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# Sphinx build info version 1
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# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
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<title>diffpy.structure &mdash; diffpy.structure 3.4.0rc1 documentation</title>
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diffpy.structure
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<li class="toctree-l1"><a class="reference internal" href="../../api/diffpy.structure.html">Package API</a></li>
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<li class="breadcrumb-item active">diffpy.structure</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<h1>Source code for diffpy.structure</h1><div class="highlight"><pre>
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<span></span><span class="ch">#!/usr/bin/env python</span>
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<span class="c1">##############################################################################</span>
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<span class="c1">#</span>
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<span class="c1"># (c) 2024-2026 The Trustees of Columbia University in the City of New York.</span>
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<span class="c1"># All rights reserved.</span>
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<span class="c1">#</span>
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<span class="c1"># File coded by: Chris Farrow, Pavol Juhas, Simon Billinge, Billinge Group members.</span>
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<span class="c1">#</span>
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<span class="c1"># See GitHub contributions for a more detailed list of contributors.</span>
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<span class="c1"># https://github.com/diffpy/diffpy.structure/graphs/contributors</span>
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<span class="c1">#</span>
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<span class="c1"># See LICENSE.rst for license information.</span>
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<span class="c1">#</span>
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<span class="c1">##############################################################################</span>
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<span class="sd">&quot;&quot;&quot;Crystal structure container and parsers for structure formats.</span>
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<span class="sd">Classes related to the structure of materials:</span>
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<span class="sd"> * Atom</span>
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<span class="sd"> * Lattice</span>
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<span class="sd"> * Structure</span>
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<span class="sd"> * PDFFitStructure</span>
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<span class="sd">Other classes:</span>
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<span class="sd"> * SpaceGroup</span>
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<span class="sd"> * SymOp</span>
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<span class="sd"> * ExpandAsymmetricUnit</span>
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<span class="sd"> * GeneratorSite</span>
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<span class="sd"> * SymmetryConstraints</span>
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<span class="sd">Exceptions:</span>
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<span class="sd"> * StructureFormatError</span>
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<span class="sd"> * LatticeError</span>
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<span class="sd"> * SymmetryError</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">diffpy.structure</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">_structure</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.structure.atom</span><span class="w"> </span><span class="kn">import</span> <span class="n">Atom</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.structure.lattice</span><span class="w"> </span><span class="kn">import</span> <span class="n">Lattice</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.structure.parsers</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_parser</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.structure.pdffitstructure</span><span class="w"> </span><span class="kn">import</span> <span class="n">PDFFitStructure</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.structure.structure</span><span class="w"> </span><span class="kn">import</span> <span class="n">Structure</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.structure.structureerrors</span><span class="w"> </span><span class="kn">import</span> <span class="n">LatticeError</span><span class="p">,</span> <span class="n">StructureFormatError</span><span class="p">,</span> <span class="n">SymmetryError</span>
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<span class="c1"># package version</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.structure.version</span><span class="w"> </span><span class="kn">import</span> <span class="n">__version__</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">diffpy.utils._deprecator</span><span class="w"> </span><span class="kn">import</span> <span class="n">build_deprecation_message</span><span class="p">,</span> <span class="n">deprecated</span>
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<span class="c1"># Deprecations -------------------------------------------------------</span>
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<span class="n">base</span> <span class="o">=</span> <span class="s2">&quot;diffpy.structure&quot;</span>
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<span class="n">removal_version</span> <span class="o">=</span> <span class="s2">&quot;4.0.0&quot;</span>
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<span class="n">loadStructure_deprecation_msg</span> <span class="o">=</span> <span class="n">build_deprecation_message</span><span class="p">(</span>
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<span class="n">base</span><span class="p">,</span>
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<span class="s2">&quot;loadStructure&quot;</span><span class="p">,</span>
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<span class="s2">&quot;load_structure&quot;</span><span class="p">,</span>
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<span class="n">removal_version</span><span class="p">,</span>
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<span class="p">)</span>
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<span class="c1"># @deprecated</span>
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<span class="c1"># custom deprecator for diffpy.Structure module</span>
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<div class="viewcode-block" id="DeprecatedStructureModule">
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<a class="viewcode-back" href="../../api/diffpy.structure.html#diffpy.structure.DeprecatedStructureModule">[docs]</a>
