--- license: other pretty_name: SupraDB-PoseFeat tags: - chemistry - supramolecular-chemistry - cb7 - glide - crc configs: - config_name: default data_files: - split: train path: features.csv --- # 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 ` 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_b6_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_b6_pull/scores.pkl --pose-feats data/dock_b6_pull/pose_feats.pkl --attempted data/dock_b6_pull/guests.csv --identity data/dock_b6_pull/identity.csv --batch batch6 --out data/publish_b6`. ## 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.