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_bond_list_creation
benchmarks/structure/benchmark_bonds.py-2%
816.3 µs831.9 µs
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py-1%
2.5 ms2.5 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py0%
8.1 ms8.1 ms
benchmark_get_structure
benchmarks/structure/benchmark_pdb.py0%
20.2 ms20.3 ms
benchmark_clustering[neighbor_joining]
benchmarks/sequence/benchmark_phylo.py0%
623.5 µs626 µs
benchmark_align_pairwise[align_local_gapped]
benchmarks/sequence/align/benchmark_pairwise.py0%
77 ms76.7 ms
benchmark_get_structure_with_bonds
benchmarks/structure/benchmark_pdb.py0%
77.3 ms77.6 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py0%
135 µs135.5 µs
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py0%
492.9 µs491.3 µs
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
185.1 µs185.7 µs
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py0%
124.5 ms124.9 ms
benchmark_get_sequences[fasta_path1-ProteinSequence]
benchmarks/sequence/benchmark_fasta.py0%
8.8 ms8.8 ms
benchmark_conversion[as_graph]
benchmarks/structure/benchmark_bonds.py0%
8.7 ms8.7 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
542.3 µs540.8 µs
benchmark_set_structure_with_bonds
benchmarks/structure/benchmark_pdb.py0%
34.2 ms34.3 ms
benchmark_cell_list_creation
benchmarks/structure/benchmark_celllist.py0%
941.9 µs944 µs
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py0%
58.6 ms58.7 ms
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_read
benchmarks/structure/benchmark_pdb.py0%
3.5 ms3.5 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py0%
30.4 ms30.5 ms
benchmark_encode
benchmarks/sequence/benchmark_alphabet.py0%
183.1 µs183.4 µs
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py0%
28.5 ms28.5 ms
benchmark_set_structure
benchmarks/structure/benchmark_pdb.py0%
34.2 ms34.3 ms
benchmark_get_coord
benchmarks/structure/benchmark_pdb.py0%
4.2 ms4.2 ms
Commits
Click on a commit to change the comparison rangeBase
main
fe75450
-0.07%
fix(structure): reject atom-to-self bonds in BondList and chem_comp_bond writer
95eb8e4
3 months ago
by haoyu-haoyu+0.01%
fix(pdbx): raise BadStructureError on ambiguous (res_name, atom_name)
aeea708
2 months ago
by haoyu-haoyu