feat(core): improve erase_hydrogens behavior

[jnooree]

Checklist

• Have you followed the guidelines for contributing?
• Have you checked that there aren't other open pull requests for the same issue?
• Have you linked the issue(s) you are working on?

If the change is related to the source code, tests, or build environments, please also check the following:

• Does ./scripts/run_clang_tools.sh pass without any warnings?
• Have you built the project locally without any warnings and errors?
• Does all tests (if new tests are added, including the new ones) pass?

If you added new feature(s), then also check the following:

• Did you also add corresponding tests?

Linked Issues

Link the tracking issue(s) of this PR, with the auto-close keywords here:

• Closes erase_hydrogens remove nontrivial hydrogens #278.

---

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.56%. Comparing base (9ba077a) to head (c685bc6).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #280   +/-   ##
=======================================
  Coverage   90.55%   90.56%           
=======================================
  Files          37       37           
  Lines        8421     8424    +3     
=======================================
+ Hits         7626     7629    +3     
  Misses        795      795           

Files	Coverage Δ
include/nuri/core/molecule.h	85.62% <ø> (ø)
python/src/nuri/core/molecule.cpp	90.35% <ø> (ø)
src/core/molecule.cpp	94.63% <100.00%> (+0.02%)	⬆️