Protenix をテンプレートにして作成
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開始行:
本家様 [[https://github.com/bytedance/Protenix>+https://g...
pipy [[https://pypi.org/project/protenix/>+https://pypi.o...
Toward High-Accuracy Open-Source Biomolecular Structure P...
pipyのサイトからPython >=3.11みたい
***pyenv-anacondaの設置 [#y442193c]
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-26.3.2-1
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
}}
***Protenix のインストール [#h2fb44b7]
#code(nonumber){{
[root@r9 ~]# conda create -n protenix python=3.11 pip
[root@r9 ~]# conda activate protenix
(protenix) [root@r9 ~]# pip install protenix
(protenix) [root@r9 ~]# conda list
# packages in environment at /apps/pyenv/versions/minifor...
#
# Name Version Build ...
_openmp_mutex 4.5 20_gnu ...
absl-py 2.4.0 pypi_0 ...
annotated-types 0.7.0 pypi_0 ...
asttokens 3.0.1 pypi_0 ...
biopython 1.85 pypi_0 ...
biotite 1.4.0 pypi_0 ...
biotraj 1.2.2 pypi_0 ...
bzip2 1.0.8 hda65f4...
ca-certificates 2026.5.20 hbd8a1c...
certifi 2026.5.20 pypi_0 ...
charset-normalizer 3.4.7 pypi_0 ...
click 8.4.1 pypi_0 ...
colorama 0.4.6 pypi_0 ...
comm 0.2.3 pypi_0 ...
contourpy 1.3.3 pypi_0 ...
cuequivariance 0.10.0 pypi_0 ...
cuequivariance-ops-cu12 0.8.0 pypi_0 ...
cuequivariance-ops-torch-cu12 0.8.0 pypi_0 ...
cuequivariance-torch 0.8.0 pypi_0 ...
cycler 0.12.1 pypi_0 ...
decorator 5.3.1 pypi_0 ...
deepspeed 0.17.5 pypi_0 ...
einops 0.8.2 pypi_0 ...
executing 2.2.1 pypi_0 ...
fair-esm 2.0.0 pypi_0 ...
filelock 3.29.3 pypi_0 ...
fonttools 4.63.0 pypi_0 ...
fsspec 2026.4.0 pypi_0 ...
gemmi 0.6.7 pypi_0 ...
gitdb 4.0.12 pypi_0 ...
gitpython 3.1.50 pypi_0 ...
hjson 3.1.0 pypi_0 ...
icecream 2.1.7 pypi_0 ...
idna 3.18 pypi_0 ...
ihm 2.11 pypi_0 ...
ipdb 0.13.13 pypi_0 ...
ipython 9.14.1 pypi_0 ...
ipython-pygments-lexers 1.1.1 pypi_0 ...
ipywidgets 8.1.7 pypi_0 ...
jedi 0.20.0 pypi_0 ...
jinja2 3.1.6 pypi_0 ...
joblib 1.5.3 pypi_0 ...
jupyterlab-widgets 3.0.16 pypi_0 ...
kiwisolver 1.5.0 pypi_0 ...
ld_impl_linux-64 2.45.1 default...
libexpat 2.8.1 hecca71...
libffi 3.5.2 h343593...
libgcc 15.2.0 he0feb6...
libgcc-ng 15.2.0 h69a702...
libgomp 15.2.0 he0feb6...
liblzma 5.8.3 hb03c66...
libnsl 2.0.1 hb9d3cd...
libsqlite 3.53.2 h0c1763...
libuuid 2.42.1 h5347b4...
libxcrypt 4.4.36 hd59030...
libzlib 1.3.2 h25fd6f...
markupsafe 3.0.3 pypi_0 ...
matplotlib 3.10.5 pypi_0 ...
matplotlib-inline 0.2.2 pypi_0 ...
ml-collections 1.1.0 pypi_0 ...
modelcif 1.4 pypi_0 ...
mpmath 1.3.0 pypi_0 ...
msgpack 1.2.0 pypi_0 ...
ncurses 6.6 hdb1482...
networkx 3.6.1 pypi_0 ...
ninja 1.13.0 pypi_0 ...
numpy 2.4.1 pypi_0 ...
nvidia-cublas-cu12 12.6.4.1 pypi_0 ...
