Identify inter-chiralcenter stereobonds in 2D MOL files

dodgywedge.py

import pybel

def dodgywedge(sdffile):
    tot = probs = potential_probs = 0
    for mol in pybel.readfile("sdf", sdffile):
        tot += 1
        facade = pybel.ob.OBStereoFacade(mol.OBMol)
        tetcenters = [atom.OBAtom for atom in mol
                      if facade.HasTetrahedralStereo(atom.OBAtom.GetId())]
        for idx, atom_a in enumerate(tetcenters[:-1]):
            for atom_b in tetcenters[idx+1:]:
                if atom_a.IsConnected(atom_b):
                    potential_probs += 1
                    bond = atom_a.GetBond(atom_b)
                    if bond.IsWedge() or bond.IsHash():
                        probs += 1

    print "Total number of molecules", tot                        
    print "Potential problems:", potential_probs
    print "Actual problems:", probs

if __name__ == "__main__":
    dodgywedge("chembl_08.sdf")