optimised the mapping code - speed up the code

Author: asad

src/test/java/org/openscience/smsd/algorithm/mcsplus1/MCSTest.java

@@ -11,6 +11,9 @@
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.smsd.AtomAtomMapping;
+import org.openscience.smsd.Isomorphism;
+import org.openscience.smsd.interfaces.Algorithm;
 
 /**
  *
@@ -35,9 +38,9 @@ public void testSet_IMolecule_IMolecule() throws Exception {
         mcs.search_cliques();
         List<List<Integer>> overlaps = mcs.getFinalMappings();
         assertEquals(overlaps.size(), 2);
-        assertEquals((mcs.getFinalMappings().iterator().next().size() / 2), 7);
+        assertEquals(7, (mcs.getFinalMappings().iterator().next().size() / 2));
     }
-    
+
     /**
      * Test of set method, of class MCSPlusHandler.
      *
@@ -51,11 +54,61 @@ public void testSet_count() throws Exception {
         IAtomContainer target = sp.parseSmiles("*[P](=O)(O)OCC1O[CH]C(OC(=O)C(N)CC2=CC=C(O)C=C2)C1O");
 
         org.openscience.smsd.algorithm.mcsplus.mcsplus1.MCSPlus mcs
-                    = new org.openscience.smsd.algorithm.mcsplus.mcsplus1.MCSPlus(query, target, true, false, false);
-            mcs.search_cliques();
+                = new org.openscience.smsd.algorithm.mcsplus.mcsplus1.MCSPlus(query, target, true, false, false);
+        mcs.search_cliques();
         List<List<Integer>> overlaps = mcs.getFinalMappings();
         assertEquals(overlaps.size(), 1);
-        assertEquals((mcs.getFinalMappings().iterator().next().size() / 2), 9);
+        assertEquals(9, (mcs.getFinalMappings().iterator().next().size() / 2));
+    }
+
+    /**
+     * Test of set method, of class MCSPlusHandler.
+     *
+     * @throws Exception
+     */
+    @Test
+    public void test_MCS_count() throws Exception {
+        ////////System.out.println("3");
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        //CHEBI:58504
+        IAtomContainer query = sp.parseSmiles("CC1=C2N3[C@H]([C@H](CC(N)=O)[C@@]2"
+                + "(C)CCC([O-])=O)[C@]2(C)[N+]4=C([C@@H](CCC(N)=O)[C@]2(C)CC(N)=O)"
+                + "C(C)=C2[N+]5=C(C=C6[N+](=C1[C@@H](CCC(N)=O)C6(C)C)[Co--]345"
+                + "C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc3c(N)ncnc13)[C@@H]"
+                + "(CCC(N)=O)[C@]2(C)CC(N)=O");
+        //CHEBI:2480
+        IAtomContainer target = sp.parseSmiles("[H][C@@]12[C@H](CC(N)=O)[C@@](C)"
+                + "(CCC(=O)NC[C@@H](C)O)C3=C(C)C4=[N+]5C(=CC6=[N+]7C(=C(C)C8=[N+]"
+                + "([C@]1(C)[C@@](C)(CC(N)=O)[C@@H]8CCC(N)=O)[Co--]57(C[C@H]1O[C@H]"
+                + "([C@H](O)[C@@H]1O)n1cnc5c(N)ncnc15)N23)[C@@](C)(CC(N)=O)"
+                + "[C@@H]6CCC(N)=O)C(C)(C)[C@@H]4CCC(N)=O");
+
+        Isomorphism mcs
+                //= new Isomorphism(query, target, Algorithm.VFLibMCS, true, true, true);
+                = new Isomorphism(query, target, Algorithm.DEFAULT, false, false, false);
+
+        List<AtomAtomMapping> allAtomMapping = mcs.getAllAtomMapping();
+        assertEquals(81, mcs.getFirstAtomMapping().getCount());
+    }
+
+    @Test
+    public void test_VFMCS_count() throws Exception {
+        ////////System.out.println("3");
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+//        IAtomContainer query = sp.parseSmiles("*C1OC(CO)C(OP=O)C1O");
+//        IAtomContainer target = sp.parseSmiles("*[P](=O)(O)OCC1O[CH]C(OC(=O)C(N)CC2=CC=C(O)C=C2)C1O");
+
+        IAtomContainer query = sp.parseSmiles("[N].[N]=C[N].[CH].[O].[NH2]");
+        IAtomContainer target = sp.parseSmiles("[C]C(=O)N.[N].[N]C=[N].[NH2]");
+
+        Isomorphism mcs
+                //= new Isomorphism(query, target, Algorithm.VFLibMCS, true, true, true);
+                = new Isomorphism(query, target, Algorithm.VFLibMCS, false, false, false);
+
+        System.out.println("mcs.getFirstAtomMapping() " + mcs.getFirstAtomMapping());
+        List<AtomAtomMapping> allAtomMapping = mcs.getAllAtomMapping();
+        // assertEquals(2, allAtomMapping.size());
+        assertEquals(7, mcs.getFirstAtomMapping().getCount());
     }
 
 }

src/test/java/uk/ac/ebi/aamtool/RXNMappingTest.java

@@ -1798,18 +1798,18 @@ public void Rhea10570() throws Exception {
     /*
      * @FIXME
      * Takes Donkey Years to Run- TO FIX
-     *12573
+     * 12573
      *
      */
-//    @Test
-//    public void Rhea12573() throws Exception {
-//
-//        String reactionID = "12573";
-//        ReactionMechanismTool testReactions = testReactions(reactionID, RHEA_RXN_DIR);
-//        IPatternFingerprinter formedCleavedWFingerprint = testReactions
-//                .getSelectedSolution()
-//                .getBondChangeCalculator()
-//                .getFormedCleavedWFingerprint();
-//        assertEquals(1, formedCleavedWFingerprint.getFeatureCount());
-//    }
+    @Test
+    public void Rhea12573() throws Exception {
+
+        String reactionID = "12573";
+        ReactionMechanismTool testReactions = testReactions(reactionID, RHEA_RXN_DIR);
+        IPatternFingerprinter formedCleavedWFingerprint = testReactions
+                .getSelectedSolution()
+                .getBondChangeCalculator()
+                .getFormedCleavedWFingerprint();
+        assertEquals(4, formedCleavedWFingerprint.getFeatureCount());
+    }
 }