Merge tag 'openchemlib-2024.2.1'

[maven-release-plugin]  copy for tag openchemlib-2024.2.1

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>2024.1.3</version>
+    <version>2024.2.1</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-2024.1.3</tag>
+      <tag>openchemlib-2024.2.1</tag>
   </scm>
 
     <distributionManagement>

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

@@ -2954,6 +2954,21 @@ public double getVarianceCol(int col) {
         return var;
     }
 
+    public double getVarianceRow(int row) {
+        double var = 0;
+
+        int cols = cols();
+        double mean = getMeanRow(row);
+        double dSum = 0;
+        for (int i = 0; i < cols; i++) {
+        	dSum += (data[row][i] - mean) * (data[row][i] - mean);
+        }
+
+        var = dSum / (cols - 1.0);
+
+        return var;
+    }
+
     public double getVarianceCentered() {
         double var = 0;
 

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

@@ -42,6 +42,7 @@
 import java.io.BufferedWriter;
 import java.io.FileWriter;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
@@ -73,8 +74,8 @@ public AtomTypeList(int mode) {
 
 	/**
 	 * Creates a new AtomTypeList from a given file using the given mode.
-	 * If the the filename references a .typ file, then the mode is checked, whether it matches the file's content.
-	 * If the the filename references a compound file, then the molecules are parsed and a new AtomTypeList is created
+	 * If the filename references a .typ file, then the mode is checked, whether it matches the file's content.
+	 * If the filename references a compound file, then the molecules are parsed and a new AtomTypeList is created
 	 * reflecting the all contained atom types.
 	 * @param filename either .typ file or a .dwar or .sdf compound file
 	 * @param mode
@@ -84,7 +85,7 @@ public AtomTypeList(String filename, int mode) throws Exception {
         this(mode);
 
         if (filename.endsWith(".typ")) {
-	        BufferedReader theReader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(filename)));
+	        BufferedReader theReader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(filename), StandardCharsets.UTF_8));
 	        String version =theReader.readLine();
 	        if (!VERSION_STRING.equals(version)) {
 	            throw new Exception("Outdated atom type list file.");

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

@@ -47,6 +47,7 @@
 import com.actelion.research.io.BOMSkipper;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.util.TreeMap;
 
 public class MolfileParser
@@ -970,7 +971,7 @@ public boolean parse(StereoMolecule mol, File file)
 	{
 		mMol = mol;
 		try{
-			BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file), "UTF-8"));
+			BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file), StandardCharsets.UTF_8));
 			BOMSkipper.skip(reader);
 			return readMoleculeFromBuffer(reader);
 		} catch(IOException e){

src/main/java/com/actelion/research/chem/chemicalspaces/ChemicalSpaceCreator.java

@@ -1,41 +1,22 @@
 package com.actelion.research.chem.chemicalspaces;
 
-import java.io.BufferedReader;
+import com.actelion.research.chem.*;
+import com.actelion.research.chem.chemicalspaces.synthon.SynthonCreator;
+import com.actelion.research.chem.chemicalspaces.synthon.SynthonReactor;
+import com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512;
+import com.actelion.research.chem.io.DWARFileCreator;
+import com.actelion.research.chem.reaction.Reaction;
+import com.actelion.research.chem.reaction.Reactor;
+
 import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.FileWriter;
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
-import java.util.Set;
+import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
 import java.util.stream.Collectors;
 
-import com.actelion.research.chem.CanonizerUtil;
-import com.actelion.research.chem.IDCodeParser;
-import com.actelion.research.chem.Molecule;
-import com.actelion.research.chem.SSSearcher;
-import com.actelion.research.chem.SSSearcherWithIndex;
-import com.actelion.research.chem.StereoMolecule;
-import com.actelion.research.chem.chemicalspaces.synthon.SynthonCreator;
-import com.actelion.research.chem.chemicalspaces.synthon.SynthonReactor;
-import com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512;
-import com.actelion.research.chem.io.DWARFileCreator;
-import com.actelion.research.chem.io.RXNFileParser;
-import com.actelion.research.chem.io.SDFileParser;
-import com.actelion.research.chem.reaction.Reaction;
-import com.actelion.research.chem.reaction.Reactor;
-
 
 
 public class ChemicalSpaceCreator {
@@ -87,7 +68,7 @@ public void create() {
 		ConcurrentMap<String,String> processedToOrigIDCode = new ConcurrentHashMap<String,String>();
 		ConcurrentMap<String,List<Map<String,String>>> reactionsWithSynthons = new ConcurrentHashMap<String,List<Map<String,String>>>(); 
 		processBuildingBlocks(this.bbs,processedToOrigIDCode,functionalizations);
-		fps = new ConcurrentHashMap<String,long[]>();
+		fps = new ConcurrentHashMap<>();
 		calcFragFPs(processedToOrigIDCode.keySet(),fps);
 		generateSynthons(reactions, processedToOrigIDCode, reactionsWithSynthons,fps,allSynthonTransformations);
 		generateCombinatoriaLibraries(reactionsWithSynthons, bbs, allSynthonTransformations);
@@ -179,7 +160,6 @@ private static void processReaction(Reaction rxn,  ConcurrentMap<String,String>
      	reactionsWithSynthons.putIfAbsent(rxn.getName(), new ArrayList<>());
 
