feat: update OCL to v2024.4.0 (#197)

__tests__/SmilesParser.js

@@ -65,11 +65,10 @@ it('should optionally skip coordinate templates', () => {
 it('should optionally make hydrogens explicit', () => {
   const smiles = '[CH4]';
   const molecule = new Molecule(0, 0);
-  const parserWithoutExplicitH = new SmilesParser({ smartsMode: 'smarts' });
+  const parserWithoutExplicitH = new SmilesParser();
   parserWithoutExplicitH.parseMolecule(smiles, { molecule });
   expect(molecule.getAllAtoms()).toBe(1);
   const parserWithExplicitH = new SmilesParser({
-    smartsMode: 'smarts',
     makeHydrogenExplicit: true,
   });
   parserWithExplicitH.parseMolecule(smiles, { molecule });

__tests__/molfileAndAtomMapNo.test.js

@@ -4,24 +4,24 @@ const { readFileSync } = require('fs');
 
 const { Molecule } = require('../minimal');
 
-
-
 test('molfile with atomMapNo', () => {
-  const molfile = readFileSync(
-    `${__dirname}/data/atomMapNo.mol`,
-    'utf8',
-  );
+  const molfile = readFileSync(`${__dirname}/data/atomMapNo.mol`, 'utf8');
   const molecule = Molecule.fromMolfile(molfile);
 
   const newMolfile = molecule.toMolfile();
-  const atomMapNo = newMolfile.split(/\r?\n/).filter((line) => line.match(/ [OCH] /))
-    .map(line => line.replace(/.* ([OCH]) .*(.) {2}0 {2}0$/, '$1 $2'));
-  expect(atomMapNo).toStrictEqual(['O 5', 'C 1', 'C 3', 'C 4', 'H 2'])
+  const atomMapNo = newMolfile
+    .split(/\r?\n/)
+    .filter((line) => line.match(/ [OCH] /))
+    // eslint-disable-next-line prefer-named-capture-group
+    .map((line) => line.replace(/.* ([OCH]) .*(.) {2}0 {2}0$/, '$1 $2'));
+  expect(atomMapNo).toStrictEqual(['O 5', 'C 1', 'C 3', 'C 4', 'H 2']);
 
   const svg = molecule.toSVG(300, 200);
-  const mapNos = svg.split(/\r?\n/).filter((line) => line.includes('data-atom-map')).map(line => line.replace(/.*atom-map-no="(.).*/, '$1'));
-  expect(mapNos).toStrictEqual(["5", "1", "3", "4", "2"])
-
-
-
-})
+  const mapNos = svg
+    .split(/\r?\n/)
+    .filter((line) => line.includes('data-atom-map'))
+    .map((line) =>
+      line.replace(/.*atom-map-no="(?<atom_map_no>.).*/, '$<atom_map_no>'),
+    );
+  expect(mapNos).toStrictEqual(['5', '1', '3', '4', '2']);
+});

scripts/openchemlib/classes.js

@@ -28,6 +28,10 @@ const changed = [
     '@org/openmolecules/chem/conf/gen/ConformerGenerator',
     changeConformerGenerator,
   ],
+  [
+    '@org/openmolecules/chem/conf/so/ConformationSelfOrganizer',
+    changeConformationSelfOrganizer,
+  ],
   [
     '@org/openmolecules/chem/conf/so/SelfOrganizedConformer',
     changeSelfOrganizedConformer,
@@ -499,7 +503,10 @@ function changeBondLengthSet(code) {
 }
 
 function changeConformerSetDiagnostics(code) {
-  code = code.replace(methodRegExp('writeEliminationRuleFile'), '');
+  code = code.replaceAll(
+    /BufferedWriter writer = new BufferedWriter.*/g,
+    'BufferedWriter writer = new BufferedWriter();',
+  );
   return code;
 }
 
@@ -659,3 +666,16 @@ function fixCompoundFileHelper(code) {
   code = code.replaceAll('file.getName()', '""');
   return code;
 }
+
+function changeConformationSelfOrganizer(code) {
+  code = code.replace('import java.io.FileOutputStream;\n', '');
+  code = code.replace(
+    'import java.io.OutputStreamWriter;\nimport java.nio.charset.StandardCharsets;\n',
+    '',
+  );
+  code = code.replace(
+    /mDWWriter = new BufferedWriter.*/,
+    'mDWWriter = new BufferedWriter();',
+  );
+  return code;
+}

