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currently doesn't preserve a lot of data from the original PDB file if this is necessary, one option would be to manually rewrite the file and change the positions on ATOM lines by playing with strings...
will have to check how mapped atoms are used on the SMARTS patterns
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This PR includes a non-oechem/oespruce code path for each time one of those functions is called. (using either rdkit or mdtraj instead).
TODO: I need to double check how mapped atoms in the SMARTS are being used in the substructure search to make sure the rdkit implementation is handling the same.