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.
Installation and Setup
Use uv when installing into an existing Python environment:
uv pip install rdkit
For reproducible chemistry environments, especially when mixing compiled scientific packages, conda-forge remains the upstream recommendation:
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
Twelve capability areas, each with worked code, are documented in
references/core_capabilities.md:
| # |
Area |
Covers |
| 1 |
Molecular I/O and creation |
SMILES, MOL files and blocks, InChI, SDF and SMILES suppliers, multithreaded reading, writers |
| 2 |
Sanitization and validation |
disabling automatic sanitization, manual and partial sanitization, detecting problems first |
| 3 |
Analysis and properties |
atom and bond iteration, ring information and SSSR, chirality and stereochemistry, fragments |
| 4 |
Descriptors |
MW, LogP, TPSA, H-bond donors/acceptors, rotatable bonds, aromatic rings, bulk calculation, drug-likeness |
| 5 |
Fingerprints and similarity |
topological, Morgan/ECFP via rdFingerprintGenerator, MACCS, atom pair, torsion, Avalon; Tanimoto and other metrics; Butina clustering |
| 6 |
Substructure searching |
SMARTS queries, match retrieval, and a library of common patterns |
| 7 |
Chemical reactions |
reaction SMARTS, applying reactions, reaction fingerprints |
| 8 |
2D and 3D coordinates |
depiction, template alignment, ETKDG embedding, force-field optimization, RMSD, constrained embedding |
| 9 |
Visualization |
single and grid images, substructure highlighting, custom drawer options, Jupyter integration, fingerprint bit environments |
| 10 |
Molecular modification |
explicit hydrogens, Kekulization, aromaticity, substructure replacement, charge neutralization |
| 11 |
Hashes and standardization |
Murcko scaffold and canonical hashes, regioisomer hashes, randomized SMILES for augmentation |
| 12 |
Pharmacophore and 3D features |
feature factories and feature extraction |
Worked workflows and the performance, thread-safety, and version-sensitivity notes are in
references/workflows_and_best_practices.md.
Prefer portable exchange formats (SMILES, SDF) for shared data; for local caches RDKit's
binary molecule representation avoids generic pickle.
Common Pitfalls
- Forgetting to check for None: Always validate molecules after parsing
- Sanitization failures: Use
DetectChemistryProblems() to debug
- Missing hydrogens: Use
AddHs() when calculating properties that depend on hydrogen
- 2D vs 3D: Generate appropriate coordinates before visualization or 3D analysis
- SMARTS matching rules: Remember that unspecified properties match anything
- 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 functionalitydescriptors_reference.md - Complete list of available molecular descriptors with descriptionssmarts_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 descriptorssimilarity_search.py - Perform fingerprint-based similarity screeningsubstructure_filter.py - Filter molecules by substructure patterns
These scripts can be executed directly or used as templates for custom workflows.
Source: K-Dense-AI/scientific-agent-skills → skills/rdkit/SKILL.md
1---2name: rdkit3description: 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.4---567# RDKit Cheminformatics Toolkit89## Overview1011RDKit 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.1213**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.1415## Installation and Setup1617Use `uv` when installing into an existing Python environment:1819```bash20uv pip install rdkit21```2223For reproducible chemistry environments, especially when mixing compiled scientific packages, conda-forge remains the upstream recommendation:2425```bash26conda create -c conda-forge -n my-rdkit-env rdkit27conda activate my-rdkit-env28```2930Avoid 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.3132## Core Capabilities3334Twelve capability areas, each with worked code, are documented in35[references/core_capabilities.md](references/core_capabilities.md):3637| # | Area | Covers |38| --- | --- | --- |39| 1 | Molecular I/O and creation | SMILES, MOL files and blocks, InChI, SDF and SMILES suppliers, multithreaded reading, writers |40| 2 | Sanitization and validation | disabling automatic sanitization, manual and partial sanitization, detecting problems first |41| 3 | Analysis and properties | atom and bond iteration, ring information and SSSR, chirality and stereochemistry, fragments |42| 4 | Descriptors | MW, LogP, TPSA, H-bond donors/acceptors, rotatable bonds, aromatic rings, bulk calculation, drug-likeness |43| 5 | Fingerprints and similarity | topological, Morgan/ECFP via `rdFingerprintGenerator`, MACCS, atom pair, torsion, Avalon; Tanimoto and other metrics; Butina clustering |44| 6 | Substructure searching | SMARTS queries, match retrieval, and a library of common patterns |45| 7 | Chemical reactions | reaction SMARTS, applying reactions, reaction fingerprints |46| 8 | 2D and 3D coordinates | depiction, template alignment, ETKDG embedding, force-field optimization, RMSD, constrained embedding |47| 9 | Visualization | single and grid images, substructure highlighting, custom drawer options, Jupyter integration, fingerprint bit environments |48| 10 | Molecular modification | explicit hydrogens, Kekulization, aromaticity, substructure replacement, charge neutralization |49| 11 | Hashes and standardization | Murcko scaffold and canonical hashes, regioisomer hashes, randomized SMILES for augmentation |50| 12 | Pharmacophore and 3D features | feature factories and feature extraction |5152Worked workflows and the performance, thread-safety, and version-sensitivity notes are in53[references/workflows_and_best_practices.md](references/workflows_and_best_practices.md).5455Prefer portable exchange formats (SMILES, SDF) for shared data; for local caches RDKit's56binary molecule representation avoids generic pickle.5758## Common Pitfalls59601. **Forgetting to check for None:** Always validate molecules after parsing612. **Sanitization failures:** Use `DetectChemistryProblems()` to debug623. **Missing hydrogens:** Use `AddHs()` when calculating properties that depend on hydrogen634. **2D vs 3D:** Generate appropriate coordinates before visualization or 3D analysis645. **SMARTS matching rules:** Remember that unspecified properties match anything656. **Thread safety with MolSuppliers:** Don't share supplier objects across threads6667## Resources6869### references/7071This skill includes detailed API reference documentation:7273- `api_reference.md` - Comprehensive listing of RDKit modules, functions, and classes organized by functionality74- `descriptors_reference.md` - Complete list of available molecular descriptors with descriptions75- `smarts_patterns.md` - Common SMARTS patterns for functional groups and structural features7677Load these references when needing specific API details, parameter information, or pattern examples.7879Only 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.8081### scripts/8283Example scripts for common RDKit workflows:8485- `molecular_properties.py` - Calculate comprehensive molecular properties and descriptors86- `similarity_search.py` - Perform fingerprint-based similarity screening87- `substructure_filter.py` - Filter molecules by substructure patterns8889These scripts can be executed directly or used as templates for custom workflows.9091---9293**Source:** [`K-Dense-AI/scientific-agent-skills`](https://github.com/K-Dense-AI/scientific-agent-skills) → `skills/rdkit/SKILL.md`
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