Add files using upload-large-folder tool

.gitattributes

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COLUMN_GUIDE.md

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+# Column guide
+
+## `data/models.parquet`
+
+### Identity and files
+
+| Columns | Meaning |
+|---|---|
+| `model_id` | Stable model key. |
+| `method_id`, `method`, `source_group` | Method family, display name, and source tranche. |
+| `ligand_id`, `seed_ordinal`, `native_seed`, `sample_index`, `native_sample_index` | Model grid identifiers. |
+| `structure_archive`, `structure_member` | Archive and member containing the aligned CIF. |
+| `coordinate_sha256`, `aligned_structure_sha256` | Native-source and aligned-CIF hashes. |
+| `source_coordinate_format`, `source_coordinate_bytes`, `aligned_structure_bytes` | Coordinate format and sizes. |
+
+### Confidence and geometry
+
+| Columns | Meaning |
+|---|---|
+| `protein_ligand_iptm`, `iptm_source_key` | Protein–ligand iPTM and the engine-native field used. |
+| `dist_<RES1>_<RES2>_sidechain_centroid_a` | Side-chain centroid distance, Å. |
+| `dist_<RES1>_<RES2>_ca_a` | Cα distance, Å. |
+| `alignment_rmsd_to_1nrl_a` | RMSD of the governed 162-Cα alignment. |
+| `alignment_rotation_json`, `alignment_translation_json` | Rigid transform applied to the source model. |
+| `model_ligand_centroid_[xyz]` | Ligand centroid in the aligned frame. |
+| `ligand_centroid_distance_to_truth_a` | Truth-relative ligand-centroid distance, Å. |
+| `protein_strict_core_rmsd_to_truth_a` | Truth-relative receptor-core RMSD, Å. |
+
+### Official OpenStructure fields
+
+`official_ost_lddt_pli`, `official_ost_lddt_lp`, `official_ost_bisyrmsd_a`, and `official_ost_bb_rmsd_a` are official scorer outputs. The adjacent `status`, `state`, `state_label`, contact-count, mapped-residue, chain-mapping, route, and graph-normalization columns describe scorer coverage and provenance.
+
+### Prepared chemistry and contacts
+
+| Columns | Meaning |
+|---|---|
+| `ligand_state_status` | Generation-state provenance status. |
+| `chemistry_feature_status`, `chemistry_feature_error` | Prepared-top chemistry feature outcome. |
+| `ligand_mapping_status`, `ligand_mapping_mode` | Authoritative graph-to-coordinate mapping outcome. |
+| `authoritative_*_bond_distance_a`, `authoritative_bad_bonded_distances` | Bonded-distance mapping audit. |
+| `ligand_pose_mmff_*`, `ligand_strain_*`, `strain_baseline_energy_kcal_mol` | MMFF94s pose energy and conformer-baseline strain. |
+| `prolif_status`, `prolif_protocol`, `prolif_total_interactions`, `prolif_contact_residue_count` | ProLIF outcome and totals. |
+| `prolif_count_<interaction>` | Count by interaction type. |
+| `prolif_contacts_json` | Residue-level interaction counts. |
+
+### PoseBusters summary
+
+`posebusters_result_status`, `posebusters_pass_all_configured_checks`, `posebusters_n_failed`, and `posebusters_failed_checks` summarize the run. The remaining PoseBusters boolean columns are individual checks: true is pass, false is fail, and null means not run.
+
+## `data/posebusters_full.parquet`
+
+This contains the raw full-report diagnostics plus staging provenance.
+
+| Column group | Meaning |
+|---|---|
+| `mol_pred_sha256`, `mol_cond_sha256` | Exact staged ligand and receptor hashes. |
+| `authoritative_prepared_smiles`, `authoritative_formal_charge`, `atom_assignment_mode` | Topology and atom mapping used for staging. |
+| `authoritative_min_bond_distance_a`, `authoritative_max_bond_distance_a` | Mapped ligand bond-length extremes, Å. |
+| `ligand_coordinate_max_abs_delta_a`, `receptor_pdb_rounding_max_abs_delta_a` | Coordinate changes introduced by staging. |
+| `mol_pred_loaded` through `volume_overlap_with_waters` | PoseBusters pass/fail checks. |
+| `number_*`, `shortest_*`, `longest_*`, `most_extreme_*` | Raw bond, angle, clash, planarity, and contact diagnostics. |
+| `mol_pred_energy`, `ensemble_avg_energy`, `energy_ratio` | Internal-energy diagnostics. |
+| `smallest_distance_<partner>`, `volume_overlap_<partner>` | Raw protein/cofactor/water proximity diagnostics. |
+| `posebusters_*` | Derived status, failed-check list, software version, and protocol. |
+
+## Lookup tables
+
+`data/ligands.parquet` contains ligand SMILES, prepared state, charge, molecular weight, and class. `data/truth_structures.parquet` contains reference hashes, archive members, alignment fields, ligand-centroid fields, and the strict-core coordinates used for truth-relative comparisons.

