Added the N.oxide atom type, for structures like (CH3)N=O

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · Jul 22, 2010 · bb431e3 · bb431e3
1 parent 3133a18
commit bb431e3
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Showing 3 changed files with 41 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -563,6 +563,11 @@ private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) th
                 }
                 // but an sp2 hyb N might N.sp2 or N.planar3 (pyrrole), so check for the latter
             	int neighborCount = atomContainer.getConnectedAtomsCount(atom);
+            	if (neighborCount == 4 &&
+            	    IBond.Order.DOUBLE == atomContainer.getMaximumBondOrder(atom)) {
+            	    IAtomType type = getAtomType("N.oxide");
+                    if (isAcceptable(atom, atomContainer, type)) return type;
+            	} else
             	if (neighborCount > 1 && bothNeighborsAreSp2(atom, atomContainer)) {
             		IRing ring = getRing(atom, atomContainer);
             		int ringSize = ring == null ? 0 : ring.getAtomCount();
@@ -655,7 +660,11 @@ private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) th
                 }
             }
         } else if (atomContainer.getConnectedBondsCount(atom) > 3) {
-            // FIXME: I don't perceive carbons with more than 3 connections yet
+            if (atomContainer.getConnectedBondsCount(atom) == 4 &&
+                countAttachedDoubleBonds(atomContainer, atom) == 1) {
+                IAtomType type = getAtomType("N.oxide");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            }
             return null;
         } else if (atomContainer.getConnectedBondsCount(atom) == 0) {
             IAtomType type = getAtomType("N.sp3");

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
@@ -487,6 +487,15 @@
     <at:hybridization rdf:resource="&at;sp2"/>
   </at:AtomType>
 
+  <at:AtomType rdf:ID="N.oxide">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;N"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>1</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp2"/>
+  </at:AtomType>
+
   <at:AtomType rdf:ID="N.thioamide">
     <at:broader rdf:resource="&cdkat;N.sp2"/>
     <at:formalCharge>0</at:formalCharge>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -642,6 +642,28 @@ public void testTetrahydropyran() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+
+    @Test public void testAmineOxide() throws Exception {
+        IMolecule mol = new Molecule();
+        IAtom atom = new Atom("O");
+        IAtom atom2 = new Atom("N");
+        IAtom atom3 = new Atom("C");
+        IAtom atom4 = new Atom("C");
+        IAtom atom5 = new Atom("C");
+        mol.addAtom(atom);
+        mol.addAtom(atom2);
+        mol.addAtom(atom3);
+        mol.addAtom(atom4);
+        mol.addAtom(atom5);
+        mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
+        mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
+        mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
+        mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
+
+        String[] expectedTypes = {"O.sp2", "N.oxide", "C.sp3", "C.sp3", "C.sp3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test public void testThioAmide() throws Exception {
         IMolecule mol = new Molecule();
         IAtom atom = new Atom("S");