Hi Grzegorz,
Nice one! This is a bug in the way Reaction SMARTS (or Reaction SMILES for
that matter) is parsed.
At the moment there's not any way to directly work around the problem. You
can add a single bond in the reaction and then manually convert that to a
dative bond in the products. Something like this could work:
In [40]: rxn = AllChem.ReactionFromSmarts('[O:1]>>[O:1]-[H+]')
In [41]: ps = rxn.RunReactants((Chem.MolFromSmiles('CCC[O-]'),))
In [42]: newPs = []
In [43]: for p in ps:
...: p = p[0]
...: match = p.GetSubstructMatch(pattern)
...: if not match:
...: continue
...: newP = Chem.RWMol(p)
...:
newP.GetBondBetweenAtoms(match[0],match[1]).SetBondType(Chem.BondType.DATIVE)
...: newPs.append(newP)
...:
In [44]: newPs[0].UpdatePropertyCache(strict=False)
In [45]: Chem.MolToSmiles(newPs[0])
Out[45]: '[H+]<-[O-]CCC'
Note that I changed the definition of your reaction: I removed the [H+]
from the reactants since you weren't mapping it into the products.
-greg
On Wed, Feb 12, 2020 at 3:27 PM Grzegorz Skoraczyński <
g.skoraczyn...@mimuw.edu.pl> wrote:
> Hello,
>
> Imagine that we want to simulate an ESI protonation of the molecule. We
> want to add a positively charged proton to a lone pair of the oxygen atom
> of the molecule. I tried to create a reaction SMARTS with extended molecule
> SMARTS definition, but unfortunately, it results in ValueError error, the
> description of which suggests a different problem (parsing problem).
>
> >>> from rdkit.Chem import AllChem
> >>> rxn = AllChem.ReactionFromSmarts('[O:1].[H+]>>[O:1]->[H+]')
> ---------------------------------------------------------------------------
> ValueError Traceback (most recent call last)
> <ipython-input-42-06f8a10b5869> in <module>()
> ----> 1 rxn = AllChem.ReactionFromSmarts('[O:1].[H+]>>[O:1]->[H+]')
>
> ValueError: ChemicalReactionParserException: multi-step reactions not
> supported
>
> RDKit version: 2020.03.1dev1.
>
> Could you help me with creating a dative bond in reaction SMARTS?
>
> Best regards
> Grzegorz Skoraczyński
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