Split the C.sp atom type into C.sp for (-C#) and C.allene for (=C=)

Change-Id: I4f496fdff6e4f04650831673bc573f3a6a3d5d1d Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Oct 7, 2012 · 001f488 · 001f488
1 parent 492a9cd
commit 001f488
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Showing 3 changed files with 39 additions and 7 deletions.
diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -36,6 +36,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IPseudoAtom;
 import org.openscience.cdk.interfaces.IRing;
@@ -375,8 +376,14 @@ private IAtomType perceiveCarbons(IAtomContainer atomContainer, IAtom atom)
 	            IAtomType type = getAtomType("C.sp3");
 	            if (isAcceptable(atom, atomContainer, type)) return type;
 	        } else if (atom.getHybridization() == Hybridization.SP1) {
-	            IAtomType type = getAtomType("C.sp");
-	            if (isAcceptable(atom, atomContainer, type)) return type;
+	        	IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
+	        	if (maxBondOrder == Order.TRIPLE) {
+		            IAtomType type = getAtomType("C.sp");
+		            if (isAcceptable(atom, atomContainer, type)) return type;
+	        	} else {
+	        		IAtomType type = getAtomType("C.allene");
+	        		if (isAcceptable(atom, atomContainer, type)) return type;
+	        	}
 	        }
 	    } else if (atom.getFlag(CDKConstants.ISAROMATIC)) {
 	        IAtomType type = getAtomType("C.sp2");
@@ -435,7 +442,7 @@ private IAtomType perceiveCarbons(IAtomContainer atomContainer, IAtom atom)
 	            // OK, one or two double bonds?
 	            int doubleBondCount = countAttachedDoubleBonds(atomContainer, atom);
 	            if (doubleBondCount == 2) {
-	                IAtomType type = getAtomType("C.sp");
+	                IAtomType type = getAtomType("C.allene");
 	                if (isAcceptable(atom, atomContainer, type)) return type;
 	            } else if (doubleBondCount == 1) {
 	                IAtomType type = getAtomType("C.sp2");

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
@@ -191,19 +191,29 @@
   <at:AtomType rdf:ID="C.sp">
     <at:formalCharge>0</at:formalCharge>
     <at:hasElement rdf:resource="&elem;C"/>
-    <at:formalNeighbourCount>2</at:formalNeighbourCount>
     <at:lonePairCount>0</at:lonePairCount>
-    <at:piBondCount>2</at:piBondCount>
     <at:hybridization rdf:resource="&at;sp1"/>
+    <at:formalBondType rdf:resource="&bo;single"/>
+    <at:formalBondType rdf:resource="&bo;triple"/>
+  </at:AtomType>
+
+  <at:AtomType rdf:ID="C.allene">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;C"/>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:hybridization rdf:resource="&at;sp1"/>
+    <at:formalBondType rdf:resource="&bo;double"/>
+    <at:formalBondType rdf:resource="&bo;double"/>
   </at:AtomType>
 
   <at:AtomType rdf:ID="C.sp2">
     <at:formalCharge>0</at:formalCharge>
     <at:hasElement rdf:resource="&elem;C"/>
-    <at:formalNeighbourCount>3</at:formalNeighbourCount>
     <at:lonePairCount>0</at:lonePairCount>
-    <at:piBondCount>1</at:piBondCount>
     <at:hybridization rdf:resource="&at;sp2"/>
+    <at:formalBondType rdf:resource="&bo;double"/>
+    <at:formalBondType rdf:resource="&bo;single"/>
+    <at:formalBondType rdf:resource="&bo;single"/>
   </at:AtomType>
 
   <at:AtomType rdf:ID="C.plus.planar">

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -1477,6 +1477,21 @@ public void testTetrahydropyran() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    @Test public void testAllene() throws Exception {
+    	IMolecule mol = new Molecule();
+        IAtom atom1 = new Atom("C");
+        IAtom atom2 = new Atom("C");
+        IAtom atom3 = new Atom("C");
+        mol.addAtom(atom1);
+        mol.addAtom(atom2);
+        mol.addAtom(atom3);
+        mol.addBond(0,1,Order.DOUBLE);
+        mol.addBond(1,2,Order.DOUBLE);
+
+        String[] expectedTypes = new String[]{"C.sp2", "C.allene", "C.sp2"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test public void testAzide2() throws Exception {
     	IAtomContainer mol = new AtomContainer();
         IAtom atom = new Atom("C");