mol_to_graph.py

import networkx as nx

def mol_to_nx(self, mol):
  G = nx.Graph()

  for atom in mol.GetAtoms():
    G.add_node(
      atom.GetIdx(), atom_type=atom.GetAtomicNum()
    )

  for bond in mol.GetBonds():
    G.add_edge(
      bond.GetBeginAtomIdx(),
      bond.GetEndAtomIdx(),
      bond_type=bond.GetBondType()
    )

  return G
  
  
graphs = []
with Chem.SDMolSupplier('file.sdf') as suppl:
  for mol in suppl:
    if mol is None: 
      continue
    graphs.append(mol_to_nx(mol))