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

@@ -1727,6 +1727,8 @@ else if (hydrogens == Molecule.cAtomQFNot3Hydrogen)
                     isoStr = append(isoStr, "h<3");
                 else if (hydrogens == Molecule.cAtomQFNot2Hydrogen+Molecule.cAtomQFNot3Hydrogen)
                     isoStr = append(isoStr, "h<2");
+			    else if (hydrogens == Molecule.cAtomQFNot0Hydrogen+Molecule.cAtomQFNot3Hydrogen)
+				    isoStr = append(isoStr, "h1-2");
                 }
             if ((queryFeatures & Molecule.cAtomQFCharge) != 0) {
                 long charge = (queryFeatures & Molecule.cAtomQFCharge);
@@ -1766,6 +1768,12 @@ else if (neighbours == Molecule.cAtomQFNot0Neighbours+Molecule.cAtomQFNot1Neighb
                     isoStr = append(isoStr, "n>2");
                 else if (neighbours == (Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot4Neighbours))
                     isoStr = append(isoStr, "n>3");
+                else if (neighbours == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot3Neighbours | Molecule.cAtomQFNot4Neighbours))
+	                isoStr = append(isoStr, "n1-2");
+                else if (neighbours == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot4Neighbours))
+	                isoStr = append(isoStr, "n1-3");
+                else if (neighbours == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot1Neighbour | Molecule.cAtomQFNot4Neighbours))
+	                isoStr = append(isoStr, "n2-3");
                 }
 			if ((queryFeatures & Molecule.cAtomQFENeighbours) != 0) {
 				long eNegNeighbours = (queryFeatures & Molecule.cAtomQFENeighbours);
@@ -1791,7 +1799,7 @@ else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNo
 					isoStr = append(isoStr, "e>2");
 				else if (eNegNeighbours == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot4ENeighbours))
 					isoStr = append(isoStr, "e>3");
-				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot3ENeighbours))
+				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot4ENeighbours))
 					isoStr = append(isoStr, "e1-2");
 				else if (eNegNeighbours == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot4ENeighbours))
 					isoStr = append(isoStr, "e1-3");

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

@@ -50,8 +50,8 @@ public class Canonizer {
 
 	// The following options CONSIDER_DIASTEREOTOPICITY, CONSIDER_ENANTIOTOPICITY
 	// and CONSIDER_STEREOHETEROTOPICITY have no influence on the idcode,
-	// i.e. the idcode is the same whether or not one of these options is
-	// used. However, if you require e.g. a pro-E atom always to appear
+	// i.e. the idcode is the same whether one of these options is used.
+	// However, if you require e.g. a pro-E atom always to appear
 	// before the pro-Z, e.g. because you can distinguish them from the
 	// encoded coordinates, then you need to use one of these options.
 	// Of course, pro-R or pro-S can only be assigned, if one of the bonds
@@ -928,7 +928,7 @@ private void canRecursivelyFindCIPParities() {
 		while ((mNoOfRanks < mMol.getAtoms()) && paritiesFound) {
 			for (int atom=0; atom<mMol.getAtoms(); atom++) {
 				mCanBase[atom].init(atom);
-				mCanBase[atom].add(mAtomBits+4, (mCanRank[atom] << 4)
+				mCanBase[atom].add(mAtomBits+4, ((long)mCanRank[atom] << 4)
 											  | (mTHParity[atom] << 2));
 				}
 
@@ -987,9 +987,9 @@ private void canRecursivelyFindCanonizedParities() {
 				// then only consider the ESR type and the rank of the group.
 
 				if (!mTHESRTypeNeedsNormalization[atom]
-						&& mTHESRType[atom] != Molecule.cESRTypeAbs)
+				 && mTHESRType[atom] != Molecule.cESRTypeAbs)
 					mCanBase[atom].add((mTHESRType[atom] << 18)
-							+ (groupRank[(mTHESRType[atom] == Molecule.cESRTypeAnd) ? 0 : 1][mTHESRGroup[atom]] << 8));
+							+ ((long)groupRank[(mTHESRType[atom] == Molecule.cESRTypeAnd) ? 0 : 1][mTHESRGroup[atom]] << 8));
 
 //				if (!mTHParityNeedsNormalization[atom]) {
 					int parity = mTHParity[atom];
@@ -1665,6 +1665,14 @@ private boolean canCalcTHParity(int atom, int mode) {
 		if (mMol.getAtomicNo(atom) == 5 && mMol.getAllConnAtoms(atom) != 4)
 			return false;
 