      	//System.out.println("bbs");
-
 
      	for(int i=0;i<reactants.size();i++) {
      		List<String> rList = reactants.get(i);

src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonCreator.java

@@ -1,27 +1,19 @@
 package com.actelion.research.chem.chemicalspaces.synthon;
 
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.Writer;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 import com.actelion.research.chem.Molecule;
 import com.actelion.research.chem.RingCollection;
 import com.actelion.research.chem.StereoMolecule;
 import com.actelion.research.chem.coords.CoordinateInventor;
 import com.actelion.research.chem.io.RXNFileCreator;
 import com.actelion.research.chem.reaction.Reaction;
 
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.Writer;
+import java.util.*;
+
 public class SynthonCreator {
-
-
+
 	/**
 	 * only works for reactions with a single product
 	 * @param rxn
@@ -32,18 +24,15 @@ public static Reaction[] create(Reaction rxn) throws Exception {
 		if(rxn.getProducts()>1)
 			throw new Exception("only reactions with one product are supported");
 		Reaction[] synthonTransformations = new Reaction[rxn.getReactants()];
-		Map<Integer,Integer> mappedAtomToReactant = new HashMap<Integer,Integer>(); //stores the information on which mapped atom in the product ist contributed by which reactant
+		Map<Integer,Integer> mappedAtomToReactant = new HashMap<>(); //stores the information on which mapped atom in the product ist contributed by which reactant
 		for(int r=0;r<rxn.getReactants();r++) {
 			if(rxn.getReactants()==0)
 				throw new Exception("cannot create Synthons for reactions with one reactant");
 			StereoMolecule reactant = rxn.getReactant(r);
 			for(int a=0;a<reactant.getAtoms();a++) {
 				int reactantMapNo = reactant.getAtomMapNo(a);
-				if(reactantMapNo==0)
-					continue;
-				else {
+				if(reactantMapNo!=0)
 					mappedAtomToReactant.put(reactantMapNo, r);
-				}
 			}
 		}
 		//find bonds in products that are formed between a) atoms from different reactants or b) between an unmapped and a mapped atom
@@ -58,10 +47,8 @@ public static Reaction[] create(Reaction rxn) throws Exception {
 			int[] atoms = rc.getRingAtoms(ringNo);
 			for(int a : atoms) {
 				int mappedA = product.getAtomMapNo(a);
-				if(mappedA==0)
-					continue;
-				int reactant = mappedAtomToReactant.get(mappedA);
-				ringReactant.add(reactant);
+				if(mappedA!=0)
+					ringReactant.add(mappedAtomToReactant.get(mappedA));
 			}
 			if(ringReactant.size()==1) {//homogeneous ring!
 				int[] ringBonds = rc.getRingBonds(ringNo);
@@ -78,17 +65,13 @@ public static Reaction[] create(Reaction rxn) throws Exception {
 			int mappedBondAtom1 = product.getAtomMapNo(bondAtom1);
 			int mappedBondAtom2 = product.getAtomMapNo(bondAtom2);
 			if(mappedBondAtom1==0) {
-				if(mappedBondAtom2==0) // both atoms unmapped
-					continue;
-				else //bond between a mapped and an unmapped atom
+				if(mappedBondAtom2!=0) //bond between a mapped and an unmapped atom
 					bondsToCut.add(b);
-
 			}
 			else if(mappedBondAtom2==0) { //bond between a mapped and an umapped atom
 				bondsToCut.add(b);
-				continue;
 			}
-			else if(mappedAtomToReactant.get(mappedBondAtom1)!=mappedAtomToReactant.get(mappedBondAtom2)) { //atoms from two different reactants
+			else if(!mappedAtomToReactant.get(mappedBondAtom1).equals(mappedAtomToReactant.get(mappedBondAtom2))) { //atoms from two different reactants
 				bondsToCut.add(b);
 			}
 		}

src/main/java/com/actelion/research/chem/conf/TorsionDB.java

@@ -38,6 +38,7 @@
 import com.actelion.research.chem.StereoMolecule;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.util.TreeMap;
 
 public class TorsionDB {
@@ -298,14 +299,14 @@ protected static BufferedReader openReader(String resourceName) throws IOExcepti
 			InputStream is = TorsionDB.class.getResourceAsStream(cBasePath+DATABASE_CSD+resourceName);
 			if (is != null) {
 				sDatabase = DATABASE_CSD;
-				return new BufferedReader(new InputStreamReader(is));
+				return new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8));
 				}
 
 			sDatabase = DATABASE_COD;
 			}
 
 	   	return new BufferedReader(new InputStreamReader(TorsionDB.class.getResourceAsStream(
-   				cBasePath+sDatabase+resourceName)));
+   				cBasePath+sDatabase+resourceName), StandardCharsets.UTF_8));
 		}
 
