![[PukiWiki]](image/picc.png "[PukiWiki]")
github https://github.com/RosettaCommons/foundry
pipy https://pypi.org/project/rc-foundry/
Protein design with Foundry
RFdiffusion3 (RFD3)
RosettaFold3 (RF3)
ProteinMPNN
pipyの内容から 「Python <3.13, >=3.12」なので python 3.12を選択
conda create -n rc-foundry python=3.12 pip
conda activate rc-foundry
pip install "rc-foundry[all]"
(rc-foundry) root@ubuntu24:~# conda list
# packages in environment at /apps/pyenv/versions/miniforge3-26.3.2-1/envs/rc-foundry:
#
# Name Version Build Channel
_openmp_mutex 4.5 20_gnu conda-forge
absl-py 2.4.0 pypi_0 pypi
aiohappyeyeballs 2.6.2 pypi_0 pypi
aiohttp 3.14.0 pypi_0 pypi
aiosignal 1.4.0 pypi_0 pypi
annotated-doc 0.0.4 pypi_0 pypi
annotated-types 0.7.0 pypi_0 pypi
antlr4-python3-runtime 4.9.3 pypi_0 pypi
assertpy 1.1 pypi_0 pypi
asttokens 3.0.1 pypi_0 pypi
atomworks 2.2.0 pypi_0 pypi
attrs 26.1.0 pypi_0 pypi
beartype 0.22.9 pypi_0 pypi
biotite 1.4.0 pypi_0 pypi
biotraj 1.2.2 pypi_0 pypi
bzip2 1.0.8 hda65f42_9 conda-forge
ca-certificates 2026.5.20 hbd8a1cb_0 conda-forge
certifi 2026.5.20 pypi_0 pypi
charset-normalizer 3.4.7 pypi_0 pypi
click 8.4.1 pypi_0 pypi
comm 0.2.3 pypi_0 pypi
cuequivariance 0.10.0 pypi_0 pypi
cuequivariance-ops-cu12 0.10.0 pypi_0 pypi
cuequivariance-ops-torch-cu12 0.10.0 pypi_0 pypi
cuequivariance-torch 0.10.0 pypi_0 pypi
cython 3.2.5 pypi_0 pypi
cytoolz 0.12.3 pypi_0 pypi
debugpy 1.8.21 pypi_0 pypi
decorator 5.3.1 pypi_0 pypi
dm-tree 0.1.10 pypi_0 pypi
einops 0.8.2 pypi_0 pypi
einx 0.4.3 pypi_0 pypi
environs 11.2.1 pypi_0 pypi
executing 2.2.1 pypi_0 pypi
filelock 3.29.1 pypi_0 pypi
frozendict 2.4.7 pypi_0 pypi
frozenlist 1.8.0 pypi_0 pypi
fsspec 2026.4.0 pypi_0 pypi
gitdb 4.0.12 pypi_0 pypi
gitpython 3.1.50 pypi_0 pypi
hydra-core 1.3.2 pypi_0 pypi
hydride 1.2.3 pypi_0 pypi
idna 3.18 pypi_0 pypi
ipykernel 7.2.0 pypi_0 pypi
ipython 9.14.0 pypi_0 pypi
ipython-pygments-lexers 1.1.1 pypi_0 pypi
jaxtyping 0.3.10 pypi_0 pypi
jedi 0.20.0 pypi_0 pypi
jinja2 3.1.6 pypi_0 pypi
jupyter-client 8.8.0 pypi_0 pypi
jupyter-core 5.9.1 pypi_0 pypi
ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge
libexpat 2.8.1 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libgcc 15.2.0 he0feb66_19 conda-forge
libgcc-ng 15.2.0 h69a702a_19 conda-forge
libgomp 15.2.0 he0feb66_19 conda-forge
liblzma 5.8.3 hb03c661_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libsqlite 3.53.1 h0c1763c_0 conda-forge
libuuid 2.42.1 h5347b49_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.2 h25fd6f3_2 conda-forge
lightning 2.6.5 pypi_0 pypi
lightning-utilities 0.15.3 pypi_0 pypi
loralib 0.1.2 pypi_0 pypi
markdown-it-py 4.2.0 pypi_0 pypi
markupsafe 3.0.3 pypi_0 pypi
marshmallow 4.3.0 pypi_0 pypi
matplotlib-inline 0.2.2 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
msgpack 1.1.2 pypi_0 pypi
multidict 6.7.1 pypi_0 pypi
ncurses 6.6 hdb14827_0 conda-forge
