<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>DeepPurpose documentation! — DeepPurpose 0.0.1 documentation</title>
<script type="text/javascript" src="_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Raleway" type="text/css" />
<link rel="stylesheet" href="../build/html/_static/css/deeppurpose_docs_theme.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home"> DeepPurpose
<img src="_static/logo_dp_2.png" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<p class="caption"><span class="caption-text">Background</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/introduction.html">Features of DeepPurpose</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/introduction.html#features">Features</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/DTI.html">What is drug repurposing, virtual screening and drug-target interaction prediction?</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/DTI.html#drug-repurposing">Drug Repurposing</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/DTI.html#virtual-screening">Virtual Screening</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/DTI.html#drug-target-interaction">Drug-Target Interaction</a></li>
</ul>
</li>
</ul>
<p class="caption"><span class="caption-text">How to run</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/download.html">Download Code & Install</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/download.html#download-code">Download Code</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/download.html#first-time-usage-setup-conda-environment">First time usage: setup conda environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/download.html#second-time-and-later">Second time and later</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/casestudy.html">Case Study</a></li>
</ul>
<p class="caption"><span class="caption-text">Package Reference</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/models.html">DeepPurpose.models</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/dtba/classifier.html">Classifier</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoders/transformer.html">Transformer</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoders/cnnrnn.html">CNN+RNN</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoders/cnn.html">CNN</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoders/mlp.html">MLP</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/dataset.html">DeepPurpose.dataset</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/read_file_training_dataset_drug_target_pairs.html">read_file_training_dataset_drug_target_pairs</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/read_file_virtual_screening_drug_target_pairs.html">read_file_virtual_screening_drug_target_pairs</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/read_file_repurposing_library.html">load bioarray dataset (read_file_training_dataset_bioassay)</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/read_file_target_sequence.html">read_file_target_sequence</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/download_BindingDB.html">download_DrugTargetCommons</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/process_BindingDB.html">process_BindingDB</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/load_process_DAVIS.html">load_process_DAVIS</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/load_process_KIBA.html">load_process_KIBA</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/load_antiviral_drugs.html">load_antiviral_drugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/data/load_broad_repurposing_hub.html">load_broad_repurposing_hub</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/chemutils.html">DeepPurpose.chemutils</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/chem/onek_encoding_unk.html">DeepPurpose.chemutils.onek_encoding_unk</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/chem/atom_features.html">DeepPurpose.chemutils.atom_features</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/chem/bond_features.html">DeepPurpose.chemutils.bond_features</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/oneliner.html">DeepPurpose.oneliner</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/oneliner_folder/repurpose.html">DeepPurpose.oneliner.repurpose</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/oneliner_folder/virtual_screening.html">DeepPurpose.oneliner.virtual_screening</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/model_helper.html">DeepPurpose.model_helper</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/utils.html">DeepPurpose.utils</a></li>
</ul>
<p class="caption"><span class="caption-text">Importance Function</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/model.html">Drug Target Binding Affinity (DTBA) Model</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/dtba/classifier.html">Classifier</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/encoder.html">Drug/Target Encoder</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#drug-encoding">Drug encoding</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#target-encoding">Target encoding</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#encoder-model">Encoder Model</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#technical-details">Technical Details</a><ul>
<li class="toctree-l3"><a class="reference internal" href="notes/encoders/transformer.html">Transformer</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/encoders/cnnrnn.html">CNN+RNN</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/encoders/cnn.html">CNN</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/encoders/mlp.html">MLP</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/process_data.html">Processing Data</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notes/process_data.html#drug-target-binding-benchmark-dataset">Drug-Target Binding Benchmark Dataset</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/process_data.html#repurposing-dataset">Repurposing Dataset</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/process_data.html#bioassay-data-for-covid-19">Bioassay Data for COVID-19</a></li>
<li class="toctree-l2"><a class="reference internal" href="notes/process_data.html#covid-19-targets">COVID-19 Targets</a><ul>
<li class="toctree-l3"><a class="reference internal" href="notes/data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/read_file_training_dataset_drug_target_pairs.html">read_file_training_dataset_drug_target_pairs</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/read_file_virtual_screening_drug_target_pairs.html">read_file_virtual_screening_drug_target_pairs</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/read_file_repurposing_library.html">load bioarray dataset (read_file_training_dataset_bioassay)</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/read_file_target_sequence.html">read_file_target_sequence</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/download_BindingDB.html">download_DrugTargetCommons</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/process_BindingDB.html">process_BindingDB</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/load_process_DAVIS.html">load_process_DAVIS</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/load_process_KIBA.html">load_process_KIBA</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/load_antiviral_drugs.html">load_antiviral_drugs</a></li>
<li class="toctree-l3"><a class="reference internal" href="notes/data/load_broad_repurposing_hub.html">load_broad_repurposing_hub</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notes/configuration.html">Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/utility_function.html">Utility Function</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">DeepPurpose</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html">Docs</a> »</li>
<li>DeepPurpose documentation!</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/contents.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="deeppurpose-documentation">
<h1>DeepPurpose documentation!<a class="headerlink" href="#deeppurpose-documentation" title="Permalink to this headline">¶</a></h1>
<p>Welcome! This is the documentation for DeepPurpose.
DeepPurpose is a Deep Learning Based Drug Repurposing and Virtual Screening Toolkit (using PyTorch).
It allows very easy usage (only one line of code!)
for non-computational domain researchers to be able to
obtain a list of potential drugs using deep learning
while facilitating deep learning method research in this topic
by providing a flexible framework (less than 10 lines of codes!) and baselines.
The Github repository is located <a class="reference external" href="https://github.com/kexinhuang12345/DeepPurpose">here</a>.</p>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Background</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/introduction.html">Features of DeepPurpose</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/DTI.html">What is drug repurposing, virtual screening and drug-target interaction prediction?</a></li>
</ul>
</div>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">How to run</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/download.html">Download Code & Install</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/casestudy.html">Case Study</a></li>
</ul>
</div>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Package Reference</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/models.html">DeepPurpose.models</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/dataset.html">DeepPurpose.dataset</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/chemutils.html">DeepPurpose.chemutils</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/oneliner.html">DeepPurpose.oneliner</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/model_helper.html">DeepPurpose.model_helper</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/utils.html">DeepPurpose.utils</a></li>
</ul>
</div>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Importance Function</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notes/model.html">Drug Target Binding Affinity (DTBA) Model</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/encoder.html">Drug/Target Encoder</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/process_data.html">Processing Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/configuration.html">Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="notes/utility_function.html">Utility Function</a></li>
</ul>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© Copyright 2020, Kexin Huang, Tianfan Fu
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>
Datasets
Models
