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base repository: ParmEd/ParmEd
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base: 4.2.2
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head repository: ParmEd/ParmEd
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compare: 4.3.0
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  • 15 commits
  • 19 files changed
  • 9 contributors

Commits on Jan 18, 2024

  1. Replaced mktemp with mkstemp (#1328) 

    Signed-off-by: fazledyn-or <ataf@openrefactory.com>
    @nydelzaf
    nydelzaf authored Jan 18, 2024
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Commits on Apr 10, 2024

  1. Add support for 12-6-4 models. (#1346) 

    * Add the support for four new water models OPC3, OPC, TIP3P-FB, and TIP4P-FB to add12_6_4 function in ParmEd.

* Update the test files to be consistent with the updated add12_6_4 function

* pin rdkit <2024.03.1

---------

Co-authored-by: Pengfei Li <ldsoar1990@gmail.com>
    @swails @pengfeili1
    swails and pengfeili1 authored Apr 10, 2024
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Commits on Apr 24, 2024

  1. Fix wildcard sorting when writing Amber parameter sets (fixes #1347) (#… 

    …1348)
    @murfalo
    murfalo authored Apr 24, 2024
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Commits on Jun 24, 2024

  1. Match tleap by ensuring parm{10|99|15}.dat are loaded no more than on… 

    …ce (#1353)

(#1352)
    @murfalo
    murfalo authored Jun 24, 2024
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  2. Ignore TURN comments in PDBs (#1351) 

    Co-authored-by: David Slochower <david_slochower@vrtx.com>
Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @slochower @davidslochower @swails
    3 people authored Jun 24, 2024
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  3. fix SyntaxWarning: invalid escape sequence (#1350)

    @njzjz
    njzjz authored Jun 24, 2024
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  4. Fix output of changeLJSingleType (#1355)

    @swails
    swails authored Jun 24, 2024
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Commits on Jun 26, 2024

  1. Bugfixed AtomType equality operator (#1360)

    @murfalo
    murfalo authored Jun 26, 2024
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Commits on Sep 18, 2024

  1. Fix the build wrt RDKit package issues (#1370) 

    * Add some debugging

* Stop testing Python 3.9 and 3.10

* Improve a test
    @swails
    swails authored Sep 18, 2024
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  2. Fixed compatibility with NumPy 2.0+ (#1374) 

    Issue #1364

Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @vedranmiletic @swails
    vedranmiletic and swails authored Sep 18, 2024
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  3. Fix serialization of structure with bond type attributes and add test (… 

    …#1376)

* Fix serialization of structure with bond type attributes and add test

* Fix default assignment.
    @swails
    swails authored Sep 18, 2024
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  4. Ensure PBC box vectors are in reduced form for OpenMM (#1368) 

    Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @nffaruk @swails
    nffaruk and swails authored Sep 18, 2024
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Commits on Sep 21, 2024

  1. Improve mdin parsing to not split restraintmask fields using '=' wild… 

    …card char (#1369)

Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @nffaruk @swails
    nffaruk and swails authored Sep 21, 2024
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Commits on Sep 22, 2024

  1. Fix velocity unit scale for existing vels passed to OpenMM (#1367) 

    Co-authored-by: Jason Swails <jason.swails@gmail.com>
    @nffaruk @swails
    nffaruk and swails authored Sep 22, 2024
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Commits on Oct 2, 2024

  1. Switch to non-deprecated miniforge (#1378)

    @swails
    swails authored Oct 2, 2024
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