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--- a +++ b/docs/build/html/index.html @@ -0,0 +1,355 @@ + + +<!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" 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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="#">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="#">Docs</a> »</li> + + <li>DeepPurpose documentation!</li> + + + <li class="wy-breadcrumbs-aside"> + + + <a href="_sources/index.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> + + <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation"> + + <a href="notes/introduction.html" class="btn btn-neutral float-right" title="Features of DeepPurpose" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a> + + + </div> + + + <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> \ No newline at end of file