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(protein) termini patching #374

Merged
merged 19 commits into from
Jul 26, 2024
Merged

(protein) termini patching #374

merged 19 commits into from
Jul 26, 2024

Commits on Jun 14, 2024

  1. Initial commit 

    - with the -ter flag, add modifications read from the force field to the n and c termini
    @csbrasnett
    csbrasnett committed Jun 14, 2024
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  2. Merge branch 'master' into termini_patching

    @csbrasnett
    csbrasnett committed Jun 14, 2024
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  3. added martini3 modifications.ff and updated martini3 aminoacids.ff to… 

    … remove terminal modifications
    @csbrasnett
    csbrasnett committed Jun 14, 2024
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  4. fixed existing tests 

    - updated m3 command to include -ter
- new m3/prot.itp with correct parameters
    @csbrasnett
    csbrasnett committed Jun 14, 2024
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  5. add cystein bridge back in

    @csbrasnett
    csbrasnett committed Jun 14, 2024
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  6. Convert apply_termini.py to apply_modifications.py to treat modificat… 

    …ions more generally
    @csbrasnett
    csbrasnett committed Jun 14, 2024
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  7. added -protter as shorthand for protein termini

    @csbrasnett
    csbrasnett committed Jun 14, 2024
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  8. fixed test failure

    @csbrasnett
    csbrasnett committed Jun 14, 2024
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Commits on Jun 18, 2024

  1. added simple modification tests

    @csbrasnett
    csbrasnett committed Jun 18, 2024
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Commits on Jun 25, 2024

  1. Merge branch 'marrink-lab:master' into termini_patching

    @csbrasnett
    csbrasnett committed Jun 25, 2024
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Commits on Jul 1, 2024

  1. addressed comments for apply_modifications.py and gen_itp.py

    @csbrasnett
    csbrasnett committed Jul 1, 2024
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  2. cleaned up tests

    @csbrasnett
    csbrasnett committed Jul 1, 2024
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  3. Update modifications.ff

    @csbrasnett
    csbrasnett committed Jul 1, 2024
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  4. modifications missed off somehow

    @csbrasnett
    csbrasnett committed Jul 1, 2024
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  5. added test for ApplyModifications class

    @csbrasnett
    csbrasnett committed Jul 1, 2024
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Commits on Jul 17, 2024

  1. Made requested changes 

    - removed -ter flag from polyply
- -ter flag is not necessary anymore because apply_modifications.py will automatically add protein termini to the resspec if no modifications are given
- the modifications in the resspec will then only be applied if the target residue is in fact a protein residue
    @csbrasnett
    csbrasnett committed Jul 17, 2024
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  2. Updated tests for latest improvements

    @csbrasnett
    csbrasnett committed Jul 17, 2024
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  3. added extra tests for modification addition

    @csbrasnett
    csbrasnett committed Jul 17, 2024
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Commits on Jul 26, 2024

  1. Merge branch 'marrink-lab:master' into termini_patching

    @csbrasnett
    csbrasnett committed Jul 26, 2024
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