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Fix PanicException for single residues in connect_inter_residue()#882

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padix-key wants to merge 1 commit intobiotite-dev:rustfrom
padix-key:rust-connect-fix
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Fix PanicException for single residues in connect_inter_residue()#882
padix-key wants to merge 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 54.34%

⚠️ 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

⚡ 21 improved benchmarks
❌ 3 regressed benchmarks
✅ 63 untouched benchmarks
🆕 3 new benchmarks
⏩ 11 skipped benchmarks1

⚠️ Please fix the performance issues or acknowledge them on CodSpeed.

Performance Changes

Benchmark BASE HEAD Efficiency
benchmark_connect[connect_via_distances] 26.1 ms 2.6 ms ×10
benchmark_concatenate 317.1 µs 206.8 µs +53.35%
benchmark_conversion[as_graph] 8.7 ms 11.9 ms -26.95%
benchmark_find_connected 304.4 µs 465.9 µs -34.67%
benchmark_connect[connect_via_residue_names] 50.9 ms 4.4 ms ×12
benchmark_bond_list_creation 813.9 µs 269.2 µs ×3
benchmark_conversion[bond_type_matrix] 1.4 ms 1.3 ms +10.04%
benchmark_find_rotatable_bonds 43.9 ms 96.2 ms -54.34%
benchmark_conversion[get_all_bonds] 180.2 µs 149.8 µs +20.26%
benchmark_get_all_bonds 181.9 µs 151.3 µs +20.18%
benchmark_get_bonds 15.3 ms 7.3 ms ×2.1
benchmark_partial_charges 729.7 µs 142.7 µs ×5.1
🆕 benchmark_cell_list_compute_contacts[PAIRS] N/A 17.9 ms N/A
🆕 benchmark_cell_list_compute_contacts[MASK] N/A 19.7 ms N/A
🆕 benchmark_cell_list_compute_contacts[MAPPING] N/A 18 ms N/A
benchmark_get_coord 4,235.8 µs 587.2 µs ×7.2
benchmark_get_remark 758.2 µs 172.4 µs ×4.4
benchmark_cell_list_creation 942.1 µs 337.3 µs ×2.8
benchmark_set_structure 34.2 ms 11.5 ms ×3
benchmark_get_structure_with_bonds 77.6 ms 9.2 ms ×8.4
... ... ... ... ...

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


Comparing padix-key:rust-connect-fix (cfcdd50) with main (00d5b98)2

Open in CodSpeed

Footnotes

  1. 11 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports.

  2. No successful run was found on rust (bd495d4) during the generation of this report, so main (00d5b98) was used instead as the comparison base. There might be some changes unrelated to this pull request in this report.

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