RDKit Skill
This skill provides up-to-date RDKit patterns. LLMs often have outdated RDKit syntax — always follow the patterns here.
Installation
bash
uv pip install rdkit
Core Imports
python
from rdkit import Chem from rdkit.Chem import AllChem, Descriptors, Draw, rdFingerprintGenerator from rdkit.Chem import rdDepictor from rdkit import DataStructs
Molecule I/O
python
# From SMILES
mol = Chem.MolFromSmiles('CCO')
# From file
mol = Chem.MolFromMolFile('molecule.mol')
mols = [m for m in Chem.SDMolSupplier('molecules.sdf') if m is not None]
# To SMILES
smiles = Chem.MolToSmiles(mol)
Fingerprints — USE THE NEW API
CRITICAL: Use rdFingerprintGenerator module, NOT the old functions like GetMorganFingerprint().
See references/fingerprints.md for complete documentation.
Quick Reference
python
from rdkit.Chem import rdFingerprintGenerator # Morgan/ECFP fingerprints (ECFP4 = radius 2) mfpgen = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048) # RDKit fingerprint rdkgen = rdFingerprintGenerator.GetRDKitFPGenerator(fpSize=2048) # Atom pairs apgen = rdFingerprintGenerator.GetAtomPairGenerator(fpSize=2048) # Topological torsions ttgen = rdFingerprintGenerator.GetTopologicalTorsionGenerator(fpSize=2048) # Generate fingerprints (same API for all types) fp = mfpgen.GetFingerprint(mol) # bit vector cfp = mfpgen.GetCountFingerprint(mol) # count vector np_fp = mfpgen.GetFingerprintAsNumPy(mol) # numpy array
Drawing Molecules
Use MolDraw2DCairo or MolDraw2DSVG with drawOptions() for customization.
See references/drawing.md for complete documentation.
Quick Reference
python
from rdkit.Chem import Draw, rdDepictor
# Generate 2D coordinates
rdDepictor.Compute2DCoords(mol)
rdDepictor.StraightenDepiction(mol)
# Simple drawing
img = Draw.MolToImage(mol, size=(300, 300))
img.save('molecule.png')
# Customized drawing
d2d = Draw.MolDraw2DCairo(350, 300)
dopts = d2d.drawOptions()
dopts.addAtomIndices = True # show atom indices
d2d.DrawMolecule(mol)
d2d.FinishDrawing()
with open('molecule.png', 'wb') as f:
f.write(d2d.GetDrawingText())
# Grid of molecules
img = Draw.MolsToGridImage(mols, molsPerRow=4, subImgSize=(200, 200))
Molecular Properties
python
from rdkit.Chem import Descriptors mw = Descriptors.MolWt(mol) logp = Descriptors.MolLogP(mol) hbd = Descriptors.NumHDonors(mol) hba = Descriptors.NumHAcceptors(mol) tpsa = Descriptors.TPSA(mol) rotatable = Descriptors.NumRotatableBonds(mol)
Substructure Search
python
# SMARTS pattern matching
pattern = Chem.MolFromSmarts('[OH]')
matches = mol.GetSubstructMatches(pattern) # returns tuple of tuples
# Check if has substructure
has_oh = mol.HasSubstructMatch(pattern)
Similarity
Always specify which fingerprint when reporting similarity — different fingerprints give very different values for the same molecule pair (e.g., RDKit FP: 0.79 vs Morgan2: 0.43).
python
from rdkit import DataStructs # Tanimoto similarity between two fingerprints sim = DataStructs.TanimotoSimilarity(fp1, fp2) # Bulk similarity (one vs many) sims = DataStructs.BulkTanimotoSimilarity(fp1, [fp2, fp3, fp4])
Molecule Properties
python
# Get/set/check properties on molecules, atoms, bonds
mol.SetProp('name', 'aspirin')
mol.GetProp('name')
mol.HasProp('name')
mol.ClearProp('name')
# Typed getters/setters
mol.SetDoubleProp('score', 3.14)
mol.GetDoubleProp('score')
mol.SetIntProp('count', 42)
# Get all properties
mol.GetPropsAsDict() # {key: value, ...}
# Private props (start with _) hidden by default
mol.GetPropsAsDict(includePrivate=True)
Pickling Gotcha
Properties are lost by default when pickling/serializing:
python
from rdkit import Chem # Enable property preservation Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AllProps) # Or per-molecule binary = mol.ToBinary(Chem.PropertyPickleOptions.AllProps)
Parsing & Sanitization
Control chemistry perception during parsing. See references/parsing.md for details.
python
# Custom parsing without sanitization params = Chem.SmilesParserParams() params.sanitize = False params.removeHs = False mol = Chem.MolFromSmiles(smiles, params=params) # Manual sanitization after preprocessing Chem.SanitizeMol(mol) Chem.AssignStereochemistry(mol, cleanIt=True, force=True)