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Do not lookup bonds for hetero residues

#820Merged
Comparing
Emrys-Merlin:disable_hetatm_bond_lookup
(
81dab9a
) with
main
(
a541322
)
CodSpeed Performance Gauge
0%
Untouched
59

Benchmarks

Passed

benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]
CodSpeed Performance Gauge
+1%
152.7 µs150.8 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
+1%
13 ms12.9 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 ms9.5 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]
CodSpeed Performance Gauge
0%
39.9 ms39.8 ms
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]
CodSpeed Performance Gauge
0%
2.4 ms2.4 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[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
10.3 ms10.2 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]
CodSpeed Performance Gauge
0%
201.4 ms201.1 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]
CodSpeed Performance Gauge
0%
118.6 ms118.5 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]
CodSpeed Performance Gauge
0%
312.4 ms312 ms
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]
CodSpeed Performance Gauge
0%
319.2 ms318.8 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]
CodSpeed Performance Gauge
0%
39 ms38.9 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]
CodSpeed Performance Gauge
0%
324.5 ms324.2 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]
CodSpeed Performance Gauge
0%
59.7 ms59.7 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]
CodSpeed Performance Gauge
0%
493.2 µs492.8 µs
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]
CodSpeed Performance Gauge
0%
462.2 µs461.8 µs
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_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_lddt[False-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]
CodSpeed Performance Gauge
0%
228.9 ms228.8 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]
CodSpeed Performance Gauge
0%
13.2 ms13.2 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]
CodSpeed Performance Gauge
0%
883.3 ms883 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_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
542.1 µs541.9 µs
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]
CodSpeed Performance Gauge
0%
126.1 ms126 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
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%
38.8 ms38.8 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_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_lddt[True-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
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[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]
CodSpeed Performance Gauge
0%
104.2 ms104.2 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[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
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_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%
17.2 ms17.2 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_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]
CodSpeed Performance Gauge
0%
12.6 ms12.6 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress
CodSpeed Performance Gauge
0%
675.2 ms675.4 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_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
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%
7.3 ms7.4 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]
CodSpeed Performance Gauge
0%
24.1 ms24.1 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%
459.6 µs460.3 µs
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]
CodSpeed Performance Gauge
0%
106.9 ms107.1 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]
CodSpeed Performance Gauge
0%
128 ms128.2 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
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]
CodSpeed Performance Gauge
0%
106.9 ms107.2 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_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]
CodSpeed Performance Gauge
0%
83.9 ms84.1 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]
CodSpeed Performance Gauge
0%
8.9 ms8.9 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%
541.1 µs542.7 µs
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]
CodSpeed Performance Gauge
0%
29.6 ms29.7 ms
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%
537.3 µs539.6 µs
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
573.3 µs575.9 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
-1%
620.8 µs624 µs
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
-1%
185.4 µs187.2 µs

Commits

Click on a commit to change the comparison range
Base
main
a541322
0%
Build non-hetero bond dict for pdbs
81dab9a
2 months ago
by Emrys-Merlin
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