Add helpers to position and shuffle membrane proteins

[iecheverria]

Random initial configurations can place membrane proteins far from the membrane or in the wrong orientation, which slows sampling under MembraneRestraint.

place_in_membrane: Place rigid bodies with MembraneRestraints in the membrane with the proper orientation.

shuffle_in_membrane: Move rigid bodies in the membrane to random x, y positions, keeping z and orientation fixed. Intended to be called after place_in_membrane.

Add tests for placement and shuffling

[codecov]

Codecov Report

❌ Patch coverage is 77.77778% with 20 lines in your changes missing coverage. Please review.
✅ Project coverage is 64.77%. Comparing base (47dc4a3) to head (3b6019b).
⚠️ Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
pyext/src/tools.py	83.07%	5 Missing and 6 partials ⚠️
pyext/src/restraints/basic.py	64.00%	6 Missing and 3 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #273      +/-   ##
===========================================
+ Coverage    63.57%   64.77%   +1.19%     
===========================================
  Files           31       31              
  Lines        13267    13921     +654     
  Branches      2421     2700     +279     
===========================================
+ Hits          8435     9017     +582     
- Misses        4341     4402      +61     
- Partials       491      502      +11     

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