Added the missing S.2minus atom type for selenide

Change-Id: Ia53e8e981b471f9cb77ed022cd46581092fe01a5 Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Oct 30, 2012 · b7d2ae6 · b7d2ae6
1 parent 23e26b9
commit b7d2ae6
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -290,6 +290,10 @@ private IAtomType perceiveSelenium(IAtomContainer atomContainer, IAtom atom) thr
                     && atomContainer.getConnectedAtomsCount(atom) == 3) {
                 IAtomType type = getAtomType("Se.plus.3");
                 if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if ((atom.getFormalCharge() != CDKConstants.UNSET && atom.getFormalCharge() == -2)
+                    && atomContainer.getConnectedAtomsCount(atom) == 0) {
+                IAtomType type = getAtomType("Se.2minus");
+                if (isAcceptable(atom, atomContainer, type)) return type;
             }
         }
         return null;

diff --git a/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl b/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl
@@ -2158,6 +2158,14 @@
     <at:lonePairCount>0</at:lonePairCount>
   </at:AtomType> 
 
+  <at:AtomType rdf:ID="Se.2minus">
+    <at:formalCharge>-2</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Se"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:lonePairCount>4</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+  </at:AtomType> 
+
   <at:AtomType rdf:ID="Se.plus.3">
     <at:formalCharge>1</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Se"/>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -568,6 +568,17 @@ public void testTetrahydropyran() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test public void testSelenide() throws Exception {
+        IMolecule mol = DefaultChemObjectBuilder.getInstance().newInstance(IMolecule.class);
+        IAtom se = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"Se");
+        se.setImplicitHydrogenCount(0);
+        se.setFormalCharge(-2);
+        mol.addAtom(se);
+
+        String[] expectedTypes = {"Se.2minus"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test public void testH2S_Hybridization() throws Exception {
         IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
         IAtom s = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"S");