Added four and six coordinate neutral platinum atom types.

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
egonw · Mar 28, 2010 · 407d793 · 407d793
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -1245,6 +1245,16 @@ private IAtomType perceiveCommonSalts(IAtomContainer atomContainer, IAtom atom)
     				atom.getFormalCharge() == +2)) {
     			IAtomType type = getAtomType("Pt.2plus");
     			if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if ((atom.getFormalCharge() == CDKConstants.UNSET ||
+                    atom.getFormalCharge() == 0)) {
+                int neighbors = atomContainer.getConnectedAtomsCount(atom);
+                if (neighbors == 4) {
+                    IAtomType type = getAtomType("Pt.4");
+                    if (isAcceptable(atom, atomContainer, type)) return type;
+                } else if (neighbors == 6) {
+                    IAtomType type = getAtomType("Pt.6");
+                    if (isAcceptable(atom, atomContainer, type)) return type;
+                }
     		}
     	} else if ("Ni".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
@@ -1177,7 +1177,21 @@
     <at:hasElement rdf:resource="&elem;Pt"/>
     <at:formalNeighbourCount>0</at:formalNeighbourCount>
     <at:piBondCount>0</at:piBondCount>
-    </at:AtomType>
+  </at:AtomType>
+
+  <at:AtomType rdf:ID="Pt.4">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Pt"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+  </at:AtomType>
+
+  <at:AtomType rdf:ID="Pt.6">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Pt"/>
+    <at:formalNeighbourCount>6</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+  </at:AtomType>
 
   <at:AtomType rdf:ID="Co.2plus">
     <at:formalCharge>2</at:formalCharge>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherSMILESTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherSMILESTest.java
@@ -94,4 +94,21 @@ public class CDKAtomTypeMatcherSMILESTest extends AbstractCDKAtomTypeTest {
             Assert.assertNotNull(type.getAtomTypeName());
         }
     }
+
+    @Test public void testPlatinum4() throws Exception {
+        String smiles1 = "Cl[Pt]1(Cl)(Cl)(Cl)NC2CCCCC2N1";
+
+        IMolecule mol1 = smilesParser.parseSmiles(smiles1);
+        Assert.assertEquals(13, mol1.getAtomCount());
+        Assert.assertEquals("Pt.6", mol1.getAtom(1).getAtomTypeName());
+    }
+
+    @Test public void testPlatinum6() throws Exception {
+        String smiles1 = "[Pt](Cl)(Cl)(N)N";
+
+        IMolecule mol1 = smilesParser.parseSmiles(smiles1);
+        Assert.assertEquals(5, mol1.getAtomCount());
+        Assert.assertEquals("Pt.4", mol1.getAtom(0).getAtomTypeName());
+    }
+
 }
diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3151,6 +3151,32 @@ public void testNOxide() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test public void testPlatinumFourCoordinate() throws Exception {
+        IMolecule mol = new Molecule();
+        mol.addAtom(new Atom("Pt"));
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,1,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,2,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,3,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,4,IBond.Order.SINGLE);
+
+        String[] expectedTypes = {"Pt.4", "Cl", "Cl", "Cl", "Cl"}; 
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test public void testPlatinumSixCoordinate() throws Exception {
+        IMolecule mol = new Molecule();
+        mol.addAtom(new Atom("Pt"));
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,1,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,2,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,3,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("Cl")); mol.addBond(0,4,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("O")); mol.addBond(0,5,IBond.Order.SINGLE);
+        mol.addAtom(new Atom("O")); mol.addBond(0,6,IBond.Order.SINGLE);
+
+        String[] expectedTypes = {"Pt.6", "Cl", "Cl", "Cl", "Cl", "O.sp3", "O.sp3"}; 
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     /**
      * @cdk.bug 2424511
      */