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Macromolecule viewer#63

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PhillipDowney merged 273 commits into
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macromolecule_viewer_moe
Sep 25, 2024
Merged

Macromolecule viewer#63
PhillipDowney merged 273 commits into
mainfrom
macromolecule_viewer_moe

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@themoenen

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Per #169:

  • Newly supported GUI file formats: cif & pdb which lets us visualize proteins but also other macromolecules like nucleic acids, carbohydrates and lipids. The cif format is the more "modern" and preferred file format, where pdb is more antiquated.
  • Introduction of the OpenAD-specific .mmol.json file format to store macromolecules. For now this is nothing more than a wrapper around a cif/pdb file, but it will allow us to store notes and tags later on.

    Note: Because cif files can be 100MB, macromolecules are not compatible with molecule sets (.molset.json), to support this we need to introduce a new reference-based format that links to individual macromolecule files.

  • Small molecules are now stored as .smol.json files, with backward compatibilty provided for .mol.json files.
  • Added macromolecule lookup in the GUI supporting FASTA and PDB id
  • Added macromolecule lookup command: show protein '2g64' supporting FASTA and PDB id

Dataframe & CSV input not yet supported but this can be done easily once it's more clear how this kind of input will look like.

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Looks good.

@PhillipDowney PhillipDowney merged commit ab73100 into main Sep 25, 2024
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