feat: update OCL to v2024.11.1 (#241)

Closes: #239
cheminfo · Nov 5, 2024 · 9cfc345 · 9cfc345
1 parent 63f7771
commit 9cfc345
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Showing 3 changed files with 13 additions and 10 deletions.
diff --git a/openchemlib b/openchemlib
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/Canonizer.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/Canonizer.java
@@ -3417,7 +3417,7 @@ private void encodeCoordinates(boolean keepPositionAndScale, Coordinates[] coord
 		mEncodingBuffer.append(includeHydrogenCoordinates ? '#' : '!');
 		encodeBits(mZCoordinatesAvailable ? 1 : 0, 1);
 		encodeBits(keepPositionAndScale ? 1 : 0, 1);
-		encodeBits(resolutionBits/2, 4);	// resolution bits devided by 2
+		encodeBits(resolutionBits >> 1, 4);	// resolution bits divided by 2
 
 		double maxDelta = 0.0;
 		for (int i=1; i<mMol.getAtoms(); i++)
@@ -3436,8 +3436,8 @@ private void encodeCoordinates(boolean keepPositionAndScale, Coordinates[] coord
 			}
 
 		int binCount = (1 << resolutionBits);
-		double increment = maxDelta / (binCount / 2.0 - 1);
-		double maxDeltaPlusHalfIncrement = maxDelta + increment / 2.0;
+		double increment = maxDelta / ((binCount >> 1) - 1);
+		double maxDeltaPlusHalfIncrement = maxDelta + 0.5 * increment;
 
 		for (int i=1; i<mMol.getAtoms(); i++)
 			encodeCoords(mGraphAtom[i], (mGraphFrom[i] == -1) ? -1 : mGraphAtom[mGraphFrom[i]], maxDeltaPlusHalfIncrement, increment, resolutionBits, coords);

diff --git a/...search/gwt/chemlib/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java b/...search/gwt/chemlib/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
@@ -771,10 +771,13 @@ 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 / 2.0));
-						mMol.setAtomY(atom, mMol.getAtomY(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
+
+						double decodedDX = factor * (decodeBits(resolutionBits) + 1 - (binCount >> 1));
+						double decodedDY = factor * (decodeBits(resolutionBits) + 1 - (binCount >> 1));
+						mMol.setAtomX(atom, mMol.getAtomX(from) + decodedDX);
+						mMol.setAtomY(atom, mMol.getAtomY(from) + decodedDY);
 						if (coordsAre3D)
-							mMol.setAtomZ(atom, mMol.getAtomZ(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
+							mMol.setAtomZ(atom, mMol.getAtomZ(from) + factor * (decodeBits(resolutionBits) + 1 - (binCount >> 1)));
 						}
 
 					if (coordinates[coordsStart] == '#') {    // we have 3D-coordinates that include implicit hydrogen coordinates
@@ -790,10 +793,10 @@ 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 / 2.0));
-								mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
+								mMol.setAtomX(hydrogen, mMol.getAtomX(atom) + (decodeBits(resolutionBits) + 1 - (binCount >> 1)));
+								mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) + 1 - (binCount >> 1)));
 								if (coordsAre3D)
-									mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
+									mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) + 1 - (binCount >> 1)));
 
 								if (selectedHydrogenBits != null && (selectedHydrogenBits[atom] & (1 << i)) != 0)
 									mMol.setAtomSelection(hydrogen, true);
+2 −2		pom.xml
+3 −3		src/main/java/com/actelion/research/chem/Canonizer.java
+9 −6		src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
+12 −0		src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistHelper.java
+1 −1		src/main/java/com/actelion/research/gui/CompoundCollectionPane.java