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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 9 new columns ({'confidence_score', 'runtime_s', 'status', 'complex_plddt', 'all_runs', 'id', 'pair_chains_iptm', 'chains_ptm', 'complex_iplddt'}) and 4 missing columns ({'avg_plddt_of_mg', 'model_id', 'ranking_score', 'avg_plddt'}).
This happened while the json dataset builder was generating data using
hf://datasets/Tenstorrent/mgtbind-boltz2/results.json (at revision 38736bb4d9f47c9fe226f17871882e791f138bbe), ['hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1000/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1001/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1002/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1003/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1004/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1005/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1006/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1007/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1008/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1009/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1010/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1011/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1012/boltz2_structure/top5_summary_confidences.json', 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'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/926/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/927/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/928/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/929/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/930/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/931/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/932/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/933/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/934/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/935/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/936/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/937/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/938/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/939/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/940/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/941/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/942/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/943/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/944/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/945/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/946/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/947/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/948/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/949/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/950/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/951/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/952/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/953/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/954/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/955/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/956/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/957/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/958/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/960/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/961/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/962/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/963/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/964/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/965/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/966/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/967/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/968/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/969/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/970/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/971/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/972/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/973/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/974/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/977/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/978/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/979/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/980/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/981/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/982/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/983/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/985/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/986/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/987/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/988/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/990/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/991/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/992/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/993/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/994/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/995/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/996/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/997/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/998/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/999/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/results.json']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1800, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 765, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 773, in _write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
id: string
status: string
confidence_score: double
ptm: double
iptm: double
ligand_iptm: double
protein_iptm: double
complex_plddt: double
complex_iplddt: double
complex_pde: double
complex_ipde: double
pair_chains_iptm: struct<0: struct<0: double, 1: double, 2: double, 3: double, 4: double>, 1: struct<0: double, 1: dou (... 236 chars omitted)
child 0, 0: struct<0: double, 1: double, 2: double, 3: double, 4: double>
child 0, 0: double
child 1, 1: double
child 2, 2: double
child 3, 3: double
child 4, 4: double
child 1, 1: struct<0: double, 1: double, 2: double, 3: double, 4: double>
child 0, 0: double
child 1, 1: double
child 2, 2: double
child 3, 3: double
child 4, 4: double
child 2, 2: struct<0: double, 1: double, 2: double, 3: double, 4: double>
child 0, 0: double
child 1, 1: double
child 2, 2: double
child 3, 3: double
child 4, 4: double
child 3, 3: struct<0: double, 1: double, 2: double, 3: double, 4: double>
child 0, 0: double
child 1, 1: double
child 2, 2: double
child 3, 3: double
child 4, 4: double
child 4, 4: struct<0: double, 1: double, 2: double, 3: double, 4: double>
child 0, 0: double
child 1, 1: double
child 2, 2: double
child 3, 3: double
child 4, 4: double
chains_ptm: struct<0: double, 1: double, 2: double, 3: double, 4: double>
child 0, 0: double
child 1, 1: double
child 2, 2: double
child 3, 3: double
child 4, 4: double
all_runs: list<item: struct<rank: int64, confidence_score: double, ptm: double, iptm: double, ligand_iptm: dou (... 117 chars omitted)
child 0, item: struct<rank: int64, confidence_score: double, ptm: double, iptm: double, ligand_iptm: double, protei (... 105 chars omitted)
child 0, rank: int64
child 1, confidence_score: double
child 2, ptm: double
child 3, iptm: double
child 4, ligand_iptm: double
child 5, protein_iptm: double
child 6, complex_plddt: double
child 7, complex_iplddt: double
child 8, complex_pde: double
child 9, complex_ipde: double
runtime_s: double
to
{'model_id': Value('int64'), 'ranking_score': Value('float64'), 'ptm': Value('float64'), 'iptm': Value('float64'), 'avg_plddt': Value('float64'), 'avg_plddt_of_mg': Value('float64'), 'ligand_iptm': Value('float64'), 'protein_iptm': Value('float64'), 'complex_pde': Value('float64'), 'complex_ipde': Value('float64')}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1343, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 907, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1646, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1802, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 9 new columns ({'confidence_score', 'runtime_s', 'status', 'complex_plddt', 'all_runs', 'id', 'pair_chains_iptm', 'chains_ptm', 'complex_iplddt'}) and 4 missing columns ({'avg_plddt_of_mg', 'model_id', 'ranking_score', 'avg_plddt'}).
