Automated structure modifications occur in a various number of situations in the life of chemical structures and reactions. The most prominent one is the so called structure normalization or standardization. It has become necessary because the graph theory related IT view into chemical depiction is much more restrictive than the perception of a chemist. In that context the most prominent example is the Nitro-Group:
While both depictions describe the same compound in the chemist’s view databases tend to see them as different ones. Similarly the same Guanidine may be drawn in three different ways like in the following example:
These structures are just 2 examples out of a list of far over 50 functional groups that do not have a unique representation in the IT sense and must be normalized for the registration into a database to maintain the consistency of the database or for the comparison of two SD files as another example.
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