Foundry をテンプレートにして作成
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開始行:
github [[https://github.com/RosettaCommons/foundry>+https...
pipy [[https://pypi.org/project/rc-foundry/>+https://pypi...
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...
conda create -n rc-foundry python=3.12 pip
conda activate rc-foundry
pip install "rc-foundry[all]"
#code(nonumber){{
(rc-foundry) root@ubuntu24:~# 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 ...
aiohappyeyeballs 2.6.2 pypi_0 ...
aiohttp 3.14.0 pypi_0 ...
aiosignal 1.4.0 pypi_0 ...
annotated-doc 0.0.4 pypi_0 ...
annotated-types 0.7.0 pypi_0 ...
antlr4-python3-runtime 4.9.3 pypi_0 ...
assertpy 1.1 pypi_0 ...
asttokens 3.0.1 pypi_0 ...
atomworks 2.2.0 pypi_0 ...
attrs 26.1.0 pypi_0 ...
beartype 0.22.9 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 ...
comm 0.2.3 pypi_0 ...
cuequivariance 0.10.0 pypi_0 ...
cuequivariance-ops-cu12 0.10.0 pypi_0 ...
cuequivariance-ops-torch-cu12 0.10.0 pypi_0 ...
cuequivariance-torch 0.10.0 pypi_0 ...
cython 3.2.5 pypi_0 ...
cytoolz 0.12.3 pypi_0 ...
debugpy 1.8.21 pypi_0 ...
decorator 5.3.1 pypi_0 ...
dm-tree 0.1.10 pypi_0 ...
einops 0.8.2 pypi_0 ...
einx 0.4.3 pypi_0 ...
environs 11.2.1 pypi_0 ...
executing 2.2.1 pypi_0 ...
filelock 3.29.1 pypi_0 ...
frozendict 2.4.7 pypi_0 ...
frozenlist 1.8.0 pypi_0 ...
fsspec 2026.4.0 pypi_0 ...
gitdb 4.0.12 pypi_0 ...
gitpython 3.1.50 pypi_0 ...
hydra-core 1.3.2 pypi_0 ...
hydride 1.2.3 pypi_0 ...
idna 3.18 pypi_0 ...
ipykernel 7.2.0 pypi_0 ...
ipython 9.14.0 pypi_0 ...
ipython-pygments-lexers 1.1.1 pypi_0 ...
jaxtyping 0.3.10 pypi_0 ...
jedi 0.20.0 pypi_0 ...
jinja2 3.1.6 pypi_0 ...
jupyter-client 8.8.0 pypi_0 ...
jupyter-core 5.9.1 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 3.53.1 h0c1763...
libuuid 2.42.1 h5347b4...
libxcrypt 4.4.36 hd59030...
libzlib 1.3.2 h25fd6f...
lightning 2.6.5 pypi_0 ...
lightning-utilities 0.15.3 pypi_0 ...
loralib 0.1.2 pypi_0 ...
markdown-it-py 4.2.0 pypi_0 ...
markupsafe 3.0.3 pypi_0 ...
marshmallow 4.3.0 pypi_0 ...
matplotlib-inline 0.2.2 pypi_0 ...
mdurl 0.1.2 pypi_0 ...
mpmath 1.3.0 pypi_0 ...
msgpack 1.1.2 pypi_0 ...
multidict 6.7.1 pypi_0 ...
ncurses 6.6 hdb1482...
nest-asyncio 1.6.0 pypi_0 ...
networkx 3.6.1 pypi_0 ...
numpy 2.4.6 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 ...
omegaconf 2.3.0 pypi_0 ...
openssl 3.6.2 h35e630...
opt-einsum 3.4.0 pypi_0 ...
packaging 26.2 pyhc364...
pandas 2.3.3 pypi_0 ...
parso 0.8.7 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 ...
propcache 0.5.2 pypi_0 ...
protobuf 7.35.0 pypi_0 ...
psutil 7.2.2 pypi_0 ...
ptyprocess 0.7.0 pypi_0 ...
pure-eval 0.2.3 pypi_0 ...
py3dmol 2.5.5 pypi_0 ...
pyarrow 17.0.0 pypi_0 ...
