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Add 3di encoding to `biotite.structure`

#665Merged
Comparing
althonos:feat-3di
(
80236c2
) with
main
(
72226ca
)
CodSpeed Performance Gauge
0%
Untouched
45

Benchmarks

45 total
benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
13.1 ms12.9 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
186.7 µs184.9 µs
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
538.5 µs535.9 µs
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
472.5 µs470.5 µs
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
494.6 µs492.6 µs
benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
554.3 µs552.1 µs
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
626.3 µs623.9 µs
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
474.2 µs472.6 µs
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.9 ms9.9 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
107.7 ms107.4 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
86.2 ms86 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
567 ms566 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.8 ms9.8 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13 ms12.9 ms
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13.9 ms13.9 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13.8 ms13.8 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
146.8 ms146.7 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
10.7 ms10.7 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
7.3 ms7.3 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.9 ms12.9 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
11.3 ms11.3 ms
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
17.3 ms17.3 ms
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
10.8 ms10.8 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
580.4 µs580.2 µs
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
40 ms40 ms

Commits

Click on a commit to change the comparison range
Base
main
72226ca
+0.06%
Test structures with missing atoms/residues
80236c2
1 year ago
by padix-key
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