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<!DOCTYPE html>
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<title>Computational Crystallography Toolbox — CCTBX Developer documentation</title>
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<section id="computational-crystallography-toolbox">
<h1><a class="toc-backref" href="#id1" role="doc-backlink">Computational Crystallography Toolbox</a><a class="headerlink" href="#computational-crystallography-toolbox" title="Link to this heading">¶</a></h1>
<div class="toctree-wrapper compound" id="introduction">
<ul>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation overview</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html#manually-building-from-sources-under-linux-and-macos">Manually building from sources under Linux and macOS</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html#manually-building-from-sources-under-windows-2000-or-higher">Manually building from sources under Windows 2000 or higher</a></li>
<li class="toctree-l1"><a class="reference internal" href="tour.html">Tour of the cctbx</a></li>
<li class="toctree-l1"><a class="reference internal" href="history.html">CCTBX development history</a></li>
<li class="toctree-l1"><a class="reference internal" href="libtbx/index.html">libtbx - low-level utilities and infrastructure for CCTBX</a></li>
<li class="toctree-l1"><a class="reference internal" href="boost_adaptbx/index.html">boost_adaptbx - wrappers for Boost functionality</a></li>
<li class="toctree-l1"><a class="reference internal" href="iotbx/index.html">iotbx - file readers and writers</a></li>
<li class="toctree-l1"><a class="reference internal" href="scitbx/index.html">scitbx - general-purpose scientific programming infrastructure</a></li>
<li class="toctree-l1"><a class="reference internal" href="cctbx/cctbx.html">cctbx - core crystallographic objects and functions</a></li>
<li class="toctree-l1"><a class="reference internal" href="mmtbx/mmtbx.html">mmtbx - macromolecular crystallography</a></li>
</ul>
</div>
<section id="welcome-to-cctbx-s-documentation">
<h2><a class="toc-backref" href="#id2" role="doc-backlink">Welcome to CCTBX’s documentation!</a><a class="headerlink" href="#welcome-to-cctbx-s-documentation" title="Link to this heading">¶</a></h2>
<nav class="contents" id="table-of-contents">
<p class="topic-title">Table of Contents</p>
<ul class="simple">
<li><p><a class="reference internal" href="#computational-crystallography-toolbox" id="id1">Computational Crystallography Toolbox</a></p>
<ul>
<li><p><a class="reference internal" href="#welcome-to-cctbx-s-documentation" id="id2">Welcome to CCTBX’s documentation!</a></p></li>
<li><p><a class="reference internal" href="#high-level-organization" id="id3">High level organization</a></p>
<ul>
<li><p><a class="reference internal" href="#libtbx" id="id4">libtbx</a></p></li>
<li><p><a class="reference internal" href="#boost-adaptbx" id="id5">boost_adaptbx</a></p></li>
<li><p><a class="reference internal" href="#scitbx" id="id6">scitbx</a></p></li>
<li><p><a class="reference internal" href="#cctbx" id="id7">cctbx</a></p></li>
<li><p><a class="reference internal" href="#iotbx" id="id8">iotbx</a></p></li>
<li><p><a class="reference internal" href="#mmtbx" id="id9">mmtbx</a></p></li>
<li><p><a class="reference internal" href="#xfel" id="id10">xfel</a></p></li>
<li><p><a class="reference internal" href="#smtbx" id="id11">smtbx</a></p></li>
<li><p><a class="reference internal" href="#dxtbx" id="id12">dxtbx</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#tour" id="id13">Tour</a></p></li>
<li><p><a class="reference internal" href="#tutorials" id="id14">Tutorials</a></p></li>
<li><p><a class="reference internal" href="#installation" id="id15">Installation</a></p></li>
<li><p><a class="reference internal" href="#reference-documentation" id="id16">Reference Documentation</a></p></li>
<li><p><a class="reference internal" href="#links" id="id17">Links</a></p></li>
<li><p><a class="reference internal" href="#contact" id="id18">Contact</a></p></li>
<li><p><a class="reference internal" href="#indices-and-tables" id="id19">Indices and tables</a></p></li>
</ul>
</li>
</ul>
</nav>
</section>
<section id="high-level-organization">
<h2><a class="toc-backref" href="#id3" role="doc-backlink">High level organization</a><a class="headerlink" href="#high-level-organization" title="Link to this heading">¶</a></h2>
<p>The SourceForge cctbx project currently contains these modules. The core
libraries required for most other applications are libtbx, boost_adaptbx,
