Computational Crystallography Toolbox

Table of Contents

Introduction

The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system. 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.

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 SourceForge. 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.

High level organization

The SourceForge cctbx project currently contains these modules:

libtbx
The build system common to all other modules. This is a very thin wrapper around the SCons software construction tool.
boost_adaptbx
A very small adaptor toolbox with platform-independent instructions for building the Boost.Python library.
scitbx
Libraries for general scientific computing (i.e. libraries that are not specific to crystallographic applications): a family of high-level C++ array types, a fast Fourier transform library, and a C++ port of the popular L-BFGS quasi-Newton minimizer, all including Python bindings. These libraries are separated from the crystallographic code base to make them easily accessible for non-crystallographic application developers.
cctbx
Libraries for general crystallographic applications, useful for both small-molecule and macro-molecular crystallography. The libraries in the cctbx module cover everything from algorithms for the handling of unit cells to high-level building blocks for refinement algorithms. Note the distinction between the cctbx project and the cctbx module. In retrospect we should have chosen a different name for the project, but the current naming reflects how the modules have evolved and it would be too disruptive to start a grand renaming.
iotbx
Libraries for reading and writing established file formats.
mmtbx
Libraries for macromolecular crystallography.

Tour

Tour of the cctbx.

Installation

Installation instructions for both binary installation and installation from sources.

The cctbx build system is based on SCons.

Reference documentation

The documentation is directly embedded in the source code and automatically processed into a web-based format for ease of navigation.

Most documented C++ interfaces are also available at the Python layer. Unfortunately the documentation tools available are not capable of merging the documentations. Therefore Python users need to also consult the C++ documention.

Acknowledgments

We would like to thank David Abrahams for creating the amazing Boost.Python library and for patiently supporting the entire open source community. We would like to thank Airlie McCoy for allowing us to adapt some parts of the Phaser package (FFT structure factor calculation). Kevin Cowtan has contributed algorithms for the handling of reciprocal space asymmetric units. We are also grateful for his development of the Clipper library from which we have adapted some source code fragments. Our work was funded in part by the US Department of Energy under Contract No. DE-AC03-76SF00098. We gratefully acknowledge the financial support of NIH/NIGMS.

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Contact

cctbx@cci.lbl.gov