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Add CLePAPS structural alphabet#681

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padix-key wants to merge 16 commits intobiotite-dev:mainbiotite-dev/biotite:mainfrom padix-key:clepapspadix-key/biotite:clepapsCopy head branch name to clipboard

+1,919-139

Commits

Commits on Oct 16, 2024

• Add mini3di classes and tests as biotite.structure.alphabet

  

  althonos

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  padix-key

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  44bdb29

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• Add a dedicated Sequence subclass to store 3di sequences

  

  althonos

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  padix-key

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  7b4a4ff

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• Rewrite 3di encoder to take AtomArray as inputs

  

  althonos

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  padix-key

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  d814948

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• Fix apply_segment_wise always expecting a function with axis parameter

  

  althonos

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  padix-key

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  4edf6d0

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• Add to_3di helper function to obtain a StructureSequence from an AtomArray

  

  althonos

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  padix-key

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  b8626e5

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• Refactor 3Di functionality

  padix-key

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  9384ebb

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• Fix typo

  padix-key

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  827c4a3

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• Add 3Di sequences for existing test structure

  padix-key

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  b27f189

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• Add 3Di substitution matrix

  padix-key

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  220b70d

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• Properly handle missing atoms

  padix-key

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  218a967

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• Organize functionalities in structure.alphabet

  padix-key

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  ef0a25c

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• Add doctest

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  edda690

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• Test structures with missing atoms/residues

  padix-key

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  5f34d28

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Commits on Oct 17, 2024

• Make dihedral_backbone() more robust against missing atoms

  padix-key

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  1f487cc

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Commits on Oct 19, 2024

• Add Protein Blocks alphabet

  padix-key

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  e0eb20d

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• Add support for CLePAPS structural alphabet

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  fa5621b

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