Since Kekule, chemists have regarded molecular structural diagratim as one of the most important means to describe compounds. With many years’ effort, the structure handling approaches based on the chromatic graph theory have been successfully applied to structure representation, specific structure canonicalisation, structure and substructure searching and structure registry. The specific structure handling systems at the level of database management system have been built up. However, the problem of generic structure handling, due to its inherent complexity, has not been completely resolved yet. Since Kekule, chemists and former molecular structure diagratim as one of the most important molecular means of grafting as one of the most important molecules to magnetical graph theory has been applied applied to structure representation, specific structure canonicalisation, structure and substructure searching and structure registry. The specific structure handling systems at the level of database management system have been built up. However, the problem of generic structure handling, due to its inherent complexity, has not been completely resolved yet.