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.6.1 pypi_0 pypi
numpy 2.4.6 pypi_0 pypi
nvidia-cublas-cu12 12.6.4.1 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.6.80 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.6.77 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.6.77 pypi_0 pypi
nvidia-cudnn-cu12 9.5.1.17 pypi_0 pypi
nvidia-cufft-cu12 11.3.0.4 pypi_0 pypi
nvidia-cufile-cu12 1.11.1.6 pypi_0 pypi
nvidia-curand-cu12 10.3.7.77 pypi_0 pypi
nvidia-cusolver-cu12 11.7.1.2 pypi_0 pypi
nvidia-cusparse-cu12 12.5.4.2 pypi_0 pypi
nvidia-cusparselt-cu12 0.6.3 pypi_0 pypi
nvidia-ml-py 13.610.43 pypi_0 pypi
nvidia-nccl-cu12 2.26.2 pypi_0 pypi
nvidia-nvjitlink-cu12 12.6.85 pypi_0 pypi
nvidia-nvtx-cu12 12.6.77 pypi_0 pypi
omegaconf 2.3.0 pypi_0 pypi
openssl 3.6.2 h35e630c_0 conda-forge
opt-einsum 3.4.0 pypi_0 pypi
packaging 26.2 pyhc364b38_0 conda-forge
pandas 2.3.3 pypi_0 pypi
parso 0.8.7 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
pillow 12.2.0 pypi_0 pypi
pip 26.1.2 pyh8b19718_0 conda-forge
platformdirs 4.10.0 pypi_0 pypi
prompt-toolkit 3.0.52 pypi_0 pypi
propcache 0.5.2 pypi_0 pypi
protobuf 7.35.0 pypi_0 pypi
psutil 7.2.2 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.3 pypi_0 pypi
py3dmol 2.5.5 pypi_0 pypi
pyarrow 17.0.0 pypi_0 pypi
pydantic 2.13.4 pypi_0 pypi
pydantic-core 2.46.4 pypi_0 pypi
pygments 2.20.0 pypi_0 pypi
pymol-remote 1.1.0 pypi_0 pypi
python 3.12.13 hd63d673_0_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-dotenv 1.2.2 pypi_0 pypi
pytorch-lightning 2.6.5 pypi_0 pypi
pytz 2026.2 pypi_0 pypi
pyyaml 6.0.3 pypi_0 pypi
pyzmq 27.1.0 pypi_0 pypi
rc-foundry 0.1.12 pypi_0 pypi
rdkit 2025.3.6 pypi_0 pypi
readline 8.3 h853b02a_0 conda-forge
requests 2.34.2 pypi_0 pypi
rich 15.0.0 pypi_0 pypi
rootutils 1.0.7 pypi_0 pypi
scipy 1.17.1 pypi_0 pypi
sentry-sdk 2.61.1 pypi_0 pypi
setuptools 81.0.0 pypi_0 pypi
shellingham 1.5.4 pypi_0 pypi
six 1.17.0 pypi_0 pypi
smmap 5.0.3 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
sympy 1.14.0 pypi_0 pypi
tk 8.6.13 noxft_h366c992_103 conda-forge
toolz 1.1.0 pypi_0 pypi
torch 2.7.1 pypi_0 pypi
torchmetrics 1.9.0 pypi_0 pypi
tornado 6.5.6 pypi_0 pypi
tqdm 4.67.3 pypi_0 pypi
traitlets 5.15.1 pypi_0 pypi
triton 3.3.1 pypi_0 pypi
typer 0.26.7 pypi_0 pypi
typing-extensions 4.15.0 pypi_0 pypi
typing-inspection 0.4.2 pypi_0 pypi
tzdata 2026.2 pypi_0 pypi
urllib3 2.7.0 pypi_0 pypi
wadler-lindig 0.1.7 pypi_0 pypi
wandb 0.27.0 pypi_0 pypi
wcwidth 0.7.0 pypi_0 pypi
wheel 0.47.0 pyhd8ed1ab_0 conda-forge
wrapt 2.2.1 pypi_0 pypi
yarl 1.24.2 pypi_0 pypi
zstandard 0.25.0 pypi_0 pypi
zstd 1.5.7 hb78ec9c_6 conda-forge
(rc-foundry) root@ubuntu24:~#foundry install rfd3 --checkpoint-dir <path/to/ckpt/dir>
rfd3 design out_dir=logs/inference_outs/demo/0 inputs=models/rfd3/docs/examples/demo.json skip_existing=False dump_trajectories=True prevalidate_inputs=True
