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SupraBench/SupraDB-LigandScore

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… See the full description on the dataset page: https://huggingface.co/datasets/SupraBench/SupraDB-LigandScore.

sourceHugging Faceotherupdated 3mo agoView on Hugging Face

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Dataset Card

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 posefeatures: Returns (vec24 in POSEFEATURES order, derived dict for mechanism scores). finalizeposevec: 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.