SupraDB-PoseFeat

What it is

SupraBench/SupraDB-PoseFeat is a SupraBench feature dataset generated from the SupraEngineering compute pipeline. Pipeline position: Phase 1 docked-subset GLIDE pose feature computation by compute_all_features; Phase 2 highest-Boltzmann pose collapse.

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.
docked	bool	none	Boolean flag emitted only with --attempted for CavityScore and PoseFeat; false rows were submitted for docking but absent from the docked pickle and have empty feature values.
batch	string	none	Optional publish batch identifier emitted for CavityScore and PoseFeat when --batch is provided; every row from the publish run receives the supplied value.
DockingScore	float32	energy units from compute_all_features delta_e	Docking energy value stored for the pose; populated from per-pose delta_e in features_lib.pose_features.
Pose_Energy	float32	unitless score	Composite pose score filled in features_lib.finalize_pose_vec from portal compatibility, occupancy, packing, and clash terms.
Distance_to_Cavity_Center	float32	angstrom	Distance from the guest heavy-atom center to the CB[7] cavity center.
Distance_to_Portal	float32	angstrom	Minimum distance from the guest heavy-atom center to either CB[7] portal center.
Insertion_Depth	float32	angstrom	Insertion depth along the CB[7] barrel axis relative to the cavity half-height.
Packing_Coefficient	float32	unitless score	Guest molecular volume divided by the CB[7] cavity volume.
Occupancy	float32	unitless score	Fraction of CB[7] cavity volume occupied by guest atoms in the pose.
Hydrophobic_Occupancy	float32	unitless score	Fraction of CB[7] cavity volume occupied by hydrophobic guest atoms in the pose.
Shape_Complementarity	float32	unitless score	Fraction of guest heavy atoms inside the CB[7] cavity region.
Steric_Clash	float32	count	Count-like steric clash measure from short host-guest contacts.
Guest_CB7_Min_Distance	float32	angstrom	Minimum atom-atom distance between the guest and CB[7] host.
Pose_RMSD_to_Template	float32	angstrom	RMSD of the docked pose to the free/template guest conformer.
Portal_Compatibility	float32	unitless score	Pose portal compatibility score from cation-portal distance, charge accessibility, hydrogen bonding, and orientation.
Positive_Center_to_Portal_Distance	float32	angstrom	Distance from the guest positive-charge center to the nearest portal.
Positive_Center_Orientation	float32	unitless score	Cosine-derived orientation of the positive center toward the nearest portal.
Charge_Accessibility	float32	unitless score	Accessible positive-charge surface fraction for the posed guest.
Portal_Facing_Accessibility	float32	unitless score	Line-of-sight accessibility from the guest positive center toward the nearest portal.
HBond_Count	float32	count	Number of guest donor atoms forming hydrogen-bond contacts with CB[7] portal oxygens.
HBond_Geometry	float32	unitless score	Geometry-weighted hydrogen-bond contact score for portal oxygen contacts.
Carbonyl_Oxygen_Contact_Count	float32	count	Number of guest atoms contacting CB[7] portal carbonyl oxygens.
Hydrophobic_Contact	float32	count	Number of hydrophobic guest atoms contacting the host while inside the cavity.
Polar_Contact_Penalty	float32	count	Count of polar guest atoms buried inside the cavity region.
Bad_Group_Portal_Exposure	float32	count	Count of anionic or unfavorable groups exposed near a portal.
Desolvation_Penalty	float32	unitless score	Pose desolvation penalty from topological polar surface area and buried polar fraction.
boltzmann_weight	float32	unitless score	Boltzmann weight of the retained pose after highest-weight pose collapse.
delta_e	float32	energy units from compute_all_features	Relative energy of the retained pose after highest-weight pose collapse.

When --attempted is used for CavityScore or PoseFeat, docked marks whether a submitted guest is present in the docked pickle. Rows with docked=False were attempted but missing from the pickle, so their feature columns are empty/NaN. This flag is not emitted without --attempted and is never emitted for LigandScore.

When --batch <id> is used with --attempted, batch is emitted immediately after docked for CavityScore and PoseFeat and contains the supplied id for every row from that publish run, including both docked rows and docked=False no-pose rows. This column is not emitted without --batch and is never emitted for LigandScore.

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 docked-subset GLIDE pose feature computation by compute_all_features; Phase 2 highest-Boltzmann pose collapse.
• Source pickle: data/dock_b7_pull/pose_feats.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: 5000.
• Exact publish.py command: /Users/billyma/Workspace/applications/SupraDashboard/.claude/worktrees/ui-beautify/app/.venv/bin/python engineering/src/publish.py --dock-scores data/dock_b7_pull/scores.pkl --pose-feats data/dock_b7_pull/pose_feats.pkl --attempted data/dock_b7_pull/guests.csv --identity data/dock_b7_pull/identity.csv --batch batch7 --out data/publish_b7.

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.