scitbx, cctbx, and usually iotbx. Functionality specific to macromolecules
and small molecules lives in mmtbx and smtbx, respectively.</p>
<section id="libtbx">
<h3><a class="toc-backref" href="#id4" role="doc-backlink">libtbx</a><a class="headerlink" href="#libtbx" title="Link to this heading">¶</a></h3>
<p>The build system common to all other modules. This includes a very thin wrapper
around the <a class="reference external" href="http://www.scons.org/">SCons</a> software construction tool. It also contains many useful
frameworks and utilities to simplify application development, including tools
for regression testing, parallelization across multiprocessor systems and
managed clusters, and a flexible, modular configuration syntax called PHIL
(Python Hierarchial Interface Language) used throughout the CCTBX.</p>
<p><a class="reference internal" href="libtbx/index.html#libtbx"><span class="std std-ref">API Documentation for libtbx</span></a></p>
</section>
<section id="boost-adaptbx">
<h3><a class="toc-backref" href="#id5" role="doc-backlink">boost_adaptbx</a><a class="headerlink" href="#boost-adaptbx" title="Link to this heading">¶</a></h3>
<p>A very small adaptor toolbox with platform-independent instructions for building
the <a class="reference external" href="http://www.boost.org/libs/python/doc/">Boost.Python</a> library.</p>
<p><a class="reference internal" href="boost_adaptbx/index.html#boost-adaptbx"><span class="std std-ref">API Documentation for boost_adaptbx</span></a></p>
</section>
<section id="scitbx">
<h3><a class="toc-backref" href="#id6" role="doc-backlink">scitbx</a><a class="headerlink" href="#scitbx" title="Link to this heading">¶</a></h3>
<p>Libraries for general scientific computing (i.e. libraries that are not specific
to crystallographic applications). This includes 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, and many mathematical utilities, all including
<a class="reference external" href="http://www.python.org/">Python</a> bindings. These libraries are
separated from the crystallographic code base to make them easily accessible for
non-crystallographic application developers.</p>
<p><a class="reference internal" href="scitbx/index.html#scitbx"><span class="std std-ref">API Documentation for scitbx</span></a></p>
</section>
<section id="cctbx">
<h3><a class="toc-backref" href="#id7" role="doc-backlink">cctbx</a><a class="headerlink" href="#cctbx" title="Link to this heading">¶</a></h3>
<p>Libraries for general crystallographic applications, useful for both
small-molecule and macro-molecular crystallography. The libraries in the cctbx
module include algorithms and data structures for the handling
of crystal symmetry, basic geometry restraints, reflection data, atomic
displacement parameters, X-ray scattering, and high-level building blocks for
refinement algorithms.
Note the distinction between the CCTBX <em>project</em> and the cctbx <em>module</em>.</p>
<p><a class="reference internal" href="cctbx/cctbx.html"><span class="doc">API Documentation for cctbx</span></a></p>
</section>
<section id="iotbx">
<h3><a class="toc-backref" href="#id8" role="doc-backlink">iotbx</a><a class="headerlink" href="#iotbx" title="Link to this heading">¶</a></h3>
<p>Libraries for reading and writing common file formats, including PDB, CIF,
many reflection formats, electron density maps, and sequences.</p>
<p><a class="reference internal" href="iotbx/index.html#iotbx"><span class="std std-ref">API Documentation for iotbx</span></a></p>
</section>
<section id="mmtbx">
<h3><a class="toc-backref" href="#id9" role="doc-backlink">mmtbx</a><a class="headerlink" href="#mmtbx" title="Link to this heading">¶</a></h3>
<p>Functionality specific to macromolecular crystallography. This includes
all of the machinery required for setup of geometry restraints, bulk solvent
correction and scaling, analysis of macromolecular diffraction data,
calculation of weighted map coefficients, and most of the methods implemented
in phenix.refine. The majority of infrastructure for the MolProbity
validation server (and Phenix equivalent) is also located here.</p>
<p><a class="reference internal" href="mmtbx/mmtbx.html"><span class="doc">API Documentation for mmtbx</span></a></p>
</section>
<section id="xfel">
<h3><a class="toc-backref" href="#id10" role="doc-backlink">xfel</a><a class="headerlink" href="#xfel" title="Link to this heading">¶</a></h3>
<p>Software for processing serial data collected using an X-ray free electron laser.
