Drug/Target Encoder¶

Drug encoding¶

Drug Encodings	Description
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

Target Encodings	Description
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

Encoder Model	Description
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

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

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

Links of details of various encoders