added back in graph invarient tie-breaking fix

Author: tylerperyea

src/main/java/lychi/LyChIStandardizer.java

@@ -2934,18 +2934,18 @@ public static String[] hashKeyArray (Molecule input) {
 
         int[] fallbackLookup = new int[atno.length];
 
-//        try{
-//        	//set the tie-breaking priority based on the layer-3 information
-//	        Molecule stdLychi3Mol=getLayer3Equivalent(m1);
-//	        MolAtom[] matarr1=stdLychi3Mol.getAtomArray();
-//	        
-//	        for (int i = 0; i < atno.length; ++i) {
-//	        	fallbackLookup[matarr1[i].getAtomMap()-1]=i;
-//	        }
-//        }catch(Exception e){
-//        	 logger.log(Level.SEVERE, 
-//                     "Can't produce simplified structure from molecule", e);
-//        }
+        try{
+        	//set the tie-breaking priority based on the layer-3 information
+	        Molecule stdLychi3Mol=getLayer3Equivalent(m1);
+	        MolAtom[] matarr1=stdLychi3Mol.getAtomArray();
+	        
+	        for (int i = 0; i < atno.length; ++i) {
+	        	fallbackLookup[matarr1[i].getAtomMap()-1]=i;
+	        }
+        }catch(Exception e){
+        	 logger.log(Level.SEVERE, 
+                     "Can't produce simplified structure from molecule", e);
+        }
 
 
         for (int i = 0; i < atno.length; ++i) {

src/test/java/lychi/LychiRegressionTest.java

@@ -459,14 +459,14 @@ public static List<Object[]> data(){
 				"M  END","C1CCCCC1").name("meaningless stereo 1"));
 
 
-//		tests.add(LychiTestInstance.equivalentLayer3("[H][C@@](O)(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]([H])(O)C=O", "[H][C@](O)(C=O)[C@@]([H])(O)[C@]([H])(O)[C@]([H])(O)C([2H])([2H])O")
-//				                   .name("Hydrogen Isotope Same Layer 3")
-//				);
-//		
-//
-//		tests.add(LychiTestInstance.equivalentLayer3("[H][C@]1(CC(O)=O)CCC2=C1N(CC3=CC=C(Cl)C=C3)C4=C2C=C(F)C=C4S(C)(=O)=O", "CS(=O)(=O)C1=CC(F)=CC2=C1N(CC3=CC=C(Cl)C=C3)C4=C2CCC4CC(O)=O")
-//                                   .name("Strange graph invariant problem")
-//				);
+		tests.add(LychiTestInstance.equivalentLayer3("[H][C@@](O)(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]([H])(O)C=O", "[H][C@](O)(C=O)[C@@]([H])(O)[C@]([H])(O)[C@]([H])(O)C([2H])([2H])O")
+				                   .name("Hydrogen Isotope Same Layer 3")
+				);
+		
+
+		tests.add(LychiTestInstance.equivalentLayer3("[H][C@]1(CC(O)=O)CCC2=C1N(CC3=CC=C(Cl)C=C3)C4=C2C=C(F)C=C4S(C)(=O)=O", "CS(=O)(=O)C1=CC(F)=CC2=C1N(CC3=CC=C(Cl)C=C3)C4=C2CCC4CC(O)=O")
+                                   .name("Strange graph invariant problem")
+				);
 
 
 		//tests.add(LychiTestInstance.of("[H][C@](C)(CC)[C@]([H])(NC(=O)[C@]([H])(CCC(O)=O)N=C(O)[C@]([H])(CCC(O)=O)N=C(O)COCCOCCNC(=O)C1=CC2=C(C=C1)C3(OC2=O)C4=C(OC5=C3C=CC(O)=C5)C=C(O)C=C4)C(=O)N[C@@]([H])(CCCC)C(O)=N[C@@]([H])(CCCN=C(N)N)C(O)=N[C@@]([H])(CCCN=C(N)N)C(O)=NCCCOCC(COCCCN=C(O)[C@]([H])(CCCN=C(N)N)N=C(O)[C@]([H])(CCCN=C(N)N)N=C(O)[C@]([H])(CCCC)NC(=O)[C@@]([H])(NC(=O)[C@]([H])(CCC(O)=O)N=C(O)[C@]([H])(CCC(O)=O)N=C(O)COCCOCCNC(=O)C6=CC7=C(C=C6)C8(OC7=O)C9=C(OC%10=C8C=CC(O)=C%10)C=C(O)C=C9)[C@@]([H])(C)CC)(COCCCN=C(O)[C@]([H])(CCCN=C(N)N)N=C(O)[C@]([H])(CCCN=C(N)N)N=C(O)[C@]([H])(CCCC)NC(=O)[C@@]([H])(NC(=O)[C@]([H])(CCC(O)=O)N=C(O)[C@]([H])(CCC(O)=O)N=C(O)COCCOCCNC(=O)C%11=CC%12=C(C=C%11)C%13(OC%12=O)C%14=C(OC%15=C%13C=CC(O)=C%15)C=C(O)C=C%14)[C@@]([H])(C)CC)N=C(N)O","PY2Z7DXNU-UTQVUB5614-U4T1XF2AQV3-U43YSFQF6PCQ").name("big structure"));