8000 Comparing 4.0.0...4.1.0 · ParmEd/ParmEd · GitHub
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base repository: ParmEd/ParmEd
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base: 4.0.0
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head repository: ParmEd/ParmEd
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compare: 4.1.0
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  • 11 commits
  • 14 files changed
  • 9 contributors

Commits on Feb 3, 2023

  1. set python_requires to >=3.8 (#1285) 

    Python support has been restricted to Python v3.8 and newer, but `python_requires` is not set. Thus, the new version of ParmEd will still be installed when one installs ParmEd on an older Python version. By setting `python_requires`, pip with old Python versions will not install the new version of ParmEd.
    @njzjz
    njzjz authored Feb 3, 2023
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Commits on Feb 17, 2023

  1. switch out copy with deepcopy for structure.copy() method (#1290) 

    * switch out copy with deepcopy for structure.copy() method

* Update parmed/structure.py

---------

Co-authored-by: Jason Swails <jason@entos.ai>
    @daico007 @swails
    daico007 and swails authored Feb 17, 2023
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Commits on Mar 23, 2023

  1. Only write body section of NUMANSIO if greater 0 (#1274)

    @florianjoerg
    florianjoerg authored Mar 23, 2023
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  2. using NUMLP instead of MOLNT (#1266)

    @JohannesKarwou
    JohannesKarwou authored Mar 23, 2023
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  3. Set atomic number when applying a patch (#1275) 

    Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @peastman @swails
    peastman and swails authored Mar 23, 2023
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  4. Prefer patch versions that replace external bonds (#1278) 

    Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @peastman @swails
    peastman and swails authored Mar 23, 2023
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  5. Enable changing C4 terms in LJ pairs individually (#1277) 

    * Enable changing C4 terms in LJ pairs individually

* Update parmed/tools/actions.py

Thanks! But I would prefer to use "== False" instead of "not",  since this can make codes clearer and easier to read.

Co-authored-by: Jason Swails <jason@entos.ai>

* Apply suggestions from code review

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Co-authored-by: Jason Swails <jason@entos.ai>
Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @Blossomstripe @swails
    3 people authored Mar 23, 2023
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  6. Fix an error with mdin changing (#1299)

    @swails
    swails authored Mar 23, 2023
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Commits on Apr 1, 2023

  1. Fix bug with adding positional restraints for OpenMM (#1301) (#1302)

    @nffaruk
    nffaruk authored Apr 1, 2023
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Commits on Apr 4, 2023

  1. Fix bug with restart reporter for OpenMM minimization (#1303)

    @nffaruk
    nffaruk authored Apr 4, 2023
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Commits on Apr 6, 2023

  1. Preserve formal charges from PDB and CIF files if present over templa… 

    …tes (#1304)
    @swails
    swails authored Apr 6, 2023
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