Poor result for constrained coord generation in rapamycin derivative.

[DavidACosgrove]

Hi,
I am calling CoordGen via RDKit, and have had a problem with constrained generation of coords for a rapamycin analogue using rapamycin as the template. The discussion is here: rdkit/rdkit#4994 (reply in thread). It was suggested that I file a bug report here. I hope the cross-link is a suitable way of doing it. I used the SMARTS string [#6]1(-[#6]2(-[#6](-[#6]-[#6]-[#6](-[#8]-2)-[#6]-[#6](-[#6](-[#6])=[#6]-[#6]=[#6]-[#6]=[#6]-[#6](-[#6])-[#6]-[#6](-[#6](-[#6](-[#6](-[#6](=[#6]-[#6](-[#6](-[#6]-[#6](-[#8]-[#6](-[#6]2-[#7](-[#6]-1=[#8])-[#6]-[#6]-[#6]-[#6]-2)=[#8])-[#6](-[#6])-[#6]-[#6]1-[#6]-[#6]-[#6](-[#6](-[#6]-1)-[#8]-[#6])-[#8])=[#8])-[#6])-[#6])-[#8])-[#8]-[#6])=[#8])-[#6])-[#8]-[#6])-[#6])-[#8])=[#8] as the reference pattern, which is that RDKit returns for the MCS for the two structures.
It's worth saying, I think, that the CoordGen algorithm lays out macrocycles like this way better than any other toolkit I've seen.

[d-b-w]

Thanks for the report, @DavidACosgrove.

There may be something that we should double check in RDKit's invocation of coordgen, but this is most likely an issue strictly on the coordgen side.