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Documentation Index

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Document	Description
Installation & Setup	Environment setup (Conda / Pip) and downloading data & model weights from Zenodo.
Sampling Guide	User guide: running examples (Docking, Design, Optimization), confidence scoring, config reference, and custom tasks.
Benchmarking	Reproducing results on standard benchmarks (PoseBusters, PepBDB, GEOM, CSD, MOAD, PROTAC-DB).
Training	Training on the reduced demo set and pointers for full-data training.
Raw Data Processing	Step-by-step guide for processing raw training data from scratch (required for full-dataset training).
Source Code Guide	Overview of code structure, train/sample workflow, and core files.