Implement BondList and connection functionalities in Rust

[padix-key]

No description provided.

[codspeed-hq]

Merging this PR will improve performance by ×2.3

⚡ 3 improved benchmarks
✅ 60 untouched benchmarks
🆕 27 new benchmarks

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
🆕	benchmark_set_structure_with_bonds	N/A	11.7 ms	N/A
🆕	benchmark_set_structure	N/A	11.6 ms	N/A
🆕	benchmark_find_connected	N/A	467.5 µs	N/A
🆕	benchmark_find_rotatable_bonds	N/A	96.3 ms	N/A
🆕	benchmark_conversion[get_all_bonds]	N/A	149.7 µs	N/A
⚡	benchmark_get_structure[bcif-True]	81.5 ms	34.7 ms	×2.3
🆕	benchmark_get_bonds	N/A	7.4 ms	N/A
🆕	benchmark_get_all_bonds	N/A	151.4 µs	N/A
🆕	benchmark_cell_list_compute_contacts[MAPPING]	N/A	16.7 ms	N/A
🆕	benchmark_cell_list_compute_contacts[MASK]	N/A	19.5 ms	N/A
🆕	benchmark_cell_list_creation	N/A	339.3 µs	N/A
🆕	benchmark_cell_list_compute_contacts[PAIRS]	N/A	16.6 ms	N/A
🆕	benchmark_partial_charges	N/A	708.9 µs	N/A
⚡	benchmark_lddt[False-all]	227.1 ms	205.1 ms	+10.76%
🆕	benchmark_sasa	N/A	233.4 ms	N/A
🆕	benchmark_get_remark	N/A	171.5 µs	N/A
🆕	benchmark_get_structure	N/A	4 ms	N/A
🆕	benchmark_get_coord	N/A	585.5 µs	N/A
🆕	benchmark_read	N/A	2.1 ms	N/A
🆕	benchmark_get_structure_with_bonds	N/A	9.2 ms	N/A
...	...	...	...	...

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 (f26d0b5) 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. ↩