fix(structure): reject atom-to-self bonds in BondList and chem_comp_bond writer
#884Comparing
haoyu-haoyu:fix/bondlist-no-self-bond
(aeea708
) withmain
(fe75450
)0%
- Untouched
- 98
Benchmarks
98 total
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py0%
8.1 ms8.1 ms
benchmark_align_pairwise[align_local_gapped]
benchmarks/sequence/align/benchmark_pairwise.py0%
77 ms76.7 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py0%
492.9 µs491.3 µs
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
542.3 µs540.8 µs
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py0%
184.7 ms184.4 ms
benchmark_similar_kmers
benchmarks/sequence/align/benchmark_kmer.py0%
318.4 µs317.7 µs
benchmark_find_connected
benchmarks/structure/benchmark_bonds.py0%
303.5 µs303.1 µs
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
623.3 µs622.4 µs
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py0%
2 s2 s
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py0%
199.6 ms199.3 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py0%
39 ms39 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py0%
459.7 µs459.2 µs
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py0%
575.5 µs574.9 µs
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py0%
13 ms13 ms
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py0%
17.3 ms17.3 ms
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
458.6 µs458.4 µs
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py0%
7 ms7 ms
benchmark_get_remark
benchmarks/structure/benchmark_pdb.py0%
758.6 µs758.2 µs
benchmark_conversion[as_array]
benchmarks/structure/benchmark_bonds.py0%
116 µs116 µs
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
38.8 ms38.8 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py0%
311.6 ms311.4 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py0%
323 ms322.9 ms
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py0%
317.7 ms317.5 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py0%
698.5 ms698.3 ms
benchmark_decode
benchmarks/sequence/benchmark_alphabet.py0%
3.4 ms3.4 ms
Commits
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main
fe75450
-0.07%
fix(structure): reject atom-to-self bonds in BondList and chem_comp_bond writer
95eb8e4
1 month ago
by haoyu-haoyu+0.01%
fix(pdbx): raise BadStructureError on ambiguous (res_name, atom_name)
aeea708
28 days ago
by haoyu-haoyu