feat: update OCL to v2023.2.1 (#160)

Closes: #155

package.json

@@ -27,9 +27,6 @@
     "test": "npm run build && npm run test-only && npm run eslint",
     "test-only": "jest"
   },
-  "jest": {
-    "testEnvironment": "node"
-  },
   "main": "./core.js",
   "files": [
     "dist",
@@ -56,12 +53,12 @@
   "homepage": "https://github.com/cheminfo/openchemlib-js",
   "devDependencies": {
     "benchmark": "^2.1.4",
-    "eslint": "^8.33.0",
+    "eslint": "^8.34.0",
     "eslint-config-cheminfo": "^8.1.3",
     "gwt-api-exporter": "^2.0.0",
-    "jest": "^29.4.1",
-    "openchemlib-utils": "^2.3.0",
-    "prettier": "^2.8.3",
+    "jest": "^29.4.2",
+    "openchemlib-utils": "^2.4.0",
+    "prettier": "^2.8.4",
     "yargs": "^17.6.2"
   }
 }

scripts/openchemlib/classes.js

@@ -21,6 +21,10 @@ const modified = [
 exports.modified = modified.map(getFilename);
 
 const changed = [
+  [
+    '@org/openmolecules/chem/conf/gen/ConformerSetDiagnostics',
+    changeConformerSetDiagnostics,
+  ],
   ['@org/openmolecules/chem/conf/gen/RigidFragmentCache', removeCacheIO],
   ['chem/ChemistryHelper', removePrintf],
   ['chem/Coordinates', removeToStringSpaceDelimited],
@@ -457,6 +461,11 @@ function changeBondLengthSet(code) {
   return code;
 }
 
+function changeConformerSetDiagnostics(code) {
+  code = code.replace(methodRegExp('writeEliminationRuleFile'), '');
+  return code;
+}
+
 function removeCacheIO(code) {
   code = removeSlice(
     code,

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

@@ -1662,32 +1662,45 @@ private void mpShortenLine(DepictorLine theLine,int pointNo,int tabuZoneNo) {
 		}
 
 
-	private int mpPreferredSide(int bnd) {
-		boolean[] isAromatic = new boolean[ExtendedMolecule.cMaxConnAtoms];
-		boolean[] isInRing = new boolean[ExtendedMolecule.cMaxConnAtoms];
+	private int mpPreferredSide(int bond) {
+		int[] value = new int[ExtendedMolecule.cMaxConnAtoms];
 		double[] angle = new double[ExtendedMolecule.cMaxConnAtoms];
 		double[] bondAngle = new double[2];
 
 		int angles = 0;
 		for (int i=0; i<2; i++) {
-			int atm = mMol.getBondAtom(i,bnd);
+			int atm = mMol.getBondAtom(i,bond);
 
 			for (int j=0; j<mMol.getConnAtoms(atm); j++) {
 				int connBond = mMol.getConnBond(atm,j);
-				if (connBond == bnd)
+				if (connBond == bond)
 					continue;
 
 				if (angles == 4)
 					return 0;
 
-				isAromatic[angles] = mMol.isAromaticBond(connBond);
-				isInRing[angles] = mMol.isRingBond(connBond);
-				angle[angles++] = mMol.getBondAngle(atm, mMol.getConnAtom(atm,j));
+				int connAtom = mMol.getConnAtom(atm,j);
+
+				value[angles] = 16;
+
+				// Prefer bond on side with conjugated pi systems
+				if (mMol.getAtomPi(connAtom) != 0)
+					value[angles] += mMol.isRingAtom(connAtom) ? 1 : 4;
+
+				// Prefer bond inside of ring. Even more, if it is aromatic.
+				if (mMol.isRingBond(bond)
+				 && mMol.isRingBond(connBond)) {
+					int sharedRing = mMol.getRingSet().getSharedRing(bond, connBond);
+					if (sharedRing != -1)
+						value[angles] += mMol.getRingSet().isAromatic(sharedRing) ? 64 : 6;
+					}
+
+				angle[angles++] = mMol.getBondAngle(atm, connAtom);
 				}
 			}
 
 		boolean changed;
-		bondAngle[0] = mMol.getBondAngle(mMol.getBondAtom(0,bnd),mMol.getBondAtom(1,bnd));
+		bondAngle[0] = mMol.getBondAngle(mMol.getBondAtom(0,bond),mMol.getBondAtom(1,bond));
 		if (bondAngle[0] < 0) {
 			bondAngle[1] = bondAngle[0] + Math.PI;
 			changed = false;
@@ -1700,18 +1713,10 @@ private int mpPreferredSide(int bnd) {
 
 		int side = 0;
 		for (int i=0; i<angles; i++) {
-			int value;
-			if (isAromatic[i])
-				value = 20;
-			else if (isInRing[i])
-				value = 17;
-			else
-				value = 16;
-
 			if ((angle[i] > bondAngle[0]) && (angle[i] < bondAngle[1]))
-				side -= value;
+				side -= value[i];
 			else
-				side += value;
+				side += value[i];
 			}
 
 		return (changed) ? -side : side;

