On Mon, Jun 15, 2015 at 9:54 AM, Greg Landrum <[email protected]> wrote: > > 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. >> > ... > > This is certainly a bug and I've put it on the list of stuff to fix: > https://github.com/rdkit/rdkit/issues/518 > > Thanks much, Greg. That is very helpful.
Pursuing another remark you made, RDKit canonicalizes C1=C*C=C1 as [*]1cccc1. This may also be unwarranted, because the wildcard could be another C, in which case the structure would not be aromatic. -P.
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