Improved documentation and testing of align_rmsd

[aarongarrison]

When verbose=True, prints out the initial alignments of the mol3Ds and the improved alignments found after reordering and realignment.

[codecov]

Codecov Report

Attention: Patch coverage is 20.68966% with 23 lines in your changes missing coverage. Please review.

Project coverage is 37.38%. Comparing base (e9b1d7b) to head (60c89ca).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
molSimplify/Scripts/rmsd.py	20.68%	23 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #268      +/-   ##
==========================================
- Coverage   37.40%   37.38%   -0.03%     
==========================================
  Files          89       89              
  Lines       29827    29854      +27     
==========================================
+ Hits        11158    11162       +4     
- Misses      18669    18692      +23     

Flag	Coverage Δ
unittests	37.38% <20.68%> (-0.03%)	⬇️

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[jwtoney]

yuh