feat: add ClustalW .aln format support for sequence alignments
#880Comparing
haoyu-haoyu:feat/clustalw-aln-format
(83b69f9
) withmain
(00d5b98
)0%
- Untouched
- 98
Benchmarks
98 total
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py+2%
18.4 ms18.1 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py+1%
15.2 ms15.1 ms
benchmark_clustering[neighbor_joining]
benchmarks/sequence/benchmark_phylo.py+1%
629.9 µs626.2 µs
benchmark_connect[connect_via_residue_names]
benchmarks/structure/benchmark_bonds.py+1%
50.9 ms50.6 ms
benchmark_align_pairwise[align_local_gapped]
benchmarks/sequence/align/benchmark_pairwise.py0%
76.9 ms76.6 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py0%
30.5 ms30.4 ms
benchmark_get_structure_with_bonds
benchmarks/structure/benchmark_pdb.py0%
77.6 ms77.3 ms
benchmark_partial_charges
benchmarks/structure/benchmark_charges.py0%
729.7 µs727.3 µs
benchmark_bond_list_creation
benchmarks/structure/benchmark_bonds.py0%
813.9 µs811.4 µs
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py0%
2.5 ms2.5 ms
benchmark_find_connected
benchmarks/structure/benchmark_bonds.py0%
304.4 µs303.6 µs
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py0%
8.1 ms8.1 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py0%
81.8 ms81.6 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py0%
124.9 ms124.6 ms
benchmark_conversion[get_all_bonds]
benchmarks/structure/benchmark_bonds.py0%
180.2 µs179.7 µs
benchmark_conversion[as_array]
benchmarks/structure/benchmark_bonds.py0%
116.1 µs115.8 µs
benchmark_cell_list_creation
benchmarks/structure/benchmark_celllist.py0%
942.1 µs940.1 µs
benchmark_get_all_bonds
benchmarks/structure/benchmark_bonds.py0%
181.9 µs181.5 µs
benchmark_connect[connect_via_distances]
benchmarks/structure/benchmark_bonds.py0%
26.1 ms26.1 ms
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py0%
184.6 ms184.2 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py0%
58.7 ms58.6 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py0%
13 ms12.9 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py0%
10 ms10 ms
benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
12.9 ms12.9 ms
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py0%
17.4 ms17.4 ms
Commits
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main
00d5b98
-0.04%
fix: address edge cases in ClustalW format (Codex review findings)
83b69f9
11 days ago
by haoyu-haoyu