This happened while the json dataset builder was generating data using
hf://datasets/Tenstorrent/mgtbind-boltz2/results.json (at revision 38736bb4d9f47c9fe226f17871882e791f138bbe), ['hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1000/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1001/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1002/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1003/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1004/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/1005/boltz2_structure/top5_summary_confidences.json', 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'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/994/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/995/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/996/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/997/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/998/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/999/boltz2_structure/top5_summary_confidences.json', 'hf://datasets/Tenstorrent/mgtbind-boltz2@38736bb4d9f47c9fe226f17871882e791f138bbe/results.json']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
model_id int64 | ranking_score float64 | ptm float64 | iptm float64 | avg_plddt float64 | avg_plddt_of_mg float64 | ligand_iptm float64 | protein_iptm float64 | complex_pde float64 | complex_ipde float64 |
|---|---|---|---|---|---|---|---|---|---|
1 | 0.68 | 0.761 | 0.6597 | 74.21 | 88.84 | 0.9849 | 0.65 | 1.2247 | 4.5429 |
2 | 0.6393 | 0.7359 | 0.6152 | 74.43 | 88.12 | 0.9833 | 0.6154 | 1.306 | 5.1827 |
3 | 0.6365 | 0.7324 | 0.6125 | 73.53 | 87.32 | 0.9852 | 0.6015 | 1.2846 | 5.0249 |
4 | 0.6063 | 0.71 | 0.5803 | 73.5 | 87.95 | 0.985 | 0.5769 | 1.3416 | 5.3417 |
5 | 0.5377 | 0.6497 | 0.5098 | 73.8 | 89.02 | 0.9847 | 0.4887 | 1.4214 | 6.2217 |
1 | 0.7324 | 0.5757 | 0.7716 | 59.44 | 91.8 | 0.9822 | 0.7639 | 2.9255 | 7.5434 |
2 | 0.7253 | 0.5827 | 0.7609 | 58.95 | 91.46 | 0.9803 | 0.7531 | 2.8734 | 7.2459 |
3 | 0.718 | 0.5865 | 0.7509 | 58.82 | 91.38 | 0.9805 | 0.7428 | 2.8866 | 7.2834 |
4 | 0.7158 | 0.5615 | 0.7543 | 59.09 | 91.29 | 0.9792 | 0.7461 | 2.9359 | 7.6318 |
5 | 0.7106 | 0.5648 | 0.7471 | 59.05 | 90.63 | 0.9786 | 0.7389 | 3.115 | 8.0878 |
1 | 0.6928 | 0.7644 | 0.675 | 74 | 88.68 | 0.9862 | 0.668 | 1.247 | 4.6379 |
2 | 0.6884 | 0.7638 | 0.6695 | 74.73 | 90.37 | 0.9843 | 0.6604 | 1.2317 | 4.6691 |
3 | 0.6408 | 0.7305 | 0.6184 | 73.58 | 87.86 | 0.9813 | 0.6163 | 1.3218 | 5.099 |
