naokob / colabgcndesign Goto Github PK

Saving a config file like this would be helpful to review the previous run's settings.

{
    "pdbcode": "1bdd"
    "chains": ["A","B"],
    "nstruct": 10,
    "prob_cut": 0.8,
    "scorefxn": "ref2015",
    "keep": ["1A", "2A", "10B"],
    "unused": ["C", "H", "W"],
    "include_init_restype": true,
    "fastdesign_iterations": 3,
    "paramin": "None"
}

Currently, the download link for pyrosetta is hard-corded as
https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.MinSizeRel.python37.linux/PyRosetta4.MinSizeRel.python37.linux.release-316.tar.bz2
but this link is now dead.

So we need to replace this to the one available today such as
https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.MinSizeRel.python37.linux/PyRosetta4.MinSizeRel.python37.linux.release-328.tar.bz2

When restarting the runtime on Google Colab
downloading pyrosetta again will be a waste of time.
I suggest adding the following line
if not os.path.isdir("/content/PyRosetta"):

to here