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fix: allow ccd residues with missing coords

#730
Comparing
davegrays:fix/allow-all-ccd-residues
(
4e931fb
) with
main
(
226f2b4
)
CodSpeed Performance Gauge
0%
Improvements
0
Regressions
0
Untouched
59
New
0
Dropped
0
Ignored
0

Benchmarks

Passed

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%
620.3 µs
614.6 µs
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]
CodSpeed Performance Gauge
+1%
214.2 ms
212.5 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]
CodSpeed Performance Gauge
+1%
495.9 µs
492.9 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
+1%
535.9 µs
533.1 µs
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
583.7 µs
581 µs
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]
CodSpeed Performance Gauge
0%
93.4 ms
93.1 ms
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%
13.7 ms
13.7 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%
547.7 µs
546.3 µs
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%
546.7 µs
545.4 µs
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]
CodSpeed Performance Gauge
0%
10.7 ms
10.6 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]
CodSpeed Performance Gauge
0%
106.9 ms
106.7 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%
15 ms
14.9 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]
CodSpeed Performance Gauge
0%
13.5 ms
13.5 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]
CodSpeed Performance Gauge
0%
38.6 ms
38.6 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]
CodSpeed Performance Gauge
0%
74.8 ms
74.6 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%
456 µs
455.2 µs
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
13.8 ms
13.8 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]
CodSpeed Performance Gauge
0%
19.6 ms
19.6 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%
13.3 ms
13.3 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%
12.2 ms
12.2 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]
CodSpeed Performance Gauge
0%
75.3 ms
75.3 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]
CodSpeed Performance Gauge
0%
169.9 ms
169.8 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%
7.2 ms
7.2 ms
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]
CodSpeed Performance Gauge
0%
295.4 ms
295.2 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%
11.3 ms
11.3 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%
7.2 ms
7.2 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]
CodSpeed Performance Gauge
0%
51.6 ms
51.6 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%
8.8 ms
8.8 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]
CodSpeed Performance Gauge
0%
904.6 ms
904.3 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress
CodSpeed Performance Gauge
0%
578.6 ms
578.5 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]
CodSpeed Performance Gauge
0%
101.7 ms
101.7 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]
CodSpeed Performance Gauge
0%
98.5 ms
98.5 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%
8.9 ms
8.9 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%
15.8 ms
15.8 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]
CodSpeed Performance Gauge
0%
12.1 ms
12.1 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]
CodSpeed Performance Gauge
0%
84 ms
84 ms
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]
CodSpeed Performance Gauge
0%
1.9 s
1.9 s
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]
CodSpeed Performance Gauge
0%
1.9 s
1.9 s
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]
CodSpeed Performance Gauge
0%
1.9 s
1.9 s
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]
CodSpeed Performance Gauge
0%
143.5 ms
143.5 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%
11.3 ms
11.3 ms
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_without_outliers]
CodSpeed Performance Gauge
0%
16.5 ms
16.5 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%
9.7 ms
9.7 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%
2.2 s
2.2 s
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]
CodSpeed Performance Gauge
0%
301.5 ms
301.7 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]
CodSpeed Performance Gauge
0%
306.9 ms
307 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%
8.9 ms
8.9 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%
9.7 ms
9.7 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]
CodSpeed Performance Gauge
0%
2.2 s
2.2 s
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]
CodSpeed Performance Gauge
0%
10.1 ms
10.1 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]
CodSpeed Performance Gauge
0%
41.3 ms
41.4 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]
CodSpeed Performance Gauge
0%
52.2 ms
52.3 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]
CodSpeed Performance Gauge
0%
458 µs
458.7 µs
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]
CodSpeed Performance Gauge
0%
15.2 ms
15.2 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%
183.2 µs
183.7 µs
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]
CodSpeed Performance Gauge
0%
2.7 ms
2.7 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]
CodSpeed Performance Gauge
0%
101.3 ms
101.6 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
-1%
38.5 ms
38.7 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]
CodSpeed Performance Gauge
-1%
193.5 µs
195 µs

Commits

Click on a commit to change the comparison range
Base
main
226f2b4
0%
fix formatting
2a7fcbd
11 days ago
by davegrays
0%
Merge pull request #2 from Croydon-Brixton/patch-1 feat(pdbx): expose flag to allow missing coorindates in `get_component`
1b110f4
5 days ago
by davegrays
0%
propagate allow_missing_coord and add test
c519913
1 day ago
by davegrays
0%
future-proof residue info test with missing coord
4e931fb
1 day ago
by davegrays
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