model/dataset.py

import random
import pandas as pd
import torch
from torch.utils.data import Dataset, DataLoader

from .enumerator import SmilesEnumerator
from .utils import split

PAD = 0
MAX_LEN = 220

class Randomizer(object):

    def __init__(self):
        self.sme = SmilesEnumerator()
    
    def __call__(self, sm):
        sm_r = self.sme.randomize_smiles(sm) # Random transoform
        if sm_r is None:
            sm_spaced = split(sm) # Spacing
        else:
            sm_spaced = split(sm_r) # Spacing
        sm_split = sm_spaced.split()
        if len(sm_split)<=MAX_LEN - 2:
            return sm_split # List
        else:
            return split(sm).split()

    def random_transform(self, sm):
        '''
        function: Random transformation for SMILES. It may take some time.
        input: A SMILES
        output: A randomized SMILES
        '''
        return self.sme.randomize_smiles(sm)

class Seq2seqDataset(Dataset):

    def __init__(self, smiles, vocab, seq_len=220, transform=Randomizer()):
        self.smiles = smiles
        self.vocab = vocab
        self.seq_len = seq_len
        self.transform = transform

    def __len__(self):
        return len(self.smiles)

    def __getitem__(self, item):
        sm = self.smiles[item]
        sm = self.transform(sm) # List
        content = [self.vocab.stoi.get(token, self.vocab.unk_index) for token in sm]
        X = [self.vocab.sos_index] + content + [self.vocab.eos_index]
        padding = [self.vocab.pad_index]*(self.seq_len - len(X))
        X.extend(padding)
        return torch.tensor(X)