4 | 0.629 | 0.7225 | 0.6056 | 74.04 | 88.74 | 0.9847 | 0.5945 | 1.3372 | 5.3127 |
5 | 0.6162 | 0.7195 | 0.5904 | 74.4 | 89.9 | 0.9857 | 0.5784 | 1.3115 | 5.2598 |
1 | 0.7461 | 0.6099 | 0.7802 | 59 | 91.21 | 0.9825 | 0.7725 | 2.7767 | 6.7766 |
2 | 0.744 | 0.5827 | 0.7843 | 59.32 | 91.39 | 0.9838 | 0.7767 | 2.8786 | 7.335 |
3 | 0.7404 | 0.594 | 0.7771 | 59.58 | 91.97 | 0.9822 | 0.7694 | 2.8176 | 6.9676 |
4 | 0.7304 | 0.5674 | 0.7712 | 58.93 | 91.86 | 0.9809 | 0.7635 | 3.0052 | 7.6832 |
5 | 0.72 | 0.5828 | 0.7543 | 58.74 | 90.93 | 0.9805 | 0.7461 | 2.8848 | 7.0971 |
1 | 0.7404 | 0.6375 | 0.7662 | 58.67 | 90.07 | 0.9806 | 0.7584 | 2.5798 | 6.0826 |
2 | 0.7331 | 0.6029 | 0.7656 | 58.25 | 90.55 | 0.9815 | 0.758 | 2.8098 | 6.9116 |
3 | 0.7308 | 0.5832 | 0.7677 | 59.06 | 91.44 | 0.9811 | 0.7598 | 2.8892 | 7.278 |
4 | 0.7204 | 0.5718 | 0.7576 | 58.4 | 90.84 | 0.9807 | 0.7493 | 2.9298 | 7.4924 |
5 | 0.7174 | 0.5669 | 0.755 | 58.42 | 90.99 | 0.9774 | 0.747 | 2.9542 | 7.5461 |
1 | 0.8678 | 0.8695 | 0.8674 | 77.1 | 95.03 | 0.9903 | 0.8624 | 0.7631 | 1.6492 |
2 | 0.8469 | 0.8437 | 0.8476 | 76.92 | 94.81 | 0.9884 | 0.8421 | 0.8652 | 1.9838 |
3 | 0.8098 | 0.8217 | 0.8069 | 76.8 | 94.01 | 0.9869 | 0.8 | 1.0025 | 2.7469 |
4 | 0.8071 | 0.8103 | 0.8063 | 76.76 | 94.75 | 0.9867 | 0.7995 | 1.0409 | 2.9201 |
5 | 0.7891 | 0.8007 | 0.7862 | 76.08 | 94.01 | 0.9849 | 0.7791 | 1.1209 | 3.3694 |
1 | 0.4913 | 0.581 | 0.4688 | 70.39 | 88.6 | 0.9823 | 0.4365 | 1.9812 | 8.7277 |
2 | 0.4901 | 0.5925 | 0.4645 | 69.04 | 85.54 | 0.98 | 0.3927 | 1.9846 | 8.673 |
3 | 0.4737 | 0.5596 | 0.4523 | 68.92 | 88.75 | 0.9827 | 0.3979 | 1.997 | 8.9172 |
4 | 0.4736 | 0.5613 | 0.4517 | 68.77 | 87.36 | 0.9797 | 0.4132 | 2.0089 | 8.6823 |
5 | 0.4582 | 0.546 | 0.4363 | 69.82 | 87.89 | 0.9803 | 0.3389 | 2.095 | 9.1985 |
1 | 0.657 | 0.7475 | 0.6344 | 84.71 | 96.44 | 0.9878 | 0.3211 | 1.0534 | 5.6858 |
2 | 0.6535 | 0.7314 | 0.634 | 83.35 | 95.25 | 0.9887 | 0.2796 | 1.1307 | 6.2532 |
3 | 0.63 | 0.7189 | 0.6078 | 83.69 | 95.89 | 0.9878 | 0.257 | 1.1754 | 6.1237 |
4 | 0.6293 | 0.7008 | 0.6114 | 81.92 | 95.11 | 0.989 | 0.1572 | 1.2352 | 7.0653 |
5 | 0.6166 | 0.701 | 0.5955 | 83.95 | 95.82 | 0.9868 | 0.1273 | 1.1533 | 6.6385 |
1 | 0.8643 | 0.8599 | 0.8654 | 77.07 | 93.69 | 0.9864 | 0.8607 | 0.8372 | 1.8595 |
2 | 0.8172 | 0.8249 | 0.8152 | 77.23 | 95.31 | 0.9876 | 0.8087 | 1.0133 | 2.6204 |
3 | 0.8052 | 0.8138 | 0.8031 | 76.65 | 94.93 | 0.9864 | 0.7964 | 1.0256 | 3.0493 |
