mol_data / ligands /shard_5_metadata.json
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Move dataset shards into shared ligands directory
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{
"base_registry_unique": 19999982,
"base_seen_lmdb": "/scratch/shai/data_20m_selfies_original_cartesian_shards/selfies_seen.lmdb",
"conformers_per_molecule": 10,
"coordinate_contract": "coordinates[:, i, :] matches atom i after SELFIES decode and RDKit parse",
"coordinate_space": "original RDKit Cartesian coordinates; atom-axis permutation only",
"discarded_after_split_filled": 0,
"duplicate_selfies_in_base_rejected": 5,
"duplicate_selfies_in_shard_rejected": 8350,
"elapsed_seconds": 17794.491253614426,
"finished_at_epoch": 1787200396.49274,
"local_registry_digest_entries": 20000000,
"local_registry_extra_entries_from_resume": 0,
"local_registry_unique": 20000000,
"molecular_property_contract": {
"calculated_from": "canonical heavy-atom molecule represented by smi; standard implicit hydrogens are included by RDKit",
"molecular_weight_kind": "average molecular weight, not exact isotope mass",
"rdkit_version": "2025.03.6",
"sa_score_implementation": "RDKit Contrib SA_Score/sascorer.py"
},
"partition_count": 5,
"partition_index": 4,
"partition_rejected": 13196282,
"raw_slices": [
5,
1,
2,
3,
4
],
"record_format": {
"atoms": "heavy-atom symbols in decoded SELFIES atom order",
"coordinates": "float32 ndarray, shape (10, n_heavy, 3)",
"mol_log_p": "float; RDKit Crippen.MolLogP",
"molecular_weight": "float; RDKit Descriptors.MolWt",
"qed": "float; RDKit QED.qed",
"sa_score": "float; RDKit Contrib SA_Score; 1 is easiest and 10 is hardest",
"smi": "SELFIES encoding of canonical isomeric heavy-atom SMILES",
"tpsa": "float; RDKit rdMolDescriptors.CalcTPSA"
},
"resume": {
"enabled": true,
"resumed_from_train": 16708446,
"resumed_from_val": 0,
"source_records_skipped": 83496064
},
"skipped_by_reason": {
"disconnected_heavy_graph": 1
},
"source_file_error_samples": [
{
"error": "Error: /scratch/shai/data_new_hydrogens/5/2/96/61100.lmdb: Bad file descriptor",
"path": "/scratch/shai/data_new_hydrogens/5/2/96/61100.lmdb"
},
{
"error": "Error: /scratch/shai/data_new_hydrogens/5/5/157/61500.lmdb: Bad file descriptor",
"path": "/scratch/shai/data_new_hydrogens/5/5/157/61500.lmdb"
}
],
"source_file_errors": {
"Error": 2
},
"source_processed": {
"raw_zinc": 16496256
},
"source_written": {
"raw_zinc": 3291554
},
"split": "all accepted records assigned to train",
"started_at_epoch": 1787182602.0014863,
"total_examples": 20000000,
"train_examples": 20000000,
"val_examples": 0,
"validation": {
"selfies_roundtrip_every": 10000,
"smoke_test": false
},
"workers": 192
}