RDKitUtils

Utilities using RDKit.

Language: Python

Start: 2021

Why

I collected here a series of utilities using RDKit (Open-Source Cheminformatics Software, version originally used: Q32017):

calcCentroidFingerprint: calculate the centroid of a set of fingerprints
calcDescriptors: calculate some basic molecular descriptors
drawMolecule: draw a molecule (even with atom index)
exportExcelMolImage: export a Pandas dataframe with molecule image to Excel
printAtomBond: print atoms and bonds of a molecule
printChiral: print chirality information of a molecule
printPeriodicTable: print periodic table information
sanitizeMol: sanitize a SMILES molecule
sanitizeMolFile: sanitize a molecular file
testBulkTanimotoSimilarity: test of BulkTanimotoSimilarity function while working on different Pandas dataset of molecules
testAddMoleculeColumnToFrame: test of AddMoleculeColumnToFrame function to add a Molecule column to a Pandas dataframe (also molecules shown using Draw.MolsToGridImage)
testMaxMinPicker: test of diversity and similarity pickers functions (e.g., HierarchicalClusterPicker)
testSmilesMolSupplier: test of the SmilesMolSupplier function

Code example

Load molecules and calculate fingerprints:

mySMILES = ['CCCCF', 'C1CCCCC1', 'C(=O)CN']
mols = [Chem.MolFromSmiles(SMILES) for SMILES in mySMILES]
fps = [Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(m, 3, 512) for m in mols]

Calculate molecular descriptor MW:

from rdkit.Chem import rdMolDescriptors
import rdkit.Chem.Descriptors as Descriptors
MW = Descriptors.ExactMolWt(mol)

Draw a molecule

from rdkit.Chem import Draw
Draw.MolToFile(mol, IMAGE_FILE_NAME, size=(1024, 768), fitImage=True)
Draw.MolsToGridImage(mols, molsPerRow=3, subImgSize=(400, 400))

Loop on bonds

bonds = mol.GetBonds()
for i in range(len(bonds)):
  bond = bonds[i]
  a1 = bond.GetBeginAtomIdx()
  a2 = bond.GetEndAtomIdx()
  atom1 = mol.GetAtomWithIdx(a1)
  atom2 = mol.GetAtomWithIdx(a2)

Sanitized and canonical SMILES

mol = Chem.MolFromSmiles(SMILES, sanitize = True)
Chem.MolToSmiles(mol)
Chem.CanonSmiles(mol)

Compare two molecules

mol1 = Chem.MolFromSmiles('Nc1ccccc1')
mol2 = Chem.MolFromSmiles('c1c(N)cccc1')
print(Chem.MolToSmiles(mol1) == Chem.MolToSmiles(mol2))

Export Excel file with molecule image

df['MolImage'] = [Chem.MolFromSmiles(s) for s in df['SMILES']]
PandasTools.SaveXlsxFromFrame(df, 'export.xlsx', molCol='MolImage', size=(100, 200))

IMPORTANT: XlsxWriter needs to be installed (pip install XlsxWriter)

mattbrepo/RDKitUtils