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#823
padix-key:issue-553
1 month ago
Benchmarks
benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]14.2 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]13.3 ms
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]17.3 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]12.4 ms
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]228.1 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress674.9 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]325.3 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]118.4 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]313.8 ms
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]12.6 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]9.5 ms
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]319.9 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]59.8 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]882.4 ms
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]1.9 s
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]83.8 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]12.4 ms
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]620.7 µs
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]1.9 s
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]1.9 s
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]150.6 µs
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]201.8 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]128.4 ms
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]13.4 ms
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]107 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]541.1 µs
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]125.9 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]20.2 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]538.7 µs
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]493.6 µs
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]107 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]104.2 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]10.2 ms
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]10.3 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]9.3 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]7.8 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]29.7 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]39.8 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-11*11*1*1***111]14.9 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]542.5 µs
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_without_outliers]17.3 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]7.4 ms
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]460 µs
benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]12.9 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]461.8 µs
test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]7.3 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]574.2 µs
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]2.5 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]24.2 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[11*11*1*1***111]185.5 µs
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]2 s
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]9.3 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]8.9 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-11*11*1*1***111]38.8 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]13.3 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]13 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]15.1 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]38.9 ms
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[11*11*1*1***111]2 s