Use CryoAtom2 consistently in benchmark resources and result tables

Rename method labels, CSV headers and prediction directories while preserving all scientific predictions and numeric metrics. Refresh the resource package, archive indexes and checksums.

resources/CryoAtlas_v1.0_benchmark_resources.tar.gz

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resources/benchmark/results.parquet

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+size 363075

resources/benchmark/results/{CryoAtom_results_618_full.csv → CryoAtom2_results_618_full.csv}

@@ -1,4 +1,4 @@
-emd_id,pdb_id,category,total_residues,resolution,n_chains,CryoAtom_train_pident,CryoAtom_train_bin,CryoAtom_tm_score,CryoAtom_ca_rmsd,CryoAtom_residue_coverage,CryoAtom_sequence_match,CryoAtom_sequence_recall,CryoAtom_completeness,CryoAtom_gt_score,CryoAtom_cc_mask,CryoAtom_cc_volume,CryoAtom_cc_peaks,CryoAtom_cc_box,CryoAtom_cc_mean,CryoAtom_qscore,CryoAtom_recall_qscore,CryoAtom_map_score,CryoAtom_rama_outlier,CryoAtom_rama_favored,CryoAtom_rotamer_outlier,CryoAtom_cbeta_deviations,CryoAtom_clashscore,CryoAtom_rms_bonds,CryoAtom_rms_angles,CryoAtom_molprobity_score,CryoAtom_geom_steric,CryoAtom_geom_backbone,CryoAtom_geom_sidechn,CryoAtom_geom_bonded,CryoAtom_geom_score
+emd_id,pdb_id,category,total_residues,resolution,n_chains,CryoAtom2_train_pident,CryoAtom2_train_bin,CryoAtom2_tm_score,CryoAtom2_ca_rmsd,CryoAtom2_residue_coverage,CryoAtom2_sequence_match,CryoAtom2_sequence_recall,CryoAtom2_completeness,CryoAtom2_gt_score,CryoAtom2_cc_mask,CryoAtom2_cc_volume,CryoAtom2_cc_peaks,CryoAtom2_cc_box,CryoAtom2_cc_mean,CryoAtom2_qscore,CryoAtom2_recall_qscore,CryoAtom2_map_score,CryoAtom2_rama_outlier,CryoAtom2_rama_favored,CryoAtom2_rotamer_outlier,CryoAtom2_cbeta_deviations,CryoAtom2_clashscore,CryoAtom2_rms_bonds,CryoAtom2_rms_angles,CryoAtom2_molprobity_score,CryoAtom2_geom_steric,CryoAtom2_geom_backbone,CryoAtom2_geom_sidechn,CryoAtom2_geom_bonded,CryoAtom2_geom_score
 EMD-10532,6TNG,Nucleic Acid Binding,2777,4.1,2,100.0,≥70%,0.331,2.13,0.705,0.78,0.5499,0.8223,0.491,0.6604,0.6666,0.512,0.702,0.6352,0.46,0.253,0.444,3.35,91.67,12.15,0,50.47,0.0457,3.5,3.5,0.5139,0.4533,0.4727,0.4703,0.478
 EMD-10549,6TQE,Membrane & Transport,1294,4.3,2,100.0,≥70%,0.661,0.61,0.997,0.994,0.991,1.0087,0.863,0.8288,0.8139,0.5491,0.6904,0.7206,0.61,0.6045,0.663,0.73,94.23,8.61,0,22.17,0.0364,2.61,2.94,0.6253,0.5467,0.5045,0.4946,0.543
 EMD-11238,6ZJY,Membrane & Transport,4767,5.5,15,59.7,50-70%,0.162,4.29,0.236,0.678,0.16,0.2604,0.196,0.6296,0.6138,-0.1155,0.3316,0.3649,0.25,0.04,0.202,6.75,87.15,23.57,0,98.93,0.0636,5.59,4.12,0.4198,0.3759,0.4057,0.4191,0.405

resources/docs/data_dictionary.md

@@ -26,7 +26,7 @@ Membership is checked against the fixed split lists. Training archive assignment
 
 `benchmark/results.parquet` has one row per **EMD ID × method**: 618 targets and five methods, totaling 3,090 rows. It combines the five original CSVs under `benchmark/results/`. Original CSV values and bytes are preserved.
 
-- `method` identifies ModelAngelo, CryoAtom, E3-CryoFold, EMProt or AF3.
+- `method` identifies ModelAngelo, CryoAtom2, E3-CryoFold, EMProt or AF3.
 - `emd_id`, `pdb_id`, `category`, `total_residues`, `resolution` and `n_chains` retain the released target descriptors.
 - Metric names lose only their method prefix: for example, `ModelAngelo_gt_score` becomes `gt_score` in a row whose `method` is `ModelAngelo`.
 - `tm_score`, `ca_rmsd`, residue coverage, sequence metrics and `gt_score` concern structure-to-reference agreement.

resources/docs/dataset_guide.md

@@ -94,7 +94,7 @@ Visit the [CryoAtlas project website](https://oulling.github.io/cryoatlas/) for
 The resource archive extracts into **`CryoAtlas_v1.0_resources/`**. It contains:
 
 - `Benchmark_outcome/`: the five original evaluation CSVs, with 618 target rows each.
-- `Benchmark_rawdata/`: predicted CIF files from AF3, CryoAtom, E3-CryoFold, EMProt and ModelAngelo, with 618 targets per method.
+- `Benchmark_rawdata/`: predicted CIF files from AF3, CryoAtom2, E3-CryoFold, EMProt and ModelAngelo, with 618 targets per method.
 - `metadata/`: source accessions, fixed split lists, alignment availability and resource-file checksums.
 - `training_utility/`: `MA_CryoAtlas.csv` and `MA_Cryo2StructData.csv` (618 target rows plus one AVERAGE row each), with the corresponding `MA_CryoAtlas/` and `MA_Cryo2StructData/` predicted CIF folders (618 per condition). These are existing paper results from the original Kaggle resource release.
 - `sample/Dataset/`: 10 self-contained examples with maps, structures, sequences and available predictions.

resources/metadata/catalog/archives.json

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     "component": "benchmark_resources",
     "entries": null,
     "size_gb": 1.757,

resources/metadata/catalog/archives.parquet

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resources/metadata/checksums/CryoAtlas_v1.0_benchmark_resources.tar.gz.sha256

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resources/metadata/checksums/SHA256SUMS

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 52e9c0b3a21f60ee2402b4168faae2f16bde4d91dc4568fb0ee8be63ec078137  test/CryoAtlas_v1.0_test_benchmark_618.tar.gz
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