Dear All,
One of my colleagues has been trying to use the RDKit to process some
intramolecular reactions (ring-closing metatheses). It seems, however,
that what Daylight would refer to as "zero-level parentheses" are not
supported in RDKit reaction SMARTS(?)
------------------------------------------------------------------------
---
ValueError Traceback (most recent call
last)
C:\Users\j.davidson\<ipython-input-5-054bfc0441df> in <module>()
1 from rdkit import Chem
2 from rdkit.Chem import AllChem, Draw
----> 3 rxn1 =
AllChem.ReactionFromSmarts("([C:1]=[C;H2].[C:2]=[C;H2])>>[*:1]=[*:2]")
4 rxn1
5
ValueError: ChemicalReactionParserException: Problems constructing
reactant from SMARTS: ([C:1]=[C;H2]
To explain a little further by example (from the Daylight manual) - here
is how intra-molecular vs inter-molecular reactions can be specified /
distinguished with zero-level parentheses:
C(=O)O.OCC>>C(=O)OCC.O Matches esterifications
(C(=O)O).(OCC)>>C(=O)OCC.O Matches intermolecular esterifications
(C(=O)O.OCC)>>C(=O)OCC.O Matches intramolecular esterifications
(lactonizations)
Is there a workaround to this, and if not is this reaction behaviour
something that should be added in the future?
Kind regards
James
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