[Rdkit-discuss] Building a molecule from scratch

[Noel O'B. <bao...@gm...>]

I am running into trouble building a molecule from scratch. Let's say
the molecule represented by "F/C=C/F" (taken from the Daylight SMILES
tutorial). Here's the code to build it (according to me):

import Chem

# Set some lookups
_bondtypes = {1: Chem.BondType.SINGLE,
              2: Chem.BondType.DOUBLE,
              3: Chem.BondType.TRIPLE}
_bondstereo = {0: Chem.rdchem.BondStereo.STEREONONE,
               1: Chem.rdchem.BondStereo.STEREOE,
               2: Chem.rdchem.BondStereo.STEREOZ}

# Build F/C=C/F
rdmol = Chem.Mol()
rdedmol = Chem.EditableMol(rdmol)
for atomnum in [9, 6, 6, 9]:
    rdatom = Chem.Atom(atomnum)
    rdedmol.AddAtom(rdatom)

for bond in [(0,1,1), (1,2,2), (2,3,1)]:
    rdedmol.AddBond(bond[0],
                    bond[1],
                    _bondtypes[bond[2]])

rdmol = rdedmol.GetMol()
for stereoID, newbond in zip([0, 1, 0], rdmol.GetBonds()):
    newbond.SetStereo(_bondstereo[stereoID])

Chem.SanitizeMol(rdmol)
# Gets here fine

# Print the result
print Chem.MolToSmiles(rdmol, isomericSmiles=True)
# RuntimeError: Pre-condition Violation


What am I missing? It works fine if I use [0, 0, 0] for stereoID, so
it's something to do with the way I handle the stereoisomer.

Noel