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<section id="module-pymatgen.util.provenance">
<span id="pymatgen-util-provenance-module"></span><h1>pymatgen.util.provenance module<a class="headerlink" href="#module-pymatgen.util.provenance" title="Permalink to this heading"></a></h1>
<p>Classes and methods related to the Structure Notation Language (SNL)</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.util.provenance.Author">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Author</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">email</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L120-L179"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.Author" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.util.provenance.Author" title="pymatgen.util.provenance.Author"><code class="xref py py-class docutils literal notranslate"><span class="pre">Author</span></code></a></p>
<p>An Author contains two fields:</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.util.provenance.Author.name">
<span class="sig-name descname"><span class="pre">name</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/util/provenance.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.Author.name" title="Permalink to this definition"></a></dt>
<dd><p>Name of author (String)</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.util.provenance.Author.email">
<span class="sig-name descname"><span class="pre">email</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/util/provenance.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.Author.email" title="Permalink to this definition"></a></dt>
<dd><p>Email of author (String)</p>
</dd></dl>
<p>Create new instance of Author(name, email)</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.Author.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L139-L143"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.Author.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>Returns: MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.Author.from_dict">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L145-L154"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.Author.from_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>d</strong> (<em>dict</em>) – Dict representation</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Author</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.Author.parse_author">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">parse_author</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">author</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L156-L179"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.Author.parse_author" title="Permalink to this definition"></a></dt>
<dd><p>Parses an Author object from either a String, dict, or tuple</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>author</strong> – A String formatted as “NAME <<a class="reference external" href="mailto:email%40domain.com">email<span>@</span>domain<span>.</span>com</a>>”,
(name, email) tuple, or a dict with name and email keys.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>An Author object.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.util.provenance.HistoryNode">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">HistoryNode</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L56-L117"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.HistoryNode" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.util.provenance.HistoryNode" title="pymatgen.util.provenance.HistoryNode"><code class="xref py py-class docutils literal notranslate"><span class="pre">HistoryNode</span></code></a></p>
<p>A HistoryNode represents a step in the chain of events that lead to a
Structure. HistoryNodes leave ‘breadcrumbs’ so that you can trace back how
a Structure was created. For example, a HistoryNode might represent pulling
a Structure from an external database such as the ICSD or CSD. Or, it might
represent the application of a code (e.g. pymatgen) to the Structure, with
a custom description of how that code was applied (e.g. a site removal
Transformation was applied).</p>
<p>A HistoryNode contains three fields:</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.util.provenance.HistoryNode.name">
<span class="sig-name descname"><span class="pre">name</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/util/provenance.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.HistoryNode.name" title="Permalink to this definition"></a></dt>
<dd><p>The name of a code or resource that this Structure encountered in
its history (String)</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.util.provenance.HistoryNode.url">
<span class="sig-name descname"><span class="pre">url</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/util/provenance.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.HistoryNode.url" title="Permalink to this definition"></a></dt>
<dd><p>The URL of that code/resource (String)</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.util.provenance.HistoryNode.description">
<span class="sig-name descname"><span class="pre">description</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/util/provenance.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.HistoryNode.description" title="Permalink to this definition"></a></dt>
<dd><p>A free-form description of how the code/resource is related to the
Structure (dict).</p>
</dd></dl>
<p>Create new instance of HistoryNode(name, url, description)</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.HistoryNode.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L83-L87"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.HistoryNode.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>Returns: Dict</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.HistoryNode.from_dict">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">h_node</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.util.provenance.HistoryNode" title="pymatgen.util.provenance.HistoryNode"><span class="pre">HistoryNode</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L89-L98"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.HistoryNode.from_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>d</strong> (<em>dict</em>) – Dict representation</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>HistoryNode</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.HistoryNode.parse_history_node">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">parse_history_node</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">h_node</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L100-L117"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.HistoryNode.parse_history_node" title="Permalink to this definition"></a></dt>
