours))
                     isoStr = append(isoStr, "n>3");
                 }
-			if ((queryFeatures & Molecule.cAtomQFZValue) != 0) {
-				long eNegNeighbours = (queryFeatures & Molecule.cAtomQFZValue);
-				if (eNegNeighbours == (Molecule.cAtomQFZValue & ~Molecule.cAtomQFZValueNot0))
+			if ((queryFeatures & Molecule.cAtomQFENeighbours) != 0) {
+				long eNegNeighbours = (queryFeatures & Molecule.cAtomQFENeighbours);
+				if (eNegNeighbours == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot0ENeighbours))
 					isoStr = append(isoStr, "e0");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValue & ~Molecule.cAtomQFZValueNot1))
+				else if (eNegNeighbours == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot1ENeighbour))
 					isoStr = append(isoStr, "e1");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValue & ~Molecule.cAtomQFZValueNot2))
+				else if (eNegNeighbours == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot2ENeighbours))
 					isoStr = append(isoStr, "e2");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValue & ~Molecule.cAtomQFZValueNot3))
+				else if (eNegNeighbours == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot3ENeighbours))
 					isoStr = append(isoStr, "e3");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValueNot2 | Molecule.cAtomQFZValueNot3 | Molecule.cAtomQFZValueNot4))
+				else if (eNegNeighbours == (Molecule.cAtomQFNot2ENeighbours | Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot4ENeighbours))
 					isoStr = append(isoStr, "e<2");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValueNot3 | Molecule.cAtomQFZValueNot4))
+				else if (eNegNeighbours == (Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot4ENeighbours))
 					isoStr = append(isoStr, "e<3");
-				else if (eNegNeighbours == Molecule.cAtomQFZValueNot4)
+				else if (eNegNeighbours == Molecule.cAtomQFNot4ENeighbours)
 					isoStr = append(isoStr, "e<4");
-				else if (eNegNeighbours == Molecule.cAtomQFZValueNot0)
+				else if (eNegNeighbours == Molecule.cAtomQFNot0ENeighbours)
 					isoStr = append(isoStr, "e>0");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValueNot0 | Molecule.cAtomQFZValueNot1))
+				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot1ENeighbour))
 					isoStr = append(isoStr, "e>1");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValueNot0 | Molecule.cAtomQFZValueNot1 | Molecule.cAtomQFZValueNot2))
+				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot1ENeighbour | Molecule.cAtomQFNot2ENeighbours))
 					isoStr = append(isoStr, "e>2");
-				else if (eNegNeighbours == (Molecule.cAtomQFZValue & ~Molecule.cAtomQFZValueNot4))
+				else if (eNegNeighbours == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot4ENeighbours))
 					isoStr = append(isoStr, "e>3");
+				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot3ENeighbours))
+					isoStr = append(isoStr, "e1-2");
+				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot4ENeighbours))
+					isoStr = append(isoStr, "e1-3");
+				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot1ENeighbour | Molecule.cAtomQFNot4ENeighbours))
+					isoStr = append(isoStr, "e2-3");
 				}
             if ((queryFeatures & Molecule.cAtomQFRingState) != 0) {
                 long ringBonds = (queryFeatures & Molecule.cAtomQFRingState);

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

@@ -3262,6 +3262,9 @@ private void idCodeCreate() {
 			addAtomQueryFeatures(29, nbits, Molecule.cAtomQFRxnParityHint, Molecule.cAtomQFRxnParityBits, Molecule.cAtomQFRxnParityShift);
 			addAtomQueryFeatures(30, nbits, Molecule.cAtomQFNewRingSize, Molecule.cAtomQFNewRingSizeBits, Molecule.cAtomQFNewRingSizeShift);
 			addAtomQueryFeatures(32, nbits, Molecule.cAtomQFStereoState, Molecule.cAtomQFStereoStateBits, Molecule.cAtomQFStereoStateShift);
+			addAtomQueryFeatures(33, nbits, Molecule.cAtomQFENeighbours, Molecule.cAtomQFENeighbourBits, Molecule.cAtomQFENeighbourShift);
+			addAtomQueryFeatures(34, nbits, Molecule.cAtomQFHeteroAromatic, 1, -1);
+			addBondQueryFeatures(35, nbits, Molecule.cBondQFMatchFormalOrder, 1, -1);
 			}
 
 		encodeBits(0, 1);