Added perception of N.sp2 and N.planar3 when SINGLE_OR_DOUBLE is used

Change-Id: Ib2b045f6801bfd23479d89d148dae7b777067079 Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Nov 11, 2012 · 7a39faa · 7a39faa
1 parent b6b13ed
commit 7a39faa
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -857,6 +857,17 @@ private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) th
         } else if (atomContainer.getConnectedBondsCount(atom) == 0) {
             IAtomType type = getAtomType("N.sp3");
             if (isAcceptable(atom, atomContainer, type)) return type;
+        } else if (hasOneOrMoreSingleOrDoubleBonds(atomContainer, atom)) {
+        	int connectedAtoms = atomContainer.getConnectedAtomsCount(atom) +
+        		(atom.getImplicitHydrogenCount() == CDKConstants.UNSET
+        		    ? 0
+        			: atom.getImplicitHydrogenCount());
+        	if (connectedAtoms == 3) {
+            	IAtomType type = getAtomType("N.planar3");
+            	if (isAcceptable(atom, atomContainer, type)) return type;
+        	}
+        	IAtomType type = getAtomType("N.sp2");
+        	if (isAcceptable(atom, atomContainer, type)) return type;
         } else { // OK, use bond order info
             IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
             if (maxBondOrder == CDKConstants.BONDORDER_SINGLE) {

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -2125,6 +2125,25 @@ public void fix_Ca_1() throws Exception {
     	assertAtomTypes(testedAtomTypes, expectedTypes, molecule);
 	}
 
+    @Test public void testPyrrole_SingleOrDouble() throws Exception {
+		String[] expectedTypes = {
+			"C.sp2",
+			"N.planar3",
+			"C.sp2",
+			"C.sp2",
+			"C.sp2"
+		};
+		IAtomContainer molecule = MoleculeFactory.makePyrrole();
+		for (IBond bond : molecule.bonds()) {
+			bond.setOrder(IBond.Order.UNSET);
+			bond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
+		}
+		for (IAtom atom : molecule.atoms()) {
+			atom.setImplicitHydrogenCount(1);
+		}
+    	assertAtomTypes(testedAtomTypes, expectedTypes, molecule);
+	}
+
     @Test public void testPyrroleAnion() throws Exception {
 		String[] expectedTypes = {
 			"C.sp2",
@@ -2272,6 +2291,23 @@ public void fix_Ca_1() throws Exception {
     	assertAtomTypes(testedAtomTypes, expectedTypes, molecule);
 	}
 
+    @Test public void testPyridine_SingleOrDouble() throws Exception {
+		String[] expectedTypes = {
+			"C.sp2",
+			"N.sp2",
+			"C.sp2",
+			"C.sp2",
+			"C.sp2",
+			"C.sp2"
+		};
+		IAtomContainer molecule = MoleculeFactory.makePyridine();
+		for (IBond bond : molecule.bonds()) {
+			bond.setOrder(IBond.Order.UNSET);
+			bond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
+		}
+		assertAtomTypes(testedAtomTypes, expectedTypes, molecule);
+	}
+
     @Test public void testPyridineDirect() throws Exception {
 		String[] expectedTypes = {
 			"N.sp2",