I run into this problem when trying to use prepend_polymer_residue_before_seqpos and I can't understand what it really means and, most importantly, what its cause is and how to prevent it from happening. There's a screenshot of the error in the attached pic.
Assertion `moving_connection.icoor().is_internal() && fixed_connection.icoor().is_internal()` failed
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Post Situation:
It's a little hard to say without more information, but that error is saying that there is something off about the connection points in either the thing you're attaching or the thing you're attaching it to.
What are the residues you're attempting to attach? (That is, what is `new_rsd.name()` and `pose.residue(seqpos).name()` for the residue and seqpos that you're passing to prepend_polymer_residue_before_seqpos() )
The prepend_polymer_residue_before_seqpos is assuming that both the residue you're prepending, and the residue to which you're prepending it are polymeric residues. If either or both are non-polymeric residues, then you might get issues.
The other issue you may run into is if the residue you're prepending to is annotated as a chain terminus. In this case, the termini to which you're prepending isn't considered to be "polymeric", and the function may fail. -- One thing to try is to use safely_prepend_polymer_residue_before_seqpos() instead of just prepend_polymer_residue_before_seqpos(). It should catch the termini annotations, and "do the right thing" to fix them up.