alphafold3

(★ 8,479)

AlphaFold 3 inference pipeline.

Owner Repos

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No description provided.

Python

File Explorer

ZIP Download
  • CMakeLists.txt
  • CONTRIBUTING.md
  • fetch_databases.sh
  • LICENSE
  • OUTPUT_TERMS_OF_USE.md
  • pyproject.toml
  • README.md
  • run_alphafold.py
  • run_alphafold_data_test.py
  • run_alphafold_test.py
  • uv.lock
  • WEIGHTS_PROHIBITED_USE_POLICY.md
  • WEIGHTS_TERMS_OF_USE.md

# Installation Guide

docker
Prerequisites

Setup Steps

docker build -f docker/Dockerfile -t alphafold3 .

Build the AlphaFold 3 Docker image.

docker run -it --volume $HOME/af_input:/root/af_input --volume $HOME/af_output:/root/af_output --volume <MODEL_PARAMETERS_DIR>:/root/models --volume <DATABASES_DIR>:/root/public_databases --gpus all alphafold3 python run_alphafold.py --json_path=/root/af_input/fold_input.json --model_dir=/root/models --output_dir=/root/af_output

Run the Docker container to perform prediction.

Key Commands

python run_alphafold.py --json_path=/root/af_input/fold_input.json --model_dir=/root/models --output_dir=/root/af_output

Runs the AlphaFold 3 inference pipeline.

You must mount the model parameters and public databases directories as volumes when running Docker.

# Use via CDN

jsDelivr

jsDelivr serves any public GitHub repository as a CDN with zero setup. Pick a version and a file to get a ready-to-paste link and snippet.

Link
Example

Command Glossary

Commands referenced in this DOCs, explained below.

🔍

docker run

View Details ▼

This command is an alias of `docker container run`.

tldr docker container run

View documentation for the original command:

🔍

python

View Details ▼

Python language interpreter.

python

Start a REPL (interactive shell):

python {{path/to/file.py}}

Execute a specific Python file:

python -i {{path/to/file.py}}

Execute a specific Python file and start a REPL:

// repository documentation