rdkit

RDKit Skill

Cheminformatics and machine learning toolkit for molecular operations, property calculation, and chemical analysis.

Official Sources:

• RDKit Documentation
• Getting Started in Python
• The RDKit Book

Installation

# Via conda (recommended)
conda install -c conda-forge rdkit

# Via pip
pip install rdkit

# Verify installation
python -c "from rdkit import Chem; print(Chem.__version__)"

Quick Start

from rdkit import Chem
from rdkit.Chem import AllChem, Descriptors, Draw

# Create molecule from SMILES
mol = Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O')  # Aspirin

# Calculate properties
mw = Descriptors.MolWt(mol)
logp = Descriptors.MolLogP(mol)

# Generate fingerprint
fp = AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048)

# Draw molecule
img = Draw.MolToImage(mol)

Molecular I/O

from rdkit import Chem

# Read/write single molecules
mol = Chem.MolFromSmiles('c1ccccc1')
mol = Chem.MolFromMolFile('input.mol')
smiles = Chem.MolToSmiles(mol)
Chem.MolToMolFile(mol, 'output.mol')

# Read/write multiple molecules
suppl = Chem.SDMolSupplier('molecules.sdf')
mols = [m for m in suppl if m is not None]

with Chem.SDWriter('output.sdf') as w:
    for mol in mols:
        w.write(mol)

Molecular Operations

# Atoms and bonds
for atom in mol.GetAtoms():
    print(atom.GetSymbol(), atom.GetAtomicNum())
atom = mol.GetAtomWithIdx(0)
bond = mol.GetBondWithIdx(0).GetBondType()

# Rings
atom.IsInRing()
atom.IsInRingSize(6)
ssr = Chem.GetSymmSSSR(mol)

# Modify
mol_with_h = Chem.AddHs(mol)
mol_no_h = Chem.RemoveHs(mol)
Chem.Kekulize(mol)
Chem.SanitizeMol(mol)

Molecular Descriptors

from rdkit.Chem import Descriptors, AllChem

# Common descriptors
Descriptors.MolWt(mol)
Descriptors.MolLogP(mol)
Descriptors.TPSA(mol)
Descriptors.NumHDonors(mol)
Descriptors.NumHAcceptors(mol)
Descriptors.NumRotatableBonds(mol)

# All descriptors
all_desc = Descriptors.CalcMolDescriptors(mol)

# Partial charges
AllChem.ComputeGasteigerCharges(mol)
charge = mol.GetAtomWithIdx(0).GetDoubleProp('_GasteigerCharge')