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8 days ago 95eb8e4 haoyu-haoyu:fix/bondlist-no-self-bond pull_requestCompare
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Comparefix(structure): reject atom-to-self bonds in BondList and chem_comp_bond writer
#884
haoyu-haoyu:fix/bondlist-no-self-bond
8 days ago
CPU Simulation
98 total
benchmark_get_sequences[fasta_path1-ProteinSequence]
benchmarks/sequence/benchmark_fasta.py8.8 ms
benchmark_similar_kmers
benchmarks/sequence/align/benchmark_kmer.py318.7 µs
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py9.2 ms
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py184.4 ms
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py2 s
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py15.2 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py15.2 ms
benchmark_get_a3m_alignments
benchmarks/sequence/benchmark_fasta.py577.6 ms
benchmark_clustering[upgma]
benchmarks/sequence/benchmark_phylo.py489.7 µs
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py7.4 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py10 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py6.9 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py7.4 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py38.9 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py2 s
benchmark_bond_list_creation
benchmarks/structure/benchmark_bonds.py830.8 µs
benchmark_align_pairwise[align_banded]
benchmarks/sequence/align/benchmark_pairwise.py28.7 ms
benchmark_align_multiple
benchmarks/sequence/align/benchmark_multiple.py20.2 s
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py10.1 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py12.3 ms
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py13.3 ms
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py17.6 ms
benchmark_create_kmers
benchmarks/sequence/align/benchmark_kmer.py232.9 µs
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py10.2 ms
benchmark_connect[connect_via_distances]
benchmarks/structure/benchmark_bonds.py26.1 ms