The evaluation of the atom mapper showed that Kartograf contains a fast mapping approach for a large number of molecules and a large number of atoms contained in their mappings, yielding often similar mapping results compared to Lomap. If the coordinates should be preserved as much as possible we want to suggest Kartograf's atom mapper as a tool of choice. However, for Kartografs' mapping algorithm, the alignment of the ligands is crucial, and a possible source of error was found. To potentially overcome alignment problems, Katograf offers shape and SIS alignment wrapping functions.