alphafold3.cpp Module Not Found During Execution

[ShiyiLin0922]

Question: alphafold3.cpp Module Not Found During Execution

Hello, I am trying to run run_alphafold.py from the AlphaFold 3 repository. However, I encountered the following issue: 🥺

ModuleNotFoundError: No module named 'alphafold3.cpp'

Steps I Followed:

1. I cloned the repository and set up the environment as described in the installation instructions.
2. Due to the limitations of cluster permissions, I did not use Docker, but instead configured the dependency packages in a conda environment.
3. Ran the script run_alphafold.py.

Observations:

• The error suggests that the alphafold3.cpp module is missing.
• The repository includes a file named cpp.cc under src/alphafold3/.
• However, the installation instructions did not mention compiling this file or how to generate the necessary .so module.

File Directory Structure:

Here is the file structure of the repository (partial):

alphafold3/
├── src/
│   └── alphafold3/
│       ├── __init__.py
│       ├── cpp.cc
│       ├── data/
│       │   └── cpp/
│       ├── structure/
│       │   ├── __init__.py
│       │   ├── bioassemblies.py
│       │   ├── mmcif.py
│       │   ├── cpp/
│       ├── parsers/
│       │   └── cpp/
│       ├── model/
│       ├── constants/
│       └── common/
├── requirements.txt
├── pyproject.toml
├── run_alphafold.py
├── CMakeLists.txt
├── ……

Note: I have not made any modifications to the directory structure, so it is identical to the one directly cloned from GitHub.

Questions: 🥺

1. Is cpp.cc supposed to be compiled into a shared library (e.g., .so file)? If yes, could you clarify the steps to compile it?
2. Could the manual setup using Conda instead of Docker cause this issue? If so, how can I troubleshoot or resolve it?
3. Are the current locations of the cpp.cc file and other modules correct, or do they need to be moved to a different directory for proper loading and execution?

Thank you for your help! 🥰

[alchemistcai]

I use conda too.Have you run pip install . --no-deps after pip install -r dev-requirements.txt?

This command copys modules and compiles the cpp into your conda environment.

I wrote a easy install guidance in #49 if you want some help.