[Rdkit-discuss] Is it possible to create a reaction SMARTS with dative bonds?

[Grzegorz S. <g.s...@mi...>]

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