Add files using upload-large-folder tool

.gitattributes

@@ -58,3 +58,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+large_files/pdb_data/pdb_mmcif.zip.part-00000 filter=lfs diff=lfs merge=lfs -text
+large_files/pdb_data/pdb_mmcif.zip.part-00001 filter=lfs diff=lfs merge=lfs -text
+metadata.csv filter=lfs diff=lfs merge=lfs -text
+large_files/pdb_data/pdb_mmcif.zip.part-00002 filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,214 @@
+---
+pretty_name: OpenProteinSet
+size_categories:
+  - 100K<n<1M
+task_categories:
+  - other
+tags:
+  - biology
+  - protein
+  - rna
+  - structure-prediction
+  - tar
+  - datasets
+configs:
+  - config_name: files
+    default: true
+    data_files:
+      - split: train
+        path: metadata.csv
+  - config_name: shards
+    data_files:
+      - split: train
+        path: shards.csv
+  - config_name: parts
+    data_files:
+      - split: train
+        path: parts.csv
+---
+
+# OpenProteinSet
+
+This dataset preserves the source folder as tar shards plus split part files for any source file larger than one shard. `metadata.csv` has one row per original file and is configured as the default Dataset Viewer table.
+
+## Summary
+
+| | |
+|---|---:|
+| Original files | 524,458 |
+| Original payload | 652.27 GiB (700,373,228,509 bytes) |
+| Tar shards | 31 |
+| Large-file parts | 3 |
+| Archive size | 601.38 GiB (645,729,484,800 bytes) |
+| Max shard payload | 20.00 GiB |
+| Max large-file part | 20.00 GiB |
+| Metadata generated | 2026-05-24T22:58:05Z |
+
+## Source Layout
+
+| Directory | Files | Size |
+| --- | --- | --- |
+| . | 1 | 4.31 MiB |
+| alignment_data | 524,454 | 600.05 GiB |
+| pdb_data | 3 | 52.22 GiB |
+
+## Common File Types
+
+| Extension | Files | Size |
+| --- | --- | --- |
+| .a3m | 393,000 | 535.65 GiB |
+| .hhr | 131,454 | 64.40 GiB |
+| .zip | 1 | 51.77 GiB |
+| .json | 2 | 456.83 MiB |
+| .txt | 1 | 4.31 MiB |
+
+## Shards
+
+| Shard | Files | Payload | Archive |
+| --- | --- | --- | --- |
+| shards/shard-00000.tar | 19,802 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00001.tar | 19,903 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00002.tar | 20,041 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00003.tar | 20,140 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00004.tar | 20,709 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00005.tar | 28,209 | 20.00 GiB | 20.05 GiB |
+| shards/shard-00006.tar | 19,067 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00007.tar | 16,872 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00008.tar | 17,166 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00009.tar | 17,521 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00010.tar | 16,548 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00011.tar | 16,286 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00012.tar | 16,155 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00013.tar | 16,390 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00014.tar | 16,995 | 20.00 GiB | 20.02 GiB |
+| shards/shard-00015.tar | 16,318 | 19.99 GiB | 20.02 GiB |
+| shards/shard-00016.tar | 18,167 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00017.tar | 16,870 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00018.tar | 15,837 | 20.00 GiB | 20.02 GiB |
+| shards/shard-00019.tar | 16,787 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00020.tar | 16,173 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00021.tar | 16,894 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00022.tar | 16,107 | 20.00 GiB | 20.02 GiB |
+| shards/shard-00023.tar | 16,371 | 20.00 GiB | 20.03 GiB |
+| shards/shard-00024.tar | 15,837 | 20.00 GiB | 20.02 GiB |
+
+Only the first 25 shards are shown here. See `shards.csv` for all 31 shards.
+
+## Metadata
+
+`metadata.csv` columns:
+
+| Column | Description |
+|---|---|
+| `path` | Original relative path in the source folder. |
+| `storage_type` | `tar` for files inside tar shards, or `parts` for oversized files split into byte parts. |
+| `shard_path` | Tar shard containing the file when `storage_type` is `tar`. |
+| `member_path` | Path of the file inside the tar shard. |
+| `parts_count` | Number of part files when `storage_type` is `parts`. |
+| `part_paths` | Semicolon-separated part paths when `storage_type` is `parts`. |
+| `top_level` | First directory under the source folder. |
+| `directory` | Parent directory of the file. |
+| `filename` | File basename. |
+| `extension` | File extension, preserving compound suffixes such as `.csv.gz`. |
+| `size_bytes` | Original file size in bytes. |
+| `size_human` | Human-readable original file size. |
+| `modified_utc` | Local file modification timestamp captured during packaging. |
+
+`shards.csv` lists one row per tar shard. `parts.csv` lists one row per split large-file part. `_MANIFEST.json` contains the aggregate build summary.
+
+## Download Everything
+
+```bash
+pip install -U huggingface_hub
+hf download LiteFold/OpenProteinSet-archive --repo-type dataset --local-dir ./OpenProteinSet-archive
+```
+
+Extract all shards:
+
+```bash
+mkdir -p ./data
+for shard in ./OpenProteinSet-archive/shards/*.tar; do
+  tar -xf "$shard" -C ./data
+done
+```
+
+Reassemble any split large files:
+
+```bash
+python - <<'PY'
+import csv
+from pathlib import Path
+
+root = Path("./OpenProteinSet-archive")
+out = Path("./data")
+with (root / "metadata.csv").open(newline="") as handle:
+    for row in csv.DictReader(handle):
+        if row["storage_type"] != "parts":
+            continue
+        target = out / row["path"]
+        target.parent.mkdir(parents=True, exist_ok=True)
+        with target.open("wb") as dst:
+            for part in row["part_paths"].split(";"):
+                with (root / part).open("rb") as src:
+                    while True:
+                        chunk = src.read(8 * 1024 * 1024)
+                        if not chunk:
+                            break
+                        dst.write(chunk)
+PY
+```
+
+## Use With `datasets`
+
+Use the `datasets` API to query file metadata, then use `huggingface_hub` to download the shard that contains the file.
+
+```python
+from datasets import load_dataset
+from huggingface_hub import hf_hub_download
+import tarfile
+
+files = load_dataset("LiteFold/OpenProteinSet-archive", "files", split="train")
+row = files[0]
+
+if row["storage_type"] == "tar":
+    shard = hf_hub_download(
+        repo_id="LiteFold/OpenProteinSet-archive",
+        repo_type="dataset",
+        filename=row["shard_path"],
+    )
+    with tarfile.open(shard) as archive:
+        archive.extract(row["member_path"], path="./data")
+else:
+    from pathlib import Path
+
+    target = Path("./data") / row["path"]
+    target.parent.mkdir(parents=True, exist_ok=True)
+    with target.open("wb") as dst:
+        for part_path in row["part_paths"].split(";"):
+            part = hf_hub_download(
+                repo_id="LiteFold/OpenProteinSet-archive",
+                repo_type="dataset",
+                filename=part_path,
+            )
+            with Path(part).open("rb") as src:
+                while True:
+                    chunk = src.read(8 * 1024 * 1024)
+                    if not chunk:
+                        break
+                    dst.write(chunk)
+```
+
+For streaming metadata:
+
+```python
+from datasets import load_dataset
+
+files = load_dataset("LiteFold/OpenProteinSet-archive", "files", split="train", streaming=True)
+for row in files:
+    print(row["path"], row["shard_path"])
+    break
+```
+
+## Notes
+
+The tar shards are uncompressed by design. This keeps packaging and random extraction simple and avoids spending CPU compressing data that is often already compressed.

