naokob / colabgcndesign Goto Github PK
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License: MIT License
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
ColabGCNdesign/ColabGCNdesign_beta_v0_2_1.ipynb
Lines 51 to 53 in 39873aa
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
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"
}
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