fix(structure): reject atom-to-self bonds in BondList and chem_comp_bond writer
#884Comparing
haoyu-haoyu:fix/bondlist-no-self-bond
(95eb8e4
) withmain
(2e5ef85
)0%
- Untouched
- 98
Benchmarks
98 total
benchmark_get_all_bonds
benchmarks/structure/benchmark_bonds.py+2%
184.8 µs181.9 µs
benchmark_concatenate
benchmarks/structure/benchmark_bonds.py+1%
320.1 µs317.1 µs
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py+1%
7 ms6.9 ms
benchmark_partial_charges
benchmarks/structure/benchmark_charges.py+1%
732.9 µs727.5 µs
benchmark_find_connected
benchmarks/structure/benchmark_bonds.py+1%
307.3 µs305.5 µs
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py0%
17.4 ms17.4 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py0%
200.2 ms199.6 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py0%
39.1 ms39 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
39 ms38.9 ms
benchmark_conversion[as_set]
benchmarks/structure/benchmark_bonds.py0%
862 µs860.1 µs
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py0%
186 µs185.6 µs
benchmark_conversion[get_all_bonds]
benchmarks/structure/benchmark_bonds.py0%
181.1 µs180.8 µs
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py0%
104 ms103.8 ms
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py0%
184.6 ms184.4 ms
benchmark_conversion[bond_type_matrix]
benchmarks/structure/benchmark_bonds.py0%
1.4 ms1.4 ms
benchmark_set_structure
benchmarks/structure/benchmark_pdb.py0%
34.3 ms34.2 ms
benchmark_create_kmers
benchmarks/sequence/align/benchmark_kmer.py0%
233.1 µs232.9 µs
benchmark_set_structure_with_bonds
benchmarks/structure/benchmark_pdb.py0%
34.2 ms34.2 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py0%
15.2 ms15.2 ms
benchmark_conversion[as_array]
benchmarks/structure/benchmark_bonds.py0%
116.1 µs116 µs
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py0%
7.4 ms7.4 ms
benchmark_align_pairwise[align_banded]
benchmarks/sequence/align/benchmark_pairwise.py0%
28.7 ms28.7 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py0%
9.5 ms9.5 ms
benchmark_cell_list_compute_contacts
benchmarks/structure/benchmark_celllist.py0%
11.6 ms11.6 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py0%
312.2 ms312.1 ms
Commits
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main
2e5ef85
-0.07%
fix(structure): reject atom-to-self bonds in BondList and chem_comp_bond writer
95eb8e4
6 days ago
by haoyu-haoyu