These atoms need to be recognised for creating extended tetrahedral (…

…allene) stereo elements. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jul 16, 2014 · cf00f01 · cf00f01
1 parent 8fea909
commit cf00f01
Showing 1 changed file with 9 additions and 3 deletions.
diff --git a/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java b/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java
@@ -71,7 +71,7 @@ public class StereocentersTest {
         none("C(C)");
         none("C(C)(N)");
         none("C(=C)(C)N");
-        none("C(=C)=C");
+        bicoordinate("C(=C)=C");
         none("C(=C)(=C)(=C)=C"); // nb abnormal valence
         none("C#N");
     }
@@ -675,8 +675,8 @@ public class StereocentersTest {
         geometric("C(=CC)C");    
         geometric("[CH](=CC)C");    
         geometric("C([H])(=CC)C");    
-        none("[CH2](=CC)");    
-        none("C(=C)(=CC)");    
+        none("[CH2](=CC)");
+        bicoordinate("C(=C)(=CC)");    
         none("C(#CC)C");    
     }  
 
@@ -719,6 +719,12 @@ void geometric(String smi) throws Exception {
         test(sp.parseSmiles(smi), Stereocenters.Type.Tricoordinate, smi + " was not accepted");
     }
 
+    // assert the first atom of the SMILES is accepted as a bicoordinate center
+    void bicoordinate(String smi) throws Exception {
+        SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        test(sp.parseSmiles(smi), Stereocenters.Type.Bicoordinate, smi + " was not accepted");
+    }
+
     // assert the first atom of the SMILES is non stereogenic
     void none(String smi) throws Exception {
         SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());