nvidia-cuda-cupti-cu12 12.6.80 pypi_0 ...
nvidia-cuda-nvrtc-cu12 12.6.77 pypi_0 ...
nvidia-cuda-runtime-cu12 12.6.77 pypi_0 ...
nvidia-cudnn-cu12 9.5.1.17 pypi_0 ...
nvidia-cufft-cu12 11.3.0.4 pypi_0 ...
nvidia-cufile-cu12 1.11.1.6 pypi_0 ...
nvidia-curand-cu12 10.3.7.77 pypi_0 ...
nvidia-cusolver-cu12 11.7.1.2 pypi_0 ...
nvidia-cusparse-cu12 12.5.4.2 pypi_0 ...
nvidia-cusparselt-cu12 0.6.3 pypi_0 ...
nvidia-ml-py 13.610.43 pypi_0 ...
nvidia-nccl-cu12 2.26.2 pypi_0 ...
nvidia-nvjitlink-cu12 12.6.85 pypi_0 ...
nvidia-nvtx-cu12 12.6.77 pypi_0 ...
openssl 3.6.3 h35e630...
opt-einsum 3.4.0 pypi_0 ...
optree 0.17.0 pypi_0 ...
packaging 26.2 pyhc364...
pandas 2.3.1 pypi_0 ...
parso 0.8.7 pypi_0 ...
pdbeccdutils 1.0.0 pypi_0 ...
pexpect 4.9.0 pypi_0 ...
pillow 12.2.0 pypi_0 ...
pip 26.1.2 pyh8b19...
platformdirs 4.10.0 pypi_0 ...
prompt-toolkit 3.0.52 pypi_0 ...
protenix 2.0.0 pypi_0 ...
protobuf 6.31.1 pypi_0 ...
psutil 7.2.2 pypi_0 ...
ptyprocess 0.7.0 pypi_0 ...
pure-eval 0.2.3 pypi_0 ...
py-cpuinfo 9.0.0 pypi_0 ...
py3dmol 2.5.2 pypi_0 ...
pydantic 2.13.4 pypi_0 ...
pydantic-core 2.46.4 pypi_0 ...
pygments 2.20.0 pypi_0 ...
pyparsing 3.3.2 pypi_0 ...
python 3.11.15 h7508c3...
python-dateutil 2.9.0.post0 pypi_0 ...
pytz 2026.2 pypi_0 ...
pyyaml 6.0.2 pypi_0 ...
rdkit 2025.9.3 pypi_0 ...
readline 8.3 h853b02...
requests 2.34.2 pypi_0 ...
scikit-learn 1.7.1 pypi_0 ...
scikit-learn-extra 0.3.0 pypi_0 ...
scipy 1.17.1 pypi_0 ...
sentry-sdk 2.62.0 pypi_0 ...
setuptools 82.0.1 pyh332e...
six 1.17.0 pypi_0 ...
smmap 5.0.3 pypi_0 ...
stack-data 0.6.3 pypi_0 ...
sympy 1.14.0 pypi_0 ...
threadpoolctl 3.6.0 pypi_0 ...
tk 8.6.13 noxft_h...
torch 2.7.1 pypi_0 ...
torchaudio 2.7.1 pypi_0 ...
torchvision 0.22.1 pypi_0 ...
tqdm 4.67.1 pypi_0 ...
traitlets 5.15.1 pypi_0 ...
triton 3.3.1 pypi_0 ...
typing-extensions 4.15.0 pypi_0 ...
typing-inspection 0.4.2 pypi_0 ...
tzdata 2026.2 pypi_0 ...
urllib3 2.7.0 pypi_0 ...
wandb 0.21.1 pypi_0 ...
wcwidth 0.8.1 pypi_0 ...
wheel 0.47.0 pyhd8ed...
widgetsnbextension 4.0.15 pypi_0 ...
zstd 1.5.7 hb78ec9...
(protenix) [root@r9 ~]#
}}
確認
#code(nonumber){{
(protenix) [root@r9 ~]# python
Python 3.11.15 | packaged by conda-forge | (main, Jun 11 ...
Type "help", "copyright", "credits" or "license" for more...
>>> import torch
>>> print(torch.cuda.is_available())
True
>>> print(torch.cuda.get_device_name())
/apps/pyenv/versions/miniforge3-26.3.2-1/envs/protenix/li...
