Drug/Target Encoder 

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Drug encoding 

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    Drug Encodings                         Description 

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      Morgan                    Extended-Connectivity Fingerprints                    

      Pubchem                 Pubchem Substructure-based Fingerprints                   

      Daylight                      Daylight-type fingerprints 

 rdkit_2d_normalized                Normalized Descriptastorus                   

        CNN                    Convolutional Neural Network on SMILES                    

      CNN_RNN                     A GRU/LSTM on top of a CNN on SMILES                   

     Transformer                    Transformer Encoder on ESPF

       MPNN                          Message-passing neural network 

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Target encoding 

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  Target Encodings                        Description   

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      AAC                       Amino acid composition up to 3-mers      

    PseudoAAC                    Pseudo amino acid composition            

   Conjoint_triad                    Conjoint triad features                  

    Quasi-seq                    Quasi-sequence order descriptor              

      CNN                    Convolutional Neural Network on target seq

    CNN_RNN                   A GRU/LSTM on top of a CNN on target seq             

   Transformer                     Transformer Encoder on ESPF

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Encoder Model 

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  Encoder Model                         Description   

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      CNN                    Convolutional Neural Network on SMILES

    CNN_RNN                   A GRU/LSTM on top of a CNN on SMILES            

   Transformer                     Transformer Encoder on SMILES

     MPNN                     Message Passing Neural Network on Molecular Graph           

      MLP                       MultiLayer Perceptron on fix-dim feature vector                   

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Technical Details

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First, we describe the common modules we import in DeepPurpose.

.. code-block:: python

    import torch

    from torch.autograd import Variable

    import torch.nn.functional as F

    from torch import nn 

    import numpy as np

    import pandas as pd 

.. toctree::

   :glob:

   :maxdepth: 1

   :caption: Links of details of various encoders 

   encoders/transformer

   encoders/mpnn

   encoders/cnnrnn

   encoders/cnn 

   encoders/mlp