README.md

metadata

license: other
pretty_name: SupraDB-LigandScore
tags:
  - chemistry
  - supramolecular-chemistry
  - cb7
  - glide
  - crc
configs:
  - config_name: default
    data_files:
      - split: train
        path: features.csv

SupraDB-LigandScore

What it is

SupraBench/SupraDB-LigandScore is a SupraBench feature dataset generated from the SupraEngineering compute pipeline. Pipeline position: Phase 1 whole-pool ligand-only scoring by score_nodock; Phase 2 publish split.

The table is designed to join with the Phase 0 SupraDB-GEOM identity table and the other feature datasets through inchikey.

Schema

Column	Dtype	Units	Meaning
inchikey	string	none	Primary InChIKey join key shared across SupraDB-GEOM, LigandScore, CavityScore, and PoseFeat.
name	string	none	Guest name from the canonical SupraDB-GEOM identity table.
smiles	string	none	Canonical largest-fragment SMILES from the canonical SupraDB-GEOM identity table.
source	string	none	Winning source from the canonical SupraDB-GEOM identity table after priority deduplication.
S_charge	float32	unitless score	Ligand charge score combining formal/partial positive charge localization; score_nodock sets pose charge accessibility to zero.
S_hydrophobic	float32	unitless score	Hydrophobicity score from logP, hydrophobic volume, hydrophobic SASA fraction, and hydrophobic atom fraction.
S_rigidity	float32	unitless score	Ligand rigidity score derived from rotatable-bond count.
S_desolvation	float32	unitless score	Ligand desolvation favorability score derived from topological polar surface area.
S_packing	float32	unitless score	Ligand packing score from molecular volume relative to the CB[7] cavity volume.
S_shape	float32	unitless score	Ligand shape score from radius of gyration, asphericity, and compactness.
S_conformer_diversity	float32	unitless score	Conformer concentration score favoring low conformer diversity.
S_boltzmann_concentration	float32	unitless score	Boltzmann concentration score from the top conformer ensemble weight mass.
S_bad	float32	unitless score	Penalty-like score for anionic groups, high polarity, flexibility, and asphericity.

Schema meanings are summarized from SupraEngineering/src/features_lib.py and SupraEngineering/src/constants.py. Local feature-code docstrings: Feature computation for CB[7]-guest: the 13 mechanism scores and the 24-dim pose pose_features: Returns (vec24 in POSE_FEATURES order, derived dict for mechanism scores). finalize_pose_vec: Fill PC-dependent + tpsa-dependent fields and the PoseScore (Pose_Energy).

Join key

inchikey is the sole join key for SupraDB-GEOM, SupraDB-LigandScore, SupraDB-PoseFeat, and SupraDB-CavityScore. Downstream loaders should join on this column and treat the feature values as produced by the pipeline order in constants.SCORE_NAMES and constants.POSE_FEATURES.

Provenance

• Pipeline position: Phase 1 whole-pool ligand-only scoring by score_nodock; Phase 2 publish split.
• Source pickle: data/pool_full/features/scores.pkl.
• Computation environment: CRC.
• Docking/software context: GLIDE 2025u2 / aISS fallback as documented in the integration spec.
• Pose collapse: pose-collapse=highest Boltzmann weight; PoseFeat keeps the real pose at np.argmax(boltz) and records its boltzmann_weight and delta_e.
• Row count: 429140.
• Exact publish.py command: /users/tma2/workspace/SupraDashboard/.venv/bin/python engineering/src/publish.py --pool-scores data/pool_full/features/scores.pkl --identity data/pool_full/guests.csv --out data/pub_full.

Regeneration

Regenerate this dataset by rerunning SupraEngineering/src/publish.py with the same pipeline pickle input and --out target. Use --push only in an authenticated environment with HF_TOKEN set; local generation is fully offline by default.