alphafold

(★ 14,796)

Open source code for AlphaFold 2.

Owner Repos

deepmind-research ★ 15,157

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AlphaFold 3 inference pipeline.

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No description provided.

Python

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  • .dockerignore
  • conftest.py
  • CONTRIBUTING.md
  • LICENSE
  • pyproject.toml
  • README.md
  • requirements.txt
  • run_alphafold.py
  • run_alphafold_test.py

# Installation Guide

docker
Prerequisites

Setup Steps

git clone https://github.com/deepmind/alphafold.git

Clone the repository.

scripts/download_all_data.sh <DOWNLOAD_DIR>

Download genetic databases and parameters.

docker build -f docker/Dockerfile -t alphafold .

Build the Docker image.

pip3 install -r docker/requirements.txt

Install runner dependencies.

python3 docker/run_docker.py --fasta_paths=your_protein.fasta --max_template_date=2022-01-01 --data_dir=$DOWNLOAD_DIR --output_dir=/home/user/absolute_path_to_the_output_dir

Run prediction via Docker.

Key Commands

scripts/download_all_data.sh /path/to/download_dir

Download all required genetic databases and model parameters for AlphaFold.

docker build -f docker/Dockerfile -t alphafold .

Build the AlphaFold Docker image based on the Dockerfile.

pip3 install -r docker/requirements.txt

Install Python dependencies required for the Docker run script.

python3 docker/run_docker.py --fasta_paths=protein.fasta --max_template_date=2022-01-01 --data_dir=/data --output_dir=/output

Run AlphaFold inference in a Docker environment using a protein FASTA file.

The download directory should not be a subdirectory inside the AlphaFold repository and requires large SSD storage.

# 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.

🔍

aria2

View Details ▼

This command is an alias of `aria2c`.

tldr aria2c

View documentation for the updated command:

🔍

aria2c

View Details ▼

Fast download utility.
Supports HTTP(S), FTP, SFTP, BitTorrent, and Metalink.
See also: `axel`.

aria2c "{{url}}"

Download a specific URI to a file:

aria2c {{[-o|--out]}} {{path/to/file}} "{{url}}"

Download a file from a URI with a specific output name:

aria2c {{[-Z|--force-sequential=true]}} {{"url1" "url2" ...}}

Download multiple different files in parallel:

🔍

docker build

View Details ▼

Build an image from a Dockerfile.

docker build .

Build a Docker image using the Dockerfile in the current directory:

docker build {{github.com/creack/docker-firefox}}

Build a Docker image from a Dockerfile at a specified URL:

docker build {{[-t|--tag]}} {{name:tag}} .

Build a Docker image and tag it:

🔍

docker run

View Details ▼

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

tldr docker container run

View documentation for the original command:

🔍

git clone

View Details ▼

Clone an existing repository.

git clone {{remote_repository_location}} {{path/to/directory}}

Clone an existing repository into a new directory (the default directory is the repository name):

git clone --recursive {{remote_repository_location}}

Clone an existing repository and its submodules:

git clone {{[-n|--no-checkout]}} {{remote_repository_location}}

Clone only the `.git` directory of an existing repository:

🔍

pickle

View Details ▼

A PHP extension installer based on Composer.

pickle install {{extension_name}}

Install a specific PHP extension:

pickle convert {{path/to/directory}}

Convert an existing PECL extension configuration to a Pickle configuration file:

pickle validate {{path/to/directory}}

Validate a PECL extension:

🔍

pip3

View Details ▼

This command is an alias of `pip`.

tldr pip

View documentation for the original command:

🔍

python3

View Details ▼

This command is an alias of `python`.

tldr python

View documentation for the original command:

🔍

rsync

View Details ▼

Transfer files either to or from a remote host (but not between two remote hosts), by default using SSH.
To specify a remote path, use `user@host:path/to/file_or_directory`.

rsync {{path/to/source}} {{path/to/destination}}

Transfer a file (use `--dry-run` to simulate the transfer):

rsync {{[-a|--archive]}} {{path/to/source}} {{path/to/destination}}

Use archive mode (recursively copy directories, copy symlinks without resolving, and preserve permissions, ownership, and modification times):

rsync {{[-zvhP|--compress --verbose --human-readable --partial --progress]}} {{path/to/source}} {{path/to/destination}}

Compress the data as it is sent to the destination, display verbose and human-readable progress, and keep partially transferred files if interrupted:

🔍

serve

View Details ▼

Static file serving and directory listing.

serve

Start an HTTP server listening on the default port to serve the current directory:

serve -p {{port}} {{path/to/directory}}

Start an HTTP server on a specific [p]ort to serve a specific directory:

serve {{[-C|--cors]}}

Start an HTTP server with CORS enabled by including the `Access-Control-Allow-Origin: *` header in all responses:

🔍

apt install

View Details ▼

Install packages for Debian-based distributions.

sudo apt install {{package}}

Install a package, or update it to the latest version:

sudo apt install {{[-V|--verbose-versions]}} {{package}}

Display verbose package version information during installation or update:

// repository documentation