WIP: New topology docs (#1078)

[dotsdl]

Fixes #1078

Changes made in this Pull Request:

• added new topology.rst doc page describing topology system
• small edits to surrounding pages for continuity and consistency

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[richardjgowers]

The existing overview page is a nice page 1 for part 1, maybe with a quick update.

After this maybe the essentials

• creating a Universe (and the two pillars a Universe is built on, Top and Traj) (this is what you've started here imo)
• working with AtomGroups
• AtomGroup selections (already there)
• working with Residues and Segments (and also the levels of different attributes)
• working with the trajectory (traj iteration and quirks of the one frame at a time system)
• coordinate manipulation (introducing distance array and friends)
• the analysis module (idea of prepackaged analysis tools, and how to write your own...)

Then past this point we're into more specific cases

• working with bonds angles torsions
• advanced Universe creation (everything left out of the previous Universe section to keep it light)
• advanced Reader usage (ChainReader, auxs)
• advanced Topology manipulation, (adding Attrs, creating new Attrs, adding/removing Res/Seg)

[dotsdl]

@richardjgowers ? I know I'm slow, but why are we merged now?

[richardjgowers]

I'm making another PR with docs, and I didn't want to cause merge conflicts

[dotsdl]

Ah gotcha. No worries, just saw it.