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#author("2026-06-03T18:11:04+00:00","default:sysosa","sysosa") github [[https://github.com/RosettaCommons/foundry>+https://github.com/RosettaCommons/foundry]] pipy [[https://pypi.org/project/rc-foundry/>+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]" #code(nonumber){{ (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
