OpenMMDL 1.1.1 Release

This is a short release adding the Amber19 forcefield in addition to implementing the OPC and OPC3 water models

What's Changed

• Update of OpenFF forcefield version by @talagayev in #155
• Implementation of OPC and OPC3 water models by @talagayev in #156
• Amber19 addition by @talagayev in #157

Full Changelog: 1.1.0...1.1.1

OpenMMDL 1.1.0 Release

This is a major release of OpenMMDL.

The main changes in this release consist of the addition of various features, a change to the code and refactoring of OpenMMDL Analysis.

The main additions consist in the following:

• Implementation of OpenFF force field selection options in OpenMMDL Setup.
• addition of PyMOL support for visualisation
• Implementation of MDonatello for additional visualisation
• Transfer to RDKitConverter for ligand recognition if none are specified in OpenMMDL Analysis.
• The addition of a Dockerfile for installation.
• The option to select the final frame for OpenMMDL Analysis has been added with the -f flag.

Additionaly various small fixes were added in this release

Here are all of changes:

• Fixing of Errors with Figures by @talagayev in #86
• OpenFF Forcecfield implementation by @talagayev in #85
• Added PyMOL support for visualization. by @NDoering99 in #92
• Fix of Implementation of Molecule Sanitization Option by @talagayev in #123
• added citation page to docs by @NDoering99 in #124
• [WIP] Addition of Dockerfile by @talagayev in #119
• Update Development branch by @NDoering99 in #126
• Update openmmdlsetup.py by @NDoering99 in #125
• Added smallMoleculeForceField description by @talagayev in #127
• Merging of developent branch into version 1.01 by @talagayev in #128
• MDonatello Visualization Implementation by @talagayev in #130
• Updated Installation.rst by @talagayev in #131
• OpenMMDL Analysis Code restructure by @talagayev in #133
• Addition of pytests to OpenMMDL Analysis by @talagayev in #134
• Change to RDKitConverter by @talagayev in #135
• Fixing of the color code for the positive and negative ionizable interactions by @talagayev in #137
• Fix missing ligand name by @talagayev in #139
• TrajectorySaver movement by @talagayev in #142
• Add last frame by @talagayev in #140
• Short fix of OpenMMDL logo by @talagayev in #143
• Fix last frame modified by @talagayev in #145
• Class restruction: image_handler.py by @talagayev in #146
• Files Structure renaming by @talagayev in #147
• File renaming documentation by @talagayev in #149
• Openmmdl 1.1.0 Release by @talagayev in #151
• Openmmdl 1.1.0 fix by @talagayev in #152

Full Changelog: 0.9.2.4...1.1.0

0.9.2.4

Final fix for correct version for conda-forge

What's Changed

• Update _version.py by @talagayev in #107

Full Changelog: 0.9.2.3...0.9.2.4

0.9.2.1

Hotfix patch.
Fixes errors during installation with python 3.11 and python 3.12

What's Changed

• Numpy upgrade by @talagayev in #101

Full Changelog: 0.9.2...0.9.2.1

v.0.9.2

What's Changed

• add flag for figure type selection default png by @NDoering99 in #80
• fix some tests by @NDoering99 in #83
• fix testcase errors by @NDoering99 in #88
• Update README.md by @NDoering99 in #90
• Update openmmdl_analysis.rst by @NDoering99 in #91

Full Changelog: Release...0.9.2

v.0.9.1

First OpenMMDL release contains:

• OpenMMDL Setup: web page for setting up protein-ligand OpenMM MD simulations
• OpenMMDL Simulation: script for MD Simulation performance with further postprocessing
• OpenMMDL Analysis: Analysis of protein ligand interactions during the simulation with interaction fingerprint generation and display of the interactions and most prominent binding modes.

VT