Merge commit '384f58f59a4029b176d2b183323badb6543f2d77'

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>2024.7.1</version>
+    <version>2024.7.2-SNAPSHOT</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-2024.7.1</tag>
+      <tag>HEAD</tag>
   </scm>
 
     <distributionManagement>

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

@@ -75,7 +75,7 @@ public void neglectSpaceDelimitedCoordinates() {
 	 * @return
 	 */
 	public StereoMolecule getCompactMolecule(String idcode) {
-		return (idcode == null || idcode.length() == 0) ? null : getCompactMolecule(idcode.getBytes(StandardCharsets.UTF_8), null);
+		return (idcode == null || idcode.isEmpty()) ? null : getCompactMolecule(idcode.getBytes(StandardCharsets.UTF_8), null);
 		}
 
 	/**
@@ -151,7 +151,7 @@ public StereoMolecule getCompactMolecule(byte[] idcode, byte[] coordinates, int
 	 * @param idcode null or idcode, which may contain coordinates separated by a space character
 	 */
 	public void parse(StereoMolecule mol, String idcode) {
-		if (idcode == null || idcode.length() == 0) {
+		if (idcode == null || idcode.isEmpty()) {
 			parse(mol, (byte[])null, (byte[])null);
 			return;
 			}
@@ -437,9 +437,10 @@ public void parse(StereoMolecule mol, byte[] idcode, byte[] coordinates, int idc
 		int offset = 0;
 		while (decodeBits(1) == 1) {
 			int dataType = offset + decodeBits(4);
+			int no;
 			switch (dataType) {
 			case 0:	//	datatype 'AtomQFNoMoreNeighbours'
-				int no = decodeBits(abits);
+				no = decodeBits(abits);
 				for (int i=0; i<no; i++) {
 					int atom = decodeBits(abits);
 					mMol.setAtomQueryFeature(atom, Molecule.cAtomQFNoMoreNeighbours, true);
@@ -762,10 +763,10 @@ 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));
-						mMol.setAtomY(atom, mMol.getAtomY(from) + factor * (decodeBits(resolutionBits) - binCount / 2));
+						mMol.setAtomX(atom, mMol.getAtomX(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
+						mMol.setAtomY(atom, mMol.getAtomY(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
 						if (coordsAre3D)
-							mMol.setAtomZ(atom, mMol.getAtomZ(from) + factor * (decodeBits(resolutionBits) - binCount / 2));
+							mMol.setAtomZ(atom, mMol.getAtomZ(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
 						}
 
 					if (coordinates[coordsStart] == '#') {    // we have 3D-coordinates that include implicit hydrogen coordinates
@@ -781,10 +782,10 @@ 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));
-								mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) - binCount / 2));
+								mMol.setAtomX(hydrogen, mMol.getAtomX(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
+								mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
 								if (coordsAre3D)
-									mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) - binCount / 2));
+									mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
 								}
 							}
 
@@ -935,10 +936,10 @@ public void parseCoordinates(byte[] encodedCoords, int coordsStart, StereoMolecu
 				from = 0;
 				factor = 8.0;
 				}
-			coords[atom].x = coords[from].x + factor * (decodeBits(resolutionBits) - binCount / 2);
-			coords[atom].y = coords[from].y + factor * (decodeBits(resolutionBits) - binCount / 2);
+			coords[atom].x = coords[from].x + factor * (decodeBits(resolutionBits) - binCount / 2.0);
+			coords[atom].y = coords[from].y + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 			if (coordsAre3D)
-				coords[atom].z = coords[from].z + factor * (decodeBits(resolutionBits) - binCount / 2);
+				coords[atom].z = coords[from].z + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 			}
 