_MANIFEST.json

@@ -0,0 +1,391 @@
+{
+  "repo_id": "LiteFold/OpenProteinSet-archive",
+  "pretty_name": "OpenProteinSet",
+  "source_data_dir": "/lambda/nfs/research/openproteinset",
+  "generated_at_utc": "2026-05-24T22:58:05Z",
+  "format": "tar shards plus metadata.csv",
+  "file_count": 524458,
+  "total_payload_bytes": 700373228509,
+  "total_payload_size": "652.27 GiB",
+  "max_shard_payload_bytes": 21474836480,
+  "max_shard_payload_size": "20.00 GiB",
+  "shard_count": 31,
+  "large_file_part_count": 3,
+  "large_file_part_bytes": 55588453165,
+  "large_file_part_size": "51.77 GiB",
+  "large_file_part_max_bytes": 21474836480,
+  "large_file_part_max_size": "20.00 GiB",
+  "total_archive_bytes": 645729484800,
+  "total_archive_size": "601.38 GiB",
+  "metadata_columns": [
+    "path",
+    "storage_type",
+    "shard_path",
+    "member_path",
+    "parts_count",
+    "part_paths",
+    "top_level",
+    "directory",
+    "filename",
+    "extension",
+    "size_bytes",
+    "size_human",
+    "modified_utc"
+  ],
+  "top_level": [
+    {
+      "name": ".",
+      "files": 1,
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+      "size": "4.31 MiB"
+    },
+    {
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+      "size": "600.05 GiB"
+    },
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+      "files": 3,
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+      "size": "52.22 GiB"
+    }
+  ],
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+      "extension": ".a3m",
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+    },
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+      "size": "64.40 GiB"
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+    },
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+    },
+    {
+      "extension": ".txt",
+      "files": 1,
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+      "size": "4.31 MiB"
+    }
+  ],
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+}

