import os from tqdm import tqdm import networkx as nx import torch from torch.utils.data import Dataset atom_number_index_dict = { 1: 0, # H 6: 1, # C 7: 2, # N 8: 3, # O 9: 4 # F } atom_index_number_dict = {v: k for k, v in atom_number_index_dict.items()} max_atom_number = max(atom_number_index_dict.keys()) def atom_number2index(atom_number): return atom_number_index_dict[atom_number] def atom_index2number(atom_index): return atom_index_number_dict[atom_index] class PreprocessedQM9Dataset(Dataset): def __init__(self, dataset): self.dataset = dataset self.processed_data = [] if dataset is not None: self._preprocess() def _preprocess(self): i = 0 for g, label in tqdm(self.dataset): g.ndata["Z_index"] = torch.tensor([atom_number2index(z.item()) for z in g.ndata["Z"]]) g.ndata["sample_idx"] = i self.processed_data.append((g, label)) def __len__(self): return len(self.processed_data) def __getitem__(self, idx): return self.processed_data[idx] def save_dataset(self, save_dir): if not os.path.exists(save_dir): os.makedirs(save_dir) torch.save(self.processed_data, os.path.join(save_dir,"QM9_dataset_processed.pt")) def load_dataset(self, dataset_path): self.processed_data = torch.load(dataset_path)