Add E3former v1.0 release assets

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README.md

@@ -1,3 +1,60 @@
 ---
 license: cc-by-4.0
+tags:
+- biology
+- protein-structure
+- inverse-folding
+- binding-site-prediction
+size_categories:
+- 10K<n<100K
 ---
+
+# E3former Datasets
+
+Processed datasets for *Energy-Adaptive Equivariant State Space Models for
+Noise-Robust Protein Structure Representation*.
+
+## Datasets
+
+| Dataset | Structure | Task | Train | Validation | Test |
+|---|---|---|---:|---:|---:|
+| [CATH](datasets/cath/README.md) | Experimental | Inverse folding | 18,009 | 607 | 1,119 |
+| [CATH-AF](datasets/cath/README.md) | AlphaFold-derived | Inverse folding | 16,467 | 559 | 1,015 |
+| [PPBS](datasets/ppbs/README.md) | Experimental | Binding-site prediction | 12,577 | 3,178 | 3,984 |
+| [PPBS-AF](datasets/ppbs/README.md) | AlphaFold-derived | Binding-site prediction | 11,345 | 2,876 | 3,636 |
+
+The archives contain processed PyTorch/PyG protein objects and fixed
+train/validation/test splits. PPBS includes the 70, homology, topology, and none
+test subsets. Family-specific manifests record split counts and archive checksums.
+
+## Download
+
+```bash
+hf download GENTEL-Lab/E3former_data --repo-type dataset --local-dir e3former_data
+```
+
+Or, from the E3former code directory:
+
+
+```bash
+python scripts/download.py --namespace GENTEL-Lab
+e3former check-data
+```
+
+To install one dataset, add `--only cath`, `--only cath-af`, `--only ppbs`, or
+`--only ppbs-af` to the download command. The script verifies SHA256 and extracts
+the archives into the matching `data/` directories.
+
+Use Python 3.10 and the dependencies pinned in the E3former installation.
+These are processed inputs for the provided data loader, not raw PDB files.
+
+## Sources
+
+CATH uses [CATH](https://www.cathdb.info/) protein classifications and benchmark
+splits. PPBS labels and evaluation subsets originate from
+[ScanNet](https://github.com/jertubiana/ScanNet).
+The AF variants provide AlphaFold-derived structures for the corresponding tasks.
+This release uses CC BY 4.0 for our contributions. Source materials retain their original licenses; see
+[THIRD_PARTY_DATA.md](THIRD_PARTY_DATA.md).
+
+Please cite E3former and the relevant source datasets when using this release.

SHA256SUMS

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+9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411  LICENSE
+8e99d361cbe8698b4c8b6387411bc68a9674334294aa4c24eba54d7cfa4919e9  README.md
+770ff095eda05d32e1074d984cff73e0c30c9d4f5d7d2516abea78c6a5233030  THIRD_PARTY_DATA.md
+86110ee0de13e9d8f1c73b2488acee08ebc7ac1a6734d495c800bfac05397826  datasets/cath/README.md
+2efc89d6503f62f98d88bc00571fce15b8c2df0f10c5417b5331efc26889be44  datasets/cath/cath.tar.gz
+f872bb706472136774dd7525fb1aa8eff43b697239c599c16bad7987db308bc2  datasets/cath/cathAF.tar.gz
+362e9fe71d4b29639c240324fdef167b23c36eb254844c943fa73a427bc777fb  datasets/cath/dataset_manifest.json
+0f52ed019318e63f10b8c30d98b8a1ac328a6b56eb874db308f5c0da8a839930  datasets/ppbs/README.md
+50a119ea4d52174dc898c41354e1ac8122f7643d03783660e1d87f770e9543fb  datasets/ppbs/binding_site.tar.gz
+9f8c8e9daad759407e276fd4812e71a160d54c312d0a130d4847ed77efcddeb4  datasets/ppbs/bindingsiteAF.tar.gz
+48f8eba20b9049bcb480c23fd3ca2c2069558b73027818851be701f2c8011842  datasets/ppbs/dataset_manifest.json
+50e6751797c50dedd75ef1b8a0d9e42f5f8472e9fbce91f34718e9f97b0c780a  licenses/ScanNet-APACHE-2.0.txt

THIRD_PARTY_DATA.md

@@ -0,0 +1,25 @@
+# Data Sources and Attribution
+
+This release packages processed protein objects, labels, and split lists for
+E3former. Source data retain their original notices and license terms.
+Our packaging and documentation are licensed under [CC BY 4.0](LICENSE).
+
+| Component | Source | Upstream license |
+|---|---|---|
+| CATH classification | [CATH](https://www.cathdb.info/wiki/doku/?id=start) | [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) |
+| PPBS labels and evaluation subsets | [ScanNet](https://github.com/jertubiana/ScanNet/tree/main/datasets/PPBS) | [Apache 2.0](licenses/ScanNet-APACHE-2.0.txt) |
+
+The upstream ScanNet license is retained unchanged. The processed objects in
+this release were prepared for the E3former data loader; they are not the
+original ScanNet distribution.
+
+ScanNet reference: Tubiana, J., Schneidman-Duhovny, D., and Wolfson, H. J.
+ScanNet: an interpretable geometric deep learning model for structure-based
+protein binding site prediction. Nature Methods 19, 730-739 (2022).
+https://doi.org/10.1038/s41592-022-01490-7
+
+AlphaFold reference: Jumper, J. et al. Highly accurate protein structure
+prediction with AlphaFold. Nature 596, 583-589 (2021).
+https://doi.org/10.1038/s41586-021-03819-2
+
+The E3former code license does not replace upstream dataset licenses.

