feat(python/core): add has_bond() interface

[jnooree]

Checklist

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Linked Issues

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• Closes Add "has bond/neighbor" interface #321.

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[codecov]

Codecov Report

Attention: Patch coverage is 80.95238% with 4 lines in your changes missing coverage. Please review.

Project coverage is 90.61%. Comparing base (fbe0d22) to head (bfe9f40).
Report is 8 commits behind head on main.

Files	Patch %	Lines
python/src/nuri/core/molecule.cpp	81.81%	2 Missing ⚠️
python/src/nuri/core/substructure.cpp	80.00%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #322   +/-   ##
=======================================
  Coverage   90.61%   90.61%           
=======================================
  Files          37       37           
  Lines        8762     8784   +22     
=======================================
+ Hits         7940     7960   +20     
- Misses        822      824    +2     

Files	Coverage Δ
python/src/nuri/core/molecule.cpp	89.90% <81.81%> (-0.24%)	⬇️
python/src/nuri/core/substructure.cpp	90.14% <80.00%> (-0.22%)	⬇️

... and 2 files with indirect coverage changes