Update OCL to v2024.2.1

package.json

@@ -75,8 +75,8 @@
     "eslint-config-cheminfo": "^9.1.1",
     "gwt-api-exporter": "^2.0.0",
     "jest": "^29.7.0",
-    "openchemlib-utils": "^5.6.1",
-    "prettier": "^3.2.4",
+    "openchemlib-utils": "^5.8.0",
+    "prettier": "^3.2.5",
     "yargs": "^17.7.2"
   }
 }

scripts/openchemlib/classes.js

@@ -43,9 +43,12 @@
   ['chem/forcefield/mmff/Vector3', changeVector3],
   ['chem/io/CompoundFileHelper', fixCompoundFileHelper],
   ['chem/io/RXNFileCreator', changeLineSeparator],
+  ['chem/io/RXNFileParser', replaceStandardCharsets(2)],
   ['chem/io/RXNFileV3Creator', changeLineSeparator, removeRXNStringFormat],
+  ['chem/io/SDFileParser', replaceStandardCharsets(2)],
   ['chem/Molecule', changeMolecule],
   ['chem/MolfileCreator', changeLineSeparator],
+  ['chem/MolfileParser', replaceStandardCharsets(1)],
   ['chem/MolfileV3Creator', changeLineSeparator],
   ['chem/Molecule3D', removeCloneInfos],
   ['chem/TautomerHelper', changeTautomerHelper],
@@ -251,11 +254,14 @@
   return code.replaceAll(methodRegExp('toStringSpaceDelimited'), '');
 }
 
-function replaceChecked(code, from, to) {
-  if (code.indexOf(from) === -1) {
-    throw new Error(`Cannot find ${from} in code`);
+function replaceChecked(code, from, to, times = 1) {
+  for (let i = 0; i < times; i++) {
+    if (code.indexOf(from) === -1) {
+      throw new Error(`Cannot find ${from} in code (iteration: ${i}}`);
+    }
+    code = code.replace(from, to);
   }
-  return code.replace(from, to);
+  return code;
 }
 
 function removeSlice(code, start, end) {
@@ -314,7 +320,7 @@
 }
 
 function changeGenericEditorArea(code) {
   // TODO: find replacements
   code = code.replaceAll(
     methodRegExp('showWarningMessage'),
     'private void showWarningMessage(String msg) {}',
@@ -588,7 +594,7 @@
   );
   code = replaceChecked(
     code,
-    'br = new BufferedReader(new InputStreamReader(Csv.class.getResourceAsStream(path)));',
+    'br = new BufferedReader(new InputStreamReader(Csv.class.getResourceAsStream(path), StandardCharsets.UTF_8));',
     'br = new BufferedReader(new StringReader(path));',
   );
   const fnfeStart = code.indexOf('catch (FileNotFoundException e) {');
@@ -597,6 +603,13 @@
   return code;
 }
 
+function replaceStandardCharsets(times) {
+  return (code) => {
+    code = replaceChecked(code, 'StandardCharsets.UTF_8', '"UTF-8"', times);
+    return code;
+  };
+}
+
 const newTables = `public static Tables newMMFF94(String tableSet) {
   return new com.actelion.research.chem.forcefield.mmff.Tables(
     CsvData.angleData,

src/com/actelion/research/gwt/chemlib/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

src/com/actelion/research/gwt/chemlib/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;
 import com.actelion.research.chem.conf.TorsionDBData;
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/forcefield/mmff/Csv.java

@@ -38,6 +38,7 @@
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.StringReader;
+import java.nio.charset.StandardCharsets;
 
 /**
  * Basic CSV parser. The Csv class provides very basic CSV file parsing

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/io/RDFileParser.java

@@ -40,6 +40,7 @@
 import com.actelion.research.io.BOMSkipper;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.util.TreeMap;
 
 /**
@@ -59,7 +60,7 @@ public class RDFileParser {
 	public RDFileParser(String fileName) {
 	    mNoOfRecords = 0;
 		try {
-			mReader = new BufferedReader(new InputStreamReader(new FileInputStream(fileName), "UTF-8"));
+			mReader = new BufferedReader(new InputStreamReader(new FileInputStream(fileName), StandardCharsets.UTF_8));
 			BOMSkipper.skip(mReader);
 			readHeader();
 		} catch (IOException e) {
@@ -70,7 +71,7 @@ public RDFileParser(String fileName) {
 	public RDFileParser(File file) {
         mNoOfRecords = 0;
 		try {
-    		mReader = new BufferedReader(new InputStreamReader(new FileInputStream(file), "UTF-8"));
+    		mReader = new BufferedReader(new InputStreamReader(new FileInputStream(file), StandardCharsets.UTF_8));
 			BOMSkipper.skip(mReader);
 			readHeader();
 		} catch (IOException e) {

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/io/RXNFileParser.java

@@ -40,6 +40,7 @@
 import com.actelion.research.io.BOMSkipper;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 
 
 public class RXNFileParser

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/io/SDFileParser.java

@@ -39,6 +39,7 @@
 import com.actelion.research.io.BOMSkipper;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 
 public class SDFileParser extends CompoundFileParser {
     private static final int DEFAULT_RECORDS_TO_INSPECT = 10240;