Mg final

cdk · Sep 4, 2011 · c562129 · c562129
1 parent 00e9aac
commit c562129
Show file tree

Hide file tree

Showing 3 changed files with 122 additions and 0 deletions.
diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -2100,6 +2100,34 @@ private IAtomType perceiveGadolinum(IAtomContainer atomContainer, IAtom atom) th
         return null;
     }
 
+    private IAtomType perceiveMagnesium(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        if (hasOneSingleElectron(atomContainer, atom)) {
+            // no idea how to deal with this yet
+            return null;
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET &&
+                    atom.getFormalCharge() == 0)) {
+            int neighbors = atomContainer.getConnectedAtomsCount(atom);
+            if (neighbors == 4) {
+                IAtomType type = getAtomType("Mg.neutral");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 2) {
+                IAtomType type = getAtomType("Mg.neutral.2");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else if (neighbors == 1) {
+                IAtomType type = getAtomType("Mg.neutral.1");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else {
+                IAtomType type = getAtomType("Mg.neutral");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            }
+        } else if ((atom.getFormalCharge() != CDKConstants.UNSET &&
+                atom.getFormalCharge() == +2)) {
+            IAtomType type = getAtomType("Mg.2plus");
+            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
@@ -1259,6 +1259,27 @@
     <at:lonePairCount>0</at:lonePairCount>
   </at:AtomType>
 
+    <at:AtomType rdf:ID="Mg.neutral.2">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Mg"/>
+    <at:formalNeighbourCount>2</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Mg.neutral.1">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Mg"/>
+    <at:formalNeighbourCount>1</at:formalNeighbourCount>
+    <at:piBondCount>1</at:piBondCount>
+    </at:AtomType>  
+
+    <at:AtomType rdf:ID="Mg.neutral">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Mg"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:piBondCount>0</at:piBondCount>
+    </at:AtomType>
+
   <at:AtomType rdf:ID="Ni.2plus">
     <at:formalCharge>2</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Ni"/>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3955,6 +3955,79 @@ public void testMethylphosphinicAcid() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test
+    public void test_Mg_neutral_2() 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,"Mg");
+        a2.setFormalCharge(0);
+        mol.addAtom(a2);
+        IAtom a3 = builder.newInstance(IAtom.class,"C");
+        a3.setFormalCharge(0);
+        mol.addAtom(a3);
+        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);
+
+        String[] expectedTypes = {"C.sp3", "Mg.neutral.2", "C.sp3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Mg_neutral_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,"C");
+        a2.setFormalCharge(0);
+        mol.addAtom(a2);
+        IAtom a3 = builder.newInstance(IAtom.class,"Mg");
+        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,a2, a3, 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,a3, a4, IBond.Order.SINGLE);
+        mol.addBond(b3);
+        IBond b4 = builder.newInstance(IBond.class,a3, a5, IBond.Order.SINGLE);
+        mol.addBond(b4);
+
+
+        String[] expectedTypes = {"C.sp3", "C.sp3", "Mg.neutral", "C.sp3", "C.sp3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    @Test
+    public void test_Mg_neutral_1() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"Mg");
+        a1.setFormalCharge(0);
+        mol.addAtom(a1);
+        IAtom a2 = builder.newInstance(IAtom.class,"C");
+        a2.setFormalCharge(0);
+        mol.addAtom(a2);
+        IBond b1 = builder.newInstance(IBond.class,a1, a2, IBond.Order.DOUBLE);
+        mol.addBond(b1);
+
+
+        String[] expectedTypes = {"Mg.neutral.1", "C.sp2"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test
     public void test_Gd_3plus() throws Exception {
         IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();