Sb final

cdk · Sep 3, 2011 · 9b1fe00 · 9b1fe00
1 parent 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
@@ -145,6 +145,8 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
             type = perceiveGallium(atomContainer, atom);
         } else if ("Ge".equals(atom.getSymbol())) {
             type = perceiveGermanium(atomContainer, atom);
+        } else if ("Sb".equals(atom.getSymbol())) {
+            type = perceiveAntimony(atomContainer, atom);
         } else if ("Pt".equals(atom.getSymbol())) {
             type = perceivePlatinum(atomContainer, atom);
         } else if ("Hg".equals(atom.getSymbol())) {
@@ -2066,6 +2068,23 @@ private IAtomType perceivePlatinum(IAtomContainer atomContainer, IAtom atom) thr
         }
         return null;
     }
+
+    private IAtomType perceiveAntimony(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (hasOneSingleElectron(atomContainer, atom)) {
+            return null;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET &&
+                    atom.getFormalCharge() == 0 &&
+                    atomContainer.getConnectedBondsCount(atom) == 3)) {
+            IAtomType type = getAtomType("Sb.3");
+            if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET && 
+                    atom.getFormalCharge() == 0 &&
+                    atomContainer.getConnectedBondsCount(atom) == 4)) {
+            IAtomType type = getAtomType("Sb.4");
+            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
@@ -1919,6 +1919,24 @@
     <at:piBondCount>0</at:piBondCount>
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
+
+  <at:AtomType rdf:ID="Sb.3">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Sb"/>
+    <at:formalNeighbourCount>3</at:formalNeighbourCount>
+    <at:lonePairCount>1</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp3"/>
+    </at:AtomType> 
+
+    <at:AtomType rdf:ID="Sb.4">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Sb"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>1</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp3"/>
+  </at:AtomType> 
 
     <at:AtomType rdf:ID="Ra.neutral">
     <at:formalCharge>0</at:formalCharge>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3646,6 +3646,64 @@ public void testPentaMethylPhosphane() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test
+    public void test_Sb_4() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"C");
+        a1.setFormalCharge(0);
+        mol.addAtom(a1);
+        IAtom a2 = builder.newInstance(IAtom.class,"Sb");
+        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.SINGLE);
+        mol.addBond(b1);
+        IBond b2 = builder.newInstance(IBond.class,a2, a3, IBond.Order.SINGLE);
+        mol.addBond(b2);
+        IBond b3 = builder.newInstance(IBond.class,a2, a4, IBond.Order.SINGLE);
+        mol.addBond(b3);
+        IBond b4 = builder.newInstance(IBond.class,a2, a5, IBond.Order.DOUBLE);
+        mol.addBond(b4);
+
+        String[] expectedTypes = {"C.sp3", "Sb.4", "C.sp3", "C.sp3", "C.sp2"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Sb_3() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Sb");
+        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);
+        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);
+        IBond b3 = builder.newInstance(IBond.class,a1, a4, IBond.Order.SINGLE);
+        mol.addBond(b3);
+
+        String[] expectedTypes = {"Sb.3", "C.sp3", "C.sp3", "C.sp3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
 
     @Test
     public void test_B_3plus() throws Exception {