Avatar for the biotite-dev user
biotite-dev
biotite
BlogDocsChangelog

Add `dihedral_side_chain()`

#827Merged
Comparing
padix-key:chi-dihedrals
(
830fc43
) with
main
(
6268d59
)
CodSpeed Performance Gauge
+35%
Improvements
3
Untouched
56

Benchmarks

Improved

benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]
CodSpeed Performance Gauge
+35%
8.9 ms6.5 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]
CodSpeed Performance Gauge
+27%
13.1 ms10.3 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]
CodSpeed Performance Gauge
+21%
39.4 ms32.5 ms

Passed

benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]
CodSpeed Performance Gauge
+1%
107.9 ms107.2 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]
CodSpeed Performance Gauge
+1%
119.2 ms118.5 ms
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]
CodSpeed Performance Gauge
+1%
228.1 ms226.8 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]
CodSpeed Performance Gauge
0%
126.2 ms125.9 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]
CodSpeed Performance Gauge
0%
19.6 ms19.6 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]
CodSpeed Performance Gauge
0%
202.1 ms201.8 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]
CodSpeed Performance Gauge
0%
38.9 ms38.8 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]
CodSpeed Performance Gauge
0%
83.9 ms83.8 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]
CodSpeed Performance Gauge
0%
13.3 ms13.3 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[11*11*1*1***111]
CodSpeed Performance Gauge
0%
185.5 µs185.4 µs
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]
CodSpeed Performance Gauge
0%
319.9 ms319.7 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]
CodSpeed Performance Gauge
0%
104.7 ms104.6 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]
CodSpeed Performance Gauge
0%
325.3 ms325.1 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]
CodSpeed Performance Gauge
0%
313.9 ms313.7 ms
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_without_outliers]
CodSpeed Performance Gauge
0%
17.3 ms17.3 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
13 ms13 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]
CodSpeed Performance Gauge
0%
38.9 ms38.9 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]
CodSpeed Performance Gauge
0%
882.4 ms882.2 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)]
CodSpeed Performance Gauge
0%
9.3 ms9.3 ms
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]
CodSpeed Performance Gauge
0%
59.8 ms59.8 ms
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[11*11*1*1***111]
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]
CodSpeed Performance Gauge
0%
24.1 ms24.1 ms
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]
CodSpeed Performance Gauge
0%
12.4 ms12.4 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
9.3 ms9.3 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]
CodSpeed Performance Gauge
0%
13.4 ms13.4 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
10.3 ms10.3 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]
CodSpeed Performance Gauge
0%
15.1 ms15.1 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]
CodSpeed Performance Gauge
0%
12.4 ms12.4 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]
CodSpeed Performance Gauge
0%
29.6 ms29.6 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]
CodSpeed Performance Gauge
0%
2 s2 s
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)]
CodSpeed Performance Gauge
0%
14.2 ms14.2 ms
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]
CodSpeed Performance Gauge
0%
12.6 ms12.7 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]
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]
CodSpeed Performance Gauge
0%
106.9 ms107 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
542.2 µs542.4 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]
CodSpeed Performance Gauge
0%
17.3 ms17.3 ms
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]
CodSpeed Performance Gauge
0%
541.2 µs541.5 µs
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress
CodSpeed Performance Gauge
0%
675.1 ms675.6 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)]
CodSpeed Performance Gauge
0%
10.3 ms10.3 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-11*11*1*1***111]
CodSpeed Performance Gauge
0%
14.9 ms14.9 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]
CodSpeed Performance Gauge
0%
7.8 ms7.8 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]
CodSpeed Performance Gauge
0%
459.3 µs459.8 µs
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
573.8 µs574.8 µs
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]
CodSpeed Performance Gauge
0%
537.4 µs538.3 µs
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]
CodSpeed Performance Gauge
0%
128.1 ms128.3 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
9.5 ms9.6 ms
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]
CodSpeed Performance Gauge
0%
2.4 ms2.5 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]
CodSpeed Performance Gauge
0%
462.1 µs463.2 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]
CodSpeed Performance Gauge
0%
620.9 µs622.4 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]
CodSpeed Performance Gauge
0%
12.9 ms12.9 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]
CodSpeed Performance Gauge
0%
493 µs495.4 µs
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]
CodSpeed Performance Gauge
-2%
150.6 µs153.5 µs

Commits

Click on a commit to change the comparison range
Base
main
6268d59
+35.48%
Add residue level functionality to get atom names per residue
830fc43
10 days ago
by padix-key
© 2025 CodSpeed Technology
Home Terms Privacy Docs