Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit
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Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit
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</> SKILL.md
rdkit.SKILL.md
---name: rdkit
description: Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
license: BSD-3-Clause license
allowed-tools:
- Read
- Write
- Edit
- Bash
compatibility: Examples target RDKit 2026.03.x. Use conda-forge for the broadest binary support or PyPI package `rdkit` for supported platform wheels; `rdkit-pypi` is the legacy PyPI name.
metadata: {"version": "1.1", "skill-author": "K-Dense Inc."}
---# RDKit Cheminformatics Toolkit
## Overview
RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks.
**Current baseline (checked 2026-06-07):** RDKit **2026.03.3** is the latest GitHub/PyPI release (`rdkit` 2026.3.3 on PyPI). Official installation docs continue to recommend conda-forge for most users, while cross-platform PyPI wheels are published under the `rdkit` package name. `rdkit-pypi` is the old PyPI package name and should only appear when maintaining legacy environments.
Use `uv` when installing into an existing Python environment:
```bash
uv pip install rdkit
```
For reproducible chemistry environments, especially when mixing compiled scientific packages, conda-forge remains the upstream recommendation:
```bash
conda create -c conda-forge -n my-rdkit-env rdkit
conda activate my-rdkit-env
```
Avoid installing both conda `rdkit` and PyPI `rdkit`/`rdkit-pypi` into the same environment unless you are deliberately debugging packaging behavior. Mixed installs can make it unclear which binary extension is being imported.
## Core Capabilities
### 1. Molecular I/O and Creation
**Reading Molecules:**
Read molecular structures from various formats:
```python
from rdkit import Chem
# From SMILES strings
mol = Chem.MolFromSmiles('Cc1ccccc1') # Returns Mol object or None
mols = [Chem.Mol(base64.b64decode(item)) for item in cached]
```
Do not load Python pickle files from untrusted sources. Pickle deserialization can execute arbitrary code; prefer SMILES/SDF for interchange and RDKit binary payloads for trusted local caches.
**Use bulk operations:**
```python
from rdkit import DataStructs
from rdkit.Chem import rdFingerprintGenerator
# Calculate fingerprints for all molecules at once
Pin RDKit versions when exact molecular identifiers or numeric features are part of a persisted dataset, model feature pipeline, or regulated report. Recent releases changed or documented behavior in several Python-facing areas:
- **Canonical SMILES and stereo:** 2026.03 changed canonical double-bond handling to avoid stereo corruption, so some stereo-containing SMILES may differ from older releases.
- **Descriptors and hashes:** 2024.09 corrected unbranched-alkane fragment descriptor SMARTS and changed some tautomer/protomer hash outputs.
- **Drawing:** legacy `rdkit.Chem.Draw` canvas modules and functions such as `MolToImageFile`, `MolToMPL`, and `MolToQPixmap` were removed; use `Draw.MolToFile`, `Draw.MolToImage`, or `rdMolDraw2D`.
- **MolStandardize:** use `rdkit.Chem.MolStandardize.rdMolStandardize`; the older Python MolStandardize implementation was removed.
- **Similarity maps:** `GetSimilarityMapFromWeights()`, `GetSimilarityMapForFingerprint()`, and `GetSimilarityMapForModel()` now require an `rdMolDraw2D` drawing object.
### Thread Safety
RDKit operations are generally thread-safe for:
- Molecule I/O (SMILES, mol blocks)
- Coordinate generation
- Fingerprinting and descriptors
- Substructure searching
- Reactions
- Drawing
**Not thread-safe:** MolSuppliers when accessed concurrently.
### Memory Management
For large datasets:
```python
# Use ForwardSDMolSupplier to avoid loading entire file
with open('large.sdf') as f:
suppl = Chem.ForwardSDMolSupplier(f)
for mol in suppl:
# Process one molecule at a time
pass
# Use MultithreadedSDMolSupplier for parallel processing
1. **Forgetting to check for None:** Always validate molecules after parsing
2. **Sanitization failures:** Use `DetectChemistryProblems()` to debug
3. **Missing hydrogens:** Use `AddHs()` when calculating properties that depend on hydrogen
4. **2D vs 3D:** Generate appropriate coordinates before visualization or 3D analysis
5. **SMARTS matching rules:** Remember that unspecified properties match anything
6. **Thread safety with MolSuppliers:** Don't share supplier objects across threads
## Resources
### references/
This skill includes detailed API reference documentation:
- `api_reference.md` - Comprehensive listing of RDKit modules, functions, and classes organized by functionality
- `descriptors_reference.md` - Complete list of available molecular descriptors with descriptions
- `smarts_patterns.md` - Common SMARTS patterns for functional groups and structural features
Load these references when needing specific API details, parameter information, or pattern examples.
Only the files listed in `references/` and `scripts/` are bundled local resources. Names such as `rdkit`, `datamol`, `scipy`, and `sklearn` refer to installable Python packages, not local files in this skill.
### scripts/
Example scripts for common RDKit workflows:
- `molecular_properties.py` - Calculate comprehensive molecular properties and descriptors
