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              <p class="caption"><span class="caption-text">Background</span></p>





  
  

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<ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/introduction.html">Features of DeepPurpose</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/introduction.html#features">Features</a></li>





  
  

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</ul>





  
  

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<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>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/DTI.html#drug-repurposing">Drug Repurposing</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/DTI.html#virtual-screening">Virtual Screening</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/DTI.html#drug-target-interaction">Drug-Target Interaction</a></li>





  
  

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<p class="caption"><span class="caption-text">How to run</span></p>





  
  

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<ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/download.html">Download Code &amp; Install</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/download.html#download-code">Download Code</a></li>





  
  

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<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>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/download.html#second-time-and-later">Second time and later</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/casestudy.html">Case Study</a></li>





  
  

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<p class="caption"><span class="caption-text">Package Reference</span></p>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/models.html">DeepPurpose.models</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/dtba/classifier.html">Classifier</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoders/transformer.html">Transformer</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoders/cnnrnn.html">CNN+RNN</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoders/cnn.html">CNN</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoders/mlp.html">MLP</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/dataset.html">DeepPurpose.dataset</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li>





  
  

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<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>





  
  

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<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>





  
  

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<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>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/read_file_target_sequence.html">read_file_target_sequence</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/download_BindingDB.html">download_DrugTargetCommons</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/process_BindingDB.html">process_BindingDB</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/load_process_DAVIS.html">load_process_DAVIS</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/load_process_KIBA.html">load_process_KIBA</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/load_antiviral_drugs.html">load_antiviral_drugs</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/data/load_broad_repurposing_hub.html">load_broad_repurposing_hub</a></li>





  
  

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</ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/chemutils.html">DeepPurpose.chemutils</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/chem/onek_encoding_unk.html">DeepPurpose.chemutils.onek_encoding_unk</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/chem/atom_features.html">DeepPurpose.chemutils.atom_features</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/chem/bond_features.html">DeepPurpose.chemutils.bond_features</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/oneliner.html">DeepPurpose.oneliner</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/oneliner_folder/repurpose.html">DeepPurpose.oneliner.repurpose</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/oneliner_folder/virtual_screening.html">DeepPurpose.oneliner.virtual_screening</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/model_helper.html">DeepPurpose.model_helper</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/utils.html">DeepPurpose.utils</a></li>





  
  

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<p class="caption"><span class="caption-text">Importance Function</span></p>





  
  

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<ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/model.html">Drug Target Binding Affinity (DTBA) Model</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/dtba/classifier.html">Classifier</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li>





  
  

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</ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/encoder.html">Drug/Target Encoder</a><ul>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#drug-encoding">Drug encoding</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#target-encoding">Target encoding</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#encoder-model">Encoder Model</a></li>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/encoder.html#technical-details">Technical Details</a><ul>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/encoders/transformer.html">Transformer</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/encoders/cnnrnn.html">CNN+RNN</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/encoders/cnn.html">CNN</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/encoders/mlp.html">MLP</a></li>





  
  

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</ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/process_data.html">Processing Data</a><ul>





  
  

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<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>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/process_data.html#repurposing-dataset">Repurposing Dataset</a></li>





  
  

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<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>





  
  

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<li class="toctree-l2"><a class="reference internal" href="notes/process_data.html#covid-19-targets">COVID-19 Targets</a><ul>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li>





  
  

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<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>





  
  

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<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>





  
  

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<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>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/read_file_target_sequence.html">read_file_target_sequence</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/download_BindingDB.html">download_DrugTargetCommons</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/process_BindingDB.html">process_BindingDB</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/load_process_DAVIS.html">load_process_DAVIS</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/load_process_KIBA.html">load_process_KIBA</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/load_antiviral_drugs.html">load_antiviral_drugs</a></li>





  
  

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<li class="toctree-l3"><a class="reference internal" href="notes/data/load_broad_repurposing_hub.html">load_broad_repurposing_hub</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/configuration.html">Configuration</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/utility_function.html">Utility Function</a></li>





  
  

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      <li>DeepPurpose documentation!</li>





  
  

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  <div class="section" id="deeppurpose-documentation">





  
  

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<h1>DeepPurpose documentation!<a class="headerlink" href="#deeppurpose-documentation" title="Permalink to this headline">ΒΆ</a></h1>





  
  

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<p>Welcome! This is the documentation for DeepPurpose.





  
  

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DeepPurpose is a Deep Learning Based Drug Repurposing and Virtual Screening Toolkit (using PyTorch).





  
  

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It allows very easy usage (only one line of code!)





  
  

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for non-computational domain researchers to be able to





  
  

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obtain a list of potential drugs using deep learning





  
  

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while facilitating deep learning method research in this topic





  
  

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by providing a flexible framework (less than 10 lines of codes!) and baselines.





  
  

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The Github repository is located <a class="reference external" href="https://github.com/kexinhuang12345/DeepPurpose">here</a>.</p>





  
  

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<p class="caption"><span class="caption-text">Background</span></p>





  
  

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<ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/introduction.html">Features of DeepPurpose</a></li>





  
  

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<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>





  
  

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<p class="caption"><span class="caption-text">How to run</span></p>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/model.html">Drug Target Binding Affinity (DTBA) Model</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/encoder.html">Drug/Target Encoder</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="notes/configuration.html">Configuration</a></li>





  
  

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