rdkit
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()
CAVEATS
Python library (conda or pip install). Requires numpy. C++ library also available.
HISTORY
RDKit was started by Greg Landrum at Rational Discovery and released as open source in 2006.