 		double avbl = coordsAre3D ? 1.5 : Molecule.getDefaultAverageBondLength();
@@ -954,10 +955,10 @@ public void parseCoordinates(byte[] encodedCoords, int coordsStart, StereoMolecu
 			for (int atom = 0; atom < atomCount; atom++) {
 				int hCount = mol.getAllConnAtoms(atom) - mol.getConnAtoms(atom);
 				for (int i = 0; i < hCount; i++) {
-					coords[hydrogen].x = coords[atom].x + (decodeBits(resolutionBits) - binCount / 2);
-					coords[hydrogen].y = coords[atom].y + (decodeBits(resolutionBits) - binCount / 2);
+					coords[hydrogen].x = coords[atom].x + (decodeBits(resolutionBits) - binCount / 2.0);
+					coords[hydrogen].y = coords[atom].y + (decodeBits(resolutionBits) - binCount / 2.0);
 					if (coordsAre3D)
-						coords[hydrogen].z = coords[atom].z + (decodeBits(resolutionBits) - binCount / 2);
+						coords[hydrogen].z = coords[atom].z + (decodeBits(resolutionBits) - binCount / 2.0);
 
 					hydrogen++;
 					}
@@ -1072,7 +1073,7 @@ else if (coordinates[coordStart] == '!' || coordinates[coordStart] == '#') {
 		}
 
 	public int getIDCodeVersion(String idcode) {
-		if (idcode == null || idcode.length() == 0)
+		if (idcode == null || idcode.isEmpty())
 			return -1;
 
 		return getIDCodeVersion(idcode.getBytes(StandardCharsets.UTF_8));
@@ -1090,7 +1091,7 @@ public int getIDCodeVersion(byte[] idcode) {
 		}
 
 	public int getAtomCount(String idcode) {
-		if (idcode == null || idcode.length() == 0)
+		if (idcode == null || idcode.isEmpty())
 			return 0;
 
 		return getAtomCount(idcode.getBytes(StandardCharsets.UTF_8), 0);
@@ -1120,7 +1121,7 @@ public int getAtomCount(byte[] idcode, int offset) {
 	 * @return int[] with atom and bond count as first and second values
 	 */
 	public int[] getAtomAndBondCounts(String idcode, int[] count) {
-		if (idcode == null || idcode.length() == 0)
+		if (idcode == null || idcode.isEmpty())
 			return null;
 
 		return getAtomAndBondCounts(idcode.getBytes(StandardCharsets.UTF_8), 0, count);
@@ -1192,7 +1193,7 @@ private double decodeShift(int value, int binCount) {
 		boolean isNegative = (value >= halfBinCount);
 		if (isNegative)
 			value -= halfBinCount;
-		double steepness = binCount/32;
+		double steepness = binCount/32.0;
 		double doubleValue = steepness * value / (halfBinCount - value);
 		return isNegative ? -doubleValue : doubleValue;
 		}
@@ -1366,9 +1367,10 @@ public void printContent(byte[] idcode, byte[] coordinates) {
 			int offset = 0;
 			while (decodeBits(1) == 1) {
 				int dataType = offset + decodeBits(4);
+				int no;
 				switch (dataType) {
 					case 0: //  datatype 'AtomQFNoMoreNeighbours'
-						int no = decodeBits(abits);
+						no = decodeBits(abits);
 						System.out.print("noMoreNeighbours:");
 						for (int i = 0; i < no; i++)
 							System.out.print(" " + decodeBits(abits));
@@ -1675,12 +1677,12 @@ public void printContent(byte[] idcode, byte[] coordinates) {
 							factor = 8.0;
 						}
 						System.out.print(atom + " (");
-						coords[0][atom] = coords[0][from] + factor * (decodeBits(resolutionBits) - binCount / 2);
+						coords[0][atom] = coords[0][from] + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 						System.out.print((int) coords[0][atom] + ",");
-						coords[1][atom] = coords[1][from] + factor * (decodeBits(resolutionBits) - binCount / 2);
+						coords[1][atom] = coords[1][from] + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 						System.out.print((int) coords[1][atom]);
 						if (coordsAre3D) {
-							coords[2][atom] = coords[2][from] + factor * (decodeBits(resolutionBits) - binCount / 2);
+							coords[2][atom] = coords[2][from] + factor * (decodeBits(resolutionBits) - binCount / 2.0);
 							System.out.print("," + (int) coords[0][atom]);
 						}
 						System.out.print("), ");
@@ -1719,12 +1721,12 @@ public void printContent(byte[] idcode, byte[] coordinates) {
 								System.out.print(atom);
 							for (int i = 0; i < hCount[atom]; i++) {
 								System.out.print(" (");
-								coords[0][hydrogen] = coords[0][atom] + (decodeBits(resolutionBits) - binCount / 2);
+								coords[0][hydrogen] = coords[0][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
 								System.out.print((int) coords[0][hydrogen] + ",");
-								coords[1][hydrogen] = coords[1][atom] + (decodeBits(resolutionBits) - binCount / 2);
+								coords[1][hydrogen] = coords[1][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
 								System.out.print((int) coords[1][hydrogen]);
 								if (coordsAre3D) {
-									coords[2][hydrogen] = coords[2][atom] + (decodeBits(resolutionBits) - binCount / 2);
+									coords[2][hydrogen] = coords[2][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
 									System.out.print("," + (int) coords[2][hydrogen]);
 								}
 								System.out.print("), ");