NVIDIA RTX PRO 2000 Blackwell with CUDA capability sm_120...
The current PyTorch install supports CUDA capabilities sm...
If you want to use the NVIDIA RTX PRO 2000 Blackwell GPU ...
warnings.warn(
NVIDIA RTX PRO 2000 Blackwell
>>> quit();
(protenix) [root@r9 ~]#
}}
っと今入っている torch 2.7.1 ではblackwellは無理みたい
なので差し替え
#code(nonumber){{
(protenix) [root@r9 ~]# python -m pip uninstall -y torch ...
(protenix) [root@r9 ~]# python -m pip cache purge
(protenix) [root@r9 ~]# python -m pip install --pre torch...
(protenix) [root@r9 ~]# conda list
:
numpy 2.4.1 pypi_0 ...
nvidia-cublas-cu12 12.8.3.14 pypi_0 ...
nvidia-cuda-cupti-cu12 12.8.57 pypi_0 ...
nvidia-cuda-nvrtc-cu12 12.8.61 pypi_0 ...
nvidia-cuda-runtime-cu12 12.8.57 pypi_0 ...
nvidia-cudnn-cu12 9.7.1.26 pypi_0 ...
nvidia-cufft-cu12 11.3.3.41 pypi_0 ...
nvidia-cufile-cu12 1.13.0.11 pypi_0 ...
nvidia-curand-cu12 10.3.9.55 pypi_0 ...
nvidia-cusolver-cu12 11.7.2.55 pypi_0 ...
nvidia-cusparse-cu12 12.5.7.53 pypi_0 ...
nvidia-cusparselt-cu12 0.6.3 pypi_0 ...
nvidia-ml-py 13.610.43 pypi_0 ...
nvidia-nccl-cu12 2.26.2 pypi_0 ...
nvidia-nvjitlink-cu12 12.8.61 pypi_0 ...
nvidia-nvtx-cu12 12.8.55 pypi_0 ...
openssl 3.6.3 h35e630...
:
python 3.11.15 h7508c3...
:
torch 2.7.1+cu128 pypi_0 ...
torchaudio 2.7.1+cu128 pypi_0 ...
torchvision 0.22.1+cu128 pypi_0 ...
:
(protenix) [root@r9 ~]#
(protenix) [root@r9 ~]# python
Python 3.11.15 | packaged by conda-forge | (main, Jun 11 ...
Type "help", "copyright", "credits" or "license" for more...
>>> import torch
>>> print(torch.cuda.is_available())
True
>>> print(torch.cuda.get_device_name())
NVIDIA RTX PRO 2000 Blackwell
>>> quit();
(protenix) [root@r9 ~]#
}}
***environment-modules [#fed55038]
「/apps/modulefiles/protenix」
#code(nonumber){{
#%Module
set root /apps/pyenv/versions/miniforge3-26.3.2-...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
***つかってみる [#w347da37]
#code(nonumber){{
[saber@r9 ~]$ module load protenix
[saber@r9 ~]$ cd test
[saber@r9 test]$ git clone https://github.com/bytedance/P...
Cloning into 'Protenix'...
remote: Enumerating objects: 2642, done.
remote: Total 2642 (delta 0), reused 0 (delta 0), pack-re...
Receiving objects: 100% (2642/2642), 105.22 MiB | 27.46 M...
Resolving deltas: 100% (1644/1644), done.
[saber@r9 test]$ cd Protenix/
[saber@r9 Protenix]$
[saber@r9 Protenix]$ protenix --version
protenix, version 2.0.0
[saber@r9 Protenix]$ protenix --help
Usage: protenix [OPTIONS] COMMAND [ARGS]...
Protenix: A trainable reproduction of AlphaFold 3.
This CLI provides tools for structure prediction, data ...
MSA/template searching.
Options:
--version Show the version and exit.
-h, --help Show this message and exit.
Commands:
json Convert PDB or CIF files to JSON files for Proten...
msa Perform MSA search using MMseqs2.
mt Perform MSA search followed by template search.
pred Run predictions with Protenix using various input...
prep Perform MSA search, template search, and RNA MSA ...
[saber@r9 Protenix]$
[saber@r9 Protenix]$
[saber@r9 Protenix]$ protenix pred -i examples/input.json...
