Hi James,
it looks like that's caused by the ambiguity between single and aromatic
bond, as the type of connecting bonds is not specified.
Specifying that all bonds should be aromatic seems to solve the problem:
tsmi = ('[cH:1]:1:[cH:2]:[c:3]([F:4]):[n:5]:[cH:6]:[cH:7]:1'
'>>[cH:1]:1:[cH:2]:[c:3]([Cl:4]):[n:5]:[cH:6]:[cH:7]:1')
rxn2 = rdChemReactions.ReactionFromSmarts(tsmi)
rdChemReactions.ChemicalReaction.Initialize(rxn2)
reacts2 = rdChemReactions.ChemicalReaction.GetReactingAtoms(
rxn2, mappedAtomsOnly=True)
reacts2
((3,),)
I thought that the bond type would default to aromatic between aromatic
atoms, but I guess there must be a reason why this is not the case;
perhaps someone else may comment on this.
Cheers,
p.
On 11/20/18 22:11, James Conroy via Rdkit-discuss wrote:
tsmi='[cH:1]1[cH:2][c:3]([F:4])[n:5][cH:6][cH:7]1>>[cH:1]1[cH:2][c:3]([Cl:4])[n:5][cH:6][cH:7]1'
rxn2 = AllChem.ReactionFromSmarts(tsmi)
rdChemReactions.ChemicalReaction.Initialize(rxn2)
reacts2=rdChemReactions.ChemicalReaction.GetReactingAtoms(rxn2,mappedAtomsOnly=True)
reacts2
((0, 1, 2, 3, 4, 5, 6),)
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