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Implementing gemmi-based mmcif reader (with easy extension to PDB/PDBx and mmJSON) #4712

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Implementing gemmi-based mmcif reader (with easy extension to PDB/PDBx and mmJSON) #4712

wants to merge 33 commits into from
+3,115 −366

Commits on May 22, 2024

  1. Start working on MMCIF parser

    @marinegor
    marinegor committed May 22, 2024
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  2. Add first (not working) version of MMCIFReader and MMCIF topology parser

    @marinegor
    marinegor committed May 22, 2024
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  3. Do some squashing

    @marinegor
    marinegor committed May 22, 2024
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  4. Remove inherited docs

    @marinegor
    marinegor committed May 22, 2024
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  5. Try improving the parsing

    @marinegor
    marinegor committed May 22, 2024
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Commits on May 30, 2024

  1. Try three independent loops over the model

    @marinegor
    marinegor committed May 30, 2024
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Commits on Jul 25, 2024

  1. Merge remote-tracking branch 'upstream/develop' into feature/mmcif

    @marinegor
    marinegor committed Jul 25, 2024
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Commits on Sep 13, 2024

  1. Add gemmi dependency

    @marinegor
    marinegor committed Sep 13, 2024
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Commits on Sep 20, 2024

  1. necessary params

    @marinegor
    marinegor committed Sep 20, 2024
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  2. finished sorting atom attrs

    @marinegor
    marinegor committed Sep 20, 2024
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  3. add function for transformation into *idx

    @marinegor
    marinegor committed Sep 20, 2024
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  4. oh damn seems to finally be working

    @marinegor
    marinegor committed Sep 20, 2024
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  5. remove TODOs

    @marinegor
    marinegor committed Sep 20, 2024
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  6. Remove debug prints

    @marinegor
    marinegor committed Sep 20, 2024
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Commits on Sep 22, 2024

  1. Merge branch 'develop' into feature/mmcif

    @marinegor
    marinegor committed Sep 22, 2024
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  2. try to pack things into separate class in utils?

    @marinegor
    marinegor committed Sep 22, 2024
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  3. remove unnecessary functions

    @marinegor
    marinegor committed Sep 22, 2024
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Commits on Sep 23, 2024

  1. copy all loops into separate functions

    @marinegor
    marinegor committed Sep 23, 2024
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  2. Move loops over structures into functions

    @marinegor
    marinegor committed Sep 23, 2024
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  3. Move coordinate fetching into function for the coordinate reader as well

    @marinegor
    marinegor committed Sep 23, 2024
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  4. Fix imports

    @marinegor
    marinegor committed Sep 23, 2024
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Commits on Sep 30, 2024

  1. Start adding documentation

    @marinegor
    marinegor committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Reference MMCIFParser in PDBParser

    @marinegor
    marinegor committed Oct 1, 2024
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  2. Add documentation for trajectory and topology parsers

    @marinegor
    marinegor committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. Add mmcif tests

    @marinegor
    marinegor committed Oct 2, 2024
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  2. Update format specifications

    @marinegor
    marinegor committed Oct 2, 2024
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  3. Write simple tests

    @marinegor
    marinegor committed Oct 2, 2024
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Commits on Oct 24, 2024

  1. Merge remote-tracking branch 'upstream/develop' into feature/mmcif

    @marinegor
    marinegor committed Oct 24, 2024
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  2. update github action with gemmi

    @marinegor
    marinegor committed Oct 24, 2024
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  3. fix gemmi import errors

    @marinegor
    marinegor committed Oct 24, 2024
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  4. add mmcif testfiles

    @marinegor
    marinegor committed Oct 24, 2024
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  5. add mmcif to __all__

    @marinegor
    marinegor committed Oct 24, 2024
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Commits on Oct 25, 2024

  1. add black instead of ruff

    @marinegor
    marinegor committed Oct 25, 2024
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