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parts.csv

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+path,part_path,part_index,part_bytes,part_size
+pdb_data/pdb_mmcif.zip,large_files/pdb_data/pdb_mmcif.zip.part-00000,0,21474836480,20.00 GiB
+pdb_data/pdb_mmcif.zip,large_files/pdb_data/pdb_mmcif.zip.part-00001,1,21474836480,20.00 GiB
+pdb_data/pdb_mmcif.zip,large_files/pdb_data/pdb_mmcif.zip.part-00002,2,12638780205,11.77 GiB

shards.csv

@@ -0,0 +1,32 @@
+shard_path,shard_index,files,payload_bytes,payload_size,archive_bytes,archive_size
+shards/shard-00000.tar,0,19802,21474086028,20.00 GiB,21509816320,20.03 GiB
+shards/shard-00001.tar,1,19903,21470426255,20.00 GiB,21506355200,20.03 GiB
+shards/shard-00002.tar,2,20041,21474678870,20.00 GiB,21510819840,20.03 GiB
+shards/shard-00003.tar,3,20140,21474359544,20.00 GiB,21510666240,20.03 GiB
+shards/shard-00004.tar,4,20709,21473055271,20.00 GiB,21510328320,20.03 GiB
+shards/shard-00005.tar,5,28209,21473616835,20.00 GiB,21524510720,20.05 GiB
+shards/shard-00006.tar,6,19067,21474675869,20.00 GiB,21508976640,20.03 GiB
+shards/shard-00007.tar,7,16872,21474518175,20.00 GiB,21504849920,20.03 GiB
+shards/shard-00008.tar,8,17166,21473906027,20.00 GiB,21504819200,20.03 GiB
+shards/shard-00009.tar,9,17521,21474115302,20.00 GiB,21505617920,20.03 GiB
+shards/shard-00010.tar,10,16548,21473016865,20.00 GiB,21502812160,20.03 GiB
+shards/shard-00011.tar,11,16286,21472884515,20.00 GiB,21502218240,20.03 GiB
+shards/shard-00012.tar,12,16155,21473828033,20.00 GiB,21502914560,20.03 GiB
+shards/shard-00013.tar,13,16390,21474638795,20.00 GiB,21504122880,20.03 GiB
+shards/shard-00014.tar,14,16995,21470587937,20.00 GiB,21501194240,20.02 GiB
+shards/shard-00015.tar,15,16318,21465653887,19.99 GiB,21495040000,20.02 GiB
+shards/shard-00016.tar,16,18167,21469809824,20.00 GiB,21502525440,20.03 GiB
+shards/shard-00017.tar,17,16870,21473790511,20.00 GiB,21504163840,20.03 GiB
+shards/shard-00018.tar,18,15837,21472194023,20.00 GiB,21500712960,20.02 GiB
+shards/shard-00019.tar,19,16787,21474710319,20.00 GiB,21504972800,20.03 GiB
+shards/shard-00020.tar,20,16173,21474822914,20.00 GiB,21504020480,20.03 GiB
+shards/shard-00021.tar,21,16894,21472765529,20.00 GiB,21503211520,20.03 GiB
+shards/shard-00022.tar,22,16107,21470795128,20.00 GiB,21499832320,20.02 GiB
+shards/shard-00023.tar,23,16371,21473507802,20.00 GiB,21502965760,20.03 GiB
+shards/shard-00024.tar,24,15837,21472092427,20.00 GiB,21500579840,20.02 GiB
+shards/shard-00025.tar,25,15663,21474824863,20.00 GiB,21503037440,20.03 GiB
+shards/shard-00026.tar,26,15701,21473128917,20.00 GiB,21501450240,20.02 GiB
+shards/shard-00027.tar,27,18362,21473681081,20.00 GiB,21506713600,20.03 GiB
+shards/shard-00028.tar,28,14207,21470389189,20.00 GiB,21495961600,20.02 GiB
+shards/shard-00029.tar,29,13239,21471806590,20.00 GiB,21495644160,20.02 GiB
+shards/shard-00030.tar,30,120,598408019,570.69 MiB,598630400,570.90 MiB

shards/shard-00000.tar

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+version https://git-lfs.github.com/spec/v1
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shards/shard-00001.tar

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shards/shard-00002.tar

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shards/shard-00003.tar

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shards/shard-00004.tar

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shards/shard-00005.tar

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shards/shard-00006.tar

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shards/shard-00007.tar

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shards/shard-00008.tar

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shards/shard-00009.tar

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shards/shard-00010.tar

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shards/shard-00011.tar

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shards/shard-00012.tar

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shards/shard-00013.tar

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shards/shard-00014.tar

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shards/shard-00015.tar

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shards/shard-00016.tar

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shards/shard-00017.tar

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shards/shard-00018.tar

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shards/shard-00019.tar

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shards/shard-00020.tar

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shards/shard-00021.tar

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shards/shard-00022.tar

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shards/shard-00023.tar

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shards/shard-00024.tar

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shards/shard-00025.tar

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shards/shard-00026.tar

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shards/shard-00027.tar

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shards/shard-00028.tar

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shards/shard-00029.tar

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shards/shard-00030.tar

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