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<h1>Source code for pyobjcryst</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) 2025 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 and 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/pyobjcryst/graphs/contributors</span>
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<span class="c1">#</span>
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<span class="c1"># See LICENSE.rst and LICENSE_DANSE.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;Python wrapping of ObjCryst++.</span>
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<span class="sd">Objects are wrapped according to their header file in the ObjCryst source.</span>
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<span class="sd">See the online ObjCryst++ documentation (https://objcryst.readthedocs.io).</span>
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<span class="sd">Modules</span>
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<span class="sd">atom -- Wrapping of Atom.h</span>
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<span class="sd">crystal -- Wrapping of Crystal.h</span>
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<span class="sd">general -- Wrapping of General.h</span>
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<span class="sd">globaloptim -- Wrapping of GlobalOptimObj.h</span>
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<span class="sd">io -- Wrapping of IO.h</span>
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<span class="sd">lsq -- Wrapping of LSQNumObj.h</span>
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<span class="sd">molecule -- Wrapping of Molecule.h</span>
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<span class="sd">polyhedron -- Wrapping of Polyhedron.h</span>
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<span class="sd">refinableobj -- Wrapping of RefinableObj.h</span>
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<span class="sd">scatterer -- Wrapping of Scatterer.h</span>
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<span class="sd">scatteringpower -- Wrapping of ScatteringPower.h</span>
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<span class="sd">scatteringpowersphere -- Wrapping of ScatteringPowerSphere.h</span>
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<span class="sd">spacegroup -- Wrapping of SpaceGroup.h</span>
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<span class="sd">unitcell -- Wrapping of UnitCell.h</span>
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<span class="sd">zscatterer -- Wrapping of ZScatterer.h</span>
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<span class="sd">General Changes</span>
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<span class="sd">- C++ methods that can return const or non-const objects return non-const</span>
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<span class="sd"> objects in python.</span>
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<span class="sd">- Classes with a Print() method have the output of this method exposed in the</span>
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<span class="sd"> __str__ python method. Thus, obj.Print() == print obj.</span>
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<span class="sd">- CrystVector and CrystMatrix are converted to numpy arrays.</span>
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<span class="sd">- Indexing methods raise IndexError when index is out of bounds.</span>
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<span class="sd">See the modules&#39; documentation for specific changes.</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">warnings</span>
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<span class="c1"># import submodules that only import from _pyobjcryst</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.atom</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.crystal</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.diffractiondatasinglecrystal</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.general</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.globaloptim</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.indexing</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.io</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.lsq</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.molecule</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.polyhedron</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.powderpattern</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.radiation</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.refinableobj</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.reflectionprofile</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.scatterer</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.scatteringdata</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.scatteringpower</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.scatteringpowersphere</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.spacegroup</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.unitcell</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">pyobjcryst.zscatterer</span>
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<span class="c1"># could be api breaking if removed</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">pyobjcryst._pyobjcryst</span><span class="w"> </span><span class="kn">import</span> <span class="n">gTopRefinableObjRegistry</span> <span class="c1"># noqa: F401</span>
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<span class="c1"># Let&#39;s put this on the package level</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">pyobjcryst.general</span><span class="w"> </span><span class="kn">import</span> <span class="n">ObjCrystException</span>
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<span class="c1"># version data</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">pyobjcryst.version</span><span class="w"> </span><span class="kn">import</span> <span class="n">__version__</span>
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<div class="viewcode-block" id="loadCrystal">
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<a class="viewcode-back" href="../api/pyobjcryst.html#pyobjcryst.loadCrystal">[docs]</a>
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<span class="k">def</span><span class="w"> </span><span class="nf">loadCrystal</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load pyobjcryst Crystal object from a CIF file.</span>
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<span class="sd"> :param filename: CIF file to be loaded.</span>
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<span class="sd"> :return: a new Crystal object.</span>
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<span class="sd"> ..deprecated:: 2.2.4</span>
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<span class="sd"> Use pyobjcryst.crystal.create_crystal_from_cif() instead,</span>
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<span class="sd"> which has more options when importing a CIF, including</span>
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<span class="sd"> using an URL instead of a file.</span>
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<span class="sd"> &quot;&quot;&quot;</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;loadCrystal is deprecated. Please use &quot;</span>
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<span class="s2">&quot;pyobjcryst.crystal.create_crystal_from_cif() 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="p">)</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">pyobjcryst.crystal</span><span class="w"> </span><span class="kn">import</span> <span class="n">CreateCrystalFromCIF</span>
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<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s2">&quot;rb&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
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<span class="n">rv</span> <span class="o">=</span> <span class="n">CreateCrystalFromCIF</span><span class="p">(</span><span class="n">fp</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 the pyflakes syntax checker</span>
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<span class="k">assert</span> <span class="n">ObjCrystException</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</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="k">assert</span> <span class="n">pyobjcryst</span><span class="o">.</span><span class="n">zscatterer</span>
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<span class="c1"># End of file</span>
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</pre></div>
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