So I have a list of molecules. They all have a common substructure, but different substitution patterns.
For example, in the figure below, the leftmost molecule is the base, and the center and rightmost molecules are both a (1,4)-substituted variants of the base.
Because the different substitution patterns result in a different numbering of the atoms, identifying the substitution locations is very difficult. Using the method
mol.HasSubstructureMatch(some_substituition), I can find the location of the substitution, but since the base pattern keeps changing, this location is meaningless for my purposes (e.g. center molecule is (4,16)-substituted, and the rightmost molecule is (4,13)-substituted)
Is it possible to modify the substituted molecules such that the base substructure always has a consistent numbering pattern (e.g. make it so both molecules above are (4,12)-substituted)? Any ideas on how to systematically identify the substitution pattern would be greatly appreciated.