4 | 0.7901 | 0.8066 | 0.7859 | 76.3 | 95.15 | 0.9859 | 0.7794 | 1.0664 | 3.5042 |
5 | 0.7884 | 0.8024 | 0.7848 | 77.32 | 95.85 | 0.9855 | 0.7776 | 1.0689 | 3.3621 |
1 | 0.752 | 0.6702 | 0.7725 | 70.1 | 92.44 | 0.9761 | 0.7662 | 1.7234 | 6.2244 |
2 | 0.7452 | 0.6624 | 0.7659 | 70.28 | 94.75 | 0.9843 | 0.759 | 1.7674 | 6.6599 |
3 | 0.7351 | 0.6546 | 0.7552 | 70.65 | 94.82 | 0.9827 | 0.7477 | 1.7857 | 6.587 |
4 | 0.7254 | 0.6377 | 0.7473 | 70.24 | 94.34 | 0.9815 | 0.7402 | 1.8789 | 7.4392 |
5 | 0.6592 | 0.6321 | 0.666 | 69.4 | 94.1 | 0.9778 | 0.6582 | 1.8861 | 7.3571 |
1 | 0.5078 | 0.5968 | 0.4855 | 70.41 | 86.46 | 0.9643 | 0.4902 | 1.8996 | 7.8255 |
2 | 0.4997 | 0.5823 | 0.4791 | 69.87 | 86.83 | 0.9679 | 0.3668 | 1.9397 | 8.2887 |
3 | 0.4942 | 0.5734 | 0.4743 | 69.17 | 78.21 | 0.9637 | 0.4075 | 2.0095 | 8.2385 |
4 | 0.4903 | 0.5719 | 0.4699 | 70.4 | 83.86 | 0.9692 | 0.3997 | 1.9945 | 8.5412 |
5 | 0.4713 | 0.5522 | 0.4511 | 70.21 | 85.62 | 0.9652 | 0.3526 | 2.1416 | 9.4313 |
1 | 0.5501 | 0.4655 | 0.5713 | 59.96 | 62.83 | 0.8566 | 0.5981 | 2.8136 | 8.707 |
2 | 0.4962 | 0.4438 | 0.5094 | 60.49 | 67.08 | 0.8986 | 0.5352 | 2.8352 | 8.634 |
3 | 0.3663 | 0.4975 | 0.3335 | 59.52 | 62.73 | 0.8776 | 0.2911 | 2.8247 | 8.8166 |
4 | 0.3319 | 0.4777 | 0.2954 | 60.96 | 69.83 | 0.9006 | 0.2474 | 2.8641 | 8.7907 |
5 | 0.2602 | 0.4393 | 0.2155 | 60.44 | 63.68 | 0.8703 | 0.1814 | 2.9027 | 9.2554 |
1 | 0.487 | 0.4446 | 0.4975 | 47.72 | 16.09 | 0.5323 | 0.5273 | 4.2613 | 14.1925 |
2 | 0.4468 | 0.4379 | 0.449 | 47.84 | 24.22 | 0.6372 | 0.4631 | 4.0992 | 13.4838 |
3 | 0.4198 | 0.4263 | 0.4182 | 47.84 | 16.06 | 0.267 | 0.4342 | 4.2958 | 14.6967 |
4 | 0.3483 | 0.4165 | 0.3312 | 46.79 | 16.22 | 0.5218 | 0.3453 | 4.2335 | 14.1909 |
5 | 0.3016 | 0.4169 | 0.2728 | 47.82 | 18.81 | 0.6064 | 0.2851 | 4.2793 | 14.007 |
1 | 0.5974 | 0.4958 | 0.6228 | 50.61 | 26.51 | 0.7437 | 0.6394 | 3.8033 | 11.1759 |
2 | 0.5082 | 0.477 | 0.516 | 49.56 | 16.22 | 0.4564 | 0.5373 | 4.0997 | 13.7406 |
3 | 0.4674 | 0.4764 | 0.4651 | 50.51 | 18.87 | 0.7341 | 0.4889 | 3.9296 | 12.2057 |
4 | 0.444 | 0.4575 | 0.4406 | 49.6 | 24.05 | 0.6623 | 0.4626 | 3.9424 | 12.443 |
5 | 0.3885 | 0.449 | 0.3734 | 50.7 | 22.87 | 0.7607 | 0.394 | 3.909 | 12.348 |
1 | 0.9147 | 0.9143 | 0.9148 | 85.45 | 93 | 0.9843 | 0.9104 | 0.577 | 1.3714 |
2 | 0.8676 | 0.8646 | 0.8684 | 84.34 | 88.47 | 0.9697 | 0.8623 | 0.767 | 2.4118 |
3 | 0.8661 | 0.8633 | 0.8668 | 85.1 | 89.77 | 0.9678 | 0.8608 | 0.7228 | 2.0614 |
