Add custom Topology

[SimonBoothroyd]

Description

This PR adds a new Topology object as a replacement for the currently used parmed.Structure. The parmed.Structure is not really maintained any longer, and somewhat limited in terms of flexibility and features.

The new Topology should be seen as basically a modernisation of the OpenMM topology, with atom selection features similar to mdtraj, pymol, etc.

Status

• Ready to go

[codecov]

Codecov Report

Attention: Patch coverage is 95.99332% with 24 lines in your changes missing coverage. Please review.

Project coverage is 95.68%. Comparing base (4023514) to head (512367e).

Files with missing lines	Patch %	Lines
femto/top/_top.py	95.07%	19 Missing ⚠️
femto/top/_sel.py	97.44%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #26      +/-   ##
==========================================
+ Coverage   95.62%   95.68%   +0.06%     
==========================================
  Files          46       51       +5     
  Lines        3039     3638     +599     
==========================================
+ Hits         2906     3481     +575     
- Misses        133      157      +24     

Flag	Coverage Δ
unittests	95.68% <95.99%> (+0.06%)	⬆️

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[SimonBoothroyd]

closed in favour of a standalone package, mdtop.