Merge tag 'openchemlib-2024.10.0'

[maven-release-plugin]  copy for tag openchemlib-2024.10.0

buildOpenChemLib

@@ -6,7 +6,7 @@ rm -rf ./build
 mkdir build
 cp -r ./src/main/resources/* ./build/
 find . -name "*.java" > sources.txt
-javac -target 8 -d ./build @sources.txt
+javac -target 8 -source 8 -d ./build @sources.txt
 rm sources.txt
 jar -cf build/OpenChemLib.jar -C ./build .
 ls -al build/OpenChemLib.jar

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>2024.7.3-SNAPSHOT</version>
+    <version>2024.10.0</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>
@@ -209,7 +209,7 @@
         <connection>scm:git:git@github.com:Actelion/openchemlib.git</connection>
         <developerConnection>scm:git:git@github.com:Actelion/openchemlib.git</developerConnection>
         <url>https://github.com/Actelion/openchemlib</url>
-      <tag>HEAD</tag>
+      <tag>openchemlib-2024.10.0</tag>
   </scm>
 
     <distributionManagement>

src/main/java/com/actelion/research/calc/ArrayUtilsCalc.java

@@ -57,15 +57,12 @@ public class ArrayUtilsCalc {
 
 	public final static int [] cat(int [] a, int [] b) {
 		int [] c = new int [a.length + b.length];
-
 		for (int i = 0; i < a.length; i++) {
 			c[i]=a[i];
 		}
-
 		for (int i = 0; i < b.length; i++) {
 			c[a.length+i]=b[i];
 		}
-
 		return c;
 	}
 
@@ -80,6 +77,16 @@ public final static boolean contains(int [] a, int b) {
 		}
 		return bFound;
 	}
+	public final static boolean containsAll(int [] a, int [] b) {
+		boolean bFound = true;
+		for (int i = 0; i < b.length; i++) {
+			if(!contains(a, b[i])){
+				bFound=false;
+				break;
+			}
+		}
+		return bFound;
+	}
 
 	public final static int [] copy(int [] a) {
 		int [] b = new int [a.length];
@@ -195,6 +202,8 @@ public final static boolean findIdentical(int [] a, int [] b) {
 
 		return bFound;
 	}
+
+
     public static final double getCorrPearson(List<PointDouble> li) {
 
     	final double [] a = new double [li.size()];
@@ -206,7 +215,7 @@ public static final double getCorrPearson(List<PointDouble> li) {
 
         return getCorrPearson(a, b);
     }
-    
+
     public static final double getCorrPearson(Matrix A, Matrix B) {
 
 

src/main/java/com/actelion/research/calc/Matrix.java

@@ -2047,7 +2047,7 @@ public boolean areRowsEqual(int row1, int row2) {
     public boolean equal(Matrix ma) {
         boolean bEQ = true;
 
-        if(equalDimension(ma) == true) {
+        if(equalDimension(ma)) {
             for (int i = 0; i < getRowDim(); i++) {
                 for (int j = 0; j < getColDim(); j++) {
                     if(data[i][j] != ma.data[i][j]) {
@@ -2066,7 +2066,7 @@ public boolean equal(Matrix ma) {
     public boolean equal(Matrix ma, double dLimit) {
         boolean bEQ = true;
 
-        if(equalDimension(ma) == true) {
+        if(equalDimension(ma)) {
             for (int i = 0; i < getRowDim(); i++) {
                 for (int j = 0; j < getColDim(); j++) {
                     double dDiff = Math.abs(data[i][j] - ma.data[i][j]);
@@ -2305,7 +2305,7 @@ final public Matrix multiply(boolean transA, boolean transB, Matrix ma) {
         //
 
         // C = A * B
-        if ( (transA == false) && (transB == false)) {
+        if (!transA && !transB) {
 
             int n = cols();
 
@@ -2364,7 +2364,7 @@ final public Matrix multiply(boolean transA, boolean transB, Matrix ma) {
         // C = A' * B
         //
         // Matrix A is transposed
-        if ( (transA == true) && (transB == false)) {
+        if (transA && !transB) {
 
             // Reverse n
             int n = rows();
@@ -2429,7 +2429,7 @@ final public Matrix multiply(boolean transA, boolean transB, Matrix ma) {
         // C = A * B'
         //
         // Matrix B is transposed
-        if ( (transA == false) && (transB == true)) {
+        if (!transA && transB) {
             int n = cols();
 
             int m = rows();
@@ -2483,7 +2483,7 @@ final public Matrix multiply(boolean transA, boolean transB, Matrix ma) {
         // C = A' * B'
         //
         // Matrix A + B are transposed
-        if ( (transA == true) && (transB == true)) {
+        if (transA && transB) {
 
