UFold Home

copy the UFold directory to your workspace

UFold is installed on white.

cp -r /home/usr/share/UFold ~/UFold
cd ~/UFold
ls 
# common  data  models  readme.md  results  run.sh  ufold  ufold_predict.py"

You should not change these files:

• common + ufold: files about the architecture of UFold
• models: pretrained weight files
• ufold_predict.py: the real script to predict the secondary structure

You can check these files:

• data: directory to put your sequence in
• results: directory that contains the prediction results
• run.sh: the direct script to be implemented
• readme.md: some explanations

put your fasta file into the directory 'data' and rename it to input.txt

cp YOURFILE ./data
unlink input.txt # you may need to delete the previous one
ln -s data/YOURFILE data/input.txt

run the script

./run.sh
# You shall modify it for yourself

# You may encounter the warning 
# '/home/xuelab/softwares/miniconda3/envs/UFold/lib/python3.6/site-packages/torch/nn/functional.py:718: UserWarning: Named tensors......'
# just ignore it.

# Your results are in the directory 'results', with the same name every time...
# So keep it carefully, every time you run a new job.