}}
終了行:
本家様 [[https://github.com/bytedance/Protenix>+https://g...
pipy [[https://pypi.org/project/protenix/>+https://pypi.o...
Toward High-Accuracy Open-Source Biomolecular Structure P...
pipyのサイトからPython >=3.11みたい
***pyenv-anacondaの設置 [#y442193c]
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-26.3.2-1
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
}}
***Protenix のインストール [#h2fb44b7]
#code(nonumber){{
[root@r9 ~]# conda create -n protenix python=3.11 pip
[root@r9 ~]# conda activate protenix
(protenix) [root@r9 ~]# pip install protenix
(protenix) [root@r9 ~]# conda list
# packages in environment at /apps/pyenv/versions/minifor...
#
# Name Version Build ...
_openmp_mutex 4.5 20_gnu ...
absl-py 2.4.0 pypi_0 ...
annotated-types 0.7.0 pypi_0 ...
asttokens 3.0.1 pypi_0 ...
biopython 1.85 pypi_0 ...
biotite 1.4.0 pypi_0 ...
biotraj 1.2.2 pypi_0 ...
bzip2 1.0.8 hda65f4...
ca-certificates 2026.5.20 hbd8a1c...
certifi 2026.5.20 pypi_0 ...
charset-normalizer 3.4.7 pypi_0 ...
click 8.4.1 pypi_0 ...
colorama 0.4.6 pypi_0 ...
comm 0.2.3 pypi_0 ...
contourpy 1.3.3 pypi_0 ...
cuequivariance 0.10.0 pypi_0 ...
cuequivariance-ops-cu12 0.8.0 pypi_0 ...
cuequivariance-ops-torch-cu12 0.8.0 pypi_0 ...
cuequivariance-torch 0.8.0 pypi_0 ...
cycler 0.12.1 pypi_0 ...
decorator 5.3.1 pypi_0 ...
deepspeed 0.17.5 pypi_0 ...
einops 0.8.2 pypi_0 ...
executing 2.2.1 pypi_0 ...
fair-esm 2.0.0 pypi_0 ...
filelock 3.29.3 pypi_0 ...
fonttools 4.63.0 pypi_0 ...
fsspec 2026.4.0 pypi_0 ...
gemmi 0.6.7 pypi_0 ...
gitdb 4.0.12 pypi_0 ...
gitpython 3.1.50 pypi_0 ...
hjson 3.1.0 pypi_0 ...
icecream 2.1.7 pypi_0 ...
idna 3.18 pypi_0 ...
ihm 2.11 pypi_0 ...
ipdb 0.13.13 pypi_0 ...
ipython 9.14.1 pypi_0 ...
ipython-pygments-lexers 1.1.1 pypi_0 ...
ipywidgets 8.1.7 pypi_0 ...
jedi 0.20.0 pypi_0 ...
jinja2 3.1.6 pypi_0 ...
joblib 1.5.3 pypi_0 ...
jupyterlab-widgets 3.0.16 pypi_0 ...
kiwisolver 1.5.0 pypi_0 ...
ld_impl_linux-64 2.45.1 default...
libexpat 2.8.1 hecca71...
libffi 3.5.2 h343593...
libgcc 15.2.0 he0feb6...
libgcc-ng 15.2.0 h69a702...
libgomp 15.2.0 he0feb6...
liblzma 5.8.3 hb03c66...
libnsl 2.0.1 hb9d3cd...
libsqlite 3.53.2 h0c1763...
libuuid 2.42.1 h5347b4...
libxcrypt 4.4.36 hd59030...
libzlib 1.3.2 h25fd6f...
markupsafe 3.0.3 pypi_0 ...
matplotlib 3.10.5 pypi_0 ...
matplotlib-inline 0.2.2 pypi_0 ...
ml-collections 1.1.0 pypi_0 ...
modelcif 1.4 pypi_0 ...
mpmath 1.3.0 pypi_0 ...
msgpack 1.2.0 pypi_0 ...
ncurses 6.6 hdb1482...
networkx 3.6.1 pypi_0 ...
ninja 1.13.0 pypi_0 ...
numpy 2.4.1 pypi_0 ...
nvidia-cublas-cu12 12.6.4.1 pypi_0 ...
nvidia-cuda-cupti-cu12 12.6.80 pypi_0 ...
