Remove hydrogens when mutating

[ayushkarnawat]

Currently, we keep all the Hs when mutating a 3D structure. Although they are (somewhat) useful, at times they add too much complexity into the 3D structure, especially when ONLY the "core" backbone of each amino acid is needed.

We should allow the user to specify if they want to add (or remove) the Hs from the 3D molecular structure. This will (a) allow for an backbone only 3D representation, and (b) result in faster computation of features since we don't have to worry about the Hs.