Molecule

Basics

A molecule is represented as a graph and has typical graph properties and accessing methods. For adding user defined data it's recommended to use the descriptor atom or bond properties (see the Section called Molecule in Chapter 3).

Molecule load example joelib/test/TestMolecule.

Chemical properties

After the molecule is loaded the aromaticity and Kekule-flags are assigned automatically (the Section called Assigning atom types, aromatic flags, hybridization and hydrogens in Chapter 3). if you want to force to write kekulized molecular structures use molecule.kekulize(). Otherwise you will work on structures with aromaticity flags, which is the recommended way. Only for visualization and some search purpose you can switch to Kekule structures.