Protex v1.2.0

New

Significant speedup for the calculation of updates. See mainly PR #68
Protex has the ability to create psf files without charmm (PR #90). Experimental!

What's Changed

• improved emoji by @JohannesKarwou in #72
• Clean up forcefield folder and testsystems.py by @florianjoerg in #71
• Docu HPTS by @florianjoerg in #73
• Update documentation by @florianjoerg in #74
• Patch drudeforce by @florianjoerg in #81
• patch resname by @florianjoerg in #80
• psf residues fix by @florianjoerg in #83
• thole particle_map by @florianjoerg in #84
• Tfa fixes by @florianjoerg in #82
• remove unnecessary extension, since parmed got an update by @florianjoerg in #92
• Create a psf file without charmm by @florianjoerg in #90
• speedup_newstuff by @florianjoerg in #94
• Speedup by @florianjoerg in #68
• removed unused 14 exclusion lists by @florianjoerg in #97

New Contributors

• @JohannesKarwou made their first contribution in #72

Full Changelog: v1.1.0...v1.2.0

Protex v1.1.0

This is a new minor release.

What's New

• Changed from setup.py to pyproject.toml
• Handling of Grotthus mechanism is now possible. Details in #56 and #57
  You can specify a new keyword "equivalent_atom" in the states dictionary for the templates

What's Changed

• Reorient by @godenymarta in #56
• Update refactor by @florianjoerg in #57
• make a deque(maxlen=10) from history by @godenymarta in #58
• Option to save and load the StateUpdate by @florianjoerg in #59
• Move from versioneer.py to setuptools_scm by @florianjoerg in #61
• ruff, pre-commit by @florianjoerg in #62
• port to pyproject.toml by @florianjoerg in #63
• improve tests by @florianjoerg in #64
• Parmed test by @florianjoerg in #67
• conda-forge by @florianjoerg in #66

Full Changelog: v1.0.0...v1.1.0

v1.0.0

Important

Please be aware of the Api changes for the two following classes:

• IonicLiquidTemplates → ProtexTemplates
• IonicLiquidSystem → ProtexSystem

What's Changed

• added DrudeTemperatureReporter to reporter.py by @florianjoerg in #38
• Fix update bug by @florianjoerg in #45
• energy fix by @florianjoerg in #43
• Energy contributions by @florianjoerg in #44
• Energyreporter by @florianjoerg in #47
• Additions to PSF file writing by @florianjoerg in #48
• Topology problem by @florianjoerg in #42
• Meoh by @godenymarta in #40
• CI Test fixes by @florianjoerg in #50
• Use dummy atomtype by @florianjoerg in #49
• Improved Error Messages by @florianjoerg in #52
• Docs by @florianjoerg in #41
• scripts by @florianjoerg in #53
• Api changes by @florianjoerg in #54

Full Changelog: v0.2.0...v1.0.0

v0.2.0

New features

• Infrastructure update to allow also updates with the photo acid.
• More robust checking for dihedral multiplicity
• Ability to specify all potential molecules separately from the actual molecules in the system

What's Changed

• Report_Update by @florianjoerg in #26
• Residue by @florianjoerg in #24
• Documentation by @florianjoerg in #15
• prob: make equilibrium setting more flexible by @florianjoerg in #28
• basic updates to docs by @florianjoerg in #29
• made function more flexibel for user input by @florianjoerg in #30
• start on psf problem by @florianjoerg in #32
• Doc bild by @florianjoerg in #31
• Psf fix2 by @florianjoerg in #33
• Update lint_python.yml by @florianjoerg in #34
• Revert "Update lint_python.yml" by @florianjoerg in #35
• started working on hpts by @godenymarta in #27
• Fix skipped tests in workflow by @florianjoerg in #37
• restructure by @florianjoerg in #36

New Contributors

• @godenymarta made their first contribution in #27

Full Changelog: v0.1.0...v0.2.0

v0.1.0

Pre-release of Protex: MD Simulations with Proton Transfers