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Suggested base runs:

Benchmarks

benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]
214.2 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]
2.2 s
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]
301.5 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]
84 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]
306.9 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]
193.5 µs
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]
12.1 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]
13.5 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
9.7 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]
11.3 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
8.8 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
8.9 ms
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]
1.9 s
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]
51.6 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]
75.3 ms
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]
1.9 s
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]
10.1 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]
101.3 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]
98.5 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]
295.4 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]
19.6 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]
904.6 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]
74.8 ms
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]
1.9 s
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]
169.9 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]
15.2 ms
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]
93.4 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress
578.6 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]
41.3 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]
143.5 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]
495.9 µs
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]
52.2 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]
38.6 ms
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]
7.2 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]
101.7 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[11*11*1*1***111]
183.2 µs
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-11*11*1*1***111]
15 ms
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]
2.7 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]
456 µs
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]
458 µs
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]
10.7 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]
583.7 µs
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]
546.7 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]
13.7 ms
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_without_outliers]
16.5 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]
12.2 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]
38.5 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]
106.9 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]
535.9 µs
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[11*11*1*1***111]
2.2 s
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]
11.3 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]
7.2 ms
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)]
8.9 ms
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)]
13.3 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
547.7 µs
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
620.3 µs
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]
15.8 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]
13.8 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)]
9.7 ms
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