Datasets:

StarLiu714
/

RNAcentral-Struct

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 1 new columns ({'id,upi,pdb_id,pdb_chain,rna_type,taxid,pdb_accession,structure_path'}) and 2 missing columns ({'bytes', 'pdb_id'}).

This happened while the csv dataset builder was generating data using

hf://datasets/StarLiu714/RNAcentral-Struct/metadata/pdb_structure_mapping_all.csv (at revision 83be45a06fa21772f7acc3e964b6916641da4f55), ['hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/cif_sizes.tsv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/pdb_structure_mapping_all.csv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/pdb_structure_mapping_downloaded.csv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/rnacentral_pdb.tsv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/summary.tsv']

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/python3.14/site-packages/datasets/builder.py", line 1837, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/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/python3.14/site-packages/datasets/arrow_writer.py", line 773, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2369, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2297, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              id,upi,pdb_id,pdb_chain,rna_type,taxid,pdb_accession,structure_path: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 515
              to
              {'pdb_id': Value('string'), 'bytes': Value('int64')}
              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 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 1683, 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 1839, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
                  ...<4 lines>...
                  )
              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 1 new columns ({'id,upi,pdb_id,pdb_chain,rna_type,taxid,pdb_accession,structure_path'}) and 2 missing columns ({'bytes', 'pdb_id'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/StarLiu714/RNAcentral-Struct/metadata/pdb_structure_mapping_all.csv (at revision 83be45a06fa21772f7acc3e964b6916641da4f55), ['hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/cif_sizes.tsv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/pdb_structure_mapping_all.csv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/pdb_structure_mapping_downloaded.csv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/rnacentral_pdb.tsv', 'hf://datasets/StarLiu714/RNAcentral-Struct@83be45a06fa21772f7acc3e964b6916641da4f55/metadata/summary.tsv']
              
              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.

pdb_id string	bytes int64
157d	103,397
17ra	741,619
1a1t	3,815,378
1a34	438,031
1a3m	2,016,367
1a4d	153,194
1a4t	1,622,103
1a51	1,079,146
1a60	3,063,061
1a9l	1,344,365
1a9n	581,250
1ac3	612,042
1afx	484,161
1ajf	97,168
1ajl	83,378
1ajt	81,695
1aju	1,883,269
1akx	128,808
1al5	832,803
1am0	485,153
1anr	1,689,943
1aq3	461,638
1aq4	474,195
1aqo	1,272,654
1arj	1,857,117
1asy	1,222,973
1asz	1,231,224
1ato	561,712
1atv	217,081
1atw	152,074
1aud	4,233,365
1b23	637,887
1b36	1,126,365
1b7f	379,599
1bau	176,149
1bgz	415,549
1biv	620,447
1bj2	952,194
1bmv	539,655
1bn0	662,537
1br3	121,392
1bvj	1,370,565
1byj	4,253,131
1bz2	75,558
1bz3	77,842
1bzt	83,187
1bzu	83,446
1c04	668,786
1c0a	800,590
1c0o	861,595
1c2w	7,826,986
1c2x	313,271
1c9s	1,611,365
1cq5	165,120
1cql	1,291,093
1csl	114,854
1cvj	1,252,581
1cx5	121,153
1d0t	668,283
1d0u	1,412,588
1d4r	283,497
1d6k	5,132,678
1ddy	407,613
1dfu	271,979
1di2	294,399
1dk1	282,838
1dqf	92,910
1dqh	80,815
1drr	597,285
1drz	316,929
1duh	162,373
1dul	311,865
1duq	304,489
1dz5	5,869,948
1e4p	1,487,308
1e7k	320,874
1e8o	430,625
1e8s	93,546
1e95	1,614,615
1ebq	453,146
1ebr	469,049
1ebs	452,737
1ec6	289,876
1efo	77,067
1efs	755,542
1efw	1,405,741
1eg0	326,885
1egk	346,219
1eht	1,072,877
1ehz	254,359
1ei2	1,471,113
1eiy	1,126,245
1ekz	7,294,988
1elh	461,837
1emi	91,461
1esh	66,435
1esy	1,206,037
1et4	580,532
1etf	193,845
1etg	2,748,929

End of preview.

RNAcentral-Struct

RNAcentral-Struct is a structure subset derived from the official RNAcentral PDB cross-reference table. It contains every unique PDB entry referenced by RNAcentral current_release/id_mapping/database_mappings/pdb.tsv, downloaded as mmCIF from official PDB mirrors.

This dataset is intended for RNA structure-conditioned modeling, inverse folding, and cross-reference analysis. RNAcentral itself is a sequence and annotation resource; the 3D coordinates here come from wwPDB/RCSB/PDBe entries linked by RNAcentral.

structures/*.cif: 7,279 unique mmCIF files, one per four-character PDB entry ID.
metadata/rnacentral_pdb.tsv: the RNAcentral official PDB cross-reference table used to build this package.
metadata/pdb_structure_mapping_all.csv: all RNAcentral chain-level mappings to the downloaded mmCIF files.
metadata/pdb_structure_mapping_downloaded.csv: mappings whose referenced mmCIF file is present. For this release it matches the full mapping table.
metadata/manifest.json: machine-readable summary.
metadata/summary.tsv: compact summary.
metadata/cif_sizes.tsv: byte size for each downloaded mmCIF file.
metadata/download_failures.json: download failure list. This release has no failures.
scripts/rnacentral_all_cif_downloader.py: downloader used to reproduce the package.

Summary

field	value
RNAcentral PDB mapping rows	18,967
Unique RNAcentral UPI IDs	4,750
Unique PDB/mmCIF entries	7,279
Downloaded mmCIF files	7,279
Download failures	0
Uncompressed package size	~54 GB

Mapping Semantics

RNAcentral pdb.tsv maps RNAcentral UPI IDs to PDB chain-level accessions such as 4UG0_L8. The four-character prefix, 4UG0, is the PDB entry ID and corresponds to one mmCIF file: structures/4ug0.cif. The suffix identifies a chain or chain-like accession within that entry. Multiple RNAcentral rows can therefore reference the same mmCIF file.

Reproducibility

The source mapping file is:

https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv

The downloader extracts unique PDB IDs from that mapping and downloads {PDB_ID}.cif from RCSB with PDBe fallback.

License

RNAcentral sequence metadata is distributed under CC0. PDB coordinate files are redistributed according to wwPDB/RCSB/PDBe terms. Please cite RNAcentral and wwPDB/PDB resources when using this dataset.

Citation

@article{rnacentral2021,
  author = {{RNAcentral Consortium}},
  title = {{RNAcentral} 2021: secondary structure integration, improved sequence search and new member databases},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {D1},
  pages = {D212--D220},
  year = {2021},
  doi = {10.1093/nar/gkaa921}
}

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