Hi Peter, On Thu, Jun 11, 2015 at 5:54 PM, Peter Shenkin <[email protected]> wrote:
> If I canonicalize *1**1 in RDKit, I get [*]1:[*]:[*]:1. > > I expected [*]1[*][*]1. > > That is indeed surprising. I can think of no reason that the wildcard type in this context should be > assumed to be aromatic. > There are a couple of things going on here that are causing this to happen. 1) A "*" in a conjugated ring can contribute 0, 1, or 2 electrons to the pi system when determining aromaticity. This allows rings like C1=CC=CC=*1 and C1=C*C=C1 to be aromatic. 2) An unspecified bond in a SMILES can be either aromatic or single. This is normally assigned based on whether or not the atoms involved in the bond are aromatic, but there is apparently some logic buried somewhere that treats dummy-dummy bonds as a special case that can always be considered for aromaticity. Consequently the SMILES '*-1-*-*-*-1' leads to an aromatic ring. The net effect of all of this is that rings containing purely dummy atoms connected by single bonds will always be aromatic. This is certainly a bug and I've put it on the list of stuff to fix: https://github.com/rdkit/rdkit/issues/518 Best, -greg > Indeed, ** is canonicalized as [*][*], demonstrating that RDKit does not > in general require wildcards to be aromatic. (Else I'd have expected some > sort of error message rejecting the input.) > > Though some other SMILES implementations do, I believe, make the same > assumption, others do not, and again, I do not think it is justified. > > Thanks, > -P. > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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