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.
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.
release
tag is deprecated, use a specific tag for a specific release version instead.
# 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
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
-
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.
-
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
-
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
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.
Contributions welcome! Please open an issue to discuess at first, fork this repository and submit a pull request.
-
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.