Cd final

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Aug 7, 2011 · 4d68c27 · 4d68c27
1 parent 0eebd74
commit 4d68c27
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Showing 3 changed files with 92 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -1677,6 +1677,27 @@ private IAtomType perceivePlutonium(IAtomContainer atomContainer, IAtom atom) th
         }
         return null;
     }
+
+    private IAtomType perceiveCadmium(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (hasOneSingleElectron(atomContainer, atom)) {
+            // no idea how to deal with this yet
+            return null;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET
+                && atom.getFormalCharge() == +2)) {
+            IAtomType type = getAtomType("Cd.2plus");
+            if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET
+                && atom.getFormalCharge() == 0)) {
+            if (atomContainer.getConnectedAtomsCount(atom) == 0) {
+                IAtomType type = getAtomType("Cd.metallic");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (atomContainer.getConnectedAtomsCount(atom) == 2) {
+                IAtomType type = getAtomType("Cd.2");
+                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
@@ -1670,4 +1670,26 @@
     <at:piBondCount>0</at:piBondCount>
     </at:AtomType>
 
+    <at:AtomType rdf:ID="Cd.metallic">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Cd"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Cd.2plus">
+    <at:formalCharge>2</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Cd"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Cd.2">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Cd"/>
+    <at:formalNeighbourCount>2</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp1"/>
+    </at:AtomType>
+
 </rdf:RDF>
diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3689,6 +3689,55 @@ public void testMethylphosphinicAcid() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test
+    public void test_Cd_2plus() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Cd");
+        a1.setFormalCharge(2);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Cd.2plus"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Cd_2() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Cd");
+        a1.setFormalCharge(0);
+        mol.addAtom(a1);
+        IAtom a2 = builder.newInstance(IAtom.class,"C");
+        a2.setFormalCharge(0);
+        mol.addAtom(a2);
+        IAtom a3 = builder.newInstance(IAtom.class,"C");
+        a3.setFormalCharge(0);
+        mol.addAtom(a3);
+        IBond b1 = builder.newInstance(IBond.class,a1, a2, IBond.Order.SINGLE);
+        mol.addBond(b1);
+        IBond b2 = builder.newInstance(IBond.class,a1, a3, IBond.Order.SINGLE);
+        mol.addBond(b2);
+
+
+        String[] expectedTypes = {"Cd.2", "C.sp3", "C.sp3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Cd_metallic() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Cd");
+        a1.setFormalCharge(0);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Cd.metallic"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test
     public void test_Pu() throws Exception {
         IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
@@ -3697,7 +3746,6 @@ public void test_Pu() throws Exception {
         a1.setFormalCharge(0);
         mol.addAtom(a1);
 
-
         String[] expectedTypes = {"Pu"};
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }