padix-key:unit-cell - Branch - biotite-dev/biotite

Support parsing unit cells

#778

Comparing

padix-key:unit-cell

(

26ff4f8

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main

(

5465b75

)

Improvements: 0

Regressions: 0

Untouched: 59

New: 0

Dropped: 0

Ignored: 0

Benchmarks

Passed

benchmark_kmer_decomposition[11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[11*11*1*1***111]

187.4 µs

186.5 µs

benchmark_lddt[False-atom]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]

297.9 ms

296.8 ms

benchmark_structural_alphabet_methods[to_protein_blocks]

benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]

8.9 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]

38.9 ms

38.8 ms

benchmark_match[KmerTable-11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]

546.9 µs

546.1 µs

benchmark_superimpose[superimpose_without_outliers]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_without_outliers]

16.8 ms

16.7 ms

benchmark_set_structure[cif-True]

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]

129.9 ms

129.7 ms

test_pickle_and_unpickle[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]

39.1 ms

39 ms

benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]

10.4 ms

benchmark_indexing_from_kmer_selection[None-KmerTable]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]

12.5 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)]

10.4 ms

benchmark_get_structure[bcif-False]

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]

21.3 ms

21.2 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]

12.5 ms

benchmark_get_structure[cif-False]

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]

58.5 ms

58.4 ms

benchmark_get_structure[bcif-True]

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]

84.9 ms

84.8 ms

benchmark_lddt[True-residue]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]

1.9 s

benchmark_lddt[True-chain]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]

1.9 s

benchmark_lddt[True-atom]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]

1.9 s

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]

17.4 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]

7.4 ms

benchmark_indexing_from_sequences[None-KmerTable]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]

12.8 ms

benchmark_get_structure[cif-True]

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]

120.6 ms

benchmark_lddt[False-residue]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]

310.2 ms

test_pickle_and_unpickle[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]

7.4 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]

13.5 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)]

14.4 ms

benchmark_match_kmer_selection[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]

470.9 µs

benchmark_serialize_pdbx[cif]

benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]

176.6 ms

benchmark_indexing_from_kmers[None-KmerTable]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]

13.4 ms

benchmark_compress

benchmarks/structure/benchmark_pdbx.py::benchmark_compress

564.9 ms

benchmark_structural_alphabet_methods[to_3di]

benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]

13.3 ms

benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]

9.8 ms

benchmark_score_threshold_rule[None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]

2.1 s

benchmark_score_threshold_rule[11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[11*11*1*1***111]

2 s

benchmark_set_structure[cif-False]

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]

108 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]

469.5 µs

469.6 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)]

9.4 ms

benchmark_lddt[False-all]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]

216.9 ms

217 ms

benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]

9.4 ms

benchmark_match_kmer_selection[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]

553.2 µs

553.5 µs

benchmark_match_table[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]

15.3 ms

benchmark_deserialize_pdbx[cif]

benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]

91.8 ms

91.9 ms

benchmark_deserialize_pdbx[bcif]

benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]

110.2 ms

benchmark_lddt[True-all]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]

907.6 ms

908.4 ms

benchmark_superimpose[superimpose]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]

2.6 ms

benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]

630.1 µs

630.9 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]

550.1 µs

550.8 µs

benchmark_superimpose[superimpose_structural_homologs]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]

40.6 ms

40.7 ms

benchmark_lddt[False-chain]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]

304.9 ms

305.4 ms

benchmark_superimpose[superimpose_homologs]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]

23.8 ms

23.9 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]

12.9 ms

benchmark_match[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]

501.8 µs

502.7 µs

benchmark_kmer_decomposition[None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]

153 µs

153.3 µs

benchmark_set_structure[bcif-True]

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]

29.1 ms

benchmark_match[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]

582.5 µs

583.7 µs

benchmark_serialize_pdbx[bcif]

benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]

84.9 ms

85.1 ms

benchmark_set_structure[bcif-False]

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]

11.1 ms

benchmark_match_table[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]

12.9 ms

13 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]

-4%

14.8 ms

15.5 ms

Commits

Click on a commit to change the comparison range

Base

main

5465b75

Allow broadcasting

a4abe53

5 days ago

by padix-key

Cleanup `get_assembly()`

26ff4f8

5 days ago

by padix-key

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