Rdkit

RDKit

The primary Python library for cheminformatics. Molecular manipulation, descriptors, fingerprints, 3D generation, reactions, and more.

When to Use This Skill

• Reading/writing molecules from SMILES, SDF, MOL, PDB files
• Calculating molecular properties and drug-likeness filters (Ro5, QED)
• Computing and comparing molecular fingerprints (Morgan/ECFP, MACCS, RDKit FP)
• Generating 3D conformers (ETKDG, MMFF, UFF)
• Substructure searching and SMARTS queries
• Maximum Common Substructure (MCS) analysis
• Chemical reactions via SMARTS or RXN files
• Molecular fragmentation (BRICS, RECAP, Murcko scaffolds)
• Stereochemistry assignment and analysis
• Tautomer enumeration and molecule standardization
• Molecular visualization (2D SVG/PNG, similarity maps)

Quick Start

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

# Load molecule
mol = Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O')  # aspirin

# Basic properties
print(Descriptors.MolWt(mol))        # 180.16
print(Descriptors.MolLogP(mol))      # 1.31
print(rdMolDescriptors.CalcNumHBD(mol))  # 1
print(rdMolDescriptors.CalcNumHBA(mol))  # 4
print(rdMolDescriptors.CalcTPSA(mol))    # 63.6

# Morgan fingerprint (ECFP4-like)
fpgen = AllChem.GetMorganGenerator(radius=2)
fp = fpgen.GetFingerprint(mol)

# 2D image
img = Draw.MolToImage(mol, size=(300, 200))

Router — What to Read

| Task | Reference | |------|-----------| | SMILES, SDF, MOL, PDB, SMARTS I/O, serialization | references/io-molecules.md | | Descriptors, Lipinski Ro5, QED, ADME, drug filters | references/properties-descriptors.md | | Morgan, MACCS, RDKit FP, atom pair, similarity, diversity | references/fingerprints-similarity.md | | 3D conformers (ETKDG), MMFF/UFF optimization, 3D descriptors | references/3d-conformers.md | | Reactions (SMARTS), BRICS, RECAP, Murcko, tautomers, standardization | references/transformations.md | | Substructure search (SMARTS), MCS, rings, stereochemistry, pharmacophores | references/analysis-search.md | | Visualization: SVG/PNG, highlighting, similarity maps, grids | references/visualization.md |

Key Modules

| Module | Import | Role | |--------|--------|------| | Chem | from rdkit import Chem | Core molecule objects, I/O | | AllChem | from rdkit.Chem import AllChem | 3D, fingerprints, reactions | | Descriptors | from rdkit.Chem import Descriptors | 200+ 2D descriptors | | rdMolDescriptors | from rdkit.Chem import rdMolDescriptors | Fast C++ descriptors | | DataStructs | from rdkit import DataStructs | Fingerprint similarity | | Draw | from rdkit.Chem import Draw | 2D visualization | | rdMolDraw2D | from rdkit.Chem.Draw import rdMolDraw2D | SVG/Cairo rendering | | MACCSkeys | from rdkit.Chem import MACCSkeys | MACCS fingerprints | | rdFMCS | from rdkit.Chem import rdFMCS | Maximum Common Substructure | | BRICS | from rdkit.Chem import BRICS | BRICS fragmentation | | Recap | from rdkit.Chem import Recap | RECAP fragmentation | | MurckoScaffold | from rdkit.Chem.Scaffolds import MurckoScaffold | Scaffold extraction | | rdMolStandardize | from rdkit.Chem.MolStandardize import rdMolStandardize | Tautomers, cleanup | | rdChemReactions | from rdkit.Chem import rdChemReactions | Reaction handling |

Installation

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

# pip (official wheel since 2022)
pip install rdkit

# verify
python -c "from rdkit import Chem; print(Chem.MolFromSmiles('c1ccccc1'))"

Related Skills

• deepchem — ML models on molecular datasets built on top of RDKit
• cheminformatics — SMILES notation, file formats, molecular representations
• nextflow — Pipeline execution for high-throughput molecular workflows

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: Kdevos12
• Source: Kdevos12/ALKYL
• License: MIT

Install and usage instructions live in the source repository linked above.