Includes spotfinding, integration, data clustering/filering and merging tools.</p>
<p><a class="reference internal" href="xfel/xfel.html"><span class="doc">API Documentation for xfel</span></a></p>
</section>
<section id="smtbx">
<h3><a class="toc-backref" href="#id11" role="doc-backlink">smtbx</a><a class="headerlink" href="#smtbx" title="Link to this heading">¶</a></h3>
<p>Functionality specific to small-molecule crystallography, including a complete
refinement program (smtbx.refine).</p>
<p><span class="xref std std-doc">API Documentation for smtbx</span></p>
</section>
<section id="dxtbx">
<h3><a class="toc-backref" href="#id12" role="doc-backlink">dxtbx</a><a class="headerlink" href="#dxtbx" title="Link to this heading">¶</a></h3>
<p>The Diffraction Image Toolbox, a library for handling X-ray detector data
of arbitrary complexity from a variety of standard formats. (Also used by
routines in iotbx.)</p>
<p><span class="xref std std-doc">API documentation for dxtbx</span></p>
</section>
</section>
<section id="tour">
<h2><a class="toc-backref" href="#id13" role="doc-backlink">Tour</a><a class="headerlink" href="#tour" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p>Tour of the <a class="reference internal" href="tour.html#tour"><span class="std std-ref">cctbx</span></a>.</p></li>
<li><p>Tour of the <a class="reference external" href="http://cci.lbl.gov/~hohn/scitbx-tour.html">scitbx (by Michael Hohn)</a></p></li>
<li><p>Tour of the <a class="reference external" href="http://cci.lbl.gov/~hohn/array-family-tour.html">array_family (by Michael Hohn)</a></p></li>
</ul>
</section>
<section id="tutorials">
<h2><a class="toc-backref" href="#id14" role="doc-backlink">Tutorials</a><a class="headerlink" href="#tutorials" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference external" href="http://cci.lbl.gov/xfel">Free-electron laser data processing (cctbx.xfel)</a></p></li>
<li><p><a class="reference external" href="http://cctbx.sourceforge.net/iucr2008/rigid_body_refinement_core.html">IUCr 2008 (Software Fayre) (rigid_body_refinement_core.py)</a></p></li>
<li><p><a class="reference external" href="http://cctbx.sourceforge.net/sbgrid2008/tutorial.html">SBGrid 2008 (Quo Vadis) (iotbx.pdb)</a></p></li>
<li><p><a class="reference external" href="http://cctbx.sourceforge.net/siena2005/">Siena 2005 IUCr Crystallographic Computing School</a></p></li>
<li><p><a class="reference external" href="http://cctbx.sourceforge.net/scitbx_rigid_body_essence/">scitbx/rigid_body/essence subset</a></p></li>
</ul>
</section>
<section id="installation">
<h2><a class="toc-backref" href="#id15" role="doc-backlink">Installation</a><a class="headerlink" href="#installation" title="Link to this heading">¶</a></h2>
<p><a class="reference internal" href="installation.html#installation"><span class="std std-ref">Installation instructions</span></a> for both binary installation and
installation from sources.</p>
<p>The cctbx build system is based on <a class="reference external" href="http://www.scons.org/">SCons</a>.</p>
</section>
<section id="reference-documentation">
<h2><a class="toc-backref" href="#id16" role="doc-backlink">Reference Documentation</a><a class="headerlink" href="#reference-documentation" title="Link to this heading">¶</a></h2>
<p><a class="reference external" href="http://cctbx.sourceforge.net/current/c_plus_plus/namespaces.html">cctbx C++ interfaces</a></p>
<p>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.</p>
</section>
<section id="links">
<h2><a class="toc-backref" href="#id17" role="doc-backlink">Links</a><a class="headerlink" href="#links" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference external" href="http://cci.lbl.gov/cctbx_build/">cctbx - Automatic multi-platform builds</a></p></li>
<li><p><a class="reference external" href="https://github.com/cctbx/cctbx_project">cctbx - Public git repository</a></p></li>
</ul>
</section>
<section id="contact">
<h2><a class="toc-backref" href="#id18" role="doc-backlink">Contact</a><a class="headerlink" href="#contact" title="Link to this heading">¶</a></h2>
<p><a class="reference external" href="mailto:cctbx%40cci.lbl.gov">cctbx<span>@</span>cci<span>.</span>lbl<span>.</span>gov</a></p>
<p>There is also a mailing list (cctbxbb) where developers can answer questions from
the community. To join/manage your subscription, please visit <a class="reference external" href="http://www.phenix-online.org/mailman/listinfo/cctbxbb">http://www.phenix-online.org/mailman/listinfo/cctbxbb</a>.</p>
</section>
<section id="indices-and-tables">
<h2><a class="toc-backref" href="#id19" role="doc-backlink">Indices and tables</a><a class="headerlink" href="#indices-and-tables" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
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<h3><a href="#">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Computational Crystallography Toolbox</a><ul>
<li><a class="reference internal" href="#welcome-to-cctbx-s-documentation">Welcome to CCTBX’s documentation!</a></li>
<li><a class="reference internal" href="#high-level-organization">High level organization</a><ul>
<li><a class="reference internal" href="#libtbx">libtbx</a></li>
<li><a class="reference internal" href="#boost-adaptbx">boost_adaptbx</a></li>
<li><a class="reference internal" href="#scitbx">scitbx</a></li>
<li><a class="reference internal" href="#cctbx">cctbx</a></li>
<li><a class="reference internal" href="#iotbx">iotbx</a></li>
<li><a class="reference internal" href="#mmtbx">mmtbx</a></li>
<li><a class="reference internal" href="#xfel">xfel</a></li>
<li><a class="reference internal" href="#smtbx">smtbx</a></li>
<li><a class="reference internal" href="#dxtbx">dxtbx</a></li>
</ul>
</li>
<li><a class="reference internal" href="#tour">Tour</a></li>
<li><a class="reference internal" href="#tutorials">Tutorials</a></li>
<li><a class="reference internal" href="#installation">Installation</a></li>
<li><a class="reference internal" href="#reference-documentation">Reference Documentation</a></li>
<li><a class="reference internal" href="#links">Links</a></li>
<li><a class="reference internal" href="#contact">Contact</a></li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
</ul>
</li>
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