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Rhea Structure search
<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml" lang="en"> <head> <title>Rhea Structure search</title> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> <meta name="google" content="notranslate"></meta> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <meta name="description" content="An expert-curated knowledgebase of chemical and transport reactions of biological interest" /> <link rel="preload" href="/style/fonts/material-design.woff2" as="font" type="font/woff2" crossorigin="anonymous"/> <link rel="stylesheet" type="text/css" media="screen" href="/style/css/home_structure.1842f22ca9e912693c4e.css" /> <script defer src="/js/customelements.js"></script> <!-- Matomo --> <script> var _paq = window._paq = window._paq || []; /* tracker methods like "setCustomDimension" should be called before "trackPageView" */ _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u="https://matomo.sib.swiss/"; _paq.push(['setTrackerUrl', u+'matomo.php']); 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margin-top: 5px;"> <rhea-search-examples></rhea-search-examples> <a id="advanced-search-button">Advanced search</a> <a id="browse-button">Browse</a> </div> </div> </header> <nav role="navigation" itemscope itemtype="http://www.schema.org/SiteNavigationElement" class="row-container"> <a itemprop="url" href="/structuresearch"> <svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 0 24 24" width="24"><path d="M0 0h24v24H0z" fill="none"/><path d="M4.59 6.89c.7-.71 1.4-1.35 1.71-1.22.5.2 0 1.03-.3 1.52-.25.42-2.86 3.89-2.86 6.31 0 1.28.48 2.34 1.34 2.98.75.56 1.74.73 2.64.46 1.07-.31 1.95-1.4 3.06-2.77 1.21-1.49 2.83-3.44 4.08-3.44 1.63 0 1.65 1.01 1.76 1.79-3.78.64-5.38 3.67-5.38 5.37 0 1.7 1.44 3.09 3.21 3.09 1.63 0 4.29-1.33 4.69-6.1H21v-2.5h-2.47c-.15-1.65-1.09-4.2-4.03-4.2-2.25 0-4.18 1.91-4.94 2.84-.58.73-2.06 2.48-2.29 2.72-.25.3-.68.84-1.11.84-.45 0-.72-.83-.36-1.92.35-1.09 1.4-2.86 1.85-3.52.78-1.14 1.3-1.92 1.3-3.28C8.95 3.69 7.31 3 6.44 3 5.12 3 3.97 4 3.72 4.25c-.36.36-.66.66-.88.93l1.75 1.71zm9.29 11.66c-.31 0-.74-.26-.74-.72 0-.6.73-2.2 2.87-2.76-.3 2.69-1.43 3.48-2.13 3.48z"/></svg> <span itemprop="name">Structure search</span> </a> <a itemprop="url" href="/mapping"> <svg xmlns="http://www.w3.org/2000/svg" enable-background="new 0 0 24 24" height="24" viewBox="0 0 24 24" width="24"><g><rect fill="none" height="24" width="24" x="0"/></g><g><g><g><path d="M9.01,14H2v2h7.01v3L13,15l-3.99-4V14z M14.99,13v-3H22V8h-7.01V5L11,9L14.99,13z"/></g></g></g></svg> <span itemprop="name">Retrieve/ID mapping</span> </a> <a itemprop="url" class="sparqlEndpoint" href="https://sparql.rhea-db.org/sparql"> <svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 0 24 24" width="24"><path d="M0 0h24v24H0z" fill="none"/><path d="M3.9 12c0-1.71 1.39-3.1 3.1-3.1h4V7H7c-2.76 0-5 2.24-5 5s2.24 5 5 5h4v-1.9H7c-1.71 0-3.1-1.39-3.1-3.1zM8 13h8v-2H8v2zm9-6h-4v1.9h4c1.71 0 3.1 1.39 3.1 3.1s-1.39 3.1-3.1 3.1h-4V17h4c2.76 0 5-2.24 5-5s-2.24-5-5-5z"/></svg> <span itemprop="name">SPARQL</span> </a> <a itemprop="url" href="/help/download"> <svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 0 24 24" width="24"><path d="M0 0h24v24H0z" fill="none"/><path d="M19.35 10.04C18.67 6.59 15.64 4 12 4 9.11 4 6.6 5.64 5.35 8.04 2.34 8.36 0 10.91 0 14c0 3.31 2.69 6 6 6h13c2.76 0 5-2.24 5-5 0-2.64-2.05-4.78-4.65-4.96zM17 13l-5 5-5-5h3V9h4v4h3z"/></svg> <span itemprop="name">Download</span> </a> <a itemprop="url" href="/help"> <svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 0 24 24" width="24"><path d="M0 0h24v24H0V0z" fill="none"/><path d="M19.07 4.93l-1.41 1.41C19.1 7.79 20 9.79 20 12c0 4.42-3.58 8-8 8s-8-3.58-8-8c0-4.08 3.05-7.44 7-7.93v2.02C8.16 6.57 6 9.03 6 12c0 3.31 2.69 6 6 6s6-2.69 6-6c0-1.66-.67-3.16-1.76-4.24l-1.41 1.41C15.55 9.9 16 10.9 16 12c0 2.21-1.79 4-4 4s-4-1.79-4-4c0-1.86 1.28-3.41 3-3.86v2.14c-.6.35-1 .98-1 1.72 0 1.1.9 2 2 2s2-.9 2-2c0-.74-.4-1.38-1-1.72V2h-1C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10c0-2.76-1.12-5.26-2.93-7.07z"/></svg> <span itemprop="name">Help</span> </a> <a itemprop="url" href="/feedback"> <svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 0 24 24" width="24"><path d="M0 0h24v24H0z" fill="none"/><path d="M20 4H4c-1.1 0-1.99.9-1.99 2L2 18c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V6c0-1.1-.9-2-2-2zm0 4l-8 5-8-5V6l8 5 8-5v2z"/></svg> <span itemprop="name">Feedback</span> </a> </nav> <main> <section class="advanced-search" style="display: none"></section> <section class="column-container structurediv"> <div class="column-container"> <div class="row-container" style="align-items: center"> Enter a SMILES string: <input type="text" id="smiles" name="smiles" size="60"></input> <set-smiles-button label="Show"></set-smiles-button> </div> <p>Or draw a molecule below:</p> </div> <div class="row-container formcontainer"> <div class="iframecontainer"> <iframe src="/ketcher/ketcher.html" id="ketcherFrame" name="ketcherFrame" width="900px" , height="500px"> </iframe> <p> The structure