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AutoDock-Vina-Docker

AutoDock Release AutoDock Develop MGLTools Image License

Package AutoDock Vina, ADFR suite, Meeko, MGLTools into Docker image.

Notice: Please makesure you will obey the License of AutoDock Vina, ADFR software suite Non-Commercial Use, Meeko before downloading this Docker image.

Introduction

We provide vina, vina-python, vina-all package for you to choose. Please refer to the table below to compare the differences.

Package Included programs Arch
vina vina binary, vice versa amd64/arm64
vina-python vina binary, vice versa, vina python bindings, Meeko amd64/arm64
vina-all vina binary, vice versa, vina python bindings, Meeko, ADFR Suite amd64
AutoDockTools (MGLTools) MGLTools amd64

Because of the lack arm64 support of ADFR Suite and MGLTools, we can't provide arm64 images with ADFR Suite and MGLTools.

Get Docker Image

⚠️Warning: The release tag is deprecated, use a specific tag for a specific release version instead.

From Github

# vina

# Build from certain version like "v1.2.5"
# To check full version supported, please click https://github.com/Metaphorme/AutoDock-Vina-Docker/pkgs/container/vina
docker pull ghcr.io/metaphorme/vina:v1.2.5

# Build from https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop
docker pull ghcr.io/metaphorme/vina:develop

# vina-python

# Build from certain version like "v1.2.5"
# To check full version supported, please click https://github.com/Metaphorme/AutoDock-Vina-Docker/pkgs/container/vina-python
docker pull ghcr.io/metaphorme/vina-python:v1.2.5

# Build from https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop
docker pull ghcr.io/metaphorme/vina-python:develop

# vina-all

# Build from certain version like "v1.2.5"
# To check full version supported, please click https://github.com/Metaphorme/AutoDock-Vina-Docker/pkgs/container/vina-all
docker pull ghcr.io/metaphorme/vina-all:v1.2.5

# Build from https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop
docker pull ghcr.io/metaphorme/vina-all:develop

# MGLTools
docker pull ghcr.io/metaphorme/mgltools

Build in local

git clone https://github.com/Metaphorme/AutoDock-Vina-Docker.git
cd AutoDock-Vina-Docker
# To build Dockerfile-vina* image
TAG_NAME=v1.2.5
docker build --build-arg BRANCHES=$TAG_NAME -t $TAG_NAME - < Dockerfile-vina-[name]
# To build MGLTools image
docker build -t mgltools - < Dockerfile-mgltools

Run Docker Image

vina

  • Exec commands and mount $PWD to /data

    docker run -v $PWD:/data --rm ghcr.io/metaphorme/vina:v1.2.5 \
      vina --ligand 1iep_ligand.pdbqt --maps 1iep_receptor --scoring ad4 \
           --exhaustiveness 32 --out 1iep_ligand_ad4_out.pdbqt

​ Notice: $PWD means the current working directory; /data is contained in $PATH.

vina-python

  • Enter the shell and mount $PWD to /data

    docker run -it -v $PWD:/data --rm ghcr.io/metaphorme/vina-python:v1.2.5

    Notice: $PWD means the current working directory; /data is contained in $PATH.

  • Commands (For example)

    # AutoDock Vina
vina
# AutoDock Vina Python bindings
mk_prepare_ligand.py

  • Software Locations

    # AutoDock Vina
/opt/AutoDock-Vina
# miniconda
/opt/conda

vina-all

  • Enter the shell and mount $PWD to /data

    docker run -it -v $PWD:/data --rm ghcr.io/metaphorme/vina-all:v1.2.5

    Notice: $PWD means the current working directory.

  • Commands (For example)

    # AutoDock Vina
vina
# AutoDock Vina Python bindings
mk_prepare_ligand.py
# ADFR Suite
prepare_receptor
autogrid4
# Python2
pythonsh

  • Software Locations

    # AutoDock Vina
/opt/AutoDock-Vina
# ADFR Suite
/opt/adfr
# miniconda
/opt/conda

MGLTools

Notice: MGLTools image is working well on macOS, it havn't been tested on other platforms. It may not be able to work directly on Linux, for more info, please check.

  • Setup XQuartz

  • Enable GLX

    # Run in Terminal
defaults write org.macosforge.xquartz.X11 enable_iglx -bool true

  • Add localhost into access control list (Run every time you restart your computer)

    # Run in Terminal
xhost +localhost

  • Mount $PWD to /data and Run MGLTools

    docker run --rm -it -v $PWD:/data -v /tmp/.X11-unix:/tmp/.X11-unix ghcr.io/metaphorme/mgltools

Notice: If the window of AutoDockTools disappeared, open XQuartz -> Windows -> AutoDockTools to turn it up.

Contribute

Contributions welcome! Please open an issue to discuess at first, fork this repository and submit a pull request.

Credits

License

  • AutoDock Vina

  • ADFR suite Non-Commercial Use

  • Meeko

  • Metaphorme/AutoDock-Vina-Docker

    MIT License

Copyright (c) 2022 Diazepam

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.