SupraDB-GEOM

What it is

SupraBench/SupraDB-GEOM is the Phase 0 guest-pool dataset for the SupraBench compute pipeline. It contains the canonical guest identity table used as the source of truth for downstream ligand-only scoring, docking-derived pose features, cavity scores, and dashboard joins.

Rows are built from GEOM source SMILES, optional QM9 source SMILES, and optional experimental CB[7] labeled guests. Each row starts from an input SMILES string, is parsed with RDKit, desalted by keeping the largest fragment, converted to canonical SMILES, and assigned an RDKit-derived InChIKey. Rows are deduplicated by derived InChIKey with priority labeled > geom_drugs > qm9.

Schema

Column	Dtype	Units	Meaning
inchikey	string	none	RDKit InChIKey derived from the canonical largest-fragment SMILES; primary join key across all SupraDB datasets.
name	string	none	Guest name from the source CSV when present, otherwise the first 14 characters of inchikey.
smiles	string	none	RDKit canonical SMILES after largest-fragment desalting.
logka	float/string nullable	log10 association constant	Optional experimental CB[7] binding label from the source CSV; empty for unlabeled guests.
source	string	none	Winning source after priority deduplication: labeled, geom_drugs, or qm9.
n_heavy	int64	atoms	Heavy-atom count of the canonical largest-fragment molecule used to derive inchikey.

Join key

inchikey is the sole join key for SupraDB-GEOM, SupraDB-LigandScore, SupraDB-PoseFeat, and SupraDB-CavityScore. It is generated once here from canonical largest-fragment SMILES so downstream compute, cache entries, 2D/3D structure lookup, and dashboard records all use the same identifier.

Provenance

• Pipeline position: Phase 0 pool builder, before CRC ligand scoring and GLIDE docking.
• GEOM source CSV: data/geom_drugs_smiles.csv.
• QM9 source CSV: data/qm9_smiles.csv.
• Labeled merge: 63 labeled rows were merged from the labeled CSV.
• Canonicalization: RDKit MolFromSmiles -> largest fragment by heavy atom count -> MolToSmiles(canonical=True) -> MolToInchiKey.
• Row count: 430904.
• Output rows by source:
• labeled: 63 rows
• geom_drugs: 301523 rows
• qm9: 129318 rows
• Downstream compute context: CRC; GLIDE 2025u2 / aISS fallback applies to later docked feature datasets, not this pool table.
• Pose collapse rule: not applicable for this dataset; later pose datasets keep the highest-Boltzmann-weight pose by default.
• Exact command: /users/tma2/workspace/SupraDashboard/.venv/bin/python engineering/src/pool_builder.py --input data/geom_drugs_smiles.csv --qm9 data/qm9_smiles.csv --labeled engineering/data/guests.csv --out data/pool_full --workers 8.