4 | 0.866 | 0.8651 | 0.8663 | 83.61 | 89.24 | 0.9731 | 0.8597 | 0.7614 | 2.4753 |
5 | 0.8522 | 0.8462 | 0.8537 | 84.2 | 90.39 | 0.9836 | 0.8454 | 0.8101 | 2.5302 |
1 | 0.762 | 0.6445 | 0.7914 | 59.63 | 82.79 | 0.9573 | 0.7828 | 2.5568 | 5.8566 |
2 | 0.7561 | 0.613 | 0.7919 | 59.46 | 84.44 | 0.9569 | 0.7827 | 2.7615 | 6.4839 |
3 | 0.7504 | 0.6149 | 0.7843 | 59.24 | 84.53 | 0.9521 | 0.7755 | 2.6926 | 6.2723 |
4 | 0.7474 | 0.592 | 0.7862 | 59.38 | 83.24 | 0.9534 | 0.7772 | 2.8218 | 6.9386 |
5 | 0.7444 | 0.6077 | 0.7785 | 59.02 | 82.27 | 0.9418 | 0.7701 | 2.7314 | 6.4348 |
1 | 0.8973 | 0.8984 | 0.897 | 84.03 | 91.33 | 0.9861 | 0.8914 | 0.5972 | 1.4579 |
2 | 0.8635 | 0.8569 | 0.8651 | 84.82 | 91.93 | 0.979 | 0.858 | 0.7664 | 2.4541 |
3 | 0.8633 | 0.8574 | 0.8647 | 84.56 | 90.93 | 0.9768 | 0.8578 | 0.7307 | 2.2391 |
4 | 0.8609 | 0.8555 | 0.8622 | 85.34 | 90.98 | 0.9785 | 0.855 | 0.7251 | 2.163 |
5 | 0.8448 | 0.8428 | 0.8453 | 85.15 | 92.55 | 0.9775 | 0.837 | 0.818 | 2.7237 |
1 | 0.7807 | 0.6528 | 0.8127 | 59.29 | 85.52 | 0.9674 | 0.8039 | 2.5232 | 5.6739 |
2 | 0.7546 | 0.5926 | 0.7951 | 59.76 | 87.03 | 0.966 | 0.7853 | 2.8399 | 6.8178 |
3 | 0.7509 | 0.5963 | 0.7895 | 59.47 | 85.96 | 0.9629 | 0.7797 | 2.827 | 6.7116 |
4 | 0.7439 | 0.5885 | 0.7828 | 59.88 | 85.85 | 0.9579 | 0.7731 | 2.8469 | 6.9883 |
5 | 0.7204 | 0.5846 | 0.7544 | 60.15 | 86.4 | 0.9604 | 0.7433 | 2.8435 | 6.9914 |
1 | 0.9217 | 0.922 | 0.9216 | 83.8 | 89.98 | 0.992 | 0.9172 | 0.5433 | 1.1866 |
2 | 0.9123 | 0.9135 | 0.912 | 84.67 | 90.74 | 0.9921 | 0.907 | 0.5488 | 1.2132 |
3 | 0.91 | 0.9136 | 0.9091 | 84.43 | 90.76 | 0.9924 | 0.9039 | 0.5796 | 1.5545 |
4 | 0.8708 | 0.8649 | 0.8723 | 84.84 | 90.51 | 0.9889 | 0.8651 | 0.7704 | 2.5123 |
5 | 0.8431 | 0.8387 | 0.8442 | 84.37 | 90.7 | 0.9867 | 0.8355 | 0.8466 | 2.8563 |
1 | 0.785 | 0.6943 | 0.8077 | 59.87 | 84.65 | 0.9739 | 0.7988 | 2.2777 | 5.0843 |
2 | 0.7423 | 0.5967 | 0.7787 | 59.66 | 84.3 | 0.9699 | 0.7687 | 2.783 | 6.7337 |
3 | 0.7313 | 0.5918 | 0.7662 | 59.24 | 83.82 | 0.9699 | 0.756 | 2.8044 | 6.8238 |
4 | 0.7312 | 0.5921 | 0.7659 | 59.68 | 85.04 | 0.9724 | 0.7553 | 2.8744 | 7.104 |
5 | 0.7246 | 0.5922 | 0.7577 | 59.55 | 84.17 | 0.9677 | 0.7472 | 2.8683 | 7.1793 |
End of preview.
MGTBind Boltz-2 Structure Predictions
 MGTBind |
 Bindbridge |
 Tenstorrent |
Boltz-2 ternary complex structure predictions for all 3,607 molecular glue complexes in the MGTBind database. Predicted in partnership with Bindbridge and computed on Tenstorrent AI accelerators using TT-Boltz.