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

@@ -23,6 +23,7 @@ public SmilesAtomParser(SmilesParser parser, int mode) {
 		mParentParser = parser;
 		mMode = mode;
 		mAllowCactvs = (mode & SmilesParser.MODE_NO_CACTUS_SYNTAX) == 0;
+		atomicNo = -1;
 		charge = 0;
 		mapNo = 0;
 		abnormalValence = -1;

src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerFlexophore.java

@@ -436,9 +436,7 @@ else if (includeNodeAtoms) {
 	public MolDistHistViz createVisualDescriptor(StereoMolecule fragBiggest) {
 
 		MolDistHistViz mdhv = null;
-
 		recentException = null;
-
 		try {
 			mdhv = creatorMolDistHistViz.create(fragBiggest);
 		} catch (Exception e) {
@@ -453,7 +451,6 @@ public MolDistHistViz createVisualDescriptor(StereoMolecule fragBiggest) {
 				recentException = e;
 			}
 		}
-
 		return mdhv;
 	}
 

src/main/java/com/actelion/research/chem/descriptor/flexophore/ConstantsFlexophore.java

@@ -11,4 +11,13 @@ public class ConstantsFlexophore {
 
 
     public static final String TAG_FLEXOPHORE_OBJECT =  "FlexDecoded";
+
+
+
+    public static final int LABEL_WEIGHT_LOW = 0;
+    public static final int LABEL_WEIGHT_NORMAL = 1;
+    public static final int LABEL_WEIGHT_MANDATORY = 2;
+    public static final double VAL_WEIGHT_LOW = 0.5;
+    public static final double VAL_WEIGHT_NORMAL = 1;
+    public static final double VAL_WEIGHT_MANDATORY = 2;
 }

src/main/java/com/actelion/research/chem/descriptor/flexophore/IMolDistHist.java

@@ -44,9 +44,11 @@ public interface IMolDistHist extends ICompleteGraph {
 
 	byte [] getDistHist(int indexAt1, int indexAt2, byte[] arr);
 
-	boolean isInevitablePharmacophorePoint(int indexNode);
-
-	int getNumInevitablePharmacophorePoints();
+	boolean isMandatoryPharmacophorePoint(int indexNode);
+
+	double getWeightPharmacophorePoint(int indexNode);
+
+	int getNumMandatoryPharmacophorePoints();
 
 
 }

src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHist.java

@@ -452,16 +452,19 @@ public int getSizeBytes(){
 	 * Only for interface compliance needed.
 	 */
 	@Override
-	public int getNumInevitablePharmacophorePoints() {
+	public int getNumMandatoryPharmacophorePoints() {
 		// TODO Auto-generated method stub
 		return 0;
 	}
 
 	@Override
-	public boolean isInevitablePharmacophorePoint(int indexNode) {
-		// TODO Auto-generated method stub
+	public boolean isMandatoryPharmacophorePoint(int indexNode) {
 		return false;
 	}
+	@Override
+	public double getWeightPharmacophorePoint(int indexNode) {
+		return 1.0;
+	}
 
 	public static int getNumBytesEntry(){
 		return PPNode.getNumBytesEntry()+1;