Added rudimentary detection of the Co.oh atom type

Change-Id: I2379c9a886f731f72c0e4dfeb4d3511334e57291

Signed-off-by: John May <john.wilkinsonmay@gmail.com>

src/main/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java

@@ -124,6 +124,11 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
             if (neighbors > 4 && neighbors <= 6) return factory.getAtomType("Cr.oh");
             else if (neighbors > 0) return factory.getAtomType("Cr.th");
         }
+        else if ("Co".equals(atom.getSymbol())) {
+            // if only I had good descriptions of the Sybyl atom types
+            int neibors = atomContainer.getConnectedBondsCount(atom);
+            if (neibors == 6) return factory.getAtomType("Co.oh");
+        }
         if (type == null) return null;
         else atom.setAtomTypeName(type.getAtomTypeName());
         String mappedType = mapCDKToSybylType(atom);

src/test/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java

@@ -818,6 +818,21 @@ public void testCroh() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test
+    public void testCooh() throws Exception {
+        IAtomContainer mol = new AtomContainer();
+        // this is made up, and may be wrong; info on the web is sparse, and PubChem has no
+        // octa-coordinate structure; lone pairs involved?
+        IAtom a1 = new Atom("Co"); mol.addAtom(a1);
+        for (int i=0; i<6; i++) {
+            IAtom atom = new Atom("O");  mol.addAtom(atom);
+            mol.addBond(new Bond(a1, atom, IBond.Order.SINGLE));
+        }
+
+        String[] expectedTypes = {"Co.oh", "O.3", "O.3", "O.3", "O.3", "O.3", "O.3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @AfterClass
     public static void testTestedAtomTypes() throws Exception {
         countTestedAtomTypes(testedAtomTypes, factory);