Mo final

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Sep 3, 2011 · a8c44bc · a8c44bc
1 parent cc46f63
commit a8c44bc
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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 ("Mo".equals(atom.getSymbol())) {
+            type = perceiveMolybdenum(atomContainer, atom);
         } else if ("Rb".equals(atom.getSymbol())) {
             type = perceiveRubidium(atomContainer, atom);
         } else if ("Te".equals(atom.getSymbol())) {
@@ -606,7 +608,23 @@ private IAtomType perceiveNitrogenRadicals(IAtomContainer atomContainer, IAtom a
         }
         return null;
     }
-
+    private IAtomType perceiveMolybdenum(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (atom.getFormalCharge() != CDKConstants.UNSET
+                && atom.getFormalCharge() == 0) {
+            int neighbors = atomContainer.getConnectedAtomsCount(atom);
+            if (neighbors == 4) {
+                IAtomType type = getAtomType("Mo.4");
+                if (isAcceptable(atom, atomContainer, type)) {
+                    return type;
+                }
+            }
+            IAtomType type1 = getAtomType("Mo.metallic");
+            if (isAcceptable(atom, atomContainer, type1)) {
+                return type1;
+            }
+        }
+        return null;
+    }
     private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) throws CDKException {
         // if hybridization is given, use that
         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
@@ -1862,6 +1862,20 @@
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
 
+ <at:AtomType rdf:ID="Mo.metallic">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Mo"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Mo.4">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Mo"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:piBondCount>2</at:piBondCount>
+    </at:AtomType> 
+
   <at:AtomType rdf:ID="Te.3">
     <at:formalCharge>0</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Te"/>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3896,6 +3896,52 @@ public void testMethylphosphinicAcid() throws Exception {
         };
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
+
+    @Test
+    public void test_Mo_4() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Mo");
+        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);
+        IAtom a4 = builder.newInstance(IAtom.class,"C");
+        a4.setFormalCharge(0);
+        mol.addAtom(a4);
+        IAtom a5 = builder.newInstance(IAtom.class,"C");
+        a5.setFormalCharge(0);
+        mol.addAtom(a5);
+        IBond b1 = builder.newInstance(IBond.class,a1, a2, IBond.Order.DOUBLE);
+        mol.addBond(b1);
+        IBond b2 = builder.newInstance(IBond.class,a1, a3, IBond.Order.DOUBLE);
+        mol.addBond(b2);
+        IBond b3 = builder.newInstance(IBond.class,a1, a4, IBond.Order.SINGLE);
+        mol.addBond(b3);
+        IBond b4 = builder.newInstance(IBond.class,a1, a5, IBond.Order.SINGLE);
+        mol.addBond(b4);
+
+
+        String[] expectedTypes = {"Mo.4", "C.sp2", "C.sp2", "C.sp3", "C.sp3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Mo_metallic() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Mo");
+        a1.setFormalCharge(0);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Mo.metallic"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
 
 
     @Test