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Support BinaryCIF file format #531

Merged
merged 14 commits into from
Mar 1, 2024
Merged

Support BinaryCIF file format #531

merged 14 commits into from
Mar 1, 2024

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padix-key
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@padix-key padix-key commented Feb 3, 2024

With the deprecation of MMTF (#525), this PR implements BinaryCIF as the new standard binary structure file format for Biotite.

  • Adds biotite.structure.io.pdbx.BinaryCIFFile
  • Adds biotite.structure.io.pdbx.CIFFile, deprecating biotite.structure.io.pdbx.PDBxFile
  • Refactors high-level functions in biotite.structure.pdbx to handle the new file interfaces
  • Supports bcif download in biotite.database.rcsb.fetch()
  • Deprecates biotite.structure.io.mmtf
  • Replaces mmtf usage with bcif in tests and documentation

Closes #525.

@padix-key padix-key force-pushed the bcif branch 6 times, most recently from 811ff40 to 8fe8b26 Compare February 12, 2024 15:57
@padix-key padix-key force-pushed the bcif branch 5 times, most recently from 7ede7b0 to b326bd4 Compare February 16, 2024 22:31
@padix-key padix-key force-pushed the bcif branch 5 times, most recently from dd31fa0 to 0f7d376 Compare February 29, 2024 22:19
@padix-key padix-key marked this pull request as ready for review March 1, 2024 07:07
@padix-key padix-key merged commit 3464598 into biotite-dev:master Mar 1, 2024
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Successfully merging this pull request may close these issues.

mmtf being officiallity deprecated & not served.
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