+		if (mMol.isFragment()) {  // don't calculate parities if atom or some neighbours are exclude groups
+			if ((mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFExcludeGroup) != 0)
+				return false;
+			for (int i=0; i<mMol.getAllConnAtoms(atom); i++)
+				if ((mMol.getAtomQueryFeatures(mMol.getConnAtom(atom, i)) & Molecule.cAtomQFExcludeGroup) != 0)
+					return false;
+			}
+
 		// don't consider tetrahedral nitrogen, unless found to qualify for parity calculation
 		if (mMol.getAtomicNo(atom) == 7
 		 && !mNitrogenQualifiesForParity[atom])
@@ -2077,6 +2085,15 @@ private boolean canCalcEZParity(int bond, int mode) {
 		if (mEZParity[bond] != 0)
 			return false;
 
+		if (mMol.isFragment()) {  // don't calculate parities if some bond atoms or their neighbours are exclude groups
+			for (int i=0; i<2; i++) {
+				int atom = mMol.getBondAtom(i, bond);
+				for (int j=0; j<mMol.getAllConnAtoms(atom); j++)
+					if ((mMol.getAtomQueryFeatures(mMol.getConnAtom(atom, j)) & Molecule.cAtomQFExcludeGroup) != 0)
+						return false;
+				}
+			}
+
 		if (mMol.getBondOrder(bond) == 1)
 			return canCalcBINAPParity(bond, mode);
 
@@ -2503,8 +2520,8 @@ else if (order == 2) {
 
 	/**
 	 * If the molecule contains exactly one stereo center and if that has unknown configuration,
-	 * than assume that the configuration is meant to be racemic and update molecule accordingly.
-	 * If stereo configuration is ill defined with a stereo bond whose pointed tip is not at the
+	 * then assume that the configuration is meant to be racemic and update molecule accordingly.
+	 * If stereo configuration is ill-defined with a stereo bond whose pointed tip is not at the
 	 * stereo center, then the molecule is not touched and the stereo center kept as undefined.
 	 * @return whether a stereo center was converted to be racemic
 	 */
@@ -3753,6 +3770,25 @@ public int getTHParity(int atom) {
 		}
 
 
+	/**
+	 * Returns the atom's enhanced stereo representation type.
+	 * @param atom
+	 * @return one of the Molecule.cESRTypeXXX constants
+	 */
+	public int getTHESRType(int atom) {
+		return mTHESRType[atom];
+		}
+
+
+	/**
+	 * @param atom
+	 * @return whether this atom's TH-parity is pseudo
+	 */
+	public boolean isPseudoTHParity(int atom) {
+		return mTHParityIsPseudo[atom];
+		}
+
+
 	/**
 	 * Returns the absolute bond parity, which is based on priority ranks.
 	 * @param bond
@@ -3763,6 +3799,25 @@ public int getEZParity(int bond) {
 		}
 
 
+	/**
+	 * Returns the bond's enhanced stereo representation type.
+	 * @param bond
+	 * @return one of the Molecule.cESRTypeXXX constants
+	 */
+	public int getEZESRType(int bond) {
+		return mEZESRType[bond];
+	}
+
+
+	/**
+	 * @param bond
+	 * @return whether this bond's EZ-parity is pseudo
+	 */
+	public boolean isPseudoEZParity(int bond) {
+		return mEZParityIsPseudo[bond];
+	}
+
+
 	/**
 	 * If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns
 	 * the number of independent relative stereo feature groups. A relative stereo

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

@@ -36,10 +36,7 @@
 
 import com.actelion.research.util.Angle;
 
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.Serializable;
+import java.io.*;
 import java.util.Arrays;
 
 /**
@@ -212,7 +209,7 @@ public int[] copyMoleculeByBonds(ExtendedMolecule destMol, boolean[] includeBond
 		destMol.mAllAtoms = 0;
 		for (int atom=0; atom<mAllAtoms;atom++) {
 			atomMap[atom] = -1;
-			for (int i=0; i< mConnAtoms[atom]; i++) {
+			for (int i=0; i<mConnAtoms[atom]; i++) {
 				if (includeBond[mConnBond[atom][i]]) {
 					atomMap[atom] = copyAtom(destMol, atom, 0, 0);
 
