Input restrictions for EFGF lifted and some general refactoring and fixing

.gitignore

@@ -13,4 +13,6 @@ build/
 .gradle
 
 # EFGF evaluation test output
-ErtlFunctionalGroupsFinderEvaluationTest_Output/
+ErtlFunctionalGroupsFinderEvaluationTest_Output/
+ChEBI_complete.sdf
+/Output/

License-header/License-header.txt

@@ -1,6 +1,6 @@
 /*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (c) $today.year Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Copyright (c) 2024 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
  * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 

build.gradle

@@ -1,6 +1,6 @@
 /*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (C) 2023 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Copyright (C) 2024 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
  * Source code is available at <https://github.com/zielesny/ErtlFunctionalGroupsFinder>
  * 

src/main/java/org/openscience/cdk/tools/efgf/app/ErtlFunctionalGroupsFinderPerformanceSnapshotApp.java

@@ -1,6 +1,6 @@
 /*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (c) 2023 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Copyright (c) 2024 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
  * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 
@@ -62,58 +62,60 @@
 /**
  * An application for testing the performance of the ErtlFunctionalGroupsFinder.find() method under parallelization on
  * multiple threads.
+ * <br><br>
+ * Legacy code that still assumes that the old input restrictions are turned on.
  *
  * @author Jonas Schaub
  * @version 1.2.0.0
  */
 public class ErtlFunctionalGroupsFinderPerformanceSnapshotApp {
-
+    //
     //<editor-fold defaultstate="collapsed" desc="Private static final constants">
     /**
      * Name of file for logging occurred exceptions
      */
     private static final String EXCEPTIONS_LOG_FILE_NAME = "Exceptions_Log.txt";
-
+    //
     /**
      * Name of file for writing results
      */
     private static final String RESULTS_FILE_NAME = "Results.txt";
-
+    //
     /**
      * All allowed atomic numbers to pass to the ErtlFunctionalGroupsFinder;
      * String will be split and resulting integers passed to a set
      */
     private static final String NON_METALLIC_ATOMIC_NUMBERS = "1,2,6,7,8,9,10,15,16,17,18,34,35,36,53,54,86";
     //</editor-fold>
-
+    //
     //<editor-fold defaultstate="collapsed" desc="Private class variables">
     /**
      * All allowed atomic numbers to pass to the ErtlFunctionalGroupsFinder as a set of integers (will be parsed from
      * NON_METALLIC_ATOMIC_NUMBERS)
      */
     private Set<Integer> nonMetallicAtomicNumbersSet;
-
+    //
     /**
      * The working directory (the jar-file's directory)
      */
     private String workingPath;
-
+    //
     /**
      * The given number of different threads to use
      */
     private int numberOfThreadsToUse;
-
+    //
     /**
      * All molecules loaded from the SD file
      */
     private IAtomContainer[] moleculesArray;
-
+    //
     /**
      * The aromaticity model in use
      */
     private Aromaticity aromaticityModel;
     //</editor-fold>
-
+    //
     //<editor-fold defaultstate="collapsed" desc="Constructor">
     /**
      * Instantiates and starts the application. It first loads all molecules from a given SD file into memory and then
@@ -265,7 +267,7 @@ public ErtlFunctionalGroupsFinderPerformanceSnapshotApp(String[] anArgs) throws
         }
     }
     //</editor-fold>
-
+    //
     //<editor-fold defaultstate="collapsed" desc="Private methods">
     /**
      * Performs all preprocessing needed for the ErtlFunctionalGroupsFinder and throws an IllegalArgumentException
@@ -311,7 +313,7 @@ private IAtomContainer applyFiltersAndPreprocessing(IAtomContainer aMolecule) th
         this.aromaticityModel.apply(aMolecule);
         return aMolecule;
     }
-
+    //
     /**
      * Appends the given exception's stack trace to a log file.
      *

src/main/java/org/openscience/cdk/tools/efgf/app/ExtractFunctionalGroupsTask.java

@@ -1,6 +1,6 @@
 /*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (c) 2023 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Copyright (c) 2024 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
  * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 
@@ -33,11 +33,11 @@
  * @version 1.2
  */
 public class ExtractFunctionalGroupsTask implements Callable<Integer> {
-
+    //
     private final IAtomContainer[] moleculesArray;
-
+    //
     private final ErtlFunctionalGroupsFinder ertlFinder;
-
+    //
     /**
      * Instantiates the thread.
      *
@@ -48,7 +48,7 @@ public ExtractFunctionalGroupsTask(IAtomContainer[] aListOfMolecules) {
         this.moleculesArray = aListOfMolecules;
         this.ertlFinder = new ErtlFunctionalGroupsFinder();
     }
-
+    //
     /**
      * Applies the ErtlFunctionalGroupsFinder.find(IAtomContainer container, boolean clone) method on all given
      * molecules (parameter clone = false) and counts the occurring exceptions.
@@ -68,5 +68,4 @@ public Integer call() throws Exception {
         }
         return tmpExceptionsCounter;
     }
-
 }

src/main/java/org/openscience/cdk/tools/efgf/app/Main.java

@@ -1,6 +1,6 @@
 /*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (c) 2023 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Copyright (c) 2024 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
  * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 
@@ -27,11 +27,11 @@
  * @version 1.2
  */
 public class Main {
-
+    //
     private Main() {
-
+        // only created because JavaDoc task complained.
     }
-
+    //
     /**
      * Starts the application. Command line arguments must be the name of an SD-file to read (must be located in the
      * same directory as the application's .jar file) and the number of different threads to use for calculation.
@@ -46,5 +46,4 @@ public static void main(String[] args) {
             System.exit(1);
         }
     }
-
 }