Definition dihedral angles

[PabloGGaray]

Hi, it may be necessary to incorporate a different dihedral definition for the glycosidic bonds (φ , ψ and ω angles) and χ (chi) angles.

In the case of the glycosidic bonds, it could be useful to have an option for selecting the preferred definition to use (NMR, crystallographic C+1 or crystallographic C-1), you can check the three possible definition in this table (the C+1 crystallographic style is useful for 1-1 bonds).

For the χ angles it's necessary to consider possible substituents, for example if a carbon has a N-acetil as subtituents the current definition used in the function set_chi it is not able to move the χ angle in that carbon (definition of NAc torsions, I have to search further to find a bibliographic reference). In the case of the ω when it behaves like a χ angle (i.e. there is no glycosidic bond 1-6), the definition of ω goes in the opposite direction to the one used in the above mentioned function, this is O5-C5-C6-O6 (definition taken from here [Experimental section - C. Theoretical Calculations], and used here).