Sire

About

Sire is a molecular modelling framework that provides extensive functionality to manipulate representations of biomolecular systems.

It is used as a key component of BioSimSpace, and is distributed and supported as an open source community project by OpenBioSim.

For more information about how to use Sire, and about application built with Sire, please visit the Sire website.

• Features
• Quick start guide
• Tutorial

Installation

The easiest way to install Sire is using our conda channel. Sire is built using dependencies from conda-forge, so please ensure that the channel takes strict priority. We recommend using miniforge3.

To create a new environment:

conda create -n openbiosim "python<3.13"
conda activate openbiosim
conda install -c conda-forge -c openbiosim sire

To install the latest development version you can use:

conda create -n openbiosim-dev "python<3.13"
conda activate openbiosim-dev
conda install -c conda-forge -c openbiosim/label/dev sire

Installing older versions

You can install a specific version of sire by specifying the version number in the conda install command, e.g.

conda install -c conda-forge -c openbiosim sire==2024.1.0

Note that limited space means that we can only keep a small number of versions of sire on the official openbiosim conda channel. Generally these are all point releases of the latest major version, plus the latest point release of the last major version.

We do provide an archive channel of all previous releases. You can search this archive channel for the release you are interested in using the following command:

conda search -c https://openbiosim.blob.core.windows.net/archive sire

This will return a list of all versions of sire available in the archive.

You can install a specific version from the archive using a command like:

conda install -c https://openbiosim.blob.core.windows.net/archive sire==2023.2.3

Installation from source

However, as you are here, it is likely you want to download the latest, greatest version of the code, which you will need to compile. To compile sire, you need a git client to download the source, and a working internet connection (needed by the sire compilation scripts to download additional dependencies).

First, you need to create and activate a conda environment, e.g.

conda create -n openbiosim-dev "python<3.12"
conda activate openbiosim-dev

Next, you need to install the Sire build dependencies.

conda install cmake pip-requirements-parser

You will also need to install compilers, e.g. on Linux use

conda install gcc gxx

on MacOS use

conda install clang clangxx

and on Windows use

conda install conda-build

Next, you can clone the sire source code and compile and install sire:

git clone https://github.com/OpenBioSim/sire
cd sire
python setup.py install

A small word of warning, the compilation can easily take over an hour!

The above will compile sire in your existing conda environment.

If you plan to build BioSimSpace on top of sire, then you will need to resolve BioSimSpace's dependencies at the time sire is installed to ensure that it is built in a self-consistent way. This can be achieved as follows:

python setup.py --install-bss-deps install

Support and Development

Bugs, Comments, Questions

For bug reports/suggestions/complaints please file an issue on GitHub.

Developers guide

Please visit the website for information on how to develop applications using sire.

GitHub actions

Since sire is quite large, a build can take quite long and might not be neccessary if a commit is only fixing a couple of typos. Simply add ci skip to your commit message and GitHub actions will not invoke an autobuild.

Note that every time you commit to devel, it will trigger a build of sire, full testing, construction of a Conda package and upload to our Anaconda channel. Please think twice before committing directly to devel. You should ideally be working in a _feature branch, and only commit to devel once you are happy the code works on your branch. Use ci skip until you are happy that you want to trigger a full build, test and deployment. This full pipeline will take several hours to complete.

Have fun :-)