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Add example for structure search based on 3Di alphabet(#704)

Comparing
padix-key:structure-search
(
e2be956
) with
main
(
77cf0f6
)
0%
IMPROVEMENTS
0
REGRESSIONS
0
UNTOUCHED
47
NEW
0
DROPPED
0
IGNORED
0

Benchmarks

Passed

test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]
+1%
40.2 ms
39.9 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]
0%
39.9 ms
39.8 ms
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]
0%
13 ms
12.9 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]
0%
113.5 ms
113.1 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]
0%
181.3 ms
180.9 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]
0%
106.9 ms
106.7 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[11*11*1*1***111]
0%
185 µs
184.6 µs
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]
0%
121.5 ms
121.2 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]
0%
154.4 µs
154.2 µs
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]
0%
146.3 ms
146.1 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]
0%
21.7 ms
21.6 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
0%
9.7 ms
9.7 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
0%
9.9 ms
9.9 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]
0%
11.3 ms
11.3 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]
0%
2.1 s
2.1 s
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
0%
624.7 µs
624.3 µs
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]
0%
139.8 ms
139.7 ms
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]
0%
12.8 ms
12.8 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]
0%
17.3 ms
17.3 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]
0%
13.9 ms
13.9 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]
0%
47.1 ms
47.1 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]
0%
534.8 µs
534.6 µs
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]
0%
13.8 ms
13.8 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]
0%
2.1 s
2.1 s
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)]
0%
14.2 ms
14.2 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]
0%
12.9 ms
12.9 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
0%
10.7 ms
10.7 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]
0%
13.2 ms
13.2 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]
0%
491.7 µs
491.7 µs
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]
0%
12.9 ms
12.9 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)]
0%
10.8 ms
10.8 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]
0%
7.3 ms
7.3 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]
0%
578.6 µs
578.9 µs
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]
0%
7.3 ms
7.3 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]
0%
86 ms
86.1 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]
0%
469.9 µs
470.2 µs
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]
0%
84.7 ms
84.8 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]
0%
553.4 µs
554.4 µs
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress
0%
565.6 ms
566.7 ms
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]
0%
77.4 ms
77.5 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]
0%
14.9 ms
14.9 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]
0%
8.8 ms
8.8 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]
0%
472.7 µs
474 µs
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)]
0%
9.9 ms
9.9 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
0%
555.7 µs
557.7 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]
0%
13 ms
13 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]
-1%
14.9 ms
15 ms

Commits

Click on a commit to change the comparison range
base
main
77cf0f6
0%
Add example for structure search based on 3Di alphabet
38cfd55
5 days ago
by padix-key
0%
Fix exception for empty structures
e2be956
3 days ago
by padix-key
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