search is powered by <a target="_blank" href="https://idsm.elixir-czech.cz/">IDSM Sachem</a>. The editor is powered by <a target="_blank" href="https://lifescience.opensource.epam.com/ketcher/index.html">Ketcher</a>. </p> </div> <div class="column-container"> <h3>Search type</h3> <ul class="row-container searchtype"> <li class="selected" id="substructure">Substructure</li> <li id="similarity">Similarity</li> </ul> <div class="substructure-container"> <p>Find compounds which contain this structure (<a href="/help/structure-search#substructure">substructure search</a>)</p> <div class="column-container"> <form target="_blank" method="GET" action="/structuresearch" id="structureSearch"> <input type="hidden" name="query"></input> <input type="hidden" name="tool" value="substructure"></input> <div class="structureForm"> <label for="charge">Charge</label> <select name="charge" id="charge"> <option value="sachem:ignoreCharges" selected="selected">Ignore</option> <option value="sachem:defaultChargeAsAny">Default any charge</option> <option value="sachem:defaultChargeAsZero">Default zero charge</option> </select> <label for="aromaticity">Aromaticity</label> <select name="aromaticity" id="aromaticity"> <option value="sachem:aromaticityFromQuery">From query</option> <option value="sachem:aromaticityDetect" selected="selected">Recompute</option> <option value="sachem:aromaticityDetectIfMissing">Compute if missing</option> </select> <label for="stereochemistry">Stereochemistry</label> <select name="stereochemistry" id="stereochemistry"> <option value="sachem:ignoreStereo" selected="selected">Ignore</option> <option value="sachem:strictStereo">Strict</option> </select> <label for="tautomerism">Tautomerism</label> <select name="tautomerism" id="tautomerism"> <option value="sachem:ignoreTautomers" selected="selected">Ignore</option> <option value="sachem:inchiTautomers">Strict</option> </select> <label for="radicals">Radicals</label> <select name="radicals" id="radicals"> <option value="sachem:ignoreSpinMultiplicity" selected="selected">Ignore</option> <option value="sachem:defaultSpinMultiplicityAsZero">Default zero</option> <option value="sachem:defaultSpinMultiplicityAsAny">Default any</option> </select> <label> </label> <div class="row-container"> <input type="checkbox" style="margin-right: 10px" id="exact" name="exact"></input> <label for="exact">Require exact match</label> </div> </div> </form> <div class="row-container"> <structure-search-button label="Search structure" data-form-id="structureSearch"></structure-search-button> <options-reset-button label="Reset options" data-form-id="structureSearch"></options-reset-button> </div> </div> </div> <div class="similarity-container" style="display:none"> <p>Find compounds that are similar to this structure (<a href="/help/structure-search#similarity">similarity search</a>)</p> <div class="column-container"> <form target="_blank" method="GET" action="/structuresearch" id="similaritySearch"> <input type="hidden" name="query"></input> <input type="hidden" name="tool" value="similarity"></input> <div class="structureForm"> <label for="cutoff">Similarity threshold</label> <div class="row-container"> <input type="range" step="0.05" id="cutoff" name="cutoff" max="1" min="0" value="0.8"> </input> <output id="slideroutput">0.8</output> </div> <label for="similarityRadius">Radius</label> <select name="similarityRadius" id="similarityRadius"> <option value="1" selected="selected">Radius 1</option> <option value="2">Radius 2</option> <option value="3">Radius 3</option> </select> <label for="aromaticity">Aromaticity</label> <select name="aromaticity" id="aromaticity"> <option value="sachem:aromaticityFromQuery">From query</option> <option value="sachem:aromaticityDetect" selected="selected">Recompute</option> <option value="sachem:aromaticityDetectIfMissing">Compute if missing</option> </select> <label for="tautomerism">Tautomerism</label> <select name="tautomerism" id="tautomerism"> <option value="sachem:ignoreTautomers" selected="selected">Ignore</option> <option value="sachem:inchiTautomers">Strict</option> </select> </div> </form> <div class="row-container"> <structure-search-button label="Search structure" data-form-id="similaritySearch"></structure-search-button> <options-reset-button label="Reset options" data-form-id="similaritySearch"></options-reset-button> </div> </div> </div> </div> </div> </section> </main> <footer class="row-container" style="text-align: center;"> <div class="row-container footer-logo"> <img alt="SIB logo" width="70px" height="37px" src="/style/images/sib_logo_short.png" /> <span> <a href="/help/license-disclaimer">License & Disclaimer</a> | <a href="https://www.sib.swiss/privacy-policy">Privacy Policy</a> </span> </div> <div class="row-container footer-logo"> <a href="https://www.elixir-europe.org/platforms/data/core-data-resources"> <img width="64px" height="64px" id="elixir-cdr-logo" alt="Elixir-cdr-logo" src="/style/images/elixir-cdr.gif"> </a> <h4>ELIXIR Core Data Resource</h4> </div> <div 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