Installation

The latest stable release is 2.11 (release notes).

Conda

OpenStructure is available as a conda package on Bioconda for a simple and portable setup. You can install it with the following command:

conda install bioconda::openstructure

This setup has been tested with miniforge.

You can then run a test script:

wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
ost test_ost.py

This should produce some output and announce that "OST is working!"

Containers

For a portable setup, we provide containerizedsolutions. OpenStructure provides its own Docker container registry. Singularity containers bootstrap from the docker container but must be built by the user. Both solution require root permissions.

Docker

This section provides a quick-start guide to help you get OpenStructure up and running using Docker. For complete documentation on using Docker with OpenStructure, see the Docker instructions.

To get the latest Docker image from the OpenStructure registry:

sudo docker pull registry.scicore.unibas.ch/schwede/openstructure:latest

And run a test script:

wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
sudo docker run --rm -v $(pwd):/home registry.scicore.unibas.ch/schwede/openstructure:latest test_ost.py

Singularity

This section provides a quick-start guide to help you get OpenStructure up and running using Singularity. Building the singularity container requires root permissions:

wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/singularity/Singularity
sudo singularity build ost.img Singularity

And run a test script:

wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
singularity run --app OST ost.img test_ost.py

Build from source

OpenStructure is developed and tested across various Linux distributions. You can find detailed build instructions and a list of required dependencies in the online documentation.

Once the dependencies are properly installed, the build process boils down to:

git clone https://git.scicore.unibas.ch/schwede/openstructure.git 
mkdir openstructure/build
cd openstructure/build
cmake ..
make
wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
stage/bin/chemdict_tool create components.cif.gz compounds.chemlib -i
cmake .. -DCOMPOUND_LIB=compounds.chemlib
make
make check
sudo make install

And you can now run a test script:

wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
ost test_ost.py