 	/**

src/main/java/com/actelion/research/chem/conf/torsionstrain/StatisticalTorsionPotential.java

@@ -9,6 +9,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicInteger;
@@ -71,7 +72,7 @@ private StatisticalTorsionPotential() {
 
 	private void initialize() {
 		BufferedReader torsionIDReader = new BufferedReader(new InputStreamReader(TorsionDB.class.getResourceAsStream(
-				BASE_PATH+database+TORSION_IDS_FILE)));
+				BASE_PATH+database+TORSION_IDS_FILE), StandardCharsets.UTF_8));
 
 		try {
 			readTorsionIDs(torsionIDReader);

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

@@ -39,6 +39,7 @@
 
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.util.BitSet;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -263,7 +264,7 @@ public static void main(String args[])
         IDCodeParser p = new IDCodeParser(false);
         StereoMolecule m = new StereoMolecule();
         BitSet referencebs = null, querybs = null;
-        BufferedReader r = new BufferedReader(new InputStreamReader(System.in));
+        BufferedReader r = new BufferedReader(new InputStreamReader(System.in, StandardCharsets.UTF_8));
         FingerPrintGenerator fp = null;
         try {
             if (args.length > 0) {

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

@@ -123,6 +123,30 @@ public static void setDistHistToOne(MolDistHist mdh){
         }
     }
 
+    public static MolDistHist getEmptyMolDistHist(){
+        PPNode ppNode0 = new PPNode();
+        ppNode0.realize();
+
+        MolDistHist mdhEmpty = new MolDistHist(1);
+        mdhEmpty.addNode(ppNode0);
+        mdhEmpty.realize();
+
+        return mdhEmpty;
+    }
+    public static boolean isEmptyMolDistHist(MolDistHist mdh){
+
+        boolean empty = true;
+        if(mdh.getNumPPNodes()>1){
+            empty = false;
+        } else if(mdh.getNumPPNodes()==1){
+            if(mdh.getNode(0).getInteractionTypeCount()>0){
+                empty = false;
+            }
+        }
+
+        return empty;
+    }
+
     public static MolDistHist getMostDistantPairOfNodes (MolDistHist mdh){
 
         int n = mdh.getNumPPNodes();

src/main/java/com/actelion/research/chem/forcefield/mmff/Csv.java

@@ -38,6 +38,7 @@
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 
 /**
  * Basic CSV parser. The Csv class provides very basic CSV file parsing
@@ -91,7 +92,7 @@ public static Object[][] readFile(String path) {
 
         try {
             String line;
-            br = new BufferedReader(new InputStreamReader(Csv.class.getResourceAsStream(path)));
+            br = new BufferedReader(new InputStreamReader(Csv.class.getResourceAsStream(path), StandardCharsets.UTF_8));
 
             int size = Integer.parseInt(br.readLine().trim());
             String[] format = br.readLine().trim().split(",");

src/main/java/com/actelion/research/chem/interactionstatistics/InteractionDistanceStatistics.java

@@ -1,23 +1,17 @@
 package com.actelion.research.chem.interactionstatistics;
 
+import com.actelion.research.util.FastSpline;
+import com.actelion.research.util.SmoothingSplineInterpolator;
+
+import java.io.*;
+import java.net.URL;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
 
-import com.actelion.research.util.FastSpline;
-import com.actelion.research.util.SmoothingSplineInterpolator;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileInputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URL;
-
 public class InteractionDistanceStatistics {
 
 	private static volatile InteractionDistanceStatistics instance = new InteractionDistanceStatistics(); //eager initialization
@@ -194,9 +188,9 @@ public void readFromFile() throws IOException {
 			}
 			InputStream is = url.openStream();
 			//InputStream is = new FileInputStream(file);
-			BufferedReader reader = new BufferedReader(new InputStreamReader(is));
+			BufferedReader reader = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8));
 			String line;
-			while((line = reader.readLine())!=null && line.length()!=0) {
+			while((line = reader.readLine())!=null && !line.isEmpty()) {
 				String s[] = line.split(" ");
 
 				long l = Long.parseLong(s[0]);