CINXE.COM
Open Babel - the chemistry toolbox — Open Babel openbabel-3-1-1 documentation
<!DOCTYPE html> <html lang="en" data-content_root="./" > <head> <meta charset="utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Open Babel - the chemistry toolbox — Open Babel openbabel-3-1-1 documentation</title> <script data-cfasync="false"> document.documentElement.dataset.mode = localStorage.getItem("mode") || ""; document.documentElement.dataset.theme = localStorage.getItem("theme") || "light"; </script> <!-- Loaded before other Sphinx assets --> <link href="_static/styles/theme.css?digest=5b4479735964841361fd" rel="stylesheet" /> <link href="_static/styles/bootstrap.css?digest=5b4479735964841361fd" rel="stylesheet" /> <link href="_static/styles/pydata-sphinx-theme.css?digest=5b4479735964841361fd" rel="stylesheet" /> <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=5b4479735964841361fd" rel="stylesheet" /> <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" /> <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" /> <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" /> <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" /> <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" /> <link rel="stylesheet" type="text/css" href="_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css?v=0a3b3ea7" /> <link rel="stylesheet" type="text/css" href="_static/custom.css" /> <!-- Pre-loaded scripts that we'll load fully later --> <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=5b4479735964841361fd" /> <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=5b4479735964841361fd" /> <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=5b4479735964841361fd"></script> <script src="_static/documentation_options.js?v=4d45eed0"></script> <script src="_static/doctools.js?v=888ff710"></script> <script src="_static/sphinx_highlight.js?v=dc90522c"></script> <script src="_static/clipboard.min.js?v=a7894cd8"></script> <script src="_static/copybutton.js?v=f281be69"></script> <script src="_static/design-tabs.js?v=36754332"></script> <script>DOCUMENTATION_OPTIONS.pagename = 'index';</script> <link rel="canonical" href="https://openbabel.github.io/index.html" /> <link rel="index" title="Index" href="genindex.html" /> <link rel="search" title="Search" href="search.html" /> <link rel="next" title="User Guide" href="docs/index.html" /> <meta name="viewport" content="width=device-width, initial-scale=1"/> <meta name="docsearch:language" content="en"/> </head> <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode=""> <a class="skip-link" href="#main-content">Skip to main content</a> <div id="pst-scroll-pixel-helper"></div> <button type="button" class="btn rounded-pill" id="pst-back-to-top"> <i class="fa-solid fa-arrow-up"></i> Back to top </button> <input type="checkbox" class="sidebar-toggle" name="__primary" id="__primary"/> <label class="overlay overlay-primary" for="__primary"></label> <input type="checkbox" class="sidebar-toggle" name="__secondary" id="__secondary"/> <label class="overlay overlay-secondary" for="__secondary"></label> <div class="search-button__wrapper"> <div class="search-button__overlay"></div> <div class="search-button__search-container"> <form class="bd-search d-flex align-items-center" action="search.html" method="get"> <i class="fa-solid fa-magnifying-glass"></i> <input type="search" class="form-control" name="q" id="search-input" placeholder="Search the docs ..." aria-label="Search the docs ..." autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/> <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span> </form></div> </div> <nav class="bd-header navbar navbar-expand-lg bd-navbar"> <div class="bd-header__inner bd-page-width"> <label class="sidebar-toggle primary-toggle" for="__primary"> <span class="fa-solid fa-bars"></span> </label> <div class="col-lg-3 navbar-header-items__start"> <div class="navbar-item"> <a class="navbar-brand logo" href="#"> <p class="title logo__title">Open Babel</p> </a></div> </div> <div class="col-lg-9 navbar-header-items"> <div class="me-auto navbar-header-items__center"> <div class="navbar-item"> <nav class="navbar-nav"> <p class="sidebar-header-items__title" role="heading" aria-level="1" aria-label="Site Navigation"> Site Navigation </p> <ul class="bd-navbar-elements navbar-nav"> <li class="nav-item"> <a class="nav-link nav-internal" href="docs/index.html"> User Guide </a> </li> <li class="nav-item"> <a class="nav-link nav-internal" href="api/index.html"> API </a> </li> </ul> </nav></div> </div> <div class="navbar-header-items__end"> <div class="navbar-item navbar-persistent--container"> <script> document.write(` <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip"> <i class="fa-solid fa-magnifying-glass"></i> <span class="search-button__default-text">Search</span> <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span> </button> `); </script> </div> <div class="navbar-item"> <script> document.write(` <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip"> <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span> <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span> <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span> </button> `); </script></div> <div