Results
Comparison against the existing AlphaFold 3 predictions in MGTBind (all 3,607 complexes):
| Metric | AF3 | Boltz-2 |
|---|---|---|
| Avg MG Chain ipTM | 0.7443 | 0.7896 |
| Delta MG Chain ipTM (Boltz-2 - AF3) | - | +0.0453 |
| MG Chain ipTM > 0.68 | 62.0% | 70.2% |
| Avg pLDDT of MG | N/A | 74.07 |
| Avg pLDDT of MG > 70 | N/A | 70.7% |
| Both criteria met (ipTM > 0.68 and pLDDT > 70) | N/A | 56.7% |
File Structure
The directory layout mirrors MGTBind's AlphaFold 3 structure convention:
{complex_id}/boltz2_structure/
Model-1/model.cif # Best-ranked (rank 0)
Model-2/model.cif # Rank 1
Model-3/model.cif # Rank 2
Model-4/model.cif # Rank 3
Model-5/model.cif # Rank 4
top5_summary_confidences.json # Per-model confidence metrics
Additional files at the repository root:
| File | Description |
|---|---|
results.json |
Complete per-complex Boltz-2 metrics for all 3,607 predictions, including per-run confidence scores, pairwise chain ipTM matrix, and inference runtime. |
results.csv |
Flattened CSV with one row per complex and key metrics for easy filtering (e.g. by quality thresholds). |
scripts/batch_download_boltz2.py |
Batch download script, mirrors MGTBind's batch_download_af3.py. |
Mapping to MGTBind
Complex IDs correspond to the id column in MGTBind's complexes.csv. For example, complex 702 maps to 702/boltz2_structure/Model-1/model.cif.
Model-1 is the best-ranked structure (by confidence score = 0.8 * ipTM + 0.2 * pTM), consistent with MGTBind's AF3 ranking convention. Five diffusion samples were generated per complex.
Download
Full Dataset
# Clone the full repository
git clone https://huggingface.co/datasets/tenstorrent/mgtbind-boltz2
Specific Complexes
# Download specific complex IDs using the batch script
python scripts/batch_download_boltz2.py -f complex_ids.txt -o output_dir
Where complex_ids.txt contains comma-separated MGTBind complex IDs (e.g. 244,245,702).
Individual Files
Access any structure directly:
https://huggingface.co/datasets/tenstorrent/mgtbind-boltz2/resolve/main/{complex_id}/boltz2_structure/Model-{N}/model.cif
Metric Definitions
- MG Chain ipTM: For each complex, the molecular glue chain's interface predicted TM-score to each protein chain, averaged across protein chains.
- Avg pLDDT of MG: Mean pLDDT across all molecular glue heavy atoms (non-hydrogen), read from each atom's
B_iso_or_equivvalue in the CIF file. - Confidence score: Boltz-2 ranking score, computed as 0.8 * ipTM + 0.2 * pTM.
The top5_summary_confidences.json per complex follows the same format as MGTBind's AF3 confidence summaries. Fields shared with AF3: model_id, ranking_score, ptm, iptm, avg_plddt, avg_plddt_of_mg. Additional Boltz-2 metrics: ligand_iptm, protein_iptm, complex_pde, complex_ipde. AF3 fields not produced by Boltz-2: has_clash, fraction_disordered.
Methodology
| Parameter | Value |
|---|---|
| Model | Boltz-2 via TT-Boltz |
| Hardware | Tenstorrent Blackhole AI accelerators |
| Precision | bfloat16 |
| Diffusion samples | 5 per complex |
| Ranking | Best model selected by confidence score (0.8 * ipTM + 0.2 * pTM) |
| MSA generation | MMseqs2 |
| Input sequences | Canonical sequences from MGTBind complexes.csv |
Partnership
This dataset was created through a collaboration between:
- Bindbridge --- Cambridge-based ag-biotech company using AI to discover molecular glues for crop protection. Bindbridge initiated the project, prepared the input data from the MGTBind database, and defined the evaluation methodology.
- Tenstorrent --- All structure predictions were computed on Tenstorrent Blackhole AI accelerators using TT-Boltz, a Boltz-2 and BoltzGen implementation for inference on Tenstorrent hardware.
- MGTBind --- Molecular Glue and Ternary Binding Database, maintained by Jianfeng Pei's group at Peking University.
Citation
If you use these structures in your research, please cite the MGTBind database:
Shuya Li, Xufan Gao, Hailin Hu, Sheng Wang, Jianfeng Pei. MGTbind: a molecular glue database with ternary complex structures, binding and functional data. Nucleic Acids Research, Volume 53, Issue D1, 2025, Pages D1500-D1507.
License
This dataset is released under the MIT License.
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