Datasets:

SupraBench
/

SupraDB-GEOM

license: other
pretty_name: SupraDB-GEOM
tags:
  - chemistry
  - supramolecular-chemistry
  - rdkit
  - cb7
configs:
  - config_name: default
    data_files:
      - split: train
        path: guests.csv

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.

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.

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.

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.
Source CSV: /Users/billyma/Workspace/applications/SupraDashboard/engineering/data/guests.csv.
Canonicalization: RDKit MolFromSmiles -> largest fragment by heavy atom count -> MolToSmiles(canonical=True) -> MolToInchiKey.
Row count: 63.
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/billyma/Workspace/SupraBench/.venv/bin/python3.11 engineering/src/pool_builder.py --push.