class="navbar-item"><ul class="navbar-icon-links navbar-nav" aria-label="Icon Links"> <li class="nav-item"> <a href="https://github.com/openbabel/openbabel" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-github fa-lg" aria-hidden="true"></i></span> <span class="sr-only">GitHub</span></a> </li> <li class="nav-item"> <a href="https://twitter.com/OpenBabel" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span> <span class="sr-only">Twitter</span></a> </li> </ul></div> </div> </div> <div class="navbar-persistent--mobile"> <script> document.write(` <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip"> <i class="fa-solid fa-magnifying-glass"></i> <span class="search-button__default-text">Search</span> <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span> </button> `); </script> </div> <label class="sidebar-toggle secondary-toggle" for="__secondary" tabindex="0"> <span class="fa-solid fa-outdent"></span> </label> </div> </nav> <div class="bd-container"> <div class="bd-container__inner bd-page-width"> <div class="bd-sidebar-primary bd-sidebar hide-on-wide"> <div class="sidebar-header-items sidebar-primary__section"> <div class="sidebar-header-items__center"> <div class="navbar-item"> <nav class="navbar-nav"> <p class="sidebar-header-items__title" role="heading" aria-level="1" aria-label="Site Navigation"> Site Navigation </p> <ul class="bd-navbar-elements navbar-nav"> <li class="nav-item"> <a class="nav-link nav-internal" href="docs/index.html"> User Guide </a> </li> <li class="nav-item"> <a class="nav-link nav-internal" href="api/index.html"> API </a> </li> </ul> </nav></div> </div> <div class="sidebar-header-items__end"> <div class="navbar-item"> <script> document.write(` <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip"> <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span> <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span> <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span> </button> `); </script></div> <div class="navbar-item"><ul class="navbar-icon-links navbar-nav" aria-label="Icon Links"> <li class="nav-item"> <a href="https://github.com/openbabel/openbabel" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-github fa-lg" aria-hidden="true"></i></span> <span class="sr-only">GitHub</span></a> </li> <li class="nav-item"> <a href="https://twitter.com/OpenBabel" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span> <span class="sr-only">Twitter</span></a> </li> </ul></div> </div> </div> <div class="sidebar-primary-items__end sidebar-primary__section"> </div> <div id="rtd-footer-container"></div> </div> <main id="main-content" class="bd-main"> <div class="bd-content"> <div class="bd-article-container"> <div class="bd-header-article"></div> <div id="searchbox"></div> <article class="bd-article" role="main"> <section class="tex2jax_ignore mathjax_ignore" id="open-babel-the-chemistry-toolbox"> <h1>Open Babel - the chemistry toolbox<a class="headerlink" href="#open-babel-the-chemistry-toolbox" title="Link to this heading">#</a></h1> <p>Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It鈥檚 an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.</p> <ul class="simple"> <li><p>Ready-to-use programs, and complete programmer鈥檚 toolkit</p></li> <li><p>Read, write and convert over 110 chemical file formats</p></li> <li><p>Filter and search molecular files using SMARTS and other methods</p></li> <li><p>Supports molecular modeling, cheminformatics, bioinformatics</p></li> <li><p>Organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry</p></li> <li><p>Downloaded over 700,000 times and used by over 40 related projects</p></li> <li><p>How to cite Open Babel: The Open Babel and Pybel papers</p></li> </ul> <div class="toctree-wrapper compound"> </div> </section> </article> <footer class="prev-next-footer"> <div class="prev-next-area"> <a class="right-next" href="docs/index.html" title="next page"> <div class="prev-next-info"> <p class="prev-next-subtitle">next</p> <p class="prev-next-title">User Guide</p> </div> <i class="fa-solid fa-angle-right"></i> </a> </div> </footer> </div> <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner"> <div class="sidebar-secondary-item"> <div class="tocsection editthispage"> <a href="https://github.com/openbabel/openbabel.github.io/edit/main/source/index.md"> <i class="fa-solid fa-pencil"></i> Edit on GitHub </a> </div> </div> </div></div> </div> <footer class="bd-footer-content"> </footer> </main> </div> </div> <!-- Scripts loaded after <body> so the DOM is not blocked --> <script src="_static/scripts/bootstrap.js?digest=5b4479735964841361fd"></script> <script src="_static/scripts/pydata-sphinx-theme.js?digest=5b4479735964841361fd"></script> <footer class="bd-footer"> <div class="bd-footer__inner bd-page-width"> <div class="footer-items__start"> <div class="footer-item"> <p class="copyright"> 漏 Copyright 漏2023 The Open Babel Team. <br/> </p> </div> <div class="footer-item"> <p class="sphinx-version"> Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6. <br/> </p> </div> </div> <div class="footer-items__end"> <div class="footer-item"> <p class="theme-version"> Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.14.4. </p></div> </div> </div> </footer> </body> </html>