pydantic 2.13.4 pypi_0 ...
pydantic-core 2.46.4 pypi_0 ...
pygments 2.20.0 pypi_0 ...
pymol-remote 1.1.0 pypi_0 ...
python 3.12.13 hd63d67...
python-dateutil 2.9.0.post0 pypi_0 ...
python-dotenv 1.2.2 pypi_0 ...
pytorch-lightning 2.6.5 pypi_0 ...
pytz 2026.2 pypi_0 ...
pyyaml 6.0.3 pypi_0 ...
pyzmq 27.1.0 pypi_0 ...
rc-foundry 0.1.12 pypi_0 ...
rdkit 2025.3.6 pypi_0 ...
readline 8.3 h853b02...
requests 2.34.2 pypi_0 ...
rich 15.0.0 pypi_0 ...
rootutils 1.0.7 pypi_0 ...
scipy 1.17.1 pypi_0 ...
sentry-sdk 2.61.1 pypi_0 ...
setuptools 81.0.0 pypi_0 ...
shellingham 1.5.4 pypi_0 ...
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 ...
tk 8.6.13 noxft_h...
toolz 1.1.0 pypi_0 ...
torch 2.7.1 pypi_0 ...
torchmetrics 1.9.0 pypi_0 ...
tornado 6.5.6 pypi_0 ...
tqdm 4.67.3 pypi_0 ...
traitlets 5.15.1 pypi_0 ...
triton 3.3.1 pypi_0 ...
typer 0.26.7 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 ...
wadler-lindig 0.1.7 pypi_0 ...
wandb 0.27.0 pypi_0 ...
wcwidth 0.7.0 pypi_0 ...
wheel 0.47.0 pyhd8ed...
wrapt 2.2.1 pypi_0 ...
yarl 1.24.2 pypi_0 ...
zstandard 0.25.0 pypi_0 ...
zstd 1.5.7 hb78ec9...
(rc-foundry) root@ubuntu24:~#
}}
foundry install rfd3 --checkpoint-dir <path/to/ckpt/dir>
rfd3 design out_dir=logs/inference_outs/demo/0 inputs=mod...
終了行:
github [[https://github.com/RosettaCommons/foundry>+https...
pipy [[https://pypi.org/project/rc-foundry/>+https://pypi...
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...
conda create -n rc-foundry python=3.12 pip
conda activate rc-foundry
pip install "rc-foundry[all]"
#code(nonumber){{
(rc-foundry) root@ubuntu24:~# 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 ...
aiohappyeyeballs 2.6.2 pypi_0 ...
aiohttp 3.14.0 pypi_0 ...
aiosignal 1.4.0 pypi_0 ...
annotated-doc 0.0.4 pypi_0 ...
annotated-types 0.7.0 pypi_0 ...
antlr4-python3-runtime 4.9.3 pypi_0 ...
assertpy 1.1 pypi_0 ...
asttokens 3.0.1 pypi_0 ...
atomworks 2.2.0 pypi_0 ...
attrs 26.1.0 pypi_0 ...
beartype 0.22.9 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 ...
comm 0.2.3 pypi_0 ...
cuequivariance 0.10.0 pypi_0 ...
cuequivariance-ops-cu12 0.10.0 pypi_0 ...
cuequivariance-ops-torch-cu12 0.10.0 pypi_0 ...
cuequivariance-torch 0.10.0 pypi_0 ...
cython 3.2.5 pypi_0 ...
cytoolz 0.12.3 pypi_0 ...
debugpy 1.8.21 pypi_0 ...
decorator 5.3.1 pypi_0 ...
dm-tree 0.1.10 pypi_0 ...
einops 0.8.2 pypi_0 ...
einx 0.4.3 pypi_0 ...
environs 11.2.1 pypi_0 ...
executing 2.2.1 pypi_0 ...
filelock 3.29.1 pypi_0 ...
frozendict 2.4.7 pypi_0 ...
frozenlist 1.8.0 pypi_0 ...
fsspec 2026.4.0 pypi_0 ...
gitdb 4.0.12 pypi_0 ...
gitpython 3.1.50 pypi_0 ...
hydra-core 1.3.2 pypi_0 ...
