Ubuntu24.04 ProteinMPNN安装

安装

建立环境，python=3.9

conda create --name proteinmpnn python=3.9
conda activate proteinmpnn
conda install pytorch=1.12.0  torchvision=0.13.0  torchaudio cudatoolkit=11.3 -c pytorch
#不指定的话cuda pytorch和GPU又不能好好配合


#验证pytorch
import torch
print(torch.__version__)          # 应显示含 'cu113' 的版本号（如 1.10.2+cu113）
print(torch.cuda.is_available())  # 输出应为 True
print(torch.cuda.get_device_name(0)) 

#git直接跑总是不顺利，先下载了source
https://github.com/dauparas/ProteinMPNN

cd  ProteinMPNN-main
chmod +x submit_example_1.sh 
./submit_example_1.sh 

line 8: activate: No such file or directory
#应该是activate环境的命令？忽略

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

conda install "numpy<2

The following packages will be DOWNGRADED:
  numpy          2.0.2-py39h9cb892a_1 --> 1.26.4-py39h474f0d3_0 
"

----------------------------------------
chain_id_jsonl is NOT loaded
----------------------------------------
fixed_positions_jsonl is NOT loaded
----------------------------------------
pssm_jsonl is NOT loaded
----------------------------------------
omit_AA_jsonl is NOT loaded
----------------------------------------
bias_AA_jsonl is NOT loaded
----------------------------------------
tied_positions_jsonl is NOT loaded
----------------------------------------
bias by residue dictionary is not loaded, or not provided
----------------------------------------
discarded {'bad_chars': 0, 'too_long': 0, 'bad_seq_length': 0}
----------------------------------------
Number of edges: 48
Training noise level: 0.2A
Generating sequences for: 5L33
2 sequences of length 106 generated in 0.6338 seconds
Generating sequences for: 6MRR
2 sequences of length 68 generated in 0.4478 seconds

一些高级功能没有开，但是基础可以运行。这个在不同的example里面有各个功能的使用，慢慢探索。

安装部分完结。
撒花。