How do I install the Chemistry Rdkit skill?

Run npx skillmds@latest add enuno/chemistry-rdkit in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Chemistry Rdkit safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Chemistry Rdkit?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Chemistry Rdkit free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Chemistry Rdkit?

enuno (@enuno) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Chemistry Rdkit by enuno — Agent Skill

Name: Chemistry Rdkit
Rating: 4.2 (5 reviews)
Author: enuno

File contents

RDKit Cheminformatics Best Practice

Molecular I/O

Create molecules from SMILES: mol = Chem.MolFromSmiles('CCO')
Always check for None: MolFromSmiles returns None on invalid input
Convert to canonical SMILES: Chem.MolToSmiles(mol)
Read SDF files: suppl = Chem.SDMolSupplier('file.sdf')
Read SMILES files: suppl = Chem.SmilesMolSupplier('file.smi')
Write molecules: writer = Chem.SDWriter('output.sdf')

Molecular Descriptors

Molecular weight: Descriptors.MolWt(mol)
LogP (lipophilicity): Descriptors.MolLogP(mol)
TPSA (polar surface area): Descriptors.TPSA(mol)
H-bond donors/acceptors: Descriptors.NumHDonors(mol), Descriptors.NumHAcceptors(mol)
Rotatable bonds: Descriptors.NumRotatableBonds(mol)
Lipinski Rule of 5: MW <= 500, LogP <= 5, HBD <= 5, HBA <= 10

Fingerprints and Similarity

Morgan (circular) fingerprints: AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048)
RDKit fingerprints: Chem.RDKFingerprint(mol)
MACCS keys: MACCSkeys.GenMACCSKeys(mol)
Tanimoto similarity: DataStructs.TanimotoSimilarity(fp1, fp2)
Use radius=2 (ECFP4 equivalent) as default for most applications
For virtual screening, Tanimoto > 0.7 suggests structural similarity

Substructure Search

SMARTS patterns: pattern = Chem.MolFromSmarts('[OH]')
Check match: mol.HasSubstructMatch(pattern)
Get all matches: mol.GetSubstructMatches(pattern)
Common SMARTS: [#6](=O)[OH] (carboxylic acid), [NH2] (primary amine)
Filter compound libraries by functional group presence

Property Calculation Patterns

Batch processing: iterate over SDMolSupplier, skip None entries
Use Chem.Descriptors.descList for all available descriptors
For ADMET filtering, calculate Lipinski, Veber, and PAINS filters
Generate 3D coordinates: AllChem.EmbedMolecule(mol, AllChem.ETKDG())
Minimize energy: AllChem.MMFFOptimizeMolecule(mol)

Common Pitfalls

Always sanitize molecules (default behavior) — disable only when needed
Add hydrogens explicitly for 3D work: Chem.AddHs(mol)
Handle stereochemistry: use Chem.AssignStereochemistry(mol)
Large SDF files: use ForwardSDMolSupplier for memory efficiency
Kekulization errors usually indicate invalid SMILES input

---name: chemistry-rdkitdescription: Computational chemistry with RDKit for molecular analysis, descriptors, fingerprints, and substructure search. Use when working with SMILES, drug discovery, or cheminformatics tasks.--- ## RDKit Cheminformatics Best Practice ### Molecular I/O 1. Create molecules from SMILES: `mol = Chem.MolFromSmiles('CCO')` 2. Always check for None: `MolFromSmiles` returns None on invalid input 3. Convert to canonical SMILES: `Chem.MolToSmiles(mol)` 4. Read SDF files: `suppl = Chem.SDMolSupplier('file.sdf')` 5. Read SMILES files: `suppl = Chem.SmilesMolSupplier('file.smi')` 6. Write molecules: `writer = Chem.SDWriter('output.sdf')` ### Molecular Descriptors 1. Molecular weight: `Descriptors.MolWt(mol)` 2. LogP (lipophilicity): `Descriptors.MolLogP(mol)` 3. TPSA (polar surface area): `Descriptors.TPSA(mol)` 4. H-bond donors/acceptors: `Descriptors.NumHDonors(mol)`, `Descriptors.NumHAcceptors(mol)` 5. Rotatable bonds: `Descriptors.NumRotatableBonds(mol)` 6. Lipinski Rule of 5: MW <= 500, LogP <= 5, HBD <= 5, HBA <= 10 ### Fingerprints and Similarity 1. Morgan (circular) fingerprints: `AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048)` 2. RDKit fingerprints: `Chem.RDKFingerprint(mol)` 3. MACCS keys: `MACCSkeys.GenMACCSKeys(mol)` 4. Tanimoto similarity: `DataStructs.TanimotoSimilarity(fp1, fp2)` 5. Use radius=2 (ECFP4 equivalent) as default for most applications 6. For virtual screening, Tanimoto > 0.7 suggests structural similarity ### Substructure Search 1. SMARTS patterns: `pattern = Chem.MolFromSmarts('[OH]')` 2. Check match: `mol.HasSubstructMatch(pattern)` 3. Get all matches: `mol.GetSubstructMatches(pattern)` 4. Common SMARTS: `[#6](=O)[OH]` (carboxylic acid), `[NH2]` (primary amine) 5. Filter compound libraries by functional group presence ### Property Calculation Patterns 1. Batch processing: iterate over SDMolSupplier, skip None entries 2. Use `Chem.Descriptors.descList` for all available descriptors 3. For ADMET filtering, calculate Lipinski, Veber, and PAINS filters 4. Generate 3D coordinates: `AllChem.EmbedMolecule(mol, AllChem.ETKDG())` 5. Minimize energy: `AllChem.MMFFOptimizeMolecule(mol)` ### Common Pitfalls 1. Always sanitize molecules (default behavior) — disable only when needed 2. Add hydrogens explicitly for 3D work: `Chem.AddHs(mol)` 3. Handle stereochemistry: use `Chem.AssignStereochemistry(mol)` 4. Large SDF files: use `ForwardSDMolSupplier` for memory efficiency 5. Kekulization errors usually indicate invalid SMILES input

Frequently asked questions

Chemistry Rdkit