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Save datasets in structure.info as BinaryCIF #540

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merged 13 commits into from
Mar 22, 2024

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First part of tackling #530.

This PR refactors the structure.info subpackage.

  • The many large MessagePack files in structure.info are replaced by a single smaller ccd/components.bcif file, containing the necessary subset of the Chemical Component Dictionary. It is stored using Git LFS to allow efficient updates of the file.
  • The setup_ccd.py script creates components.bcif along with the JSON files for molecule groups. This makes https://github.com/biotite-dev/biotite-util/tree/master/datasets obsolete.
  • The functions structure.info are refactored, decreasing the complexity and initial loading time of structure.info.
  • The functions bond_order() (was already deprecated) and bond_dataset() is removed.

@padix-key padix-key merged commit 241211a into biotite-dev:master Mar 22, 2024
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