| --- |
| license: other |
| pretty_name: moses_train |
| tags: |
| - chemistry |
| - molecules |
| - graph-generation |
| - flow-matching |
| size_categories: |
| - 1M<n<10M |
| --- |
| |
| # nico8771/moses_train — cleaned MOSES (train split) |
| |
| Each row is a molecule as **canonical SMILES** plus RDKit-recomputed targets. MOSES is |
| neutral by construction, so molecules are featurized over **7 atom types** with **no |
| formal charges**, and **aromatic bonds are kept as their own class** (no kekulization) |
| so the model learns aromaticity directly. |
| |
| > Source: official MOSES `train.csv.gz` (molecularsets/moses). Code: |
| > <https://github.com/Nico-Conti/flow-matching-molecules> (`dataset/`). |
| |
| ## Schema |
| |
| | column | type | description | |
| |---|---|---| |
| | `smiles` | string | canonical, single-fragment SMILES (post-sanitize) | |
| | `y` | list[float] | RDKit targets, columns = `logP`, `qed`, `SAS` | |
| |
| ## Pipeline |
| |
| 1. **Parse** with RDKit; unparseable dropped. |
| 2. **Standardize** — remove stereochemistry, sanitize (MOSES is neutral; *no* Uncharger). |
| 3. **Featurize** over atom vocab (`C`, `N`, `S`, `O`, `F`, `Cl`, `Br`); atoms outside the vocab dropped. |
| 4. **Round-trip check** — `smiles -> (X, E) -> mol -> smiles`, aromatic bonds preserved. |
| |
| Bonds use 5 classes (none / single / double / triple / aromatic). |
| Targets (`logP`, `qed`, `SAS`) are recomputed from the sanitized SMILES with RDKit. |
| |
| ### Drop / keep counts (this build) |
| |
| | outcome | count | |
| |---|---| |
| | `kept` | 1,415,728 | |
| | `kept_no_roundtrip` | 168,935 | |
| |
| Kept: **1,584,663** molecules. |
| |
