• 1. What is molecular graph?
• 2. How to construct a molecular graph?

1. What is molecular graph?

A graph \(\mathcal{G}\) is a set of nodes (vertices) \(\mathcal{V}\) and edges \(\mathcal{E}\). A molecular graph is a representation of the structural formula of a chemical compound in terms of graph theory, whose vertices correspond to the atoms of the compound and edges correspond to chemical bonds. Molecular Graphs are widely used in cheminfomatics area as it is a natural way to represent molecules in a machine-readable language.

2. How to construct a molecular graph?

By using RDKit, Openbabel, ASE and Pymatgen, you could easily encode a molecule into a molecular graph. The input of molecule in this case could be SMILES, InChI or other type of Mol file (e.g., xyz, cif, pdb, sdf, mol, and so on). An example of using RDKit is shown here:

from rdkit import Chem
from rdkit.Chem import Draw
mol = Chem.MolFromSmiles('Cc1ccccc1')
mol2 = Chem.MolFromPDBFile('data/mol.pdb')

img = Draw.MolToImage(mol)