@@ -294,35 +291,30 @@ && isAtomStereoCenter(atom)) {
 				int lostStereoBond = -1;
 				int lostAtom = -1;
 				for (int i=0; i<mAllConnAtoms[atom]; i++) {
-//if (mConnAtom.length>=atom || atomMap.length>=mConnAtom[atom][i])
-// System.out.println("mConnAtom.length:"+mConnAtom.length+" atom:"+atom+" atomMap.length:"+atomMap.length+" i:"+i+" mConnAtom[atom][i]:"+mConnAtom[atom][i]+" mAtoms:"+mAtoms+" mAllAtoms:"+mAllAtoms);
-					if (atomMap.length>mConnAtom[atom][i]
-					 && atomMap[mConnAtom[atom][i]] != -1)
+					if (bondMap[mConnBond[atom][i]] != -1)
 						remainingNeighbours++;
 					else if (mConnBondOrder[atom][i] == 1
-							&& isStereoBond(mConnBond[atom][i])
-							&& mBondAtom[0][mConnBond[atom][i]] == atom) {
+						 && isStereoBond(mConnBond[atom][i])
+						 && mBondAtom[0][mConnBond[atom][i]] == atom) {
 						lostStereoBond = mConnBond[atom][i];
 						lostAtom = mConnAtom[atom][i];
+						}
 					}
-				}
-				if (lostStereoBond != -1
-						&& remainingNeighbours >= 3) {
+				if (lostStereoBond != -1 && remainingNeighbours >= 3) {
 					double angle = getBondAngle(atom, lostAtom);
 					double minAngleDif = 10.0;
 					int minConnBond = -1;
 					for (int i=0; i<mAllConnAtoms[atom]; i++) {
 						if (mConnBondOrder[atom][i] == 1
-								&& (!isStereoBond(mConnBond[atom][i]) || mBondAtom[0][mConnBond[atom][i]] == atom)
-								&& atomMap.length>mConnAtom[atom][i]
-								&& atomMap[mConnAtom[atom][i]] != -1) {
+						 && (!isStereoBond(mConnBond[atom][i]) || mBondAtom[0][mConnBond[atom][i]] == atom)
+						 && bondMap[mConnBond[atom][i]] != -1) {
 							double angleDif = Math.abs(getAngleDif(angle, getBondAngle(atom, mConnAtom[atom][i])));
 							if (minAngleDif > angleDif) {
 								minAngleDif = angleDif;
 								minConnBond = mConnBond[atom][i];
+								}
 							}
 						}
-					}
 					if (minConnBond != -1) {
 						int destBond = bondMap[minConnBond];
 						destMol.setBondType(destBond, mBondType[minConnBond] == cBondTypeUp ? cBondTypeDown : cBondTypeUp);
@@ -629,7 +621,7 @@ public int getNonHydrogenNeighbourCount(int atom) {
 	public int getExcludedNeighbourCount(int atom) {
 		int count = 0;
 		for (int i=0; i<mConnAtoms[atom]; i++)
-			if ((mAtomQueryFeatures[i] & Molecule.cAtomQFExcludeGroup) != 0)
+			if ((mAtomQueryFeatures[mConnAtom[atom][i]] & Molecule.cAtomQFExcludeGroup) != 0)
 				count++;
 		return count;
 		}
@@ -4070,7 +4062,14 @@ else if ((mAtomQueryFeatures[atom] & cAtomQFAromatic) != 0)
 				mAtomQueryFeatures[atom] &= ~cAtomQFNotChain;   // redundant
 
 			if (mAtomCharge[atom] != 0)	// explicit charge supersedes query features
-				mAtomFlags[atom] &= ~cAtomQFCharge;
+				mAtomQueryFeatures[atom] &= ~cAtomQFCharge;
+
+			if (getOccupiedValence(atom) == getMaxValence(atom)) {
+				mAtomQueryFeatures[atom] &= ~cAtomQFNeighbours;
+				mAtomQueryFeatures[atom] &= ~cAtomQFENeighbours;
+				mAtomQueryFeatures[atom] &= ~cAtomQFHydrogen;
+				mAtomQueryFeatures[atom] &= ~cAtomQFPiElectrons;
+				}
 			}
 		}
 
@@ -4107,37 +4106,7 @@ else if (bondType == cBondTypeDelocalized)
 			}
 		}
 
-
 	private void writeObject(ObjectOutputStream stream) throws IOException {}
-	private void readObject(ObjectInputStream stream) throws IOException {}
-
-
-	public final static Coordinates getCenterGravity(ExtendedMolecule mol) {
-
-		int n = mol.getAllAtoms();
-
-		int [] indices = new int [n];
-
-		for (int i = 0; i < indices.length; i++) {
-			indices[i]=i;
-		}
-
-		return getCenterGravity(mol, indices);
-	}
-
-	public final static Coordinates getCenterGravity(ExtendedMolecule mol, int[] indices) {
-
-		Coordinates c = new Coordinates();
-		for (int i = 0; i < indices.length; i++) {
-			c.x += mol.getAtomX(indices[i]);
-			c.y += mol.getAtomY(indices[i]);
-			c.z += mol.getAtomZ(indices[i]);
-		}
-		c.x /= indices.length;
-		c.y /= indices.length;
-		c.z /= indices.length;
-
-		return c;
-	}
 
+	private void readObject(ObjectInputStream stream) throws IOException {}
 }