The Design API runs the rosetta FastDesign protocol given an input PDB file and a resfile.
The PDB file should be cleaned prior to input using the Clean PDB API. The Resfile is a standard Rosetta Resfile, documented here: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles
The API is used as follows:
cyrus submit design input.pdb input.res --repeats 10
where the repeats flag will result in the creation of 10 new models.