             // Reverse n
             int n = rows();
@@ -2792,7 +2792,7 @@ public void resize(int rowsNew, int colsNew) {
     public List<Double> getRowAsList(int row) {
         List<Double> list = new ArrayList<Double>();
         for (int ii = 0; ii < data[0].length; ii++) {
-          list.add(new Double(data[row][ii]));
+          list.add(data[row][ii]);
         }
         return list;
     }
@@ -3878,9 +3878,6 @@ public String toStringWithRowTags(List<String> liRowTags, DecimalFormat nf, Stri
     	return sbAll.toString();
     }
 
-
-
-
 	public void writeSerialized(File fiOut) throws IOException {
 		FileOutputStream fos = new FileOutputStream(fiOut);
 		ObjectOutputStream oos = new ObjectOutputStream(fos);
@@ -3934,7 +3931,7 @@ public void write(String sFile, boolean bApppend, int digits, int totalWidth) {
             BufferedWriter writer = new BufferedWriter(new FileWriter(new File(
                 sFile), bApppend));
 
-            StringBuffer sVal = new StringBuffer();
+            StringBuffer sVal;
             for (int ii = 0; ii < data.length; ii++) {
                 sVal = new StringBuffer();
                 for (int jj = 0; jj < data[0].length; jj++) {

src/main/java/com/actelion/research/calc/combinatorics/CombinationGenerator.java

@@ -32,6 +32,7 @@
 package com.actelion.research.calc.combinatorics;
 
 import com.actelion.research.util.ListUtils;
+import com.actelion.research.util.StringFunctions;
 
 import java.math.BigInteger;
 import java.util.ArrayList;
@@ -312,7 +313,7 @@ public static BigInteger getBinomialCoefficient(int n, int k){
 	}
 
 	public static void main(String[] args) {
-		examplePermutations();
+		exampleGetAllOutOf2();
 
 	}
 	public static void examplePermutations() {
@@ -355,6 +356,27 @@ public static void exampleCombinations() {
 		}
 	}
 
+	public static void exampleGetAllOutOf() {
+
+		int object = 4;
+		int sampleSize = 3;
+		List<int[]>  liComb = getAllOutOf(object, sampleSize);
+		for(int [] a : liComb) {
+			System.out.println(StringFunctions.toString(a, ","));
+		}
+	}
+	public static void exampleGetAllOutOf2() {
+
+		int object = 4;
+		for (int sampleSize = 1; sampleSize < object; sampleSize++) {
+			List<int[]>  liComb = getAllOutOf(object, sampleSize);
+			for(int [] a : liComb) {
+				System.out.println(StringFunctions.toString(a, ","));
+			}
+		}
+
+	}
+
 
 
 

src/main/java/com/actelion/research/calc/histogram/Histogram.java

@@ -38,6 +38,7 @@
 import java.text.DecimalFormat;
 import java.text.DecimalFormatSymbols;
 import java.text.NumberFormat;
+import java.util.Collection;
 import java.util.Locale;
 import java.util.Random;
 
@@ -83,6 +84,15 @@ public Histogram(double [] arrRaw, double min, double max, int bins) {
 		initialize(arrRaw,min,max,bins);
 	}
 
+	public Histogram(Collection<Double> values, double min, double max, int bins) {
+		double [] v = new double[values.size()];
+		int c=0;
+		for (Double value : values) {
+			v[c++]=value;
+		}
+		initialize(v,min,max,bins);
+	}
+
 	public Histogram(double [] arrRaw, int bins) {
 
 		double max = -Double.MAX_VALUE;
@@ -96,7 +106,6 @@ public Histogram(double [] arrRaw, int bins) {
 				min=v;
 			}
 		}
-
 		initialize(arrRaw,min,max,bins);
 	}
 

src/main/java/com/actelion/research/calc/statistics/median/MedianStatisticFunctions.java

@@ -34,6 +34,10 @@
 
 package com.actelion.research.calc.statistics.median;
 
+import com.actelion.research.util.ArrayUtils;
+
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 
@@ -212,23 +216,18 @@ public static double getPercentileFromSortedLong(List<Long> liScore, double frac
 	 * @return
 	 */
 	public static ModelMedianInteger getMedianForInteger(List<Integer> liScore) {
-
 		Collections.sort(liScore);
-
 		ModelMedianInteger modelMedian = new ModelMedianInteger();
-
 		modelMedian.lowerQuartile = (int)(MedianStatisticFunctions.getPercentileFromSortedInt(liScore, 0.25) + 0.5);
-
 		modelMedian.median = (int)(MedianStatisticFunctions.getPercentileFromSortedInt(liScore, 0.5) + 0.5);
-
 		modelMedian.upperQuartile = (int)(MedianStatisticFunctions.getPercentileFromSortedInt(liScore, 0.75) + 0.5);
-
 		modelMedian.size = liScore.size();
-
 		return modelMedian;
-
 	}
-
+	public static ModelMedianInteger getMedianForInteger(int [] a) {
+		return getMedianForInteger(ArrayUtils.toList(a));
+	}
+
 	public static ModelMedianLong getMedianForLong(List<Long> liScore) {
 
