---
license: other
pretty_name: zinc_clean
tags:
- chemistry
- molecules
- graph-generation
- flow-matching
size_categories:
- 100K<n<1M
---

# nico8771/zinc_clean — cleaned ZINC-250k

Each row is a molecule as **canonical SMILES** plus RDKit-recomputed targets. Charged
groups (`N+`/`O-`) are preserved. 

> Source: torch_molecule ZINC-250k (HuggingFace). Code:
> <https://github.com/Nico-Conti/flow-matching-molecules> (`dataset/`).

## Schema

| column | type | description |
|---|---|---|
| `smiles` | string | canonical, kekulizable, 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 (charges preserved; `N+`/`O-` kept).
3. **Kekulize** over atom vocab (`C`, `N`, `O`, `F`, `P`, `S`, `Cl`, `Br`, `I`, `N+`, `O-`); atoms outside the vocab dropped.
4. **Round-trip check** — `smiles -> (X, E) -> mol -> smiles` must reproduce the
   canonical molecule as a single fragment (**filter applied**).

Bonds use 4 classes (none / single / double / triple). Targets
(`logP`, `qed`, `SAS`) are recomputed from the canonical SMILES with RDKit.

### Drop / keep counts (this build)

| outcome | count |
|---|---|
| `drop_roundtrip` | 1 |
| `drop_vocab` | 2,005 |
| `kept` | 247,449 |

Kept: **247,449** molecules.