Turbo mode MCS search added Signed-off-by: Syed Asad Rahman <s9asad@g…

…mail.com> Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · May 17, 2010 · 8ac67bf · 8ac67bf
1 parent ea4960c
commit 8ac67bf
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Showing 2 changed files with 31 additions and 2 deletions.
diff --git a/src/main/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithms.java b/src/main/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithms.java
@@ -146,6 +146,9 @@ private void chooseAlgorithm(int rBondCount, int pBondCount) {
             case VFLibMCS:
                 vfLibMCSAlgorithm(rBondCount, pBondCount);
                 break;
+            case TURBOMCS:
+                vfLibTurboMCSAlgorithm(rBondCount, pBondCount);
+                break;
         }
     }
 
@@ -225,6 +228,20 @@ private void vfLibMCS() {
         allAtomMCS.addAll(mcs.getAllAtomMapping());
     }
 
+    private void vfLibTurboMCS() {
+        VFlibMCSHandler mcs = null;
+        mcs = new VFlibMCSHandler();
+        mcs.set(rMol, pMol);
+        mcs.searchMCS();
+
+        clearMaps();
+        firstSolution.putAll(mcs.getFirstMapping());
+        allMCS.addAll(mcs.getAllMapping());
+
+        firstAtomMCS.putAll(mcs.getFirstAtomMapping());
+        allAtomMCS.addAll(mcs.getAllAtomMapping());
+    }
+
     private void singleMapping() {
         SingleMappingHandler mcs = null;
 
@@ -307,6 +324,14 @@ private void vfLibMCSAlgorithm(int rBondCount, int pBondCount) {
         }
     }
 
+    private void vfLibTurboMCSAlgorithm(int rBondCount, int pBondCount) {
+        if (rBondCount >= 6 && pBondCount >= 6) {
+            vfLibTurboMCS();
+        } else {
+            mcsPlusAlgorithm();
+        }
+    }
+
     private void setTime(boolean bondTypeFlag) {
         if (bondTypeFlag) {
             TimeOut tmo = TimeOut.getInstance();
@@ -377,6 +402,7 @@ public void init(IAtomContainer Reactant, IAtomContainer Product, boolean remove
         this.pMol = new MolHandler(Product, false, removeHydrogen);
         init(rMol, pMol, removeHydrogen);
     }
+
     /**
      * Initialize the query and target mol via mol files
      * @param sourceMolFileName

diff --git a/src/main/org/openscience/cdk/smsd/interfaces/Algorithm.java b/src/main/org/openscience/cdk/smsd/interfaces/Algorithm.java
@@ -41,7 +41,6 @@
  * @cdk.githash
  * @author Syed Asad Rahman <asad@ebi.ac.uk>
  */
-
 @TestClass("org.openscience.cdk.smsd.interfaces.AlgorithmTest")
 public enum Algorithm {
 
@@ -61,10 +60,14 @@ public enum Algorithm {
      * CDK UIT MCS.
      */
     CDKMCS(3, "CDK UIT MCS"),
+    /**
+     * Turbo Mode based MCS search.
+     */
+    TURBOMCS(4, "Turbo Mode based MCS search"),
     /**
      * Turbo Mode based Substructure search.
      */
-    SubStructure(4, "Turbo Mode based Substructure search");
+    SubStructure(5, "Turbo Mode based Substructure search");
     private final int type;
     private final String description;