Issue363 Changes

Note: Issue-363 is a work in progress, nothing is final yet, everything is up for debate!

Issue #363 brings many changes, these are summarised here:

All Groups are no longer subclassed from AtomGroup.

Explanation

Previously, every object except Atom subclassed from AtomGroup. This meant that calling .positions of would give you the positions of the Atoms contained within that group.

Previous class structure:

Atom

AtomGroup  -> Residue
           -> ResidueGroup -> Segment
                           -> SegmentGroup

New class structure:

Group    -> AtomGroup
         -> ResidueGroup
         -> SegmentGroup

Atom
Residue
Segment

Now each object only contains information pertaining to that particular object. A Residue object only yields information about the Residue, to get to the atoms, use Residue.atoms

Why this was changed

Previously everything inheriting from AtomGroup made it unclear at what level of topology a given method or attribute was working on. Ie does ResidueGroup.charges give the charge of the Residues or the Atoms? Also, it was unclear what size a given output would be (see Issue-411)

How to work around this

To access Atom level information from anything that isn't an AtomGroup, use the .atoms level accessor. For example, changing all .positions calls on anything that isn't an AtomGroup to .atoms.positions.