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GitHub - ProteinQure/molecular-converter: A CLI tool to seamlessly convert between various molecular file formats such as PDB, MOL2, mmCIF and many more.
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class=\"heading-element\" dir=\"auto\"\u003eMolecular File Converter\u003c/h1\u003e\u003ca id=\"user-content-molecular-file-converter\" class=\"anchor\" aria-label=\"Permalink: Molecular File Converter\" href=\"#molecular-file-converter\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe Molecular File Converter is designed to seamlessly convert between the Protein Data Bank (PDB) and the Macromolecular Crystallographic Information File (mmCIF) format. These types of conversions are typically needed when downloading data from the RCSB databank - depending on the computational biology tool at hand you either need input files in PDB or mmCIF format. This converter makes it easy to switch back and forth between them.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eDesigned with a user-friendly interface, Molecular File Converter is crafted to be intuitively accessible to both novices and experienced users alike. It provides an easily navigable conversion process that significantly reduces the amount of time and effort researchers typically invest in manually transforming these file types. Additionally, the software is capable of batch conversions, enabling users to process multiple files concurrently.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eHow to install\u003c/h2\u003e\u003ca id=\"user-content-how-to-install\" class=\"anchor\" aria-label=\"Permalink: How to install\" href=\"#how-to-install\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe install the package dependencies run\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"$ poetry install\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003e$ poetry install\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThen activate the\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"$ poetry shell\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003e$ poetry shell\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eand you should be ready to go!\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eHow to convert\u003c/h2\u003e\u003ca id=\"user-content-how-to-convert\" class=\"anchor\" aria-label=\"Permalink: How to convert\" href=\"#how-to-convert\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can find example input files in \u003ccode\u003edata/mmcif_files\u003c/code\u003e and \u003ccode\u003edata/pdb_files\u003c/code\u003e. Here's an example how to convert from mmCIF to PDB:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"$ molconverter data/mmcif_files/7lcj.cif --pdb-file converted_7lcj.pdb\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003e$ molconverter data/mmcif_files/7lcj.cif --pdb-file converted_7lcj.pdb\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003ewhich will create a new file called \u003ccode\u003econverted_7lcj.pdb\u003c/code\u003e in the current working directory.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eHow to test\u003c/h2\u003e\u003ca id=\"user-content-how-to-test\" class=\"anchor\" aria-label=\"Permalink: How to test\" href=\"#how-to-test\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can execute the test suite locally by running\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"pytest .\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003epytest .\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe tests can be found in the \u003ccode\u003etests/\u003c/code\u003e directory.\u003c/p\u003e\n\u003c/article\u003e","loaded":true,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":[{"level":1,"text":"Molecular File Converter","anchor":"molecular-file-converter","htmlText":"Molecular File Converter"},{"level":2,"text":"How to install","anchor":"how-to-install","htmlText":"How to install"},{"level":2,"text":"How to convert","anchor":"how-to-convert","htmlText":"How to convert"},{"level":2,"text":"How to test","anchor":"how-to-test","htmlText":"How to 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class="heading-element" dir="auto">Molecular File Converter</h1><a id="user-content-molecular-file-converter" class="anchor" aria-label="Permalink: Molecular File Converter" href="#molecular-file-converter"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The Molecular File Converter is designed to seamlessly convert between the Protein Data Bank (PDB) and the Macromolecular Crystallographic Information File (mmCIF) format. These types of conversions are typically needed when downloading data from the RCSB databank - depending on the computational biology tool at hand you either need input files in PDB or mmCIF format. This converter makes it easy to switch back and forth between them.</p> <p dir="auto">Designed with a user-friendly interface, Molecular File Converter is crafted to be intuitively accessible to both novices and experienced users alike. It provides an easily navigable conversion process that significantly reduces the amount of time and effort researchers typically invest in manually transforming these file types. Additionally, the software is capable of batch conversions, enabling users to process multiple files concurrently.</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">How to install</h2><a id="user-content-how-to-install" class="anchor" aria-label="Permalink: How to install" href="#how-to-install"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The install the package dependencies run</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="$ poetry install"><pre class="notranslate"><code>$ poetry install </code></pre></div> <p dir="auto">Then activate the</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="$ poetry shell"><pre class="notranslate"><code>$ poetry shell </code></pre></div> <p dir="auto">and you should be ready to go!</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">How to convert</h2><a id="user-content-how-to-convert" class="anchor" aria-label="Permalink: How to convert" href="#how-to-convert"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">You can find example input files in <code>data/mmcif_files</code> and <code>data/pdb_files</code>. Here's an example how to convert from mmCIF to PDB:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="$ molconverter data/mmcif_files/7lcj.cif --pdb-file converted_7lcj.pdb"><pre class="notranslate"><code>$ molconverter data/mmcif_files/7lcj.cif --pdb-file converted_7lcj.pdb </code></pre></div> <p dir="auto">which will create a new file called <code>converted_7lcj.pdb</code> in the current working directory.</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">How to test</h2><a id="user-content-how-to-test" class="anchor" aria-label="Permalink: How to test" href="#how-to-test"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">You can execute the test suite locally by running</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="pytest ."><pre class="notranslate"><code>pytest . </code></pre></div> <p dir="auto">The tests can be found in the <code>tests/</code> directory.</p> </article></div></div></div></div></div> <!-- --> <!-- --> <script type="application/json" id="__PRIMER_DATA_:R0:__">{"resolvedServerColorMode":"day"}</script></div> </react-partial> <input type="hidden" data-csrf="true" 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