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CPU Simulation
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CPU Simulation instrument
to collect CPU performance metrics.
2 days ago
9caf813
danielkovtun:optimize-rcsb-bcif-fetch
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fix: speedup rcsb fetch of bcif files
#852
danielkovtun:optimize-rcsb-bcif-fetch
2 days ago
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Benchmarks
benchmark_get_assembly
benchmarks/structure/benchmark_pdbx.py
663.6 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
81.4 ms
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
105.5 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
12.3 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
39.1 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
9.2 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
18.4 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
38.9 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
12.3 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
58.6 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
9.1 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
10.1 ms
benchmark_get_a3m_alignments
benchmarks/sequence/benchmark_fasta.py
574.3 ms
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
10.2 ms
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
13.3 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
199.4 ms
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py
184 ms
benchmark_get_sequences[fasta_path1-ProteinSequence]
benchmarks/sequence/benchmark_fasta.py
8.8 ms
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py
2.5 ms
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py
17.3 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
29.9 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
111.7 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
124.1 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py
28.2 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
8 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
13.2 ms
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
625.7 µs
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
9.5 ms
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
457 µs
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
540.8 µs
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py
6.9 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py
10 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
575.2 µs
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
184.9 µs
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py
32.2 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py
147.2 µs
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
12.6 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
458.4 µs
benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
14.5 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
540.8 µs
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
103.5 ms
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
17.6 ms
benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
12.9 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
127.4 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
539.4 µs
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py
310.9 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
490.2 µs
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py
884.3 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
12.9 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
15.2 ms
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py
318.7 ms
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py
1.9 s
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
15.1 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py
2 s
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py
324 ms
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py
225.7 ms
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py
1.9 s
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
2 s
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py
1.9 s
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
110.3 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
7.4 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
7.4 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py
697.8 ms
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