All pull requests

Pull requests

• Return an empty array from segment-wise functions for an empty atom array

  #1032·musharna opened Nov 9, 2026·

  ·

• Vectorize nucleotide SequenceProfile.to_consensus()

  #1031·padix-key opened Nov 8, 2026Member·

  ·
  1

• Vectorize SequenceProfile.from_alignment()

  #1030·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up Feature.get_location_range() and thus feature sorting

  #1029·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up CodonTable.codon_dict()

  #1028·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up LetterAlphabet.get_symbols()

  #1027·padix-key opened Nov 8, 2026Member·

  ·
  1

• Vectorize find_subsequence()

  #1026·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up Sequence.__iter__()

  #1025·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up pseudoknots() and dot_bracket()

  #1024·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up dihedral_side_chain() by computing all chi angles at once

  #1023·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up PDBFile.get_sequence()

  #1022·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up SubstitutionMatrix creation from dictionary or matrix name

  #1021·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up MOL/SDF structure writing

  #1020·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up find_stacking_interactions() and find_pi_cation_interactions()

  #1019·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up to_3di() by avoiding masked arrays in partner search

  #1018·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up filter_intersection()

  #1017·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up base_pairs_edge()

  #1016·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up ScoreThresholdRule.similar_kmers() and thus KmerTable.match() with similarity rule

  #1015·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up align.score() by vectorization

  #1014·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up get_component() with res_name

  #1013·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up filter_polymer()

  #1012·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up connect_via_distances(periodic=True)

  #1011·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up periodic distance measurement and move_inside_box()

  #1010·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up to_sequence()

  #1009·padix-key opened Nov 8, 2026Member·

  ·
  1

• Speed up find_rotatable_bonds()

  #1008·padix-key opened Nov 8, 2026Member·

  ·
  1