Add CHARGE_TRANSFER/RADICAL_CHANGE flags, remove last DEBUG guards

- Add CHARGE_TRANSFER (14) and RADICAL_CHANGE (15) to
  ECBLAST_BOND_CHANGE_FLAGS enum for extended R-matrix support
- Remove unused DEBUG boolean from Reactor.java (5 guards → direct LOGGER)
- Remove unused DEBUG boolean from TestUtility.java
- Remove unused generic() import from Reactor.java
- Remove stale SMILES generation in Reactor debug path

135/135 tests pass.

Author: asad

src/main/java/com/bioinceptionlabs/reactionblast/mapping/Reactor.java

@@ -41,7 +41,6 @@
 import static org.openscience.cdk.interfaces.IReaction.Direction.BIDIRECTIONAL;
 import org.openscience.cdk.layout.StructureDiagramGenerator;
 import org.openscience.cdk.smiles.SmilesGenerator;
-import static org.openscience.cdk.smiles.SmilesGenerator.generic;
 import static org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator.getTotalFormalCharge;
 import com.bioinceptionlabs.reactionblast.mapping.algorithm.CalculationProcess;
 import com.bioinceptionlabs.reactionblast.mapping.container.MoleculeMoleculeMapping;
@@ -74,7 +73,6 @@
  */
 public class Reactor extends AbstractReactor implements Serializable {
 
-    private static final boolean DEBUG = false;
     private static final long serialVersionUID = 197816786981017L;
     private final static ILoggingTool LOGGER
             = createLoggingTool(Reactor.class);
@@ -146,22 +144,16 @@ public class Reactor extends AbstractReactor implements Serializable {
         LOGGER.debug("|++++++++++++++++++++++++++++|");
         LOGGER.debug("|i. Reactor Initialized");
         cleanMapping(reaction);
-        if (DEBUG) {
-            LOGGER.debug("|++++++++++++++++++++++++++++|");
-            printReaction(reaction);
-            LOGGER.debug("|ii. Create Mapping Objects");
-        }
+        LOGGER.debug("|++++++++++++++++++++++++++++|");
+        printReaction(reaction);
+        LOGGER.debug("|ii. Create Mapping Objects");
         copyReferenceReaction(reaction);
         expandReaction();
         checkReactionBalance();
         LOGGER.debug("|iii. Compute atom-atom Mappings");
         calculateAtomAtomMapping();
-        if (DEBUG) {
-            printReaction(reactionWithUniqueSTOICHIOMETRY);
-            LOGGER.debug("|++++++++++++++++++++++++++++|");
-            LOGGER.debug("|iv. Done|");
-            LOGGER.debug("|++++++++++++++++++++++++++++|" + NEW_LINE + NEW_LINE);
-        }
+        printReaction(reactionWithUniqueSTOICHIOMETRY);
+        LOGGER.debug("|iv. Done|");
     }
 
     @Override
@@ -1099,14 +1091,11 @@ public IMappingAlgorithm getAlgorithm() {
     private IAtomContainer prepareMol(IAtomContainer cloneMolecule)
             throws CloneNotSupportedException, CDKException {
 
-        if (DEBUG) {
-            LOGGER.debug("Orignal");
-            printAtoms(cloneMolecule);
-        }
+        LOGGER.debug("Original");
+        printAtoms(cloneMolecule);
         /*
         Use the Canonical labelling from the SMILES
         IMP: Suggested by John May
-        It throws java.util.concurrent.ExecutionException
          */
         int[] p = new int[cloneMolecule.getAtomCount()];
 
@@ -1119,10 +1108,8 @@ private IAtomContainer prepareMol(IAtomContainer cloneMolecule)
         }
         permuteWithoutClone(p, cloneMolecule);
 
-        if (DEBUG) {
-            LOGGER.debug("mol after: ");
-            printAtoms(cloneMolecule);
-        }
+        LOGGER.debug("mol after: ");
+        printAtoms(cloneMolecule);
 
         /*
         Generate 2D Diagram without cloning
@@ -1147,13 +1134,8 @@ private IAtomContainer prepareMol(IAtomContainer cloneMolecule)
             atom.setID("-1");
         }
 
-        if (DEBUG) {
-            LOGGER.debug("Processed");
-            printAtoms(cloneMolecule);
-            LOGGER.debug("canonicalMolecule: "
-                    + generic().create(cloneMolecule)
-                    + NEW_LINE + NEW_LINE);
-        }
+        LOGGER.debug("Processed");
+        printAtoms(cloneMolecule);
 
         return cloneMolecule;
     }

src/main/java/com/bioinceptionlabs/reactionblast/mechanism/interfaces/ECBLAST_BOND_CHANGE_FLAGS.java

@@ -55,6 +55,14 @@ public enum ECBLAST_BOND_CHANGE_FLAGS {
      * BONDCHANGEORDERREDUCED
      */
     BOND_ORDER_REDUCED(13, "BOND_CHANGE_ORDER_REDUCED"),
+    /**
+     * Formal charge transfer between atoms (e.g., protonation/deprotonation)
+     */
+    CHARGE_TRANSFER(14, "CHARGE_TRANSFER"),
+    /**
+     * Radical (unpaired electron) change
+     */
+    RADICAL_CHANGE(15, "RADICAL_CHANGE"),
     /**
      * BONDCHANGEPSEUDOBOND
      */

src/main/java/com/bioinceptionlabs/reactionblast/tools/TestUtility.java

@@ -55,7 +55,6 @@ public class TestUtility {
     public static final String MACIE_RXN = "rxn/macie/";
     private final static ILoggingTool LOGGER
             = createLoggingTool(TestUtility.class);
-    private static final boolean DEBUG = false;
 
     /**
      *
@@ -95,14 +94,12 @@ protected IReaction readReactionFile(String name, String dir, boolean reMap, boo
         try (MDLRXNV2000Reader reader = new MDLRXNV2000Reader(getFileWithUtil(filepath))) {
             reaction = reader.read(new Reaction());
             reaction.setID(name);
-            if (DEBUG) {
-                LOGGER.debug("Read Reaction ");
-                for (IAtomContainer ac : reaction.getReactants().atomContainers()) {
-                    LOGGER.debug("r " + ac.getTitle() + ":" + reaction.getReactantCoefficient(ac));
-                }
-                for (IAtomContainer ac : reaction.getProducts().atomContainers()) {
-                    LOGGER.debug("p " + ac.getTitle() + ":" + reaction.getProductCoefficient(ac));
-                }
+            LOGGER.debug("Read Reaction ");
+            for (IAtomContainer ac : reaction.getReactants().atomContainers()) {
+                LOGGER.debug("r " + ac.getTitle() + ":" + reaction.getReactantCoefficient(ac));
+            }
+            for (IAtomContainer ac : reaction.getProducts().atomContainers()) {
+                LOGGER.debug("p " + ac.getTitle() + ":" + reaction.getProductCoefficient(ac));
             }
         } catch (Exception ex) {
             LOGGER.error(SEVERE, "Unable to parse the RXN file", ex.getMessage());