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schrodinger / coordgenlibs

Schrodinger-developed 2D Coordinate Generation
BSD 3-Clause "New" or "Revised" License
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Poor result for constrained coord generation in rapamycin derivative. #110

Open DavidACosgrove opened 2 years ago

DavidACosgrove commented 2 years ago

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: https://github.com/rdkit/rdkit/discussions/4994#discussioncomment-2127071. 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 commented 2 years ago

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.