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Computational Crystallography Toolbox
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.. contents:: 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 <tour.html>`_.

Installation
============

`Installation instructions <installation.html>`_ for both binary
installation and installation from sources.

The cctbx build system `is based on SCons <build_system.html>`_.

Reference documentation
=======================

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

- cctbx Python interfaces:
  `libtbx <python/libtbx.html>`_
  `scitbx <python/scitbx.html>`_
  `cctbx <python/cctbx.html>`_
  `iotbx <python/iotbx.html>`_
  `mmtbx <python/mmtbx.html>`_

- `cctbx C++ interfaces <c_plus_plus/namespaces.html>`_

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.

Links
=====

- `cctbx - Automatic multi-platform builds`_

- `cctbx - Public SVN repository`_

- `cctbx - Project page at SourceForge`_

- `cctbx - Development history <history.html>`_

.. _`cctbx - Automatic multi-platform builds`: http://cci.lbl.gov/cctbx_build/

.. _`cctbx - Public SVN repository`: http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/

.. _`cctbx - Project page at SourceForge`: http://sourceforge.net/projects/cctbx/

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.

The cctbx SVN development tree is hosted by

__SOURCEFORGE_LOGO_HERE__

Contact
=======

cctbx@cci.lbl.gov


.. _Boost: http://www.boost.org/

.. _Boost.Python: http://www.boost.org/libs/python/doc/

.. _Clipper: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html

.. _PHENIX: http://phenix-online.org/

.. _Python: http://www.python.org/

.. _SCons: http://www.scons.org/

.. _SourceForge: http://sourceforge.net/