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<span class="k">class</span><span class="w"> </span><span class="nc">DeprecatedStructureModule</span><span class="p">:</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Proxy for backward compatibility of diffpy.Structure.&quot;&quot;&quot;</span>
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<span class="k">def</span><span class="w"> </span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
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<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span>
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<span class="s2">&quot;Module &#39;diffpy.Structure&#39; is deprecated and will be removed in version 4.0. &quot;</span>
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<span class="s2">&quot;Use &#39;diffpy.structure&#39; instead.&quot;</span><span class="p">,</span>
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<span class="ne">DeprecationWarning</span><span class="p">,</span>
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<span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
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<span class="p">)</span>
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<span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">_structure</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span></div>
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<span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="s2">&quot;diffpy.Structure&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">DeprecatedStructureModule</span><span class="p">()</span>
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<span class="c1"># top level routines</span>
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<span class="nd">@deprecated</span><span class="p">(</span><span class="n">loadStructure_deprecation_msg</span><span class="p">)</span>
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<span class="k">def</span><span class="w"> </span><span class="nf">loadStructure</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">fmt</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;This function has been deprecated and will be removed in version</span>
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<span class="sd"> 4.0.0.</span>
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<span class="sd"> Please use diffpy.structure.load_structure instead.</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="k">return</span> <span class="n">load_structure</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">fmt</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
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<div class="viewcode-block" id="load_structure">
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<a class="viewcode-back" href="../../api/diffpy.structure.html#diffpy.structure.load_structure">[docs]</a>
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<span class="k">def</span><span class="w"> </span><span class="nf">load_structure</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">fmt</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load new structure object from the specified file.</span>
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<span class="sd"> Parameters</span>
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<span class="sd"> ----------</span>
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<span class="sd"> filename : str</span>
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<span class="sd"> Path to the file to be loaded.</span>
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<span class="sd"> fmt : str, Optional</span>
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<span class="sd"> Format of the structure file such as &#39;cif&#39; or &#39;xyz&#39;. Must be</span>
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<span class="sd"> one of the formats listed by the `parsers.inputFormats` function.</span>
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<span class="sd"> When &#39;auto&#39;, all supported formats are tried in a sequence.</span>
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<span class="sd"> kw : Optional</span>
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<span class="sd"> Extra keyword arguments that are passed to `parsers.getParser`</span>
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<span class="sd"> function. These configure the dedicated Parser object that</span>
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<span class="sd"> is used to read content in filename.</span>
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<span class="sd"> Returns</span>
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<span class="sd"> -------</span>
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<span class="sd"> stru : `Structure`, `PDFFitStructure`</span>
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<span class="sd"> The new Structure object loaded from the specified file.</span>
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<span class="sd"> Return a more specific PDFFitStructure type for &#39;pdffit&#39;</span>
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<span class="sd"> and &#39;discus&#39; formats.</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="n">filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">fspath</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
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<span class="n">p</span> <span class="o">=</span> <span class="n">get_parser</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
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<span class="n">rv</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">parse_file</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
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<span class="k">return</span> <span class="n">rv</span></div>
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<span class="c1"># silence pyflakes checker</span>
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<span class="k">assert</span> <span class="n">StructureFormatError</span> <span class="ow">and</span> <span class="n">LatticeError</span> <span class="ow">and</span> <span class="n">SymmetryError</span>
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<span class="k">assert</span> <span class="n">Atom</span>
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<span class="k">assert</span> <span class="n">Lattice</span>
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<span class="k">assert</span> <span class="n">Structure</span>
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<span class="k">assert</span> <span class="n">PDFFitStructure</span>
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<span class="c1"># silence the pyflakes syntax checker</span>
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<span class="k">assert</span> <span class="n">__version__</span> <span class="ow">or</span> <span class="kc">True</span>
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<span class="c1"># End of file</span>
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</pre></div>
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