The documentation for PyRosetta functionality is sparse, at best, but what documentation there is for the API can be found at http://www.pyrosetta.org/documentation — particularly the link to http://graylab.jhu.edu/PyRosetta.documentation/
Alternatively, most of the PyRosetta functionality is just a thin wrapper around the Rosetta functionality. Much of the information in the Rosetta documentation (both the user guide at https://www.rosettacommons.org/docs/latest/Home and the code documentation at https://www.rosettacommons.org/manuals/latest/ — much of the PyRosetta documentation is just a differently formatted version of the latter.)
… and if you’re confused about anything, feel free to ask. We realize that the documentation is rather scant, and not necessarily as helpful as it could be.
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