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Fix PanicException for single residues in connect_inter_residue()#882

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padix-key merged 1 commit intobiotite-dev:rustfrom
padix-key:rust-connect-fix
Apr 13, 2026
Merged

Fix PanicException for single residues in connect_inter_residue()#882
padix-key merged 1 commit intobiotite-dev:rustfrom
padix-key:rust-connect-fix

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codspeed-hq bot commented Apr 8, 2026

Merging this PR will degrade performance by 54.29%

⚡ 21 improved benchmarks
❌ 3 (👁 3) regressed benchmarks
✅ 73 untouched benchmarks
🆕 3 new benchmarks
⏩ 1 skipped benchmark1

Performance Changes

Benchmark BASE HEAD Efficiency
benchmark_bond_list_creation 815.7 µs 269.3 µs ×3
benchmark_concatenate 320.1 µs 206.4 µs +55.08%
benchmark_connect[connect_via_distances] 26.1 ms 2.6 ms ×10
benchmark_encode 183.1 µs 156.5 µs +17.01%
👁 benchmark_conversion[as_graph] 8.7 ms 11.8 ms -26.16%
benchmark_connect[connect_via_residue_names] 50.6 ms 4.3 ms ×12
👁 benchmark_find_rotatable_bonds 43.9 ms 96 ms -54.29%
benchmark_conversion[get_all_bonds] 181.1 µs 149.5 µs +21.15%
benchmark_conversion[bond_type_matrix] 1.4 ms 1.3 ms +10.17%
benchmark_get_all_bonds 184.8 µs 150.5 µs +22.79%
benchmark_partial_charges 732.9 µs 142.7 µs ×5.1
benchmark_cell_list_creation 941.6 µs 336.9 µs ×2.8
🆕 benchmark_cell_list_compute_contacts[MAPPING] N/A 18.6 ms N/A
benchmark_get_bonds 15.3 ms 7.3 ms ×2.1
👁 benchmark_find_connected 307.3 µs 459.9 µs -33.18%
🆕 benchmark_cell_list_compute_contacts[PAIRS] N/A 18.5 ms N/A
🆕 benchmark_cell_list_compute_contacts[MASK] N/A 19.7 ms N/A
benchmark_get_structure 20.2 ms 4 ms ×5
benchmark_get_coord 4,234.1 µs 586.6 µs ×7.2
benchmark_get_remark 757.9 µs 171.4 µs ×4.4
... ... ... ... ...

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


Comparing padix-key:rust-connect-fix (9227c51) with main (2e5ef85)2

Open in CodSpeed

Footnotes

  1. 1 benchmark was skipped, so the baseline result was used instead. If it was deleted from the codebase, click here and archive it to remove it from the performance reports.

  2. No successful run was found on rust (d97c654) during the generation of this report, so main (2e5ef85) was used instead as the comparison base. There might be some changes unrelated to this pull request in this report.

@padix-key padix-key merged commit 619b723 into biotite-dev:rust Apr 13, 2026
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