add prepare_QM9_dataset.py

Graph/GraphMAE_MQ9/prepare_QM9_dataset.py

@@ -0,0 +1,48 @@
+import argparse
+import os
+import time
+
+from dgl.data import QM9Dataset
+from dgl.dataloading import GraphDataLoader
+from rdkit import Chem
+from rdkit import RDLogger;
+from torch.utils.data import Dataset
+import torch.nn.functional as F
+from tqdm import tqdm
+import ast
+
+from QM9_dataset_class import PreprocessedQM9Dataset
+
+RDLogger.DisableLog('rdApp.*')
+import torch
+import torch.nn as nn
+import torch.optim as optim
+
+
+QM9_label_keys = ['mu','alpha','homo','lumo','gap','r2','zpve','U0','U','H','G','Cv']
+
+
+
+def prepare_main(label_keys=None, cutoff=5.0,save_path="dataset"):
+    assert save_path !="","save_path shouldn't be empty"
+    if label_keys is None:
+        raise ValueError('label_keys cannot be None')
+    for label_key in label_keys:
+        if label_key not in QM9_label_keys:
+            raise ValueError('label_key must be in QM9_label_keys,refer:https://docs.dgl.ai/en/0.8.x/generated/dgl.data.QM9Dataset.html')
+    dataset = QM9Dataset(label_keys=label_keys, cutoff=5.0)
+    dataset_processed = PreprocessedQM9Dataset(dataset)
+    print("Store processed QM9 dataset:",save_path)
+    dataset_processed.save_dataset("dataset")
+    return dataset_processed
+
+def main():
+    parser = argparse.ArgumentParser(description="Prepare QM9 dataset")
+    parser.add_argument('--label_keys', nargs='+', help="label keys in QM9 dataset,like 'mu' 'gap'....")
+    parser.add_argument('--cutoff', type=float, default=5.0, help="cutoff for atom number")
+    parser.add_argument('--save_path', type=str, default="dataset", help="processed_dataset save path")
+    args = parser.parse_args()
+    prepare_main(label_keys=args.label_keys, cutoff=args.cutoff)
+
+if __name__ == '__main__':
+    main()