Rachel Walker

@ptosco do you know if these changes fix #3965?

A few of the examples that Greg gave seem to be fixed (no clashes and RMSD between all the mols and the scaffold is < .2), including doc16404: However, doc55715,...

This is interesting! @ZontaNicola, here are the animations (sorry about the mirrored coordinates) Fragment DOF minimization stage: https://user-images.githubusercontent.com/39069546/120018608-40ecdb80-bf9c-11eb-8e7e-be5cd26ce352.mp4 FF Minimization stage: https://user-images.githubusercontent.com/39069546/120018642-5104bb00-bf9c-11eb-9210-4d5084f620df.mp4

Thank you @ptosco, and sorry for the late reply! We are going to try to update RDKit's coordinate generation method to address cases like this.

Thank you @d-b-w and @joseerlang! Closing this issue.