Added Ag+ and Ag-* atom types (addressing #3388240)

cdk · Sep 10, 2011 · 033fb9f · 033fb9f
1 parent d98ec5b
commit 033fb9f
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Showing 3 changed files with 56 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -2045,8 +2045,17 @@ private IAtomType perceiveSilver(IAtomContainer atomContainer, IAtom atom) throw
             return null;
         } else if ((atom.getFormalCharge() != CDKConstants.UNSET
                 && atom.getFormalCharge() == 0)) {
+            int neighbors = atomContainer.getConnectedAtomsCount(atom);
+            if (neighbors == 1) {
+                IAtomType type = getAtomType("Ag.1");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            }
             IAtomType type = getAtomType("Ag.neutral");
             if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET
+                && atom.getFormalCharge() == 1)) {
+            IAtomType type = getAtomType("Ag.plus");
+            if (isAcceptable(atom, atomContainer, type)) return type;
         }
         return 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
@@ -2136,7 +2136,21 @@
     <at:formalNeighbourCount>0</at:formalNeighbourCount>
     <at:piBondCount>0</at:piBondCount>
     </at:AtomType>
-
+
+  <at:AtomType rdf:ID="Ag.plus">
+    <at:formalCharge>+1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Ag"/>
+    <at:formalNeighbourCount>0</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+  </at:AtomType>
+
+  <at:AtomType rdf:ID="Ag.1">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Ag"/>
+    <at:formalNeighbourCount>1</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+  </at:AtomType>
+
     <at:AtomType rdf:ID="Ge.3">
     <at:formalCharge>0</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Ge"/>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -4725,6 +4725,38 @@ public void test_Ag_neutral() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    /**
+     * For example PubChem CID 3808730.
+     */
+    @Test
+    public void test_Ag_plus() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Ag");
+        a1.setFormalCharge(1);
+        mol.addAtom(a1);
+
+        String[] expectedTypes = {"Ag.plus"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    /**
+     * For example PubChem CID 139654.
+     */
+    @Test
+    public void test_Ag_covalent() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Ag");
+        mol.addAtom(a1);
+        IAtom a2 = builder.newInstance(IAtom.class,"Cl");
+        mol.addAtom(a2);
+        mol.addBond(0, 1, IBond.Order.SINGLE);
+
+        String[] expectedTypes = {"Ag.1", "Cl"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test
     public void test_In_3plus() throws Exception {
         IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();