Rb final

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Aug 12, 2011 · af5f764 · af5f764
1 parent 5ebe425
commit af5f764
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -131,6 +131,8 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
             type = perceiveChromium(atomContainer, atom);
         } else if ("Se".equals(atom.getSymbol())) {
             type = perceiveSelenium(atomContainer, atom);
+        } else if ("Rb".equals(atom.getSymbol())) {
+            type = perceiveRubidium(atomContainer, atom);
         } else if ("Te".equals(atom.getSymbol())) {
             type = perceiveTellurium(atomContainer, atom);
         } else if ("Ba".equals(atom.getSymbol())) {
@@ -1224,6 +1226,24 @@ private IAtomType perceiveThorium(IAtomContainer atomContainer, IAtom atom)
         return null;
     }
 
+    private IAtomType perceiveRubidium(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (hasOneSingleElectron(atomContainer, atom)) {
+            return null;
+        } else if (atom.getFormalCharge() != CDKConstants.UNSET
+                && atom.getFormalCharge() == +1) {
+            IAtomType type = getAtomType("Rb.plus");
+            if (isAcceptable(atom, atomContainer, type)) {
+                return type;
+            }
+        } else if (atom.getFormalCharge() != CDKConstants.UNSET
+                && atom.getFormalCharge() == 0) {
+            IAtomType type = getAtomType("Rb.neutral");
+            if (isAcceptable(atom, atomContainer, type)) {
+                return type;
+            }
+        }
+        return null;
+    }
     private IAtomType perceiveCommonSalts(IAtomContainer atomContainer, IAtom atom) throws CDKException {
         if ("Ca".equals(atom.getSymbol())) {
     		if (hasOneSingleElectron(atomContainer, atom)) {

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
@@ -1666,6 +1666,22 @@
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
 
+<at:AtomType rdf:ID="Rb.plus">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Rb"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType> 
+
+    <at:AtomType rdf:ID="Rb.neutral">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Rb"/>
+    <at:formalNeighbourCount>1</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>
+
   <at:AtomType rdf:ID="Se.3">
     <at:formalCharge>0</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
@@ -3751,6 +3751,32 @@ public void test_Cr_neutral() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test
+    public void test_Rb_neutral() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Rb");
+        a1.setFormalCharge(0);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Rb.neutral"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Rb_plus() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Rb");
+        a1.setFormalCharge(1);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Rb.plus"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test
     public void test_Cr_4() throws Exception {
         IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();