Merge tag 'openchemlib-2024.3.1'

[maven-release-plugin]  copy for tag openchemlib-2024.3.1

buildOpenChemLib

@@ -6,6 +6,6 @@ rm -rf ./build
 mkdir build
 cp -r ./src/main/resources/* ./build/
 find . -name "*.java" > sources.txt
-javac -d ./build @sources.txt
+javac -target 8 -d ./build @sources.txt
 rm sources.txt
 jar -cf build/OpenChemLib.jar -C ./build .

pom.xml

@@ -8,7 +8,7 @@
     Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH
     (eg. 2016.4.1 for second release in Apr 2016)
     -->
-    <version>2024.2.2</version>
+    <version>2024.3.1</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>
@@ -209,7 +209,7 @@
         <connection>scm:git:[email protected]:Actelion/openchemlib.git</connection>
         <developerConnection>scm:git:[email protected]:Actelion/openchemlib.git</developerConnection>
         <url>https://github.com/Actelion/openchemlib</url>
-      <tag>openchemlib-2024.2.2</tag>
+      <tag>openchemlib-2024.3.1</tag>
   </scm>
 
     <distributionManagement>

src/main/java/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];
@@ -2503,8 +2503,8 @@ 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 +3753,25 @@ public int getTHParity(int atom) {
 		}
 
 
+	/**
+	 * Returns the atoms'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 +3782,25 @@ 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/main/java/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;
 
 /**
@@ -629,7 +626,7 @@ 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 +4067,14 @@ 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 +4111,7 @@ 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 {}
 }

src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java

@@ -1163,9 +1163,7 @@ public static boolean isSulfoxyGroup(StereoMolecule mol, int atom) {
 	public static boolean isIsolatedCarbon(StereoMolecule mol, int indexAtCentral, int [] arrIndexAt){
 
 		boolean isolated=true;
-
 		int nConnected = mol.getConnAtoms(indexAtCentral);
-
 		boolean [] arrConnected = new boolean[mol.getAtoms()];
 
 		for (int i = 0; i < nConnected; i++) {
@@ -1176,7 +1174,6 @@ public static boolean isIsolatedCarbon(StereoMolecule mol, int indexAtCentral, i
 			if(!arrConnected[indexAt]){
 				continue;
 			}
-
 			if(mol.getAtomicNo(indexAt)==6){
 				isolated=false;
 				break;

src/main/java/com/actelion/research/chem/Molecule.java

@@ -2289,6 +2289,28 @@ public Coordinates getCoordinates(int atom) {
 	}
 
 
+	public Coordinates getCenterOfGravity() {
+		if (mAllAtoms == 0)
+			return null;
+
+		Coordinates c = new Coordinates();
+		for (int atom = 0; atom<mAllAtoms; atom++)
+			c.add(mCoordinates[atom]);
+		return c.scale(1.0 / mAllAtoms);
+		}
+
+
+	public Coordinates getCenterOfGravity(int[] atomIndex) {
+		if (atomIndex == null || atomIndex.length==0 || atomIndex.length>mAllAtoms)
+			return null;
+
+		Coordinates c = new Coordinates();
+		for (int atom:atomIndex)
+			c.add(mCoordinates[atom]);
+		return c.scale(1.0 / atomIndex.length);
+		}
+
+
 	public double getAtomX(int atom) {
 		return mCoordinates[atom].x;
 		}
@@ -2604,10 +2626,26 @@ public double getBondLength(int bond) {
 	 * Returns the formal bond order. Delocalized rings have alternating single and double
 	 * bonds, which are returned as such. Bonds that are explicitly marked as being delocalized
 	 * are returned as 1. Dative bonds are returned as 0.
+	 * In fragments with at least one bond type set as bond query feature, the smallest
+	 * non-zero order of allowed bonds is returned.
 	 * @param bond
 	 * @return formal bond order 0 (dative bonds), 1, 2, 3, 4, or 5
 	 */
 	public int getBondOrder(int bond) {
+		if (mIsFragment && (mBondQueryFeatures[bond] & cBondQFBondTypes) != 0) {
+			if ((mBondQueryFeatures[bond] & (cBondQFSingle | cBondQFDelocalized)) != 0)
+				return 1;
+			if ((mBondQueryFeatures[bond] & cBondQFDouble) != 0)
+				return 2;
+			if ((mBondQueryFeatures[bond] & cBondQFTriple) != 0)
+				return 3;
+			if ((mBondQueryFeatures[bond] & cBondQFQuadruple) != 0)
+				return 4;
+			if ((mBondQueryFeatures[bond] & cBondQFQuintuple) != 0)
+				return 5;
+			if ((mBondQueryFeatures[bond] & cBondQFMetalLigand) != 0)
+				return 0;
+			}
 		switch (mBondType[bond] & cBondTypeMaskSimple) {
 		case cBondTypeSingle:
 		case cBondTypeDelocalized: return 1;
@@ -2796,11 +2834,11 @@ public int getMaxBonds() {
 	 * @param v
 	 */
 	public void setMaxBonds(int v) {
-		mBondAtom[0] = (int[])copyOf(mBondAtom[0], v);
-		mBondAtom[1] = (int[])copyOf(mBondAtom[1], v);
-		mBondType = (int[])copyOf(mBondType, v);
-		mBondFlags = (int[])copyOf(mBondFlags, v);
-		mBondQueryFeatures = (int[])copyOf(mBondQueryFeatures, v);
+		mBondAtom[0] = copyOf(mBondAtom[0], v);
+		mBondAtom[1] = copyOf(mBondAtom[1], v);
+		mBondType = copyOf(mBondType, v);
+		mBondFlags = copyOf(mBondFlags, v);
+		mBondQueryFeatures = copyOf(mBondQueryFeatures, v);
 		mMaxBonds = v;
 		}
 

src/main/java/com/actelion/research/chem/MoleculeStandardizer.java

@@ -36,7 +36,7 @@ public static StereoMolecule getStandardized(String idcode, String coordinates,
 
 	/**
 	 * Standardises a molecule and fixes some structural errors.
-	 * Typically this is done before canonicalization.
+	 * Typically, this is done before canonicalization.
 	 * It includes the following changes:<br>
 	 * - different forms of functional groups (e.g. nitro) are normalized to a preferred one<br>
 	 * - charged acidic or basic atoms are (de-)protonated to remove charges and neutralize the molecule, if possible.<br>
@@ -77,7 +77,6 @@ public static void standardize(StereoMolecule mol, int mode) throws Exception {
 	 * sulfonic acid, phosphoric acid, phenolic oxygen. Means: negative charges are removed.
 	 * Adds Na+ or Cl- for final charge equilibration.
 	 * @param mol
-	 * @return true if an atom was added.
 	 */
 	private static void repairAndUnify(StereoMolecule mol) {
 		mol.ensureHelperArrays(Molecule.cHelperRings);