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feat: allow setting the `label_entity_id` from the AtomArray, if annotated

#732
Comparing
Croydon-Brixton:feat/allow_setting_entity_id
(
68e593a
) with
main
(
e76eb24
)
CodSpeed Performance Gauge
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Improvements
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Benchmarks

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test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]
CodSpeed Performance Gauge
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38.7 ms
36.7 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]
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+1%
195 µs
192.2 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 µs
183.6 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%
13.8 ms
13.7 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]
CodSpeed Performance Gauge
+1%
496.5 µs
493.4 µs
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
+1%
13.8 ms
13.7 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]
CodSpeed Performance Gauge
+1%
460.3 µs
457.5 µs
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%
38.7 ms
38.5 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
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455.8 µs
454 µs
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]
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170.1 ms
169.4 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]
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benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
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622 µs
620.9 µs
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]
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93.1 ms
93 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]
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98.5 ms
98.4 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]
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19.6 ms
19.6 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]
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583 µs
582.4 µs
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]
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15.2 ms
15.2 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]
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13.5 ms
13.5 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
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15.8 ms
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benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]
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benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
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9.7 ms
9.7 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]
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51.7 ms
51.7 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
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13.3 ms
13.3 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
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7.2 ms
7.2 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
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12.2 ms
12.2 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]
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75.2 ms
75.3 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
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546.3 µs
546.3 µs
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
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2.2 s
2.2 s
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
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7.2 ms
7.2 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]
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2.2 s
2.2 s
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
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8.9 ms
8.9 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]
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74.6 ms
74.6 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]
CodSpeed Performance Gauge
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11.3 ms
11.3 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]
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101.4 ms
101.4 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]
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143.5 ms
143.6 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]
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12.1 ms
12.1 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
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9.7 ms
9.7 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
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11.3 ms
11.3 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
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8.8 ms
8.8 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
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8.9 ms
8.9 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]
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84 ms
84 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress
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578.7 ms
579.1 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]
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106.8 ms
106.9 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]
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10.6 ms
10.6 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
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547.1 µs
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benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]
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52.2 ms
52.4 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
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15.1 ms
15.3 ms

Commits

Click on a commit to change the comparison range
Base
main
e76eb24
0%
feat: allow setting the `label_entity_id` in the cif from the atom array, if it is annotated. This is a standard category that comes with CIF files (https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_entity_id.html)
68e593a
2 days ago
by Croydon-Brixton
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