Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
Home Page: https://discord.gg/7VckQVxvKk
License: MIT License
Describe the bug
Problems with local install.
To Reproduce
Steps to reproduce the behavior:
❯ pip install alphafold3
Collecting alphafold3
Using cached alphafold3-0.0.4-py3-none-any.whl.metadata (4.9 kB)
Collecting einops (from alphafold3)
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting openfold (from alphafold3)
Using cached openfold-0.0.1.tar.gz (164 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [17 lines of output]
Traceback (most recent call last):
File "/media/fkt/82c1c9f8-5b60-449e-b3b1-2710aabe45ee/learn_AF3/venv/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/media/fkt/82c1c9f8-5b60-449e-b3b1-2710aabe45ee/learn_AF3/venv/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/media/fkt/82c1c9f8-5b60-449e-b3b1-2710aabe45ee/learn_AF3/venv/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-8x0rxkos/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-8x0rxkos/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-8x0rxkos/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 487, in run_setup
super().run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-8x0rxkos/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 311, in run_setup
exec(code, locals())
File "<string>", line 19, in <module>
ModuleNotFoundError: No module named 'torch'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.Since I saw the ModuleNotFoundError: No module named 'torch' massage, I checked it but torch is already installed.
❯ pip list
Package Version
------------------------ ----------
filelock 3.14.0
fsspec 2024.3.1
Jinja2 3.1.4
MarkupSafe 2.1.5
mpmath 1.3.0
networkx 3.3
nvidia-cublas-cu12 12.1.3.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12 8.9.2.26
nvidia-cufft-cu12 11.0.2.54
nvidia-curand-cu12 10.3.2.106
nvidia-cusolver-cu12 11.4.5.107
nvidia-cusparse-cu12 12.1.0.106
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.4.127
nvidia-nvtx-cu12 12.1.105
pip 24.0
setuptools 65.5.0
sympy 1.12
torch 2.3.0
triton 2.3.0
typing_extensions 4.11.0
I had the same issue #2, however, when I installed torch+cu117 manually,
pip install -U torch==2.0.0+cu117 torchtext==0.15.1 --extra-index-url https://download.pytorch.org/whl/cu117
this problem was gone.
However, now, I am seeing the different problem,
pip install alphafold3
Collecting alphafold3
Using cached alphafold3-0.0.4-py3-none-any.whl.metadata (4.9 kB)
Collecting einops (from alphafold3)
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting openfold (from alphafold3)
Using cached openfold-0.0.1.tar.gz (164 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [6 lines of output]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-8nl_52c_/openfold_e8ccf631ed2748ad8eff0a1e6a8da60b/setup.py", line 21, in <module>
from scripts.utils import get_nvidia_cc
ModuleNotFoundError: No module named 'scripts'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
with python3.10 (or higher version) showing up when I try to install openfold alone.
Many Thanks,
Thanks for your job~
Thanks a lot for your work.
May I ask a naive question on how to submit the sequence of the target protein to the model? Kind for your reply
Describe the bug
I tried to pip install AlphaFold3 locally on a Linux server, but encountered an error ( "ModuleNotFoundError: No modulel name 'scripts'.").
$ pip install alphafold3
ERROR: Could not find a version that satisfies the requirement alphafold3 (from versions: none)
ERROR: No matching distribution found for alphafold3
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