- Introduction
- Installation
- Building a development version
- Contributing to the cctbx
- Nightly builds and tests
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.
The easiest way to install cctbx is through the Conda package manager. We recommend the Miniforge installers since they provide a minimal environment and default to the conda-forge
channel.
There are two packages available, cctbx
and cctbx-base
. The cctbx
package is cctbx-base
with some additional GUI packages (e.g. wxpython
, pyside2
, ipython
).
With the 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
To install cctbx-base
into the currently active environment, use
conda install -c conda-forge cctbx-base
The 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://github.com/raw/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py in the directory where the cctbx and its dependencies shall be installed
- Run
python bootstrap.py
(you may want to run it with the--help
option first to discover the available options).
- For better compatibility with newer operating systems,
conda
packages can be used for dependencies. Add the--use-conda
flag and the command becomespython bootstrap.py --use-conda
. This will run theminiconda
installer ifconda
cannot be found. The environment with the dependencies will be located in theconda_base
directory. See the description of the--use-conda
flag from the--help
output for more details.
The installation will take a long while but the script will verbosely describe what it does.
For a more detailed description on how to contribute to the cctbx please visit our contribution guide.
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 conda-forge
.
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 from the conda-forge
and cctbx-nightly
channels every night (10 pm Pacific) to test compatibility with the latest packages from conda-forge
. Additional source files for fable
and antlr3
are needed for the tests. The nightly test details can be viewed by clicking the "Nightly conda package tests" badge near the beginning of this README.