<dd><p>Parses a History Node object from either a dict or a tuple.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>h_node</strong> – A dict with name/url/description fields or a 3-element
tuple.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>History node.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.util.provenance.StructureNL">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StructureNL</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct_or_mol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">authors</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projects</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remarks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">history</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">created_at</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L182-L407"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.StructureNL" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>The Structure Notation Language (SNL, pronounced ‘snail’) is a container
for a pymatgen Structure/Molecule object with some additional fields for
enhanced provenance. It is meant to be imported/exported in a JSON file
format with the following structure:</p>
<ul class="simple">
<li><dl class="simple">
<dt>about</dt><dd><ul>
<li><p>created_at</p></li>
<li><p>authors</p></li>
<li><p>projects</p></li>
<li><p>references</p></li>
<li><p>remarks</p></li>
<li><p>data</p></li>
<li><p>history</p></li>
</ul>
</dd>
</dl>
</li>
<li><p>lattice (optional)</p></li>
<li><p>sites</p></li>
</ul>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct_or_mol</strong> – A pymatgen.core.structure Structure/Molecule object</p></li>
<li><p><strong>authors</strong> – <em>List</em> of {“name”:’’, “email”:’’} dicts,
<em>list</em> of Strings as ‘John Doe <<a class="reference external" href="mailto:johndoe%40gmail.com">johndoe<span>@</span>gmail<span>.</span>com</a>>’,
or a single String with commas separating authors</p></li>
<li><p><strong>projects</strong> – List of Strings [‘Project A’, ‘Project B’]</p></li>
<li><p><strong>references</strong> – A String in BibTeX format</p></li>
<li><p><strong>remarks</strong> – List of Strings [‘Remark A’, ‘Remark B’]</p></li>
<li><p><strong>data</strong> – A free form dict. Namespaced at the root level with an
underscore, e.g. {“_materialsproject”: <custom data>}</p></li>
<li><p><strong>history</strong> – List of dicts - [{‘name’:’’, ‘url’:’’, ‘description’:{}}]</p></li>
<li><p><strong>created_at</strong> – A datetime object</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.StructureNL.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L283-L299"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.StructureNL.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>Returns: MSONable dict</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.StructureNL.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L301-L327"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.StructureNL.from_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>d</strong> (<em>dict</em>) – Dict representation</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Class</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.util.provenance.StructureNL.from_structures">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_structures</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structures</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">authors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projects</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remarks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">histories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">created_at</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L329-L382"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.StructureNL.from_structures" title="Permalink to this definition"></a></dt>
<dd><p>A convenience method for getting a list of StructureNL objects by
specifying structures and metadata separately. Some of the metadata
is applied to all of the structures for ease of use.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structures</strong> – A list of Structure objects</p></li>
<li><p><strong>authors</strong> – <em>List</em> of {“name”:’’, “email”:’’} dicts,
<em>list</em> of Strings as ‘John Doe <<a class="reference external" href="mailto:johndoe%40gmail.com">johndoe<span>@</span>gmail<span>.</span>com</a>>’,
or a single String with commas separating authors</p></li>
<li><p><strong>projects</strong> – List of Strings [‘Project A’, ‘Project B’]. This
applies to all structures.</p></li>
<li><p><strong>references</strong> – A String in BibTeX format. Again, this applies to all
structures.</p></li>
<li><p><strong>remarks</strong> – List of Strings [‘Remark A’, ‘Remark B’]</p></li>
<li><p><strong>data</strong> – A list of free form dict. Namespaced at the root level
with an underscore, e.g. {“_materialsproject”:<custom data>}
. The length of data should be the same as the list of
structures if not None.</p></li>
<li><p><strong>histories</strong> – List of list of dicts - [[{‘name’:’’, ‘url’:’’,
‘description’:{}}], …] The length of histories should be the
same as the list of structures if not None.</p></li>
<li><p><strong>created_at</strong> – A datetime object</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.util.provenance.is_valid_bibtex">
<span class="sig-name descname"><span class="pre">is_valid_bibtex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../util/provenance.py#L37-L53"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.util.provenance.is_valid_bibtex" title="Permalink to this definition"></a></dt>
<dd><p>Use pybtex to validate that a reference is in proper BibTeX format</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>reference</strong> – A String reference in BibTeX format.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Boolean indicating if reference is valid bibtex.</p>
</dd>
</dl>
</dd></dl>
</section>
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