rdkit
Open-source cheminformatics and molecular toolkit
TLDR
Import RDKit in Python
$ python -c "from rdkit import Chem"
Read molecule from SMILES$ python -c "from rdkit import Chem; m = Chem.MolFromSmiles('CCO'); print(m)"
Calculate molecular weight$ python -c "from rdkit.Chem import Descriptors; from rdkit import Chem; print(Descriptors.MolWt(Chem.MolFromSmiles('CCO')))"
SYNOPSIS
rdkit Python library for cheminformatics
DESCRIPTION
RDKit is an open-source cheminformatics library. It provides functionality for reading, writing, and manipulating chemical structures, calculating molecular descriptors, and performing substructure searches.
EXAMPLES
$ from rdkit import Chem
from rdkit.Chem import AllChem, Descriptors, Draw
# Read molecule
mol = Chem.MolFromSmiles('c1ccccc1') # Benzene
# Calculate properties
mw = Descriptors.MolWt(mol)
logp = Descriptors.MolLogP(mol)
# Generate 2D coordinates
AllChem.Compute2DCoords(mol)
# Generate 3D conformer
mol3d = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol3d)
# Substructure search
pattern = Chem.MolFromSmarts('c1ccccc1')
mol.HasSubstructMatch(pattern)
# Save as image
Draw.MolToFile(mol, 'molecule.png')
from rdkit.Chem import AllChem, Descriptors, Draw
# Read molecule
mol = Chem.MolFromSmiles('c1ccccc1') # Benzene
# Calculate properties
mw = Descriptors.MolWt(mol)
logp = Descriptors.MolLogP(mol)
# Generate 2D coordinates
AllChem.Compute2DCoords(mol)
# Generate 3D conformer
mol3d = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol3d)
# Substructure search
pattern = Chem.MolFromSmarts('c1ccccc1')
mol.HasSubstructMatch(pattern)
# Save as image
Draw.MolToFile(mol, 'molecule.png')
INPUT FORMATS
$ SMILES - Chem.MolFromSmiles()
SDF - Chem.SDMolSupplier()
MOL - Chem.MolFromMolFile()
SDF - Chem.SDMolSupplier()
MOL - Chem.MolFromMolFile()
INSTALL
sudo pacman -S rdkit
brew install rdkit
CAVEATS
Python library installed via conda or pip (`pip install rdkit`). Requires numpy. A C++ library is also available. Some features require additional optional dependencies such as matplotlib for drawing.
HISTORY
RDKit was started by Greg Landrum at Rational Discovery and released as open source in 2006.
