I am looking at ../simulate/torsion_angle_monte_carlo/monte_carlo_utilities/torsion.py and noticing a method that "...prepares a group for a flexible isopeptide bond region". This actually seem to be more general, in which case the comment should be updated. Or if it is isopeptide specific, it should be moved to the isopeptide_bond_torsion directory.
The code in this file seems to be a divergence from the methods used originally, which the B-DNA module follows.
I am looking at
../simulate/torsion_angle_monte_carlo/monte_carlo_utilities/torsion.pyand noticing a method that "...prepares a group for a flexible isopeptide bond region". This actually seem to be more general, in which case the comment should be updated. Or if it is isopeptide specific, it should be moved to theisopeptide_bond_torsiondirectory.The code in this file seems to be a divergence from the methods used originally, which the B-DNA module follows.