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Integrate pdbprep into codebase #592

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Integrate pdbprep into codebase #592

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Commits on Mar 13, 2024

  1. minor formatting improvements

    @DaniBodor
    DaniBodor committed Mar 13, 2024
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Commits on Mar 19, 2024

  1. add dependencies to env files

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  2. style: update ruff settings for TODOs

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  3. mimic do_pdbtools from pdbprep

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  4. start testing pdbtools

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  5. create function to run PRAS 

    PRAS only allows files as in- and output, so function is wrapped in a `TemporaryDirectory` to have variable in- and outputs
    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  6. add pdb2pqr functionality

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  7. rename file

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  8. temporarily add test notebooks

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  9. add detect protonation functions

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  10. add add_hydrogens functions

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  11. add PRAS to preprocess file

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  12. move pdb2pqr function into detect protonation module

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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  13. rename hydrogenation

    @DaniBodor
    DaniBodor committed Mar 19, 2024
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