11.2 Kekule Form Assignment

A number of file formats don't represent a connection table as a single representative Kekulé form but instead denote some bonds, such as those in benzene, as aromatic. OEChem provides a method for determining a valid, but arbitrary, Kekulé form for such connection tables using the OEKekulize function. On input to OEKekulize, the integer bond type property of each bond represents either the bond order (1 for single, 2 for double, 3 for triple or 4 for quadruple) or a the value 5 indicating the bond is aromatic or resonant. The algorithm sets the bond order property from the bond type property, with the exception of bond type 5, which is assigned a bond order of either 1 or 2 representing either a single or double bond. The Boolean return value indicates whether a valid Kekulé form could be assigned.

Note that OEKekulize requires that the implicit hydrogen counts and formal charges have been correctly set on all atoms before being called.

OEKekulize is normally only used by low-level file readers for interpreting input connection tables. To write out a Kekulé SMILES string, use the OEChem function OEClearAromaticity that clears the aromaticity property of all atoms and bonds in a molecule, causing the molecule to be written out as aliphatic with explicit bond orders.

				OEChem - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1