Merge 27 files: GameTheory, checks, mechanism helpers/enums (88→64 files)

- mapping/algorithm: 7 GameTheory files → GameTheoryEngine.java
- mapping/algorithm: 6 check files → MappingChecks.java
- mechanism: 9 helper files → MechanismHelpers.java
- mechanism: 5 enum/abstract files → BondChangeCalculator.java inner types

345 → 64 files (81% reduction). All tests pass.

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

Author: asad

src/main/java/com/bioinceptionlabs/aamtool/Annotator.java

@@ -18,6 +18,8 @@
  */
 package com.bioinceptionlabs.aamtool;
 
+
+import com.bioinceptionlabs.reactionblast.mechanism.MechanismHelpers;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
@@ -49,7 +51,6 @@
 import com.bioinceptionlabs.reactionblast.mechanism.BondChangeCalculator;
 import com.bioinceptionlabs.reactionblast.mechanism.MappingSolution;
 import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
-import com.bioinceptionlabs.reactionblast.mechanism.MoleculeMoleculePair;
 import static com.bioinceptionlabs.reactionblast.tools.ReactionSimilarityTool.getSimilarity;
 import com.bioinceptionlabs.reactionblast.tools.StandardizeReaction;
 
@@ -224,27 +225,27 @@ private void printRPAIRPatternAsText(MappingSolution s, StringBuilder sb) throws
             index++;
         }
 
-        Collection<MoleculeMoleculePair> reactionTransform = s.getBondChangeCalculator().getReactionCentreTransformationPairs();
+        Collection<MechanismHelpers.MoleculeMoleculePair> reactionTransform = s.getBondChangeCalculator().getReactionCentreTransformationPairs();
 
         StringBuilder pair1 = new StringBuilder();
         index = 1;
-        for (MoleculeMoleculePair m : reactionTransform) {
+        for (MechanismHelpers.MoleculeMoleculePair m : reactionTransform) {
             pair1.append(index).append(": ").append(m.getSmirks1());
             pair1.append(NEW_LINE);
             index++;
         }
 
         StringBuilder pair2 = new StringBuilder();
         index = 1;
-        for (MoleculeMoleculePair m : reactionTransform) {
+        for (MechanismHelpers.MoleculeMoleculePair m : reactionTransform) {
             pair2.append(index).append(": ").append(m.getSmirks2());
             pair2.append(NEW_LINE);
             index++;
         }
 
         StringBuilder pair3 = new StringBuilder();
         index = 1;
-        for (MoleculeMoleculePair m : reactionTransform) {
+        for (MechanismHelpers.MoleculeMoleculePair m : reactionTransform) {
             pair3.append(index).append(": ").append(m.getSmirks3());
             pair3.append(NEW_LINE);
             index++;
@@ -365,7 +366,7 @@ private void printRPAIRPatternAsXML(MappingSolution s, org.w3c.dom.Document doc,
             }
         });
 
-        Collection<MoleculeMoleculePair> reactionTransform = s.getBondChangeCalculator().getReactionCentreTransformationPairs();
+        Collection<MechanismHelpers.MoleculeMoleculePair> reactionTransform = s.getBondChangeCalculator().getReactionCentreTransformationPairs();
 
         //Start of Fingerprint elements
         org.w3c.dom.Element transform = doc.createElement("TRANSFORMATION");
@@ -378,7 +379,7 @@ private void printRPAIRPatternAsXML(MappingSolution s, org.w3c.dom.Document doc,
 
         int index = 1;
 
-        for (MoleculeMoleculePair m : reactionTransform) {
+        for (MechanismHelpers.MoleculeMoleculePair m : reactionTransform) {
             // RAIR elements
             org.w3c.dom.Element rpairMATCH = doc.createElement("MMP" + index);
             rpairMATCH.appendChild(doc.createTextNode(m.getSmirks1()));
@@ -396,7 +397,7 @@ private void printRPAIRPatternAsXML(MappingSolution s, org.w3c.dom.Document doc,
         transform.setAttributeNode(attr);
         index = 1;
 
-        for (MoleculeMoleculePair m : reactionTransform) {
+        for (MechanismHelpers.MoleculeMoleculePair m : reactionTransform) {
             // RAIR elements
             org.w3c.dom.Element rpairMATCH = doc.createElement("MMP" + index);
             rpairMATCH.appendChild(doc.createTextNode(m.getSmirks2()));
@@ -414,7 +415,7 @@ private void printRPAIRPatternAsXML(MappingSolution s, org.w3c.dom.Document doc,
         transform.setAttributeNode(attr);
         index = 1;
 
-        for (MoleculeMoleculePair m : reactionTransform) {
+        for (MechanismHelpers.MoleculeMoleculePair m : reactionTransform) {
             // RAIR elements
             org.w3c.dom.Element rpairMATCH = doc.createElement("MMP" + index);
             rpairMATCH.appendChild(doc.createTextNode(m.getSmirks3()));

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

@@ -8,7 +8,7 @@
 import com.bioinceptionlabs.reactionblast.mapping.ReactionContainer.MoleculeMoleculeMapping;
 import com.bioinceptionlabs.reactionblast.mapping.ReactionContainer;
 import com.bioinceptionlabs.reactionblast.mapping.algorithm.CalculationProcess;
-import com.bioinceptionlabs.reactionblast.mapping.algorithm.ChooseWinner;
+import com.bioinceptionlabs.reactionblast.mapping.algorithm.MappingChecks;
 import com.bioinceptionlabs.reactionblast.mapping.algorithm.Holder;
 import com.bioinceptionlabs.reactionblast.tools.CDKSMILES;
 import com.bioinceptionlabs.reactionblast.tools.EBIMatrix;
@@ -1289,7 +1289,7 @@ protected void printSimMatrix(Holder mh, List<String> EdMap, List<String> PdMap)
          * @param EdMap
          * @param PdMap
          */
-        protected void printFlagMatrix(ChooseWinner winner, List<String> EdMap, List<String> PdMap) {
+        protected void printFlagMatrix(MappingChecks.ChooseWinner winner, List<String> EdMap, List<String> PdMap) {
 
             StringBuilder sb = new StringBuilder();
             sb.append(NEW_LINE);