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Merge pull request #891 from padix-key/fix-missing-intra-bonds Fix missing intra-residue bonds in PDBx files

main

17 hours ago

Adapt doctests to updated database outputs

padix-key:fix-missing-intra-bonds

20 hours ago

Merge pull request #889 from padix-key/fix-segments Fix missing stop entry for empty atom arrays

main

21 hours ago

Fix missing intra-residue bonds in PDBx files

padix-key:fix-missing-intra-bonds

4 days ago

Fix missing stop entry for empty atom arrays

padix-key:fix-segments

4 days ago

fix(clustal): apply review feedback on PR #880 - Credit __author__ in the three new clustal modules (__init__.py, convert.py, file.py). - Replace the two-part consensus-line check in ClustalFile._parse() with a single precompiled regex (_CONSENSUS_LINE = re.compile(r"[ *:.]+")). The old `line[0] == " " and all(c in _CONSENSUS_CHARS for c in line)` was redundant (the all-check already excludes real sequence lines, since those contain alphanumeric characters) and technically also passed empty lines (harmless only because of the preceding blank-line skip). Regex is simpler and doesn't rely on that ordering. - Raise InvalidFileError on malformed sequence lines (< 2 whitespace- separated parts) instead of silently dropping them. Same exception class already used by the header check. - Tests: round-trip checks now compare Alignment objects directly via `alignment == alignment2/3` instead of `str(alignment) == str(...)`, per reviewer suggestion. Rebased onto current main; ruff format + ruff check --fix applied.

haoyu-haoyu:feat/clustalw-aln-format

6 days ago

Merge pull request #887 from padix-key/fix-ion-filter Make `filter_monoatomic_ions()` more rigorous

main

8 days ago

Merge pull request #886 from padix-key/nucleotide-dihedrals Add measurements of nucleotide dihedral angles

main

8 days ago

Latest Branches

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Fix missing intra-residue bonds in PDBx files#891

21 hours ago

7b2f910

padix-key:fix-missing-intra-bonds

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Fix missing stop entry for empty atom arrays#889

4 days ago

8900c8d

padix-key:fix-segments

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feat: add ClustalW .aln format support for sequence alignments#880

8 days ago

7e6fb6e

haoyu-haoyu:feat/clustalw-aln-format

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