Added aromaticity-based perception: N.planar3

Added perception of PLANAR3 hyrbidization for aromatic nitrogens that are not in kekule representation (i.e. atomaticity has been read). This patch adds a unit test on pyrrole that demonstrates the functionality is working.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>

Author: Stephan Beisken

src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java

@@ -637,7 +637,10 @@ private boolean atLeastTwoNeighborsAreSp2(IAtom atom, IAtomContainer atomContain
     			} else if (countAttachedDoubleBonds(atomContainer, nextAtom) > 0) {
     				// OK, it's SP2
     				count++;
-    			} // OK, not SP2
+    			} else if (atomContainer.getBond(atom, nextAtom).getFlag(CDKConstants.ISAROMATIC)) {
+                    // two aromatic bonds indicate sp2
+                    count++;
+                } // OK, not SP2
     		}
     	}
     	return count >= 2;
@@ -845,9 +848,14 @@ private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) th
                             bonds.get(1).getFlag(CDKConstants.ISAROMATIC)) {
                         Integer hCount = atom.getImplicitHydrogenCount();
                         if (hCount == CDKConstants.UNSET || hCount == 0) {
-                            IAtomType type = getAtomType("N.sp2");
-                            if (isAcceptable(atom, atomContainer, type))
-                                return type;
+                            if (atomContainer.getMaximumBondOrder(atom) == CDKConstants.BONDORDER_SINGLE &&
+                                    isSingleHeteroAtom(atom, atomContainer)) {
+                                IAtomType type = getAtomType("N.planar3");
+                                if (isAcceptable(atom, atomContainer, type)) return type;
+                            } else {
+                                IAtomType type = getAtomType("N.sp2");
+                                if (isAcceptable(atom, atomContainer, type)) return type;
+                            }
                         } else if (hCount == 1) {
                             IAtomType type = getAtomType("N.planar3");
                             if (isAcceptable(atom, atomContainer, type))
@@ -901,6 +909,25 @@ private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) th
     	return null;
     }
 
+    private boolean isSingleHeteroAtom(IAtom atom, IAtomContainer atomContainer) {
+
+        for (IAtom atom1 : atomContainer.getConnectedAtomsList(atom)) {
+            if (atomContainer.getBond(atom, atom1).getFlag(CDKConstants.ISAROMATIC) && !atom1.getSymbol().equals("C")) {
+                return false;
+            } else if (atomContainer.getBond(atom, atom1).getFlag(CDKConstants.ISAROMATIC)) {
+                for (IAtom atom2 : atomContainer.getConnectedAtomsList(atom1)) {
+                    if (atom2 != atom && atomContainer.getBond(atom1, atom2).getFlag(CDKConstants.ISAROMATIC) &&
+                            !atom2.getSymbol().equals("C")) {
+                        return false;
+                    }
+                }
+            } else {
+                continue;
+            }
+        }
+        return true;
+    }
+
     private boolean isRingAtom(IAtom atom, IAtomContainer atomContainer) {
     	SpanningTree st = new SpanningTree(atomContainer);
         return st.getCyclicFragmentsContainer().contains(atom);

src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java

@@ -50,6 +50,7 @@
 import org.openscience.cdk.nonotify.NNAtomType;
 import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
 import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
@@ -6374,6 +6375,47 @@ public void test_Ru_6() throws Exception {
         String[] expectedTypes = {"Ru.6", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
+
+    @Test
+    public void test_n_planar3_sp2_aromaticity() throws Exception {
+
+        IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
+
+        // simulate an IAtomContainer returned from a SDFile with bond order 4 to indicate aromaticity
+        IAtomContainer pyrrole = builder.newInstance(IAtomContainer.class);
+
+        IAtom n1 = builder.newInstance(IAtom.class,"N");
+        IAtom c2 = builder.newInstance(IAtom.class,"C");
+        IAtom c3 = builder.newInstance(IAtom.class,"C");
+        IAtom c4 = builder.newInstance(IAtom.class,"C");
+        IAtom c5 = builder.newInstance(IAtom.class,"C");
+
+        IBond b1 = builder.newInstance(IBond.class,n1, c2, IBond.Order.SINGLE);
+        b1.setFlag(CDKConstants.ISAROMATIC, true);
+        IBond b2 = builder.newInstance(IBond.class,c2, c3, IBond.Order.SINGLE);
+        b2.setFlag(CDKConstants.ISAROMATIC, true);
+        IBond b3 = builder.newInstance(IBond.class,c3, c4, IBond.Order.SINGLE);
+        b3.setFlag(CDKConstants.ISAROMATIC, true);
+        IBond b4 = builder.newInstance(IBond.class,c4, c5, IBond.Order.SINGLE);
+        b4.setFlag(CDKConstants.ISAROMATIC, true);
+        IBond b5 = builder.newInstance(IBond.class,c5, n1, IBond.Order.SINGLE);
+        b5.setFlag(CDKConstants.ISAROMATIC, true);
+
+        pyrrole.addAtom(n1);
+        pyrrole.addAtom(c2);
+        pyrrole.addAtom(c3);
+        pyrrole.addAtom(c4);
+        pyrrole.addAtom(c5);
+        pyrrole.addBond(b1);
+        pyrrole.addBond(b2);
+        pyrrole.addBond(b3);
+        pyrrole.addBond(b4);
+        pyrrole.addBond(b5);
+
+        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(pyrrole);
+
+        Assert.assertEquals(pyrrole.getAtom(0).getHybridization().name(), "PLANAR3");
+    }
 
     /*
      * This method *must* be the last method in the class.