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fix: speedup rcsb fetch of bcif files

#852Merged
Comparing
danielkovtun:optimize-rcsb-bcif-fetch
(
9caf813
) with
main
(
5d1e30a
)
CodSpeed Performance Gauge
0%
Untouched
63

Benchmarks

Passed

benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
104 ms103.5 ms
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
0%
184.9 ms184 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13 ms12.9 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
127.8 ms127.4 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
8.1 ms8 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
200 ms199.4 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
147.5 µs147.2 µs
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
457.7 µs457 µs
benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
540.2 µs539.4 µs
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
81.5 ms81.4 ms
benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.9 ms12.9 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
110.5 ms110.3 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
32.3 ms32.2 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py
CodSpeed Performance Gauge
0%
6.9 ms6.9 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
29.9 ms29.9 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
18.5 ms18.4 ms
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
10.2 ms10.2 ms
benchmark_get_assembly
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
663.9 ms663.6 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.1 ms9.1 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
698.1 ms697.8 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
311 ms310.9 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.3 ms12.3 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
490.3 µs490.2 µs
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
324.1 ms324 ms
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
318.8 ms318.7 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
39.1 ms39.1 ms
benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
14.5 ms14.5 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
458.5 µs458.4 µs
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
2.5 ms2.5 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
111.7 ms111.7 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
17.6 ms17.6 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
15.2 ms15.2 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
15.1 ms15.1 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
17.3 ms17.3 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
884.3 ms884.3 ms
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
225.7 ms225.7 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13.2 ms13.2 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py
CodSpeed Performance Gauge
0%
9.9 ms10 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
10.1 ms10.1 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
38.9 ms38.9 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.3 ms12.3 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13.3 ms13.3 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.2 ms9.2 ms
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.6 ms12.6 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
124.1 ms124.1 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
540.3 µs540.8 µs
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
625.2 µs625.7 µs
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.5 ms9.5 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
58.5 ms58.6 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
540.2 µs540.8 µs
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
28.2 ms28.2 ms
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
105.4 ms105.5 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
184.7 µs184.9 µs
benchmark_get_a3m_alignments
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
0%
573 ms574.3 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
573.3 µs575.2 µs
benchmark_get_sequences[fasta_path1-ProteinSequence]
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
0%
8.7 ms8.8 ms

Commits

Click on a commit to change the comparison range
Base
main
5d1e30a
+0.02%
fix: speedup rcsb fetch of bcif files which was previously slow when accessing response.text
0b540ec
4 days ago
+0.01%
fix: still need to check for error codes if content-type is text or html; bcif uses application/octet-stream
9caf813
4 days ago
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