Problem loading aromatic SMILES or kekulized molecules with RDKit

[stevenkbennett]

There is an issue with loading aromatic SMILES or kekulized molecules from RDKit where bonds involved in aromatic rings are converted to single bonds.

Discovered by @joshkamm, @andrewtarzia and myself.

stk is able to handle to handle the aromatic bond order of 1.5, however, when converting back into the RDKit molecule, or writing to a .mol file, the aromatic bond information is lost.
When converting back into the RDKit molecule with to_rdkit_mol, I believe this occurs due to line 739 in https://github.com/lukasturcani/stk/blob/5987b0aa7ce73175701ba267d392b4fe5c651707/src/stk/molecular/molecules/molecule/molecule.py. When rdkit.BondType is called with a floating point bond order, it is converted into an int.
This behaviour can be seen just by executing

rdkit.BondType(1.6)

For writing to a .mol file, this issue appears due to line 82 in https://github.com/andrewtarzia/stk/blob/main/src/stk/molecular/molecules/molecule/utilities/writers/mdl_mol.py, as mentioned by @andrewtarzia on Discord as bond orders are all converted to ints.

To reproduce this, the following code can be used:

import stk
from rdkit.Chem import AllChem as rdkit

smiles = 'C1=CC=CC=C1'

mol = rdkit.MolFromSmiles(smiles)
rdkit.MolToMolFile(mol, 'rdkit.mol')
mol = rdkit.AddHs(mol)
rdkit.EmbedMolecule(mol)
stk.BuildingBlock.init_from_rdkit_mol(mol).write('prekc.mol')
rdkit.Kekulize(mol)
rdkit.MolToMolFile(mol, 'rdkit2.mol')
stk.BuildingBlock.init_from_rdkit_mol(mol).write('postkc.mol')

stk.BuildingBlock(smiles).write('stk.mol')

To fix, maybe an error can be raised if the user passes in non-integer bond types when initialising from an RDKit molecule, or some different handling of non-integer bond types within stk itself.

[lukasturcani]

stk does not deal in aromatic bonds. It is quite right for it to convert to integers. The problem, as I see it, is that it is not sanitizing user input. By which I mean, that when receiving an rdkit molecule, it does not kekulize it.

[stevenkbennett]

Hey Lukas, just wanted to bring this issue up again as it has appeared quite a few times in our work. I was planning on submitting a PR in which a warning is issued to the user if an aromatic molecule is received in the init_from_rdkit function. What do you think of this?

[lukasturcani]

#407 (comment)