I am trying to preform PSIPRED secondary structure prediction in PyRosetta. This is my code so far:
psipred = pyrosetta.rosetta.core.io.external.PsiPredInterface(' ') #<--- What goes here? psipred.run_psipred(pose , 'blueprint') #<--- Is this correct?
I think I am close at getting it to work, but I am not there yet; what goes in the first line? (pydoc3 says the argument in the first line should be cmd: str and I don't know what that is)
Is the second line correct? are there any other methods I should include to preform a correct PSIPRED secondary structure prediction for Abinitio?
I have attached the blueprint file that I think is required.