Re: [Rdkit-discuss] RDKit appears to be parsing SMILES stereochemistry differently

[Brian C. <co...@gm...>]

Here's an example of why this is useful at maintaining molecular
fragmentation inside your molecular representation:

>>> from rdkit import Chem
>>> smiles = 'F9.[C@]91(C)CCO1'
>>> fluorine, core = smiles.split('.')
>>> fluorine
'F9'
>>> fragment = core.replace('9', '([*:9])')
>>> fragment
'[C@]([*:9])1(C)CCO1'
>>> mol = Chem.RWMol(Chem.MolFromSmiles(fragment))  ### RDKit is flipping
the stereo on me here even the order of the bonds has not changed
>>> idx = mol.AddAtom(Chem.Atom(0))
>>> mol.AddBond(idx, 4, Chem.rdchem.BondType.SINGLE)
7
>>> mol.GetAtomWithIdx(idx).SetIntProp("molAtomMapNumber", 8)
>>> new_core = Chem.MolToSmiles(mol, True)
>>> new_core = new_core.replace('([*:9])', '9').replace('([*:8])', '8')
>>> new_core
'C[C@]19CC8O1'
>>> analog_smiles = 'Cl8.' + fluorine + '.' + new_core
>>> analog_smiles
'Cl8.F9.C[C@]19CC8O1'
>>> analog = Chem.MolFromSmiles(analog_smiles)
>>> analog.HasSubstructMatch(Chem.MolFromSmiles(smiles),
useChirality=True)      # Uh oh! My original molecule didn't match
False
>>> analog.HasSubstructMatch(Chem.MolFromSmiles(smiles.replace('@', '@@')),
useChirality=True)   # flipping the stereo of the original causes it to
match again
True




On Thu, Nov 9, 2017 at 4:41 AM, Andrew Dalke <da...@da...>
wrote:

> On Nov 9, 2017, at 08:13, Greg Landrum <gre...@gm...> wrote:
> > As was discussed in the comments of https://github.com/rdkit/
> rdkit/issues/786, I think it's pretty gross that the second syntax is
> even legal. But that's a side point.
>
> To belabor that point. Neither Daylight SMILES nor OpenSMILES accept it,
> which are the only two explicit sources of "legal" that people use.
>
> "allowed" might be a better term.
>
>                                 Andrew
>                                 da...@da...
>
>
>
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