Tl final

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Sep 4, 2011 · ae54e0c · ae54e0c
1 parent 81ce6e5
commit ae54e0c
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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 ("Tl".equals(atom.getSymbol())) {
+            type = perceiveThallium(atomContainer, atom);
         } else if ("Sb".equals(atom.getSymbol())) {
             type = perceiveAntimony(atomContainer, atom);
         } else if ("Pt".equals(atom.getSymbol())) {
@@ -2129,6 +2131,26 @@ private IAtomType perceiveMagnesium(IAtomContainer atomContainer, IAtom atom) th
         }
         return null;
     }
+
+    private IAtomType perceiveThallium(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (atom.getFormalCharge() != CDKConstants.UNSET &&
+            atom.getFormalCharge() == +1 &&
+            atomContainer.getConnectedBondsCount(atom) == 0) {
+            IAtomType type = getAtomType("Tl.plus");
+            if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if (atom.getFormalCharge() != CDKConstants.UNSET &&
+                   atom.getFormalCharge() == 0 &&
+                   atomContainer.getConnectedBondsCount(atom) == 0) {
+            IAtomType type = getAtomType("Tl");
+            if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if (atom.getFormalCharge() != CDKConstants.UNSET &&
+                   atom.getFormalCharge() == 0 &&
+                   atomContainer.getConnectedBondsCount(atom) == 1) {
+            IAtomType type = getAtomType("Tl.1");
+            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 +1941,31 @@
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
 
+    <at:AtomType rdf:ID="Tl.plus">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Tl"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType> 
+
+    <at:AtomType rdf:ID="Tl.1">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Tl"/>
+    <at:formalNeighbourCount>1</at:formalNeighbourCount>
+    <at:lonePairCount>1</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp1"/>
+    </at:AtomType> 
+
+    <at:AtomType rdf:ID="Tl">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Tl"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+  </at:AtomType>
+
   <at:AtomType rdf:ID="Gd.3plus">
     <at:formalCharge>3</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Gd"/>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3954,6 +3954,51 @@ public void testMethylphosphinicAcid() throws Exception {
         };
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
+
+
+    @Test
+    public void test_Tl_neutral() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Tl");
+        a1.setFormalCharge(0);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Tl"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Tl_1() 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,"Tl");
+        a2.setFormalCharge(0);
+        mol.addAtom(a2);
+        IBond b1 = builder.newInstance(IBond.class,a1, a2, IBond.Order.SINGLE);
+        mol.addBond(b1);
+
+
+        String[] expectedTypes = {"C.sp3", "Tl.1"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Tl_plus() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Tl");
+        a1.setFormalCharge(1);
+        mol.addAtom(a1);
+
+
+        String[] expectedTypes = {"Tl.plus"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
 
     @Test
     public void test_Mg_neutral_2() throws Exception {