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

@@ -42,7 +42,7 @@
 import java.math.RoundingMode;
 import java.util.ArrayList;
 
-public class SVGDepictor extends AbstractDepictor {
+public class SVGDepictor extends AbstractDepictor<Void> {
     public static final int DEFAULT_ELEM_WIDTH = 8;
 
     private static final String FONTNAME = "Helvetica";

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

@@ -78,7 +78,7 @@ public static StereoMolecule getMurckoScaffold(StereoMolecule mol, boolean skele
 		return scaffold;
 		}
 
-	private static void makeSkeleton(StereoMolecule mol) {
+	public static void makeSkeleton(StereoMolecule mol) {
 		for (int bond=0; bond<mol.getAllBonds(); bond++)
 			mol.setBondType(bond, Molecule.cBondTypeSingle);
 		for (int atom=0; atom<mol.getAllAtoms(); atom++)

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

@@ -34,7 +34,11 @@
 
 package com.actelion.research.chem;
 
-import java.io.*;
+import com.actelion.research.chem.coords.CoordinateInventor;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
 
 public class StereoMolecule extends ExtendedMolecule {
     static final long serialVersionUID = 0x2006CAFE;
@@ -191,6 +195,13 @@ public void ensureHelperArrays(int required) {
         if ((required & ~mValidHelperArrays) == 0)
 			return;
 
+        // If we have valid parities, but no atom coordinates, and if we need to run the Canonizer
+		// for extended stereo features, then we need to create 2D-coordinates first to not loose
+		// the given parities, because the Canonizer recalculates parities from coords and up/down bonds.
+		if ((mValidHelperArrays & cHelperParities) != 0
+		 && (mAllAtoms > 1) && mCoordinates[0].equals(mCoordinates[1]))
+			new CoordinateInventor(0).invent(this);
+
         if (mAssignParitiesToNitrogen)
         	required |= cHelperBitIncludeNitrogenParities;
 
@@ -367,6 +378,8 @@ public int getSymmetryRank(int atom) {
      */
     public String getIDCode() {
         ensureHelperArrays(cHelperParities);
+        if (mCanonizer == null && (getAtoms() < 2 || !mCoordinates[0].equals(mCoordinates[1])))
+        	mCanonizer = new Canonizer(this);
         return mCanonizer == null ? null : mCanonizer.getIDCode();
         }
 
@@ -380,6 +393,8 @@ public String getIDCode() {
      */
     public String getIDCoordinates() {
         ensureHelperArrays(cHelperParities);
+	    if (mCanonizer == null && (getAtoms() < 2 || !mCoordinates[0].equals(mCoordinates[1])))
+		    mCanonizer = new Canonizer(this);
         return mCanonizer == null ? null : mCanonizer.getEncodedCoordinates();
         }
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/conf/Conformer.java

@@ -184,7 +184,7 @@ public void setZ(int atom, double z) {
 	/**
 	 * Removes atoms Coordinates objects from those atoms that are marked in the given array.
 	 * Make sure to also remove those atoms from the underlying Molecule.
-	 *
+	 * When this method is used, bond torsion angles are lost.
 	 * @param isToBeDeleted
 	 * @return
 	 */
@@ -196,18 +196,13 @@ public int deleteAtoms(boolean[] isToBeDeleted) {
 
 		if (count != 0) {
 			Coordinates[] newCoords = new Coordinates[mCoordinates.length - count];
-			short[] newBondTorsion = (mBondTorsion == null) ? null : new short[mCoordinates.length - count];
 			int newIndex = 0;
-			for (int i = 0; i < mCoordinates.length; i++) {
-				if (!isToBeDeleted[i]) {
-					newCoords[newIndex] = mCoordinates[i];
-					if (newBondTorsion != null)
-						newBondTorsion[newIndex] = mBondTorsion[i];
-					newIndex++;
-				}
-			}
+			for (int i = 0; i < mCoordinates.length; i++)
+				if (!isToBeDeleted[i])
+					newCoords[newIndex++] = mCoordinates[i];
+
 			mCoordinates = newCoords;
-			mBondTorsion = newBondTorsion;
+			mBondTorsion = null;
 		}
 
 		return count;
@@ -242,8 +237,7 @@ public double calculateTorsion(int[] atom) {
 	}
 
 	/**
-	 * Returns the current bond torsion angle in degrees, it is was set before.
-	 *
+	 * Returns the current bond torsion angle in degrees, as it was set before.
 	 * @param bond
 	 * @return -1 or previously set torsion angle in the range 0 ... 359
 	 */
@@ -258,8 +252,10 @@ public int getBondTorsion(int bond) {
 	 * @param torsion in degrees
 	 */
 	public void setBondTorsion(int bond, short torsion) {
-		if (mBondTorsion == null)
+		if (mBondTorsion == null) {
 			mBondTorsion = new short[mMol.getAllBonds()];
+			Arrays.fill(mBondTorsion, (short)-1);
+			}
 		mBondTorsion[bond] = torsion;
 	}
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/conf/TorsionDescriptorHelper.java

@@ -96,7 +96,7 @@ public TorsionDescriptor getTorsionDescriptor() {
 
 	/**
 	 * Creates a TorsionDescriptor from the coordinates of the passed conformer assuming that its
-	 * underlying molecule is the same that waas passed to this TorsionDescriptorHelper's constructor.
+	 * underlying molecule is the same that was passed to this TorsionDescriptorHelper's constructor.
 	 * This TorsionDescriptorHelper uses the default method to detect rotatable bonds.
 	 * The torsion descriptor is not canonical, unless the passed molecule is canonical.
 	 * Rotatable bonds need to carry at least one external non-hydrogen neighbor on each side.

