Dataset Viewer
The dataset viewer is not available for this subset.
Cannot get the split names for the config 'default' of the dataset.
Exception: SplitsNotFoundError
Message: The split names could not be parsed from the dataset config.
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/inspect.py", line 286, in get_dataset_config_info
for split_generator in builder._split_generators(
~~~~~~~~~~~~~~~~~~~~~~~~~^
StreamingDownloadManager(base_path=builder.base_path, download_config=download_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 81, in _split_generators
first_examples = list(islice(pipeline, self.NUM_EXAMPLES_FOR_FEATURES_INFERENCE))
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
fs: fsspec.AbstractFileSystem = fsspec.filesystem("memory")
~~~~~~~~~~~~~~~~~^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/fsspec/registry.py", line 302, in filesystem
cls = get_filesystem_class(protocol)
File "/usr/local/lib/python3.14/site-packages/fsspec/registry.py", line 239, in get_filesystem_class
raise ValueError(f"Protocol not known: {protocol}")
ValueError: Protocol not known: memory
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/split_names.py", line 71, in compute_split_names_from_streaming_response
for split in get_dataset_split_names(
~~~~~~~~~~~~~~~~~~~~~~~^
path=dataset,
^^^^^^^^^^^^^
config_name=config,
^^^^^^^^^^^^^^^^^^^
token=hf_token,
^^^^^^^^^^^^^^^
)
^
File "/usr/local/lib/python3.14/site-packages/datasets/inspect.py", line 340, in get_dataset_split_names
info = get_dataset_config_info(
path,
...<6 lines>...
**config_kwargs,
)
File "/usr/local/lib/python3.14/site-packages/datasets/inspect.py", line 291, in get_dataset_config_info
raise SplitsNotFoundError("The split names could not be parsed from the dataset config.") from err
datasets.inspect.SplitsNotFoundError: The split names could not be parsed from the dataset config.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.
AnewOmni Training Datasets — non-SIU subset
Preprocessed, training-ready datasets for AnewOmni
("Programming Biomolecular Interactions with an All-Atom Generative Model"), in the codebase's
memory-mapped format (data.bin + index.txt + split/cluster index files).
This bundle holds 7 of the 8 training sources — everything except SIU (SIU is ~156 GB and is
distributed separately). After extraction the datasets/ tree matches the paths in
configs/train_ldm.yaml / configs/train_vae.yaml with 0 missing files.
Contents
| Dataset | Modality | Entries | Splits | Original source |
|---|---|---|---|---|
| PepBench | peptide | 6,105 | train 4,157 / valid 114 (LNR 93 test held out) | Zenodo 13373108 (PepGLAD) |
| ProtFrag | peptide (augmentation) | 70,498 | — | Zenodo 13373108 (PepGLAD) |
| SAbDab | antibody | 16,947 | train 9,473 / valid 400 | OPIG / UniMoMo |
| PDBbind v2020 | small molecule | 16,200 | refined 4,628 (+train/valid) + other-PL 11,572 | PDBbind v2020 |
| BioLiP2-nr | small molecule | 51,114 | pretrain / finetune (by resolution) | zhanggroup.org/BioLiP |
| CrossDocked2020 | small molecule | 100,081 | train 99,881 / valid 100 / test 100 | TargetDiff Google Drive |
| SIU (separate upload) | small molecule | 4,289,980 | cluster-weighted | HuggingFace bgao95/SIU |
Bundle total: ~261k entries, 17.2 GB (anewomni_datasets_noSIU.tar).
Usage
# on your training server, from the AnewOmni repo root:
hf download Windsao/anewomni-train-data anewomni_datasets_noSIU.tar --repo-type dataset --local-dir .
tar -xf anewomni_datasets_noSIU.tar # -> ./datasets/...
rm anewomni_datasets_noSIU.tar
The extracted layout:
datasets/
peptide/pepbench/processed/ (+ ../train.cluster)
peptide/ProtFrag/processed/
antibody/SAbDab/processed/
molecule_v2/PDBbind/processed/{refined-set,v2020-other-PL}/
molecule_v2/biolip2_nr/processed/
molecule_v2/CrossDocked/processed/
Format
Each dataset is a memory-mapped store:
data.bin— concatenated, per-entry zlib-compressed complexes (receptor + binder).index.txt— one line per entry:id \t start \t end \t properties-json(byte range[start,end)intodata.bin).*_index.txt— train / valid / test subsets (an entry list).*.cluster— sequence / scaffold clusters used for size- and redundancy-aware sampling.
Loadable via the AnewOmni MoleculeDataset / PeptideDataset / AntibodyDataset classes (mmap_dir=…, specify_index=…, cluster=…).
Notes
- Counts are from raw processing of each source. The AnewOmni paper applies an additional ligand-quality filtering pipeline (CCD exclusion list, cross-source dedup by PDB code, 40% sequence-identity train/test cutoff) that is not applied here — so the small-molecule counts above are somewhat higher than the paper's final training numbers (PDBbind 14,200 / BioLiP2 18,012 / CrossDocked 85,938). PepBench (4,157) and SAbDab (9,473/400) splits match the paper exactly.
- Derived from publicly available datasets (mostly CC-BY); refer to each original source for its license.
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