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base repository: ParmEd/ParmEd
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base: 4.1.0
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head repository: ParmEd/ParmEd
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compare: 4.2.0
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  • 6 commits
  • 24 files changed
  • 4 contributors

Commits on Apr 7, 2023

  1. Added 3D-RISM and GBNSR6 to mdin configuration (#1305) 

    * added 3D-rism and GBNSR6 mdins

* updated copyright date

* removed debugging prints

* fixed sander fail when all variable values in rism are default

* fixed rism mdin when some variable is defined as a list or tuple
    @Valdes-Tresanco-MS
    Valdes-Tresanco-MS authored Apr 7, 2023
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Commits on Jun 9, 2023

  1. Basic routines for internal to cartesian coordinate conversion (#1311) 

    I hope there is agreement as to how something like this could be useful.
I included a test to show how you can place atoms based on internal
coordinates using a Z-matrix-like entry.
    @bradakta
    bradakta authored Jun 9, 2023
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  2. Transfer chain IDs to OpenMM topology. (#1310)

    Jeff Thompson authored Jun 9, 2023
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Commits on Sep 12, 2023

  1. Add a library of all CCD residues separate from modified amino/nuclei… 

    …c acids (#1315)

* Add templates for all CCD residues other than currently stored amino/nucleic acids

* Fix file name

* Fix issues in RDKit interconversions

* Fix copying of qualitative bond type

* Update dependencies.

* Do not arbitrarily override residue number

* Fix tests to work with newer OpenMM versions.

* Fix for newer scipy
    @swails
    swails authored Sep 12, 2023
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Commits on Sep 13, 2023

  1. Fix Python 3.8 support (#1319)

    @swails
    swails authored Sep 13, 2023
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Commits on Sep 14, 2023

  1. Preserve residue IDs, insertion codes, and bond orders in OpenMM topo… 

    …logy conversions (#1316)

* Preserve residue IDs, insertion codes, and bond orders in OpenMM topology conversions.

* Remove type conversion.

---------

Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @swails
    Jeff Thompson and swails authored Sep 14, 2023
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