Looking for a better way of writing this code

def calculate_scores(population):
  scores = []
  for gene in population:
    mol=prepare_molecule(gene)
    Chem.SDWriter('mol_%i.sdf'%(population.index(gene))).write(mol) #add hs, optimize mol, remove hs, write all to sdf file
    shell('obabel mol_%i.sdf -O ligand_%i.pdbqt'%(population.index(gene),population.index(gene)),shell=False)
    score = sc.smina_score('ligand_%i.pdbqt'%(population.index(gene)))
    print(score)
    scores.append(max(float(score),0.0))

  return scores