| --- |
| 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. |
|
|
| 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`. |
|
|
