213 lines
5.5 KiB
HTML
213 lines
5.5 KiB
HTML
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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<title>
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File: README
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— Documentation by YARD 0.8.7.6
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</title>
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<link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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<link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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<script type="text/javascript" charset="utf-8">
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hasFrames = window.top.frames.main ? true : false;
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relpath = '';
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framesUrl = "frames.html#!file.README.html";
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</script>
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<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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</head>
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<body>
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<div id="header">
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<div id="menu">
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<a href="_index.html">Index</a> »
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<span class="title">File: README</span>
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<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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</div>
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<div id="search">
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<a class="full_list_link" id="class_list_link"
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href="class_list.html">
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Class List
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</a>
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<a class="full_list_link" id="method_list_link"
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href="method_list.html">
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Method List
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</a>
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<a class="full_list_link" id="file_list_link"
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href="file_list.html">
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File List
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</a>
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</div>
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<div class="clear"></div>
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</div>
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<iframe id="search_frame"></iframe>
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<div id="content"><div id='filecontents'>
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<p><a href="http://classyfire.wishartlab.com">ClassyFire</a> is a resource
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that allows you to automatically classify any chemical compound based on
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its structure. This is the repository for the ClassyFire API allows you to
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send requests to and pull information from the ClassyFire web server.</p>
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<h1 id="label-What+is+this+repository+for-3F"><strong>What is this repository for?</strong></h1>
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<ul><li>
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<p>Quick summary</p>
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</li><li>
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<p>Version</p>
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</li><li>
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<p><a href="https://bitbucket.org/tutorials/markdowndemo">Learn Markdown</a></p>
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</li></ul>
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<h1 id="label-How+do+I+get+set+up-3F"><strong>How do I get set up?</strong></h1>
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<ul><li>
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<p>Summary of set up</p>
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</li><li>
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<p>Configuration</p>
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</li><li>
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<p>Dependencies</p>
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</li><li>
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<p>Database configuration</p>
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</li><li>
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<p>How to run tests</p>
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</li><li>
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<p>Deployment instructions</p>
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</li></ul>
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<h1 id="label-Contribution+guidelines"><strong>Contribution guidelines</strong></h1>
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<ul><li>
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<p>Writing tests</p>
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</li><li>
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<p>Code review</p>
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</li><li>
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<p>Other guidelines</p>
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</li></ul>
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<h1 id="label-Endpoints"><strong>Endpoints</strong></h1>
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<blockquote>
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<h2 id="label-1.+Entity">1. Entity</h2>
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<blockquote>
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<p>Chemical compounds are represented by the Entity model, through which one
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can access the compound's structure-based classification.</p>
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<h3 id="label-GET">GET</h3>
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<p><strong>/entities/entityInchikey</strong></p>
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<p>A chemical compound's classification can be retrieved in the JSON or
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XML format. The compound's information is accessed via the InChIkey as
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show in the following examples. In this example, the entity has the
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InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.</p>
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<blockquote>
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<p>ClassyFireAPI.get_entity_classification(“BDAGIHXWWSANSR-UHFFFAOYSA-N”,“json”)</p>
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</blockquote>
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<p>Where:</p>
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<blockquote>
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<p>The entity's InChIKey is “BDAGIHXWWSANSR-UHFFFAOYSA-N”,</p>
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<p>The output format is “json” (JSON).</p>
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</blockquote>
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</blockquote>
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<h2 id="label-2.+Query">2. Query</h2>
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<blockquote>
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<p>The Query model represents the chemical structure to be classified. Its
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attributes are the query label and the query input.</p>
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<blockquote>
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<p>The query label is an identifier</p>
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<p>The query input contains the compound's identifier (optional) and its
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structural representation, separated by a comma. The chemical structure is
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represented either in the <a
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href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight
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SMILES</a> or the <a
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href="http://www.iupac.org/home/publications/e-resources/inchi.html">InChI</a>
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format.</p>
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</blockquote>
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<h3 id="label-POST">POST</h3>
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<p>A query can be submitted using the POST method as demonstrated in the
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following example.</p>
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<blockquote>
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<p>ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)</p>
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</blockquote>
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<p>where the parameters are:</p>
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<blockquote>
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<p>The query label: curl_test,</p>
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<p>The entity identifiers: MOL1,MOL2</p>
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<p>The entity's structure represented in the SMILES format: CCCOCC and
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COCC=CCCC.</p>
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<p>The query is of type 'STRUCTURE'</p>
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</blockquote>
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<h3 id="label-GET">GET</h3>
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<p><strong>/queries/queryId</strong></p>
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<p>The classification results can be retrieved via a GET method in the JSON or
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XML format.</p>
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<blockquote>
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<p>ClassyFireAPI.get_query(443431,“json”)</p>
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</blockquote>
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<p>where:</p>
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<blockquote>
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<p>The query id is 443431, The output format is “json” (JSON)</p>
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</blockquote>
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</blockquote>
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</blockquote>
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<h1 id="label-Directory+Structure"><strong>Directory Structure</strong></h1>
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<ul><li>
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<p>lib</p>
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</li></ul>
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<h1 id="label-Who+do+I+talk+to-3F"><strong>Who do I talk to?</strong></h1>
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<ul><li>
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<p>Repo owner or admin</p>
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</li><li>
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<p>Other community or team contact</p>
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</li></ul>
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</div></div>
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<div id="footer">
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Generated on Wed Mar 9 19:25:38 2016 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.8.7.6 (ruby-2.3.0).
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</div>
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</body>
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</html>
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