united atom translational axes

[skfegan]

We want the translational axes to be the same as the rotational axes for the unit one level larger. This would have the united atom translational axes being the same as the residue rotational axes. The residue rotational axes are based on the bonds between residues.

Currently, the united atom translational axes are based on the principal axes of the residue.

[skfegan]

Closed by merge #246 using principal axes for translation and rotation at all levels.

[ioanaapapa]

At the moment, we use principal axes at all levels. For bonded residues, such as in a protein, we will likely need to move to bonded axes again to properly capture the motions of the beads with respect to their bonded neighbours.