Major effort has been expended in order to obtain a standard internal representation of molecules regardless of the format of the input files. The aim was to obtain unique descriptor values for a give molecule starting from different representations. 

It's well-known that the common MDL file represents the molecule by means of an aliphatic structure (i.e. a Kekulè-like structure), while HyperChem files and SMILES notations can give different molecule representations according to how the user has defined conjugated systems and aromaticity.

 

In the DRAGON molecule representation, all bonds belonging to aromatic rings are assigned a conventional bond order of 1.5 while bonds belonging to non-aromatic conjugated systems are alternating single and double bonds. The nitro group is represented by two double bonds N = O and the N-oxide by one double bond N = O. Aromaticity detection is performed by an internal algorithm and thus it is independent of the aromatic bonds labelled by the user.

The user is free to choose whether to use the standard DRAGON molecule representation or keep the one defined in the input file, by the option 'User defined bond orders' in the window 'Select files'. This option is not available in DRAGON running in background mode.