diff --git a/Docs/Book/RDKit_Book.rst b/Docs/Book/RDKit_Book.rst index 46744fa90..a46c0c6f6 100644 --- a/Docs/Book/RDKit_Book.rst +++ b/Docs/Book/RDKit_Book.rst @@ -20,7 +20,6 @@ The rules are relatively straightforward. Aromaticity is a property of atoms and bonds in rings. An aromatic bond must be between aromatic atoms, but a bond between aromatic atoms does not need to be aromatic. - For example the fusing bonds here are not considered to be aromatic by the RDKit: .. image:: images/picture_9.png @@ -83,6 +82,31 @@ True >>> m.GetBondBetweenAtoms(6,7).GetIsAromatic() False +A special case, heteroatoms with radicals are not considered candidates for aromaticity: + +.. image:: images/picture_10.png + +>>> m = Chem.MolFromSmiles('C1=C[N]C=C1') +>>> m.GetAtomWithIdx(0).GetIsAromatic() +False +>>> m.GetAtomWithIdx(2).GetIsAromatic() +False +>>> m.GetAtomWithIdx(2).GetNumRadicalElectrons() +1 + +Carbons with radicals, however, are still considered: + +.. image:: images/picture_11.png + +>>> m = Chem.MolFromSmiles('C1=[C]NC=C1') +>>> m.GetAtomWithIdx(0).GetIsAromatic() +True +>>> m.GetAtomWithIdx(1).GetIsAromatic() +True +>>> m.GetAtomWithIdx(1).GetNumRadicalElectrons() +1 + + **Note:** For reasons of computation expediency, aromaticity perception is only done for fused-ring systems where all members are at most 24 atoms in size. diff --git a/Docs/Book/images/picture_10.png b/Docs/Book/images/picture_10.png new file mode 100644 index 000000000..7a66a2be7 Binary files /dev/null and b/Docs/Book/images/picture_10.png differ diff --git a/Docs/Book/images/picture_11.png b/Docs/Book/images/picture_11.png new file mode 100644 index 000000000..0de9d1297 Binary files /dev/null and b/Docs/Book/images/picture_11.png differ