Computational Crystallography Toolbox
Table of Contents
- Building a development version
- Contributing to the cctbx
- Nightly builds
- Checks of nightly builds
The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications.
The cctbx also provides some of the key component of the Olex 2 software. Olex 2 is dedicated to the workflow of small molecule crystallographic studies. It features a powerful and flexible refinement engine, olex2.refine, which is developed as part of the cctbx, in the smtbx top-module.
To maximize reusability and, maybe even more importantly, to give individual developers a notion of privacy, the cctbx is organized as a set of smaller modules. This is very much like a village (the cctbx project) with individual houses (modules) for each family (groups of developers, of any size including one).
The cctbx code base is available without restrictions and free of charge to all interested developers, both academic and commercial. The entire community is invited to actively participate in the development of the code base. A sophisticated technical infrastructure that enables community based software development is provided by GitHub. This service is also free of charge and open to the entire world.
The cctbx is designed with an open and flexible architecture to promote extendability and easy incorporation into other software environments. The package is organized as a set of ISO C++ classes with Python bindings. This organization combines the computational efficiency of a strongly typed compiled language with the convenience and flexibility of a dynamically typed scripting language in a strikingly uniform and very maintainable way.
Use of the Python interfaces is highly recommended, but optional. The cctbx can also be used purely as a C++ class library.
There are two packages available,
cctbx package is
cctbx-base with some additional packages (
conda command available, a new
cctbx-base environment named
my_env can be created with
conda create -n my_env -c conda-forge cctbx-base
To choose a specific version of Python, add the
python package with the specific version
conda create -n my_env -c conda-forge cctbx-base python=3.8
Then the environment can be activated with
conda activate my_env
cctbx-base into the currently active environment, use
conda install -c conda-forge cctbx-base
python package with a specific version can be added to change the version of
python that is already installed in the active environment.
- Download https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py in the directory where the cctbx and its dependencies shall be installed
python bootstrap.py(you may want to run it with the
--helpoption first to discover the available options).
- For better compatibility with newer operating systems,
condapackages can be used for dependencies. Add the
--use-condaflag and the command becomes
python bootstrap.py --use-conda. This will run the
condacannot be found. The environment with the dependencies will be located in the
conda_basedirectory. See the description of the
--use-condaflag from the
--helpoutput for more details.
The installation will take a long while but the script will verbosely describe what it does.
A nightly build of the
conda packages are available on the
cctbx-nightly channel. To use these packages, prepend
-c cctbx-nightly as a channel to the commands above. For example, the command to create a new
my_env environment would become
conda create -n my_env -c cctbx-nightly -c conda-forge cctbx-base
This will use the
cctbx-base package from the
cctbx-nightly channel, but pull the remaining dependencies from
Nightly builds are only updated if there are additional commits from the previous build.
A subset of tests is run on the current
cctbx-base packages every night (10 pm Pacific) to test compatibility with the latest packages from
conda-forge. Additional source files for
antlr3 are needed for the tests.