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--- a +++ b/docs/build/html/notes/utils.html @@ -0,0 +1,315 @@ + + +<!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.utils — 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" /> + <link rel="next" title="Drug Target Binding Affinity (DTBA) Model" href="model.html" /> + <link rel="prev" title="DeepPurpose.model_helper" href="model_helper.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="introduction.html">Features of DeepPurpose</a><ul> +<li class="toctree-l2"><a class="reference internal" href="introduction.html#features">Features</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="DTI.html">What is drug repurposing, virtual screening and drug-target interaction prediction?</a><ul> +<li class="toctree-l2"><a class="reference internal" href="DTI.html#drug-repurposing">Drug Repurposing</a></li> +<li class="toctree-l2"><a class="reference internal" href="DTI.html#virtual-screening">Virtual Screening</a></li> +<li class="toctree-l2"><a class="reference internal" href="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="download.html">Download Code & Install</a><ul> +<li class="toctree-l2"><a class="reference internal" href="download.html#download-code">Download Code</a></li> +<li class="toctree-l2"><a class="reference internal" href="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="download.html#second-time-and-later">Second time and later</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="casestudy.html">Case Study</a></li> +</ul> +<p class="caption"><span class="caption-text">Package Reference</span></p> +<ul class="current"> +<li class="toctree-l1"><a class="reference internal" href="models.html">DeepPurpose.models</a><ul> +<li class="toctree-l2"><a class="reference internal" href="dtba/classifier.html">Classifier</a></li> +<li class="toctree-l2"><a class="reference internal" href="dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/transformer.html">Transformer</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/cnnrnn.html">CNN+RNN</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/cnn.html">CNN</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/mlp.html">MLP</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="dataset.html">DeepPurpose.dataset</a><ul> +<li class="toctree-l2"><a class="reference internal" href="data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li> +<li class="toctree-l2"><a class="reference internal" href="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="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="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="data/read_file_target_sequence.html">read_file_target_sequence</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/download_BindingDB.html">download_DrugTargetCommons</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/process_BindingDB.html">process_BindingDB</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_process_DAVIS.html">load_process_DAVIS</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_process_KIBA.html">load_process_KIBA</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_antiviral_drugs.html">load_antiviral_drugs</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_broad_repurposing_hub.html">load_broad_repurposing_hub</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="chemutils.html">DeepPurpose.chemutils</a><ul> +<li class="toctree-l2"><a class="reference internal" href="chem/onek_encoding_unk.html">DeepPurpose.chemutils.onek_encoding_unk</a></li> +<li class="toctree-l2"><a class="reference internal" href="chem/atom_features.html">DeepPurpose.chemutils.atom_features</a></li> +<li class="toctree-l2"><a class="reference internal" href="chem/bond_features.html">DeepPurpose.chemutils.bond_features</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="oneliner.html">DeepPurpose.oneliner</a><ul> +<li class="toctree-l2"><a class="reference internal" href="oneliner_folder/repurpose.html">DeepPurpose.oneliner.repurpose</a></li> +<li class="toctree-l2"><a class="reference internal" href="oneliner_folder/virtual_screening.html">DeepPurpose.oneliner.virtual_screening</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="model_helper.html">DeepPurpose.model_helper</a></li> +<li class="toctree-l1 current"><a class="current reference internal" href="#">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="model.html">Drug Target Binding Affinity (DTBA) Model</a><ul> +<li class="toctree-l2"><a class="reference internal" href="dtba/classifier.html">Classifier</a></li> +<li class="toctree-l2"><a class="reference internal" href="dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="encoder.html">Drug/Target Encoder</a><ul> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#drug-encoding">Drug encoding</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#target-encoding">Target encoding</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#encoder-model">Encoder Model</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#technical-details">Technical Details</a><ul> +<li class="toctree-l3"><a class="reference internal" href="encoders/transformer.html">Transformer</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/cnnrnn.html">CNN+RNN</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/cnn.html">CNN</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/mlp.html">MLP</a></li> +</ul> +</li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="process_data.html">Processing Data</a><ul> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#drug-target-binding-benchmark-dataset">Drug-Target Binding Benchmark Dataset</a></li> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#repurposing-dataset">Repurposing Dataset</a></li> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#bioassay-data-for-covid-19">Bioassay Data for COVID-19</a></li> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#covid-19-targets">COVID-19 Targets</a><ul> +<li class="toctree-l3"><a class="reference internal" href="data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li> +<li class="toctree-l3"><a class="reference internal" href="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="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="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="data/read_file_target_sequence.html">read_file_target_sequence</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/download_BindingDB.html">download_DrugTargetCommons</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/process_BindingDB.html">process_BindingDB</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_process_DAVIS.html">load_process_DAVIS</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_process_KIBA.html">load_process_KIBA</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_antiviral_drugs.html">load_antiviral_drugs</a></li> +<li class="toctree-l3"><a class="reference internal" href="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="configuration.html">Configuration</a></li> +<li class="toctree-l1"><a class="reference internal" href="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.utils</li> + + + <li class="wy-breadcrumbs-aside"> + + + <a href="../_sources/notes/utils.rst.txt" rel="nofollow"> View page source</a> + + + 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