| import os |
| import pickle |
| import lmdb |
| from tqdm import tqdm, trange |
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| def read_lmdb(lmdb_path): |
| env = lmdb.open( |
| lmdb_path, |
| subdir=False, |
| readonly=True, |
| lock=False, |
| readahead=False, |
| meminit=False, |
| max_readers=256, |
| ) |
| txn = env.begin() |
| keys = list(txn.cursor().iternext(values=False)) |
| out_list = [] |
| for idx in tqdm(keys): |
| datapoint_pickled = txn.get(idx) |
| data = pickle.loads(datapoint_pickled) |
| out_list.append(data) |
| |
| env.close() |
| return out_list |
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| def write_lmdb(out_list, save_path): |
| |
| env = lmdb.open( |
| save_path, |
| subdir=False, |
| lock=False, |
| readahead=False, |
| meminit=False, |
| max_readers=64, |
| map_size=1099511627776 |
| ) |
|
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| with env.begin(write=True) as lmdb_txn: |
| for i in tqdm(range(len(out_list))): |
| lmdb_txn.put(str(i).encode('ascii'), pickle.dumps(out_list[i])) |
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| if __name__ == "__main__": |
| |
| |
| lmdb_path = "/HOME/nsccgz_ywang/nsccgz_ywang_wzh/HDD_POOL/qiaoaj/DrugCLIP/data/train_no_test_af/train.lmdb" |
| data = read_lmdb(lmdb_path) |
| print(len(data)) |
| print(data[0].keys()) |
| |
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| dic = { |
| "atoms": "atom types for each atom in the ligand", |
| "coordinates": "3D coordinates for each atom in the ligand generated by RDKit. Max number of conformations is 10", |
| "pocket_atoms": "atom types for each atom in the pocket", |
| "pocket_coordinates": "3D coordinates for each atom in the pocket", |
| "mol": "RDKit molecule object for the ligand", |
| "smi": "SMILES string for the ligand", |
| "pocket": "pdbid of the pocket", |
| } |
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