Customised Axes Argument
Problem / Motivation
Currently, the customised_axes argument gives the principal axes if False and the axes calculated from the topology if True. At the moment, this obscures the new customised axes for residue level rotation and UA level translation.
Proposed Solution
This argument can become a string instead of a boolean, having the options 'principal', 'topology', and 'custom'/'coordinate-based'? (we should discuss possible names that would be clearer)
Alternatives Considered
A topology version of the residue rotation/UA translation axes can be implemented, making the topology axes the same as the new custom axes. They do however, employ a significant number of MDAnalysis selections. The atoms in the selections stay the same in each frame but their positions do not.
Expected Impact
The more robust residue rotation/UA translation axes are easily accessible. We will explain in the documentation what each of the arguments mean and which is recommended for different systems.
Customised Axes Argument
Problem / Motivation
Currently, the customised_axes argument gives the principal axes if False and the axes calculated from the topology if True. At the moment, this obscures the new customised axes for residue level rotation and UA level translation.
Proposed Solution
This argument can become a string instead of a boolean, having the options 'principal', 'topology', and 'custom'/'coordinate-based'? (we should discuss possible names that would be clearer)
Alternatives Considered
A topology version of the residue rotation/UA translation axes can be implemented, making the topology axes the same as the new custom axes. They do however, employ a significant number of MDAnalysis selections. The atoms in the selections stay the same in each frame but their positions do not.
Expected Impact
The more robust residue rotation/UA translation axes are easily accessible. We will explain in the documentation what each of the arguments mean and which is recommended for different systems.