final_data/mol_data/data/README.md

MolWeaver pretraining datasets

This directory contains the finalized LMDB inputs used for MolWeaver pretraining.

Free ligands

ligands/ contains five heavy-atom molecular training shards. Shards 1–4 contain 20,000,000 records each. The last 3,000 records were removed from shard 5 and placed in valid.lmdb, leaving 19,997,000 training records in shard 5 and 99,997,000 training records overall.

Each record contains a SELFIES representation, heavy-atom identities, ten aligned Cartesian conformers, and five RDKit-derived properties: QED, synthetic accessibility score, molecular weight, MolLogP, and TPSA.

Protein pockets

pockets_center_frame_cartesian/ contains 3,123,776 protein-pocket training records in a deterministic heavy-atom Cartesian frame. There is no pocket validation LMDB in this release.

CrossDocked complexes

crossdock/ contains paired heavy-atom pocket-ligand records with ligand SELFIES, pocket and ligand coordinates, and Vina docking scores. The training split contains 326,896 records after excluding seven examples whose conservative sequence length exceeded 4,356. The validation split contains 3,000 records.

Loading

import lmdb
import pickle

env = lmdb.open(
    "ligands/shard_1.lmdb",
    readonly=True,
    subdir=False,
    lock=False,
    readahead=False,
)
with env.begin() as txn:
    length = pickle.loads(txn.get(b"length"))
    record = pickle.loads(txn.get(b"0"))

Pickled records should only be loaded from a trusted dataset source.