Sr final

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Sep 4, 2011 · 458d1aa · 458d1aa
1 parent 6207b4f
commit 458d1aa
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -147,6 +147,8 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
             type = perceiveGadolinum(atomContainer, atom);
         } else if ("Ge".equals(atom.getSymbol())) {
             type = perceiveGermanium(atomContainer, atom);
+        } else if ("Sr".equals(atom.getSymbol())) {
+            type = perceiveStrontium(atomContainer, atom);
         } else if ("Pb".equals(atom.getSymbol())) {
             type = perceiveLead(atomContainer, atom);
         } else if ("Tl".equals(atom.getSymbol())) {
@@ -2173,6 +2175,17 @@ private IAtomType perceiveLead(IAtomContainer atomContainer, IAtom atom) throws
         }
         return null;
     }
+
+    private IAtomType perceiveStrontium(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (hasOneSingleElectron(atomContainer, atom)) {
+            return null;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET
+                && atom.getFormalCharge() == 2)) {
+            IAtomType type = getAtomType("Sr.2plus");
+            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
@@ -1941,6 +1941,14 @@
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
 
+    <at:AtomType rdf:ID="Sr.2plus">
+    <at:formalCharge>2</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Sr"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>
+
     <at:AtomType rdf:ID="Pb.neutral">
     <at:formalCharge>0</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Pb"/>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3737,6 +3737,20 @@ public void test_B_3plus() throws Exception {
         String[] expectedTypes = {"B.3plus", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
+
+
+    @Test
+    public void test_Sr_2plus() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Sr");
+        a1.setFormalCharge(2);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Sr.2plus"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
 
     @Test
     public void test_Te_4plus() throws Exception {