代码改变世界

alphafold2的几项便利性修改。

2021-08-31 16:34  丨o聽乄雨o丨  阅读(120)  评论(0编辑  收藏  举报
#Run alphafold2
# conda activate af2
# run_alphafold.py --fasta_paths=Test.fasta --max_template_date=2020-05-14
# run_alphafold.py --fasta_paths=N7.fasta > N7.Log 2>&1

#Changelog
1. vim /home/wangq/Programs/miniconda3/envs/af2/lib/python3.8/site-packages/absl/flags/_validators.py
# annotate line 202-206
2. vim ~/Programs/alphafold2/run_alphafold.py
# add !/usr/bin/env python3
3. chmod +x ~/Programs/alphafold2/run_alphafold.py
4. vim ~/Programs/alphafold2/run_alphafold.py
# add time module
5. vim ./alphafold/data/tools/jackhmmer.py
# change cpu:8 to cpu:20
6. vim ./alphafold/data/tools/hhblits.py
# change cpu:4 to cpu:20
7. vim alphafold/common/residue_constants.py
#change line 23 28 409
    import subprocess
    AF2_PATH = subprocess.getoutput("echo $alphafold2")
    stereo_chemical_props_path = (f'{AF2_PATH}/alphafold/common/stereo_chemical_props.txt')

 

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