Merge 10 small classes into consumers (68 files total)

Mapping package: merged Cache, IKey, IResult, IGameTheory,
IGraphTheoryMatrix, AbstractGraphMatching, MappingThread into
their primary consumers (ThreadSafeCache, ReactionContainer,
MappingChecks, GameTheoryEngine, GraphMatcher, CallableAtomMappingTool).

Mechanism package: merged StereoChange into DUModel,
StereoCenteralityTool into DUModel, CaseHandler into CalculationProcess.

IMappingAlgorithm kept standalone (9+ consumers across packages).

345 → 68 Java files (80% reduction). 150/150 tests pass.

Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>

Author: asad

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

@@ -286,4 +286,37 @@ private void putSolution(IMappingAlgorithm choice, Reactor reactor) {
         this.solution.put(choice, reactor);
     }
 
+    /**
+     * @author Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
+     */
+    static class MappingThread implements java.util.concurrent.Callable<Reactor> {
+
+        private static final ILoggingTool MT_LOGGER = createLoggingTool(MappingThread.class);
+
+        private final IReaction cleanedReaction;
+        private final IMappingAlgorithm algorithm;
+        private final boolean removeHydrogen;
+
+        MappingThread(String message, IReaction cleanedReaction,
+                IMappingAlgorithm algorithm, boolean removeHydrogen) {
+            this.cleanedReaction = cleanedReaction;
+            this.algorithm = algorithm;
+            this.removeHydrogen = removeHydrogen;
+            MT_LOGGER.info("|++++++++++++++++++++++++++++|");
+            MT_LOGGER.info("|Atom Atom Mapping Tool Initialized for " + message);
+        }
+
+        @Override
+        public Reactor call() throws Exception {
+            try {
+                Reactor reactor;
+                reactor = new Reactor(cleanedReaction, removeHydrogen, algorithm);
+                MT_LOGGER.info("|Done " + reactor.getAlgorithm() + " |");
+                return reactor;
+            } catch (Exception ex) {
+                throw ex;
+            }
+        }
+    }
+
 }

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

@@ -4,7 +4,6 @@
  */
 package com.bioinceptionlabs.reactionblast.mapping;
 
-import com.bioinceptionlabs.reactionblast.mapping.AbstractGraphMatching;
 import com.bioinceptionlabs.reactionblast.mapping.BestMatch;
 import com.bioinceptionlabs.reactionblast.mapping.Reactor.Debugger;
 import com.bioinceptionlabs.reactionblast.mapping.IMappingAlgorithm;
@@ -77,6 +76,28 @@
  */
 public class GraphMatcher extends Debugger {
 
+    /**
+     * @author Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
+     */
+    public static abstract class AbstractGraphMatching {
+
+        public static void setMCSUpdationFlags(Holder holder, int substrateIndex, int productIndex) throws Exception {
+            ReactionContainer reactionStructureInformation = holder.getReactionContainer();
+            reactionStructureInformation.setEductModified(substrateIndex, true);
+            reactionStructureInformation.setProductModified(productIndex, true);
+        }
+
+        public abstract IAtomContainer getMatchedPart();
+
+        public abstract IAtomContainer getRemainingEduct();
+
+        public abstract IAtomContainer getRemainingProduct();
+
+        public abstract boolean mcsMatch(Holder holder, boolean removeHydrogen, Integer I, Integer J, BitSet eductFP, BitSet prodFP);
+
+        public abstract int removeMatchedAtomsAndUpdateAAM(IReaction reaction);
+    }
+
     private static final int LARGE_JOB_THRESHOLD = 1000;
     private final static ILoggingTool LOGGER
             = createLoggingTool(GraphMatcher.class);