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Chemistry Rdkit | Skills Pool

Archivo del skill

Chemistry Rdkit

Computational chemistry with RDKit for molecular analysis, descriptors, fingerprints, and substructure search. Use when working with SMILES, drug discovery, or cheminformatics tasks.

aiming-lab11,332 estrellas31 mar 2026

Ocupación
Categorías: Química Computacional

Contenido de la habilidad

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)

Skills relacionados

Instalación rápida

Chemistry Rdkit

npx skillvault add aiming-lab/aiming-lab-autoresearchclaw-claude-skills-chemistry-rdkit-skill-md

Descargar Skill Abrir repositorio

Autor: aiming-lab
estrellas: 11,332
Actualizado: 31 mar 2026
Ocupación

En esta página

01RDKit Cheminformatics Best Practice

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

02

Molecular I/O

03Molecular Descriptors

04Fingerprints and Similarity

05Substructure Search

06Property Calculation Patterns

07Common Pitfalls

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