Add lightweight PDB (Protein Data Bank) file support

[behroozazarkhalili]

Summary

This PR adds support for loading PDB (Protein Data Bank) files with load_dataset(), following the ImageFolder pattern where one row = one structure.

Based on feedback from @lhoestq in #7930, this approach makes datasets more practical for ML workflows:

• Each row is independent, enabling train/test splits and shuffling
• Easy to add labels (folder-based) and metadata (metadata.jsonl)
• Compatible with Dataset Viewer (one 3D render per row)

Architecture

Uses FolderBasedBuilder pattern (like ImageFolder, AudioFolder):

class PdbFolder(FolderBasedBuilder):
    BASE_FEATURE = ProteinStructure
    BASE_COLUMN_NAME = "structure"
    EXTENSIONS = [".pdb", ".ent"]

New ProteinStructure Feature Type

# Arrow schema for lazy loading
pa.struct({"bytes": pa.binary(), "path": pa.string()})

# Decoded: returns structure file content as string
dataset = load_dataset("pdb", data_dir="structures/")
print(dataset[0]["structure"])  # Full PDB file content

Supported Extensions

.pdb, .ent

Usage

from datasets import load_dataset

# Load from directory
dataset = load_dataset("pdb", data_dir="protein_structures/")

# Load with folder-based labels
# structures/
#   enzymes/
#     1abc.pdb
#   receptors/
#     2def.pdb
dataset = load_dataset("pdb", data_dir="structures/")
print(dataset[0])  # {"structure": "HEADER...", "label": "enzymes"}

# Load with metadata
# structures/
#   1abc.pdb
#   metadata.jsonl  # {"file_name": "1abc.pdb", "resolution": 2.5}
dataset = load_dataset("pdb", data_dir="structures/")
print(dataset[0])  # {"structure": "HEADER...", "resolution": 2.5}

# Drop labels or metadata
dataset = load_dataset("pdb", data_dir="structures/", drop_labels=True)
dataset = load_dataset("pdb", data_dir="structures/", drop_metadata=True)

Test Results

All 28 PDB tests + 15 ProteinStructure feature tests pass.

Related PRs

• feat: Add mmCIF file support for macromolecular structures #7925 - mmCIF support (same pattern)
• Proposal: Protein 3D Structure Visualization for Dataset Viewer #7930 - Protein 3D visualization proposal

cc @lhoestq @georgia-hf