Implement BondList and connection functionalities in Rust

[padix-key]

No description provided.

[codspeed-hq]

Merging this PR will improve performance by ×2.4

⚠️ Different runtime environments detected

Some benchmarks with significant performance changes were compared across different runtime environments,
which may affect the accuracy of the results.

Open the report in CodSpeed to investigate

⚡ 2 improved benchmarks
✅ 61 untouched benchmarks
🆕 27 new benchmarks

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
🆕	benchmark_conversion[get_all_bonds]	N/A	149.4 µs	N/A
🆕	benchmark_find_connected	N/A	466.8 µs	N/A
🆕	benchmark_find_rotatable_bonds	N/A	96.4 ms	N/A
🆕	benchmark_set_structure	N/A	11.5 ms	N/A
🆕	benchmark_get_bonds	N/A	7.3 ms	N/A
🆕	benchmark_get_all_bonds	N/A	150.5 µs	N/A
🆕	benchmark_cell_list_compute_contacts[MAPPING]	N/A	16.5 ms	N/A
🆕	benchmark_cell_list_compute_contacts[MASK]	N/A	19.2 ms	N/A
🆕	benchmark_cell_list_compute_contacts[PAIRS]	N/A	16.4 ms	N/A
🆕	benchmark_partial_charges	N/A	709.8 µs	N/A
⚡	benchmark_get_structure[bcif-True]	81.5 ms	34.6 ms	×2.4
🆕	benchmark_sasa	N/A	233.5 ms	N/A
🆕	benchmark_set_structure_with_bonds	N/A	11.8 ms	N/A
🆕	benchmark_get_structure_with_bonds	N/A	9.2 ms	N/A
🆕	benchmark_get_remark	N/A	171.4 µs	N/A
🆕	benchmark_get_structure	N/A	4 ms	N/A
🆕	benchmark_cell_list_creation	N/A	337 µs	N/A
🆕	benchmark_read	N/A	2.1 ms	N/A
🆕	benchmark_get_coord	N/A	585 µs	N/A
⚡	benchmark_get_structure[cif-True]	124.5 ms	77.8 ms	+59.94%
...	...	...	...	...

ℹ️ Only the first 20 benchmarks are displayed. Go to the app to view all benchmarks.

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_{Comparing padix-key:rust-bondlist (15cec43) with main (8f348b6)¹}

Footnotes

1. No successful run was found on rust (1845904) during the generation of this report, so main (8f348b6) was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