On Mon, Jun 15, 2015 at 6:11 PM, Peter Shenkin <[email protected]> wrote:
> 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. > That's correct.[1] There's not really a right answer when treating molecules with query features as "real" molecules, this is just the convention that the RDKit takes when canonicalizing structures containing dummy atoms. -greg [1] Though, technically, if the * is a [CH-], then the ring would be aromatic again. There's no way to win here. :-)
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