datasets/cath/README.md

@@ -0,0 +1,43 @@
+# E3former CATH and CATH-AF
+
+Preprocessed CATH inverse-folding benchmarks for E3former, including experimental structures and
+their AlphaFold-derived counterpart. Data are stored as PyTorch/PyG protein
+objects in `.pt` files, using the feature pipeline supplied with the code.
+
+## Splits
+
+| Dataset | Train | Validation | Test |
+|---|---:|---:|---:|
+| cath | 18,009 | 607 | 1,119 |
+| cath-af | 16,467 | 559 | 1,015 |
+
+Each archive preserves its dataset directory, processed proteins, and fixed
+train/validation/test ID lists. Only proteins referenced by these lists are
+included. Experimental and predicted versions have different available samples;
+their split sizes are not assumed to be identical.
+
+`dataset_manifest.json` records counts, preprocessing dependencies, split-file
+checksums, and the SHA256 checksum of each archive. The repository-level
+[`SHA256SUMS`](../../SHA256SUMS) covers all release files.
+
+## Usage
+
+With the E3former code installed:
+
+```bash
+python scripts/download.py --namespace GENTEL-Lab --only cath cath-af
+```
+
+After installing both dataset families, run `e3former check-data` to verify
+all four datasets.
+
+Use Python 3.10, PyTorch 2.1.0, PyG 2.4.0, and Graphein 1.7.5 as pinned by the
+E3former installation. These archives contain processed inputs, not the
+original PDB files or AlphaFold prediction pipeline.
+
+## Source
+
+CATH protein classification and the inverse-folding benchmark splits distributed with E3former.
+See [CATH](https://www.cathdb.info/) for the source database.
+
+Please cite the source dataset and the E3former paper when using this release.

datasets/cath/cath.tar.gz

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+size 463111507

datasets/cath/cathAF.tar.gz

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+size 790538916

datasets/cath/dataset_manifest.json

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+        }
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+      "archive": {
+        "group": "cath-af",
+        "repository": "e3former",
+        "filename": "datasets/cath/cathAF.tar.gz",
+        "archive_root": "cathAF",
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+    "python": "3.10",
+    "torch": "2.1.0",
+    "torch_geometric": "2.4.0",
+    "graphein": "1.7.5"
+  }
+}

datasets/ppbs/README.md

@@ -0,0 +1,43 @@
+# E3former PPBS and PPBS-AF
+
+Preprocessed protein-protein binding-site prediction benchmarks for E3former, including experimental structures and
+their AlphaFold-derived counterpart. Data are stored as PyTorch/PyG protein
+objects in `.pt` files, using the feature pipeline supplied with the code.
+
+## Splits
+
+| Dataset | Train | Validation | Test |
+|---|---:|---:|---:|
+| ppbs | 12,577 | 3,178 | 3,984 |
+| ppbs-af | 11,345 | 2,876 | 3,636 |
+
+Each archive preserves its dataset directory, processed proteins, and fixed
+train/validation/test ID lists. Only proteins referenced by these lists are
+included. Experimental and predicted versions have different available samples;
+their split sizes are not assumed to be identical.
+
+`dataset_manifest.json` records counts, preprocessing dependencies, split-file
+checksums, and the SHA256 checksum of each archive. The repository-level
+[`SHA256SUMS`](../../SHA256SUMS) covers all release files.
+
+## Usage
+
+With the E3former code installed:
+
+```bash
+python scripts/download.py --namespace GENTEL-Lab --only ppbs ppbs-af
+```
+
+After installing both dataset families, run `e3former check-data` to verify
+all four datasets.
+
+Use Python 3.10, PyTorch 2.1.0, PyG 2.4.0, and Graphein 1.7.5 as pinned by the
+E3former installation. These archives contain processed inputs, not the
+original PDB files or AlphaFold prediction pipeline.
+
+## Source
+
+The protein-protein binding-site benchmark originates from ScanNet;
+the released ID lists preserve its homology-based evaluation subsets.
+
+Please cite the source dataset and the E3former paper when using this release.

datasets/ppbs/binding_site.tar.gz

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+size 547503822

datasets/ppbs/bindingsiteAF.tar.gz

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+size 738478697

datasets/ppbs/dataset_manifest.json

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+        "repository": "e3former",
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+    "python": "3.10",
+    "torch": "2.1.0",
+    "torch_geometric": "2.4.0",
+    "graphein": "1.7.5"
+  }
+}

licenses/ScanNet-APACHE-2.0.txt

@@ -0,0 +1,201 @@
+Apache License
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