![[PukiWiki]](image/picc.png "[PukiWiki]")
本家様 https://jclinic.mit.edu/boltzgen/
github https://github.com/HannesStark/boltzgen
BoltzGen is a new, generative model for designing proteins and peptides of any modality that can bind to a wide range of biomolecular targets.
(deepL訳)
BoltzGenは、あらゆるモダリティのタンパク質およびペプチドを設計するための新たな生成モデルであり、幅広い生体分子標的と結合することが可能です。
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install --list <--これでanaconda,minicondaのバージョンが一覧されます.
pyenv install miniforge3-25.3.1-0
source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profile.d/conda.sh
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profile.d/conda.sh[root@rockylinux9 ~]# conda create -n bg python=3.12
[root@rockylinux9 ~]# conda activate bg
(bg) [root@rockylinux9 ~]# pip install boltzgen
(bg) [root@rockylinux9 ~]# conda list
:
boltzgen 0.2.0 pypi_0 pypi
:
numpy 2.0.2 pypi_0 pypi
nvidia-cublas-cu12 12.8.4.1 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.8.90 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.8.93 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.8.90 pypi_0 pypi
nvidia-cudnn-cu12 9.10.2.21 pypi_0 pypi
nvidia-cufft-cu12 11.3.3.83 pypi_0 pypi
nvidia-cufile-cu12 1.13.1.3 pypi_0 pypi
nvidia-curand-cu12 10.3.9.90 pypi_0 pypi
nvidia-cusolver-cu12 11.7.3.90 pypi_0 pypi
nvidia-cusparse-cu12 12.5.8.93 pypi_0 pypi
nvidia-cusparselt-cu12 0.7.1 pypi_0 pypi
nvidia-ml-py 13.590.44 pypi_0 pypi
nvidia-nccl-cu12 2.27.5 pypi_0 pypi
nvidia-nvjitlink-cu12 12.8.93 pypi_0 pypi
nvidia-nvshmem-cu12 3.3.20 pypi_0 pypi
nvidia-nvtx-cu12 12.8.90 pypi_0 pypi
:
python 3.12.12 hd63d673_1_cpython conda-forge
:
rdkit 2025.9.3 pypi_0 pypi
:
torch 2.9.1 pypi_0 pypi
:
(bg) [root@rockylinux9 ~]# pip install torch==2.9.1+cu128 --index-url https://download.pytorch.org/whl/cu128
(bg) [root@rockylinux9 ~]# conda list
:
torch 2.9.1+cu128 pypi_0 pypi
:
(bg) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#「/apps/modulefiles/BoltzGen」
#%Module
set root /apps/pyenv/versions/miniforge3-25.3.1-0/envs/bg
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/libgithubにexampleがあるのでそれを拝借
[saber@rockylinux9 ~]$ git clone https://github.com/HannesStark/boltzgen
[saber@rockylinux9 ~]$ cd boltzgen/
[saber@rockylinux9 boltzgen]$ ls -l
total 1852
drwxr-xr-x. 2 saber saber 117 Oct 31 12:53 assets
drwxr-xr-x. 3 saber saber 174 Oct 31 12:53 config
-rw-r--r--. 1 saber saber 1617 Oct 31 12:53 Dockerfile
drwxr-xr-x. 20 saber saber 4096 Oct 31 12:53 example
-rw-r--r--. 1 saber saber 1841516 Oct 31 12:53 filter.ipynb
-rw-r--r--. 1 saber saber 1070 Oct 31 12:53 LICENSE
-rwxr-xr-x. 1 saber saber 1861 Oct 31 12:53 main.py
-rwxr-xr-x. 1 saber saber 3271 Oct 31 12:53 pyproject.toml
-rwxr-xr-x. 1 saber saber 29301 Oct 31 12:53 README.md
drwxr-xr-x. 3 saber saber 22 Oct 31 12:53 src
[saber@rockylinux9 boltzgen]$
[saber@rockylinux9 boltzgen]$ cat example/vanilla_protein/1g13prot.yaml
entities:
- protein:
id: C
sequence: 80..140
- file:
path: 1g13.cif
include:
- chain:
id: A
[saber@rockylinux9 boltzgen]$
[saber@rockylinux9 boltzgen]$ module use /apps/modulefiles/
[saber@rockylinux9 boltzgen]$ module load BoltzGen
[saber@rockylinux9 boltzgen]$ mkdir workbench
[saber@rockylinux9 boltzgen]$ boltzgen run example/vanilla_protein/1g13prot.yaml \
--output workbench/test_run \
--protocol protein-anything \
--num_designs 10 \
--budget 2
[saber@rockylinux9 boltzgen]$
[saber@rockylinux9 boltzgen]$ ls -l workbench/test_run/
total 116
-rw-r--r--. 1 saber saber 106129 Oct 31 12:57 1g13prot.cif
drwxr-xr-x. 2 saber saber 143 Oct 31 12:59 config
drwxr-xr-x. 4 saber saber 161 Oct 31 13:24 final_ranked_designs
drwxr-xr-x. 4 saber saber 4096 Oct 31 13:05 intermediate_designs
drwxr-xr-x. 11 saber saber 4096 Oct 31 13:23 intermediate_designs_inverse_folded
-rw-r--r--. 1 saber saber 347 Oct 31 12:59 steps.yaml
[saber@rockylinux9 boltzgen]$