nvidia-cuda-nvrtc-cu12 12.6.77 pypi_0 ...
nvidia-cuda-runtime-cu12 12.6.77 pypi_0 ...
nvidia-cudnn-cu12 9.5.1.17 pypi_0 ...
nvidia-cufft-cu12 11.3.0.4 pypi_0 ...
nvidia-cufile-cu12 1.11.1.6 pypi_0 ...
nvidia-curand-cu12 10.3.7.77 pypi_0 ...
nvidia-cusolver-cu12 11.7.1.2 pypi_0 ...
nvidia-cusparse-cu12 12.5.4.2 pypi_0 ...
nvidia-cusparselt-cu12 0.6.3 pypi_0 ...
nvidia-ml-py 13.610.43 pypi_0 ...
nvidia-nccl-cu12 2.26.2 pypi_0 ...
nvidia-nvjitlink-cu12 12.6.85 pypi_0 ...
nvidia-nvtx-cu12 12.6.77 pypi_0 ...
openssl 3.6.3 h35e630...
opt-einsum 3.4.0 pypi_0 ...
optree 0.17.0 pypi_0 ...
packaging 26.2 pyhc364...
pandas 2.3.1 pypi_0 ...
parso 0.8.7 pypi_0 ...
pdbeccdutils 1.0.0 pypi_0 ...
pexpect 4.9.0 pypi_0 ...
pillow 12.2.0 pypi_0 ...
pip 26.1.2 pyh8b19...
platformdirs 4.10.0 pypi_0 ...
prompt-toolkit 3.0.52 pypi_0 ...
protenix 2.0.0 pypi_0 ...
protobuf 6.31.1 pypi_0 ...
psutil 7.2.2 pypi_0 ...
ptyprocess 0.7.0 pypi_0 ...
pure-eval 0.2.3 pypi_0 ...
py-cpuinfo 9.0.0 pypi_0 ...
py3dmol 2.5.2 pypi_0 ...
pydantic 2.13.4 pypi_0 ...
pydantic-core 2.46.4 pypi_0 ...
pygments 2.20.0 pypi_0 ...
pyparsing 3.3.2 pypi_0 ...
python 3.11.15 h7508c3...
python-dateutil 2.9.0.post0 pypi_0 ...
pytz 2026.2 pypi_0 ...
pyyaml 6.0.2 pypi_0 ...
rdkit 2025.9.3 pypi_0 ...
readline 8.3 h853b02...
requests 2.34.2 pypi_0 ...
scikit-learn 1.7.1 pypi_0 ...
scikit-learn-extra 0.3.0 pypi_0 ...
scipy 1.17.1 pypi_0 ...
sentry-sdk 2.62.0 pypi_0 ...
setuptools 82.0.1 pyh332e...
six 1.17.0 pypi_0 ...
smmap 5.0.3 pypi_0 ...
stack-data 0.6.3 pypi_0 ...
sympy 1.14.0 pypi_0 ...
threadpoolctl 3.6.0 pypi_0 ...
tk 8.6.13 noxft_h...
torch 2.7.1 pypi_0 ...
torchaudio 2.7.1 pypi_0 ...
torchvision 0.22.1 pypi_0 ...
tqdm 4.67.1 pypi_0 ...
traitlets 5.15.1 pypi_0 ...
triton 3.3.1 pypi_0 ...
typing-extensions 4.15.0 pypi_0 ...
typing-inspection 0.4.2 pypi_0 ...
tzdata 2026.2 pypi_0 ...
urllib3 2.7.0 pypi_0 ...
wandb 0.21.1 pypi_0 ...
wcwidth 0.8.1 pypi_0 ...
wheel 0.47.0 pyhd8ed...
widgetsnbextension 4.0.15 pypi_0 ...
zstd 1.5.7 hb78ec9...
(protenix) [root@r9 ~]#
}}
確認
#code(nonumber){{
(protenix) [root@r9 ~]# python
Python 3.11.15 | packaged by conda-forge | (main, Jun 11 ...
Type "help", "copyright", "credits" or "license" for more...
>>> import torch
>>> print(torch.cuda.is_available())
True
>>> print(torch.cuda.get_device_name())
/apps/pyenv/versions/miniforge3-26.3.2-1/envs/protenix/li...