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/prediction/CLogPPredictor.java

@@ -233,9 +233,13 @@ public CLogPPredictor() {
 		}
 
 	/**
-	 * Ambiguous bonds are normalized. 
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
+	 * This method may normalize ambiguous bonds of the molecule.
 	 * @param mol
-	 * @return
+	 * @return logP value estimated from atom type specific increments
 	 */
 	public float assessCLogP(StereoMolecule mol) {
 		float cLogP = 0.0f;

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/prediction/DruglikenessPredictorWithIndex.java

@@ -64,6 +64,14 @@ public DruglikenessPredictorWithIndex() {
 			}
 		}
 
+	/**
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
+	 * @param mol
+	 * @return druglikeness value estimated from atom type specific increments
+	 */
 	public double assessDruglikeness(StereoMolecule mol, long[] index, ThreadMaster threadMaster) {
 		if (!sInitialized)
 			return cDruglikenessUnknown;

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/prediction/PolarSurfaceAreaPredictor.java

@@ -111,8 +111,12 @@ public static int getPolarAtomTypeCount() {
 	 * Calculates the topological polar surface area (TPSA) of a molecule as a sum of
 	 * contributions of its polar atom-types. This method uses the polar atom contributions
 	 * originally published by Peter Ertl et al. in J. Med. Chem. 2000, 43, 3714-3717.
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
 	 * @param mol
-	 * @return
+	 * @return topological polar surface area estimated from atom type specific increments
 	 */
 	public float assessPSA(StereoMolecule mol) {
 		int[] count = getPolarAtomTypeCounts(mol);

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/prediction/SolubilityPredictor.java

@@ -155,6 +155,15 @@ public SolubilityPredictor() {
 		}
 
 
+	/**
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
+	 * This method may normalize ambiguous bonds of the molecule.
+	 * @param mol
+	 * @return aquous solubility value estimated from atom type specific increments
+	 */
 	public float assessSolubility(StereoMolecule mol) {
 		float logS = -0.530f;
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/prediction/TotalSurfaceAreaPredictor.java

@@ -120,8 +120,12 @@ public static int getNonPolarAtomTypeCount() {
 	 * as solvent accessible surface using Van der Waals radii and a probe of 1.4 angstrom
 	 * radius. Surface contribution values were for 43 polar and 20 non polar atom types were
 	 * calculated as a multi-linear regression with a PLS approach.
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
 	 * @param mol
-	 * @return
+	 * @return topological total surface area estimated from atom type specific increments
 	 */
 	public float assessTotalSurfaceArea(StereoMolecule mol) {
 		return assessNonPolarSurfaceArea(mol) + assessPolarSurfaceArea(mol);
@@ -137,8 +141,12 @@ public float assessTotalSurfaceArea(StereoMolecule mol) {
 	 * as solvent accessible surface using Van der Waals radii and a probe of 1.4 angstrom
 	 * radius. Surface contribution values were for 43 polar and 20 non polar atom types were
 	 * calculated as a multi-linear regression with a PLS approach.
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
 	 * @param mol
-	 * @return
+	 * @return topological polar surface area estimated from atom type specific increments
 	 */
 	public float assessPolarSurfaceArea(StereoMolecule mol) {
 		int[] count = getPolarAtomTypeCounts(mol);
@@ -160,8 +168,12 @@ public float assessPolarSurfaceArea(StereoMolecule mol) {
 	 * as solvent accessible surface using Van der Waals radii and a probe of 1.4 angstrom
 	 * radius. Surface contribution values were for 43 polar and 20 non polar atom types were
 	 * calculated as a multi-linear regression with a PLS approach.
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
 	 * @param mol
-	 * @return
+	 * @return topological non-polar surface area estimated from atom type specific increments
 	 */
 	public float assessNonPolarSurfaceArea(StereoMolecule mol) {
 		int[] count = getNonPolarAtomTypeCounts(mol);
@@ -176,8 +188,12 @@ public float assessNonPolarSurfaceArea(StereoMolecule mol) {
 	/**
 	 * Calculates the relative (fractional) polar surface area from polar and non-polar atom
 	 * contributions. This method does not use the Peter Ertl increments.
+	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
+	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
+	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
+	 * MoleculeStandardizer.
 	 * @param mol
-	 * @return
+	 * @return topological relative surface area estimated from atom type specific increments
 	 */
 	public float assessRelativePolarSurfaceArea(StereoMolecule mol) {
 		float psa = assessPolarSurfaceArea(mol);