云上安装软件

云上安装
%%time
#@title install
#@markdown install ESMFold, OpenFold and download Params (~2min 30s)

import os, time
if not os.path.isfile(“esmfold.model”):

download esmfold params

os.system(“apt-get install aria2 -qq”)
os.system(“aria2c -q -x 16 https://colabfold.steineggerlab.workers.dev/esm/esmfold.model &”)

install libs

os.system(“pip install -q omegaconf pytorch_lightning biopython ml_collections einops py3Dmol”)
os.system(“pip install -q git+https://github.com/NVIDIA/dllogger.git”)

install openfold

commit = “6908936b68ae89f67755240e2f588c09ec31d4c8”
os.system(f"pip install -q git+https://github.com/aqlaboratory/openfold.git@{commit}")

install esmfold

os.system(f"pip install -q git+https://github.com/sokrypton/esm.git")

wait for Params to finish downloading…

if not os.path.isfile(“esmfold.model”):
# backup source!
os.system(“aria2c -q -x 16 https://files.ipd.uw.edu/pub/esmfold/esmfold.model”)
else:
while os.path.isfile(“esmfold.model.aria2”):
time.sleep(5)