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README.md

@@ -29,11 +29,22 @@ the other feature datasets through `inchikey`.
 | 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. |
 | `S_occupancy` | float32 | unitless score | Cavity occupancy score from the hydrophobic occupied volume of the selected docked pose. |
 | `S_portal` | float32 | unitless score | Portal compatibility score from cation-portal distance, charge accessibility, hydrogen bonding, and orientation. |
 | `S_accessibility` | float32 | unitless score | Charge accessibility score from solvent-accessible positive atoms in the selected docked pose. |
 | `S_orientation` | float32 | unitless score | Orientation score measuring whether the positive center points from the cavity center toward the near portal. |
 
+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).
 
@@ -47,12 +58,12 @@ this column and treat the feature values as produced by the pipeline order in
 ## Provenance
 
 - Pipeline position: Phase 1 docked-subset GLIDE feature computation by compute_all_features; Phase 2 publish split.
-- Source pickle: `/tmp/validate63/scores.pkl`.
+- Source pickle: `data/dock5000/dock/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: 60.
-- Exact publish.py command: `/Users/billyma/Workspace/SupraBench/.venv/bin/python3.11 engineering/src/publish.py --dock-scores /tmp/validate63/scores.pkl --pose-feats /tmp/validate63/pose_feats.pkl --push`.
+- Row count: 4177.
+- Exact publish.py command: `/users/tma2/workspace/SupraDashboard/.venv/bin/python engineering/src/publish.py --dock-scores data/dock5000/dock/features/scores.pkl --pose-feats data/dock5000/dock/features/pose_feats.pkl --identity data/pool_full/guests.csv --attempted /tmp/b1_docked.csv --batch batch1 --out data/publish_b1`.
 
 ## Regeneration