Hello RDKit users, I have a large set of cropped transition state structures that I would like to sort. An atom that is common to every transition state is set as the coordinate origin in every structure file. The cropped transition state regions are collected by expanding a sphere about the origin atom until a fixed number of atoms (say 7) are collected. Note that the set of cropped transition states will not, in general, have the same types of atoms.
I am looking for a suitable method to cluster this data and look for patterns. Since the environment about each reaction is highly variable, I am most interested in a distance weighted analysis where the atoms nearest the origin atoms are assigned a much higher "value." I notice that rdkit has tools to rank the similarity between molecular structures. Are these tools suitable for my task? Best, Eric
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