hydride 1.2.3 pypi_0 ...
idna 3.18 pypi_0 ...
ipykernel 7.2.0 pypi_0 ...
ipython 9.14.0 pypi_0 ...
ipython-pygments-lexers 1.1.1 pypi_0 ...
jaxtyping 0.3.10 pypi_0 ...
jedi 0.20.0 pypi_0 ...
jinja2 3.1.6 pypi_0 ...
jupyter-client 8.8.0 pypi_0 ...
jupyter-core 5.9.1 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 3.53.1 h0c1763...
libuuid 2.42.1 h5347b4...
libxcrypt 4.4.36 hd59030...
libzlib 1.3.2 h25fd6f...
lightning 2.6.5 pypi_0 ...
lightning-utilities 0.15.3 pypi_0 ...
loralib 0.1.2 pypi_0 ...
markdown-it-py 4.2.0 pypi_0 ...
markupsafe 3.0.3 pypi_0 ...
marshmallow 4.3.0 pypi_0 ...
matplotlib-inline 0.2.2 pypi_0 ...
mdurl 0.1.2 pypi_0 ...
mpmath 1.3.0 pypi_0 ...
msgpack 1.1.2 pypi_0 ...
multidict 6.7.1 pypi_0 ...
ncurses 6.6 hdb1482...
nest-asyncio 1.6.0 pypi_0 ...
networkx 3.6.1 pypi_0 ...
numpy 2.4.6 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 ...
omegaconf 2.3.0 pypi_0 ...
openssl 3.6.2 h35e630...
opt-einsum 3.4.0 pypi_0 ...
packaging 26.2 pyhc364...
pandas 2.3.3 pypi_0 ...
parso 0.8.7 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 ...
propcache 0.5.2 pypi_0 ...
protobuf 7.35.0 pypi_0 ...
psutil 7.2.2 pypi_0 ...
ptyprocess 0.7.0 pypi_0 ...
pure-eval 0.2.3 pypi_0 ...
py3dmol 2.5.5 pypi_0 ...
pyarrow 17.0.0 pypi_0 ...
pydantic 2.13.4 pypi_0 ...
pydantic-core 2.46.4 pypi_0 ...
pygments 2.20.0 pypi_0 ...
pymol-remote 1.1.0 pypi_0 ...
python 3.12.13 hd63d67...
python-dateutil 2.9.0.post0 pypi_0 ...
python-dotenv 1.2.2 pypi_0 ...
pytorch-lightning 2.6.5 pypi_0 ...
pytz 2026.2 pypi_0 ...
pyyaml 6.0.3 pypi_0 ...
pyzmq 27.1.0 pypi_0 ...
rc-foundry 0.1.12 pypi_0 ...
rdkit 2025.3.6 pypi_0 ...
readline 8.3 h853b02...
requests 2.34.2 pypi_0 ...
rich 15.0.0 pypi_0 ...
rootutils 1.0.7 pypi_0 ...
scipy 1.17.1 pypi_0 ...
sentry-sdk 2.61.1 pypi_0 ...
setuptools 81.0.0 pypi_0 ...
shellingham 1.5.4 pypi_0 ...
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 ...
tk 8.6.13 noxft_h...
toolz 1.1.0 pypi_0 ...
torch 2.7.1 pypi_0 ...
torchmetrics 1.9.0 pypi_0 ...
tornado 6.5.6 pypi_0 ...
tqdm 4.67.3 pypi_0 ...
traitlets 5.15.1 pypi_0 ...
triton 3.3.1 pypi_0 ...
typer 0.26.7 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 ...
wadler-lindig 0.1.7 pypi_0 ...
wandb 0.27.0 pypi_0 ...
wcwidth 0.7.0 pypi_0 ...
wheel 0.47.0 pyhd8ed...
wrapt 2.2.1 pypi_0 ...
yarl 1.24.2 pypi_0 ...
zstandard 0.25.0 pypi_0 ...
zstd 1.5.7 hb78ec9...
(rc-foundry) root@ubuntu24:~#
}}
foundry install rfd3 --checkpoint-dir <path/to/ckpt/dir>
rfd3 design out_dir=logs/inference_outs/demo/0 inputs=mod...
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