I'm trying to determine the bond lengths between consecutive residues in a Pose/Conformation, to determine whether they are actually close enough to be bonded, or if there is a gap between the residues that needs to be closed or filled in. Is there a straightforward way to do this?
There's actually a bit of code in Rosetta which does something similar already. It's not encapsulated in an easy-to-use form, but you can potentially crib from it.
This is the code in PoseFromSFRBuilder::build_initial_pose() which handles the `-missing_density_to_jump`. The core of this is as follows:
(Yes, that 3.0 is hard-coded)
Alternatively, you could run with the -missing_density_to_jump option on, and look for residues with the UPPERTERM_TRUNC_VARIANT and LOWERTERM_TRUNC_VARIANT.