OneScience-Group/AlphaFold3
Updated
Dataset Viewer
The dataset viewer is not available for this split.
Cannot extract the features (columns) for the split 'train' of the config 'default' of the dataset.
Error code: FeaturesError
Exception: ArrowInvalid
Message: JSON parse error: Missing a name for object member. in row 0
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 324, in _generate_tables
df = pandas_read_json(f)
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 38, in pandas_read_json
return pd.read_json(path_or_buf, **kwargs)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/pandas/io/json/_json.py", line 815, in read_json
return json_reader.read()
~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/pandas/io/json/_json.py", line 1014, in read
obj = self._get_object_parser(self.data)
File "/usr/local/lib/python3.14/site-packages/pandas/io/json/_json.py", line 1040, in _get_object_parser
obj = FrameParser(json, **kwargs).parse()
File "/usr/local/lib/python3.14/site-packages/pandas/io/json/_json.py", line 1176, in parse
self._parse()
~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/pandas/io/json/_json.py", line 1391, in _parse
self.obj = DataFrame(
~~~~~~~~~^
ujson_loads(json, precise_float=self.precise_float), dtype=None
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/usr/local/lib/python3.14/site-packages/pandas/core/frame.py", line 782, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/usr/local/lib/python3.14/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/usr/local/lib/python3.14/site-packages/pandas/core/internals/construction.py", line 114, in arrays_to_mgr
index = _extract_index(arrays)
File "/usr/local/lib/python3.14/site-packages/pandas/core/internals/construction.py", line 677, in _extract_index
raise ValueError("All arrays must be of the same length")
ValueError: All arrays must be of the same length
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 249, in compute_first_rows_from_streaming_response
iterable_dataset = iterable_dataset._resolve_features()
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 4379, in _resolve_features
features = _infer_features_from_batch(self.with_format(None)._head())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2661, in _head
return next(iter(self.iter(batch_size=n)))
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2839, in iter
for key, pa_table in ex_iterable.iter_arrow():
~~~~~~~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2377, in _iter_arrow
yield from self.ex_iterable._iter_arrow()
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 536, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 419, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 327, in _generate_tables
raise e
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 290, in _generate_tables
pa_table = paj.read_json(
io.BytesIO(batch), read_options=paj.ReadOptions(block_size=block_size)
)
File "pyarrow/_json.pyx", line 342, in pyarrow._json.read_json
File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
return check_status(status)
File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
raise convert_status(status)
pyarrow.lib.ArrowInvalid: JSON parse error: Missing a name for object member. in row 0Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
AlphaFold3 Dataset
Dataset Description
AlphaFold3_dataset is the companion dataset for the OneScience-Group/AlphaFold3/ model. It includes inference input examples, public search databases, MMseqs databases, sharded Jackhmmer databases, and alignment-related directories. The dataset ID is fixed as OneScience-Group/AlphaFold3_dataset.
Supported Tasks
This dataset supports the AlphaFold3 biomolecular structure prediction workflow. It provides both AlphaFold3 JSON examples that already contain MSAs and the database directories required to search for MSAs from sequences. The model can use these data for preflight checks, inference with MSAs, the MMseqs data pipeline, and the Jackhmmer data pipeline.
Dataset Format and Structure
| Path | Type | Purpose | Required | Capability | Placement After Download | Notes |
|---|---|---|---|---|---|---|
manifest.yaml |
Manifest file | Machine-readable dataset description | Yes | All capabilities | Dataset package root directory | The LLM must parse this file |
onescience_run_manifest.yaml |
Runtime Manifest | Web interface read entry point | Yes | All capabilities | Dataset package root directory | Consistent with manifest.yaml |
metadata/file_manifest.yaml |
Integrity manifest | Records the source path, organized path, size, and SHA256 of key files | Yes | Preflight check | metadata/ |
Verifies consistency after organization |
scripts/validate_dataset.py |
Validation script | Checks directories, JSON schema, sizes, and SHA256 | Yes | Data read validation | scripts/ |
Does not run the model |
data/infer_input_data/ |
Input examples | AlphaFold3 JSON examples containing all_data and pressure_data | Yes | Inference and preflight checks | data/infer_input_data/ |
The smallest example is all_data/7r6r_data.json |
data/public_databases/ |
Public databases | Databases for Jackhmmer and template searches | Yes | Data pipeline | data/public_databases/ |
The upload view uses pdb_2022_09_28_mmcif_files.tar instead of the extracted mmcif_files/ directory to avoid file-count limits |
data/mmseqsDB/ |
MMseqs databases | MMseqs search databases | Yes | MMseqs data pipeline | data/mmseqsDB/ |
Includes small_bfd, mgnify, uniprot, and uniref90 |
data/jackhmmer_split/ |
Sharded database | Sharded FASTA files for Jackhmmer searches | Yes | Jackhmmer data pipeline | data/jackhmmer_split/ |
See the directory filenames for the shard count |
data/alignDB/ |
Alignment database | Alignment-related data | No | Advanced workflows | data/alignDB/ |
Optional |
How to Use the Dataset
Files and Download
Download the dataset:
hf download --dataset OneScience-Group/AlphaFold3_dataset
Download the compatible model:
hf download --model OneScience-Group/AlphaFold3/
If you use --cache_dir, you must switch to the root directory of the downloaded dataset package before validation.
Data Placement
After downloading the dataset separately, you can run validation from the dataset package root directory. To use it with the model, place this repository's data subdirectory in the model package:
<model-package>/data/alphafold3_dataset
You can do this by copying or linking the directory:
mkdir -p /path/to/model-package/data
ln -s /path/to/AlphaFold3_dataset/data /path/to/model-package/data/alphafold3_dataset
Data Read Validation
Run the following command from the dataset package root directory:
python scripts/validate_dataset.py --root .
The validation script parses metadata/file_manifest.yaml and checks that key directories exist, JSON examples are readable, and filenames, sizes, and SHA256 values are consistent. On success, it outputs dataset_validation_ok: true.
Official OneScience Information
| Platform | OneScience Main Repository | Skills Repository |
|---|---|---|
| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |
Limitations and License
mmseqs is a locally generated database. The public databases and AlphaFold3-related data are subject to their respective upstream licenses and terms of use.
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