feat(algo): support guessing atom/bond properties from geometry

[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 Detection of atom/bonds from molecular geometry #180.

---

[codecov]

Codecov Report

Attention: 256 lines in your changes are missing coverage. Please review.

Comparison is base (5af7e78) 95.67% compared to head (f34a9a2) 90.85%.
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #189      +/-   ##
==========================================
- Coverage   95.67%   90.85%   -4.82%     
==========================================
  Files          13       17       +4     
  Lines        2889     4188    +1299     
==========================================
+ Hits         2764     3805    +1041     
- Misses        125      383     +258     

Files	Coverage Δ
include/nuri/algo/rings.h	100.00% <100.00%> (ø)
include/nuri/core/element.h	100.00% <100.00%> (ø)
include/nuri/eigen_config.h	100.00% <100.00%> (ø)
src/algo/rings.cpp	95.27% <100.00%> (ø)
src/core/element.cpp	100.00% <100.00%> (ø)
src/fmt/mol2.cpp	91.66% <100.00%> (+0.09%)	⬆️
src/fmt/smiles.cpp	96.00% <100.00%> (+0.06%)	⬆️
include/nuri/core/geometry.h	98.43% <98.38%> (-1.57%)	⬇️
include/nuri/utils.h	94.32% <98.18%> (+0.73%)	⬆️
include/nuri/core/graph.h	97.47% <93.10%> (-0.23%)	⬇️
... and 4 more