All pull requests

Pull requests

• Make Nexus CharBuffer tokenizing linear instead of quadratic

  #5397·TheNetherWatcher opened Oct 31, 2026·3 tasks done·

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• Fix :param fields in Bio.PDB.vectors docstrings

  #5394·mmporong opened Oct 28, 2026·1 of 3 tasks·

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• Correct LWL85 twofold-site numerator weights in both APIs

  #5392·ArtificialZeng opened Oct 27, 2026·3 tasks done·

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• Write PDBIO TER records within 80 columns and with their own serial

  #5391·RubenChM opened Oct 26, 2026·3 tasks done·

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• Fix distance inflation when re-rooting on a root-adjacent branch

  #5390·dnncha opened Oct 25, 2026·1 task done·

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• PDB deprecation warnings

  #5389·mdehoon opened Oct 23, 2026Contributor·3 tasks done·

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• Create AIPOLICY.rst

  #5388·idoerg opened Oct 22, 2026Contributor·2 tasks done·

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• Move ruff linter settings to pyproject.toml

  #5386·peterjc opened Oct 21, 2026Member·3 tasks done·

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• Fix FastaBlastIterator to properly advance header line (closes #5377)

  #5384·thanvish21 opened Oct 20, 2026·

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• Add write_ter option to PDBIO.save

  #5381·shubhodeepcx opened Oct 17, 2026·3 tasks done·

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• Add NeighborSearch residue examples to the tutorial

  #5380·shubhodeepcx opened Oct 17, 2026·3 tasks done·

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• Skip GLY with missing atoms in HSExposureCB

  #5378·shubhodeepcx opened Oct 16, 2026·3 tasks done·

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• Fix QCPSuperimposer RMSD for a perfect fit of collinear points

  #5373·Mohit-Ak opened Oct 14, 2026Contributor·3 tasks done·

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• Assign hydrogen to four character atom names like HNZ1

  #5366·popcoder565 opened Oct 9, 2026·

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• Fix DistanceCalculator identity model with skip_letters

  #5365·barlowa124 opened Oct 8, 2026·2 tasks done·

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• Fix protein_scale for window 1 and even window sizes

  #5363·barlowa124 opened Oct 8, 2026·3 tasks done·

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• Fix CAI calculation for alternative genetic codes

  #5353·cipgi opened Oct 5, 2026Contributor·3 tasks done·

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• Fix undefined vector angles and preserve planar dihedrals

  #5352·Oblivionis028 opened Oct 4, 2026Contributor·3 tasks done·

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• GenBank: allow NA molecule type and fix LOCUS strandedness position

  #5350·bmokrytz opened Oct 2, 2026·3 tasks done·

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• Fix D105 missing magic method docstrings in Bio.Seq and Bio.SeqRecord

  #5349·aashnology opened Oct 1, 2026·2 of 3 tasks·

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• Clip negative scores in DistanceCalculator._pairwise to keep distance in [0, 1]

  #5348·ChenziqiAdam opened Oct 1, 2026Contributor·2 of 3 tasks·

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• Require AI usage declaration in PR template

  #5334·peterjc opened Sep 29, 2026Member·3 tasks done·

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• When the residue or atom serial number is empty or invalid, PDBPar…

  #5328·Lucioric2000 opened Sep 27, 2026·

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• Fix: Update allowed mol_type values in EmblWriter

  #5323·corneliusroemer opened Sep 18, 2026Contributor·3 tasks done·

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• Parse EMBL DT lines as record date

  #5318·NinjagoJaden1 opened Sep 16, 2026·3 tasks done·

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