Member Site Forums Rosetta 3 Rosetta 3 – General How to set up options in rosetta Reply To: How to set up options in rosetta


    The first thing to notice is that most lines of Rosetta output are prepended with a string matching where the result came from:

    core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
    protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
    protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
    protocols.jd2.PDBJobInputter: pushing complex_readytail_final_nozn.pdb nstruct index 1 Database file opened: /users/smlewis/minirosetta_database/env_log.txt

    You can mute these individually or in groups with the mute and unmute command line flags:
    -mute protocols
    will mute all of protocols’ tracers, including subchannels like protocols.jd2.PDBJobInputter
    -mute protocols.jd2.PDBJobInputter
    will mute only PDBJobInputter
    -mute all
    will mute all mutable output in the program (which is nearly all of it).

    Second, if you want to modify the value of options from within the code, the add_relevant function is not quite the right one. add_relevant reorganizes the -help option in the option system but does not change values. You want to do this:

    where whatever_option is the option you want to modify (probably mute, but you can try run::silent), and argument is the value you want to give it. Note that this is the same syntax as ACCESSING the value of an option, but .value() now receives an argument instead of returning the argument.