Datasets:

tonynzh2
/

afdb

Error code:   DatasetGenerationError
Exception:    TypeError
Message:      int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1531, in _prepare_split_single
                  for key, record in generator:
                                     ^^^^^^^^^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
                  for item in generator(*args, **kwargs):
                              ~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 127, in _generate_examples
                  for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
                                              ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
                  for filename, f in tar_iterator:
                                     ^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
                  for x in self.generator(*self.args):
                           ~~~~~~~~~~~~~~^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1405, in _iter_from_urlpath
                  with xopen(urlpath, "rb", download_config=download_config, block_size=0) as f:
                       ~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 982, in xopen
                  file_obj = fs.open(paths[0], mode)
                File "<string>", line 3, in open
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1176, in __call__
                  return self._mock_call(*args, **kwargs)
                         ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1180, in _mock_call
                  return self._execute_mock_call(*args, **kwargs)
                         ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1247, in _execute_mock_call
                  result = effect(*args, **kwargs)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 786, in wrapped
                  tracker.files[urlpath] = {"read": 0, "size": int(f.size)}
                                                               ~~~^^^^^^^^
              TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      builder, max_dataset_size_bytes=max_dataset_size_bytes
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1393, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^
                      gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  ):
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1571, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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cif.gz unknown	__key__ string	__url__ string
"ZGF0YV9BRi1BMEEwMDlQSkY0LUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAwOVBKRjQtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A009PJF4-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMDlTRko3LUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAwOVNGSjctRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A009SFJ7-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBQWlA4LUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFBaUDgtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010PZP8-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBQWlYzLUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFBaVjMtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010PZV3-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBRMFozLUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFEwWjMtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010Q0Z3-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBRMTQ4LUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFExNDgtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010Q148-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBRMUI2LUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFExQjYtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010Q1B6-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBRMUk5LUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFExSTktRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010Q1I9-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBRMVUwLUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFExVTAtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010Q1U0-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar
"ZGF0YV9BRi1BMEEwMTBRMkM4LUYxCiMKX2VudHJ5LmlkIEFGLUEwQTAxMFEyQzgtRjEKIwpsb29wXwpfYXRvbV90eXBlLnN5bWJ(...TRUNCATED)	AF-A0A010Q2C8-F1-model_v6	hf://datasets/tonynzh2/afdb@492370387c189d4d038e60381e5416ecf9e1be9f/gpbridge/afdb/A0.tar

End of preview.

afdb — AlphaFold 3 predicted structures for the GO + ASR sequence catalog

Predicted monomer structures for 292,804 unique protein sequences: 38,934 from a Gene Ontology molecular-function coupling set and 254,182 audited ancestral sequence reconstructions (312 sequences occur in both). The predictions serve as teacher labels for 1,421,494 training pairs; one structure is reused by every pair referencing that exact sequence.

Sequence IDs are seq_<sha256(sequence)[:20]>, so a prediction can always be matched back to its exact sequence.

Protocol

Stock open-source AlphaFold 3 with default settings — no protocol deviations:

Setting	Value
Code	google-deepmind/alphafold3 v3.0.4 (`c0f97ed`)
Genetic search	full standard pipeline: UniRef90, MGnify, small BFD, UniProt
Templates	searched (PDB seqres + mmCIF, `max_template_date` default 2021-09-30)
Diffusion samples	5 (default)
Recycles	10 (default)
Model seed	20260916
Databases	AlphaFold 3 paper versions

Both MSAs AlphaFold 3 builds are retained: the unpaired MSA and the paired (UniProt) MSA. The paired MSA is kept even though every input is a single chain, because AlphaFold 3 featurises it as msa_all_seq regardless of chain count and its presence also changes the unpaired crop size — omitting it would not be the standard protocol.

Layout

Per shard (590 shards, ≤500 sequences each, grouped by sequence length):

predictions/<band>/<part>.tar    predicted structures, confidences, *_data.json
msa/<band>/<part>.tar            unpaired and paired A3M files

Files are bundled per shard rather than stored loose: 292,804 predictions would otherwise be well over a million objects.

Terms of use

These structures are AlphaFold 3 Output and are provided under, and subject to, the AlphaFold 3 Output Terms of Use. See LEGALLY_BINDING_TERMS_OF_USE.txt. Each per-shard archive also carries AlphaFold 3's own TERMS_OF_USE.md.

Released openly for non-commercial research.

Citation

Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024). https://doi.org/10.1038/s41586-024-07487-w

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