LICENSE

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+  "created_at": "2026-07-28T13:22:14Z",
+  "gates": {
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+    "structure184_five_method_preparedtop_1nrl_20260723_v1",
+    "structure184_five_method_preparedtop_analysis_core_20260725_v1",
+    "structure184_five_method_posebusters_full_20260727_v1"
+  ],
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+}

README.md

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+---
+license: cc-by-4.0
+language:
+- en
+tags:
+- protein-ligand
+- structural-biology
+- drug-discovery
+- PXR
+- cofolding
+- PoseBusters
+pretty_name: Structure184 Five-Method PXR Cofolding Dataset
+size_categories:
+- 10K<n<100K
+configs:
+- config_name: models
+  data_files:
+  - split: models
+    path: data/models.parquet
+- config_name: posebusters_full
+  data_files:
+  - split: models
+    path: data/posebusters_full.parquet
+- config_name: ligands
+  data_files:
+  - split: ligands
+    path: data/ligands.parquet
+- config_name: truth_structures
+  data_files:
+  - split: structures
+    path: data/truth_structures.parquet
+---
+
+# Structure184 five-method PXR cofolding dataset
+
+This repository contains 92,000 PXR–ligand cofolded models:
+
+- 184 ligands
+- 20 seed positions
+- 5 samples per seed
+- Boltz2, Chai-1, ESMFold2, OpenFold3, and Protenix
+- 18,400 models per method
+
+Models use the governed prepared top solution-state ligand representation. Coordinates are harmonized to the 1NRL PXR frame using a 162-Cα core. The original generated coordinates are preserved up to that rigid alignment.
+
+## Repository contents
+
+| Path | Contents |
+|---|---|
+| `data/models.parquet` | Primary 92,000-row table: identifiers, confidence, structural metrics, OpenStructure scores, chemistry features, ProLIF, and compact PoseBusters status. |
+| `data/posebusters_full.parquet` | Full PoseBusters 0.6.5 report for 91,734 topology-safe models. |
+| `data/ligands.parquet` | One row per ligand and prepared state. |
+| `data/truth_structures.parquet` | Reference-structure metadata. |
+| `structures/<method>.tar.zst` | Aligned model CIFs, one archive per method. |
+| `structures/truth_structures.tar.zst` | Aligned reference structures. |
+| `COLUMN_GUIDE.md` | Concise column descriptions. |
+| `MANIFEST.json` and `checksums.sha256` | Counts, sizes, and SHA-256 checksums. |
+
+`models.parquet` has 119 columns. `structure_archive` and `structure_member` locate each CIF.
+
+## Load the tables
+
+```python
+from datasets import load_dataset
+
+models = load_dataset("dargason/structure184-five-method-cofolding", "models", split="models")
+posebusters = load_dataset("dargason/structure184-five-method-cofolding", "posebusters_full", split="models")
+```
+
+Or with pandas:
+
+```python
+import pandas as pd
+
+models = pd.read_parquet("hf://datasets/dargason/structure184-five-method-cofolding/data/models.parquet")
+```
+
+## Extract structures
+
+```bash
+tar --use-compress-program=unzstd -xf structures/boltz2.tar.zst
+```
+
+Archive members follow `method/ligand_id/model_id.cif`. Join them through `structure_member`.
+
+## PoseBusters
+
+PoseBusters was recomputed from scratch using generated ligand coordinates, authoritative prepared-state topology, and generated receptor coordinates.
+
+- Computed: 91,734
+- Explicit topology quarantine: 266
+- Passed all configured checks: 75,668
+- Failed one or more configured checks: 16,066
+
+Quarantined rows remain in `models.parquet` with `posebusters_result_status=not_run_topology_quarantine`.
+
+## Important interpretation notes
+
+- PoseBusters is physical-validity QC, not pose-accuracy evidence.
+- `protein_ligand_iptm` is the primary model-native confidence field; `iptm_source_key` records the engine-specific source.
+- Columns beginning `official_ost_`, plus truth-relative RMSD and centroid-distance fields, are evaluation labels. Do not use them as blind model-selection inputs.
+- ESMFold2 models are the campaign's no-MSA, 50-step protocol, not upstream-default ESMFold2.
+- The public tables remove machine-local paths. File hashes and source-group identifiers are retained.
+- This release does not claim that every engine parameter can be reconstructed from the public tables alone.
+
+## Source and attribution
+
+The ligand set and challenge context come from the [OpenADMET PXR Induction Blind Challenge](https://openadmet.ghost.io/announcing-the-next-openadmet-blind-challenge-predicting-pxr-induction/) and its [public challenge dataset](https://huggingface.co/datasets/openadmet/pxr-challenge-train-test). Please cite the OpenADMET challenge and this dataset repository when using these models or derived tables.
+
+## Repository size
+
+The packaged repository is approximately 4.6 GB compressed. The Parquet tables and `.tar.zst` structure archives are configured for Git LFS through `.gitattributes`.
+
+## License
+
+The tables, generated/aligned structures, truth-relative metrics, aligned truth structures, packaging, and documentation in this repository are provided under CC BY 4.0. Model-generating software remains under its respective license. See `LICENSE`.

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