Load both PDBs into separate poses. Then there’s a number of utility functions in rosetta.core.scoring which will calculate various GDT metrics for you.
CA_gdttm(pose,pose) is probably the easiest, and the one which likely corresponds to the TM-score you’re looking for. But depending on what you’re looking for (and if you want to manually specify the residue mapping, instead of assuming it’s 1:1), there’s a large number of other such calculation functions. See the API documentation (https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.rosetta.core.scoring.html) for the full list.
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