JJKK1212/3d-syntree-multidataset

3D-SynTree Verified Production Dataset

This dataset contains verified retrosynthetic molecular design trajectories derived from CrossDocked2020 paired with the Enamine 3D-Diversity building-block catalog.

Splits Summary:

• —Train Samples: 2194 (1 shards)
• —Validation Samples: 286 (1 shards)
• —Test Samples: 328 (1 shards)
• —Target Pockets: Staged in targets/ for Stage 2 RL & docking benchmarking.

Verified Schema:

Every sample is a certified real-structure PyTorch Geometric Data object comprising:

• —pocket_pos, pocket_z, pocket_charge: SE(3) protein pocket point cloud (pH 7.4 formal charges).
• —ligand_pos, ligand_z, ligand_charge: Scaffold heavy atoms at step $t$.
• —handle_features: 64-dimensional chemical feature vector.
• —handle_pos: 3D position vector in the pocket reference frame.
• —target_synthon, target_reaction_family_idx, target_dihedral: Supervised expert actions.
• —is_real_sample: True (100% verified real structures, zero synthetic fallback).