NVIDIA RTX PRO 2000 Blackwell with CUDA capability sm_120...
The current PyTorch install supports CUDA capabilities sm...
If you want to use the NVIDIA RTX PRO 2000 Blackwell GPU ...
warnings.warn(
NVIDIA RTX PRO 2000 Blackwell
>>> quit();
(protenix) [root@r9 ~]#
}}
っと今入っている torch 2.7.1 ではblackwellは無理みたい
なので差し替え
#code(nonumber){{
(protenix) [root@r9 ~]# python -m pip uninstall -y torch ...
(protenix) [root@r9 ~]# python -m pip cache purge
(protenix) [root@r9 ~]# python -m pip install --pre torch...
(protenix) [root@r9 ~]# conda list
:
numpy 2.4.1 pypi_0 ...
nvidia-cublas-cu12 12.8.3.14 pypi_0 ...
nvidia-cuda-cupti-cu12 12.8.57 pypi_0 ...
nvidia-cuda-nvrtc-cu12 12.8.61 pypi_0 ...
nvidia-cuda-runtime-cu12 12.8.57 pypi_0 ...
nvidia-cudnn-cu12 9.7.1.26 pypi_0 ...
nvidia-cufft-cu12 11.3.3.41 pypi_0 ...
nvidia-cufile-cu12 1.13.0.11 pypi_0 ...
nvidia-curand-cu12 10.3.9.55 pypi_0 ...
nvidia-cusolver-cu12 11.7.2.55 pypi_0 ...
nvidia-cusparse-cu12 12.5.7.53 pypi_0 ...
nvidia-cusparselt-cu12 0.6.3 pypi_0 ...
nvidia-ml-py 13.610.43 pypi_0 ...
nvidia-nccl-cu12 2.26.2 pypi_0 ...
nvidia-nvjitlink-cu12 12.8.61 pypi_0 ...
nvidia-nvtx-cu12 12.8.55 pypi_0 ...
openssl 3.6.3 h35e630...
:
python 3.11.15 h7508c3...
:
torch 2.7.1+cu128 pypi_0 ...
torchaudio 2.7.1+cu128 pypi_0 ...
torchvision 0.22.1+cu128 pypi_0 ...
:
(protenix) [root@r9 ~]#
(protenix) [root@r9 ~]# python
Python 3.11.15 | packaged by conda-forge | (main, Jun 11 ...
Type "help", "copyright", "credits" or "license" for more...
>>> import torch
>>> print(torch.cuda.is_available())
True
>>> print(torch.cuda.get_device_name())
NVIDIA RTX PRO 2000 Blackwell
>>> quit();
(protenix) [root@r9 ~]#
}}
***environment-modules [#fed55038]
「/apps/modulefiles/protenix」
#code(nonumber){{
#%Module
set root /apps/pyenv/versions/miniforge3-26.3.2-...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
***つかってみる [#w347da37]
#code(nonumber){{
[saber@r9 ~]$ module load protenix
[saber@r9 ~]$ cd test
[saber@r9 test]$ git clone https://github.com/bytedance/P...
Cloning into 'Protenix'...
remote: Enumerating objects: 2642, done.
remote: Total 2642 (delta 0), reused 0 (delta 0), pack-re...
Receiving objects: 100% (2642/2642), 105.22 MiB | 27.46 M...
Resolving deltas: 100% (1644/1644), done.
[saber@r9 test]$ cd Protenix/
[saber@r9 Protenix]$
[saber@r9 Protenix]$ protenix --version
protenix, version 2.0.0
[saber@r9 Protenix]$ protenix --help
Usage: protenix [OPTIONS] COMMAND [ARGS]...
Protenix: A trainable reproduction of AlphaFold 3.
This CLI provides tools for structure prediction, data ...
MSA/template searching.
Options:
--version Show the version and exit.
-h, --help Show this message and exit.
Commands:
json Convert PDB or CIF files to JSON files for Proten...
msa Perform MSA search using MMseqs2.
mt Perform MSA search followed by template search.
pred Run predictions with Protenix using various input...
prep Perform MSA search, template search, and RNA MSA ...
[saber@r9 Protenix]$
[saber@r9 Protenix]$
[saber@r9 Protenix]$ protenix pred -i examples/input.json...
}}
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