Gd final

cdk · Sep 3, 2011 · 770dc99 · 770dc99
1 parent ef34cca
commit 770dc99
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -2085,6 +2085,18 @@ private IAtomType perceiveAntimony(IAtomContainer atomContainer, IAtom atom) thr
         }
         return null;
     }
+
+    private IAtomType perceiveGadolinum(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (atom.getFormalCharge() != CDKConstants.UNSET &&
+            atom.getFormalCharge() == +3 &&
+            atomContainer.getConnectedBondsCount(atom) == 0) {
+            IAtomType type = getAtomType("Gd.3plus");
+            if (isAcceptable(atom, atomContainer, type)) {
+                return type;
+            }
+        }
+        return null;
+    }
 
     private int countAttachedDoubleBonds(IAtomContainer container, IAtom atom) {
     	return countAttachedDoubleBonds(container, atom, 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
@@ -1920,6 +1920,14 @@
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
 
+  <at:AtomType rdf:ID="Gd.3plus">
+    <at:formalCharge>3</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Gd"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>
+
   <at:AtomType rdf:ID="Sb.3">
     <at:formalCharge>0</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Sb"/>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3955,6 +3955,18 @@ public void testMethylphosphinicAcid() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test
+    public void test_Gd_3plus() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Gd");
+        a1.setFormalCharge(3);
+        mol.addAtom(a1);
+
+        String[] expectedTypes = {"Gd.3plus"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test
     public void test_Mo_4() throws Exception {
         IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();