Dear RDkit users, I am writing to you because I need help. I am trying to calculate the RMSD between two molecules through AllChem.GetBestRMS function but it only works when I run it on the same molecule. If I try to perform the function with two different molecules I get a generic error RuntimeError: std::exception
I also tried using the map parameter providing a list of tuples with the atom-atom mappings of the two molecules but it still doesn't work. I think this kind of error is very strange because using the AllChem.AlignMol function to align the two molecules (I use this function before calculating the RMSD with AllChem.GetBestRMS() you actually get the RMSD between the two aligned molecules. Can anyone tell me how to solve the problem or what are the causes? Best, Salvatore -- Salvatore Galati PhD Visiting Student Bonn Aachen International Center for Information Technology BIT Life Science Informatics Endenicher Allee 19c 53115 Bonn Tel : +39 340721431
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