 		Collections.sort(liScore);
@@ -249,11 +248,16 @@ public static ModelMedianLong getMedianForLong(List<Long> liScore) {
 
 	/**
 	 * 
-	 * @param liScore the list is sorted in the method.
+	 * @param
 	 * @return
 	 */
-	public static ModelMedianDouble getMedianForDouble(List<Double> liScore) {
-
+	public static ModelMedianDouble getMedianForDouble(Collection<Double> liScoreRaw) {
+
+		if(liScoreRaw.size()<1)
+			return null;
+
+		List<Double> liScore = new ArrayList<>(liScoreRaw);
+
 		Collections.sort(liScore);
 
 		ModelMedianDouble modelMedian = new ModelMedianDouble();

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

@@ -168,7 +168,13 @@ public boolean locateDelocalizedDoubleBonds(boolean[] isAromaticBond, boolean ma
                     }
                 }
 
-            if (!bondsPromoted) {
+
+			if (bondsPromoted) {
+				promoteObviousBonds();
+				continue;
+				}
+
+			if (!bondsPromoted) {
                 // find and promote one aromatic bond
                 // (should never happen, but to prevent an endless loop nonetheless)
                 for (int bond=0; bond<mMol.getBonds(); bond++) {

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

@@ -195,8 +195,12 @@ public static boolean hasUnbalancedAtomCharge(StereoMolecule mol, int atom) {
 	}
 
 	public static boolean isAcidicOxygen(StereoMolecule mol, int atom) {
+		return isAcidicOxygen(mol, atom, true);
+		}
+
+	public static boolean isAcidicOxygen(StereoMolecule mol, int atom, boolean considerCharge) {
 		if (mol.getAtomicNo(atom) != 8
-		 || mol.getAtomCharge(atom) != 0
+		 || (considerCharge && mol.getAtomCharge(atom) != 0)
 		 || mol.getConnAtoms(atom) != 1
 		 || mol.getConnBondOrder(atom, 0) != 1)
 			return false;
@@ -246,13 +250,18 @@ public static boolean isAcidicOxygen(StereoMolecule mol, int atom) {
 
 			if(nDoubleBondedO2S == 2)
 				return true;
-		} else if(isAcidicOxygenAtPhosphoricAcid(mol, atom)) // CP=O(OH)(OH)
+
+		} else if(isAcidicOxygenAtPhosphoricAcid(mol, atom, considerCharge)) // CP=O(OH)(OH)
 			return true;
 
 		return false;
 	}
-	
+
 	public static boolean isAcidicOxygenAtPhosphoricAcid(StereoMolecule mol, int atom) {
+		return isAcidicOxygenAtPhosphoricAcid(mol, atom, true);
+	}
+
+	public static boolean isAcidicOxygenAtPhosphoricAcid(StereoMolecule mol, int atom, boolean considerCharge) {
 		if (mol.getAtomicNo(atom) != 8)
 			return false;
 
@@ -351,11 +360,15 @@ public static boolean isNitroGroupN(StereoMolecule mol, int atom) {
 		return nitro;
 	}
 
-
-
+
 	public static boolean isBasicNitrogen(StereoMolecule mol, int atom) {
+		return isBasicNitrogen(mol, atom, true);
+	}
+
+
+	public static boolean isBasicNitrogen(StereoMolecule mol, int atom, boolean considerCharge) {
 		if (mol.getAtomicNo(atom) != 7
-		 || mol.getAtomCharge(atom) != 0
+		 || (considerCharge && mol.getAtomCharge(atom) != 0)
 		 || (mol.getConnAtoms(atom) + mol.getAtomPi(atom) > 3))
 			return false;
 
@@ -552,5 +565,23 @@ && getFakeOxoCount(mol, mol.getConnAtom(conn, j)) != 0)
 				}
 			}
 		return false;
+	}
+
+	public static boolean isAmphiphilic(StereoMolecule mol) {
+		boolean amphiphilic=true;
+
+		boolean acidic=false;
+		boolean basic=false;
+		for (int at = 0; at < mol.getAtoms(); at++) {
+			if(isAcidicOxygen(mol, at)){
+				acidic=true;
+			}
+			if(isBasicNitrogen(mol, at)){
+				basic=true;
+			}
 		}
+
+		amphiphilic = basic && acidic;
+		return amphiphilic;
 	}
+}