Release History

v1.2.0

(10/26/2022)

This release adds minor new features bug fixes to the paprika code.

  • Integrate OpenFF-units (a wrapper for Pint units) used in defining restraints.

  • Enhances the restraints/openmm module to include centroid-based anchor atom selection.

  • Updates the analysis module for pymbar v4.0

  • Minor bug fixes

v1.1.0

(02/17/2021)

This release provides a number of enhancements to the paprika code and changes to the API.

  • Adds support for writing APR restraints to Plumed and Colvars format.

  • Refactoring of the AMBER simulation wrapper code and expanded to include wrappers for GROMACS and NAMD.

  • Namespace refactoring for the align, dummy, and tleap modules (now under paprika.build).

  • Namespace refactoring for the OpenFF-Evaluator related modules (now under paprika.evaluator).

  • Enhancements to the tleap class, which includes a wrapper around InterMol for converting AMBER files to other MD formats and support for solvating with the Bind3P water model.

  • Migrate continuous integration (CI) to Github Actions (GHA).

  • Minor bug fixes.

v1.0.4

(08/18/2020)

  • Refactor codes for setup.py and analysis.py modules to allow a smoother integration with OpenFF-Evaluator

  • OpenMM restraints code is now decoupled from setup.py and placed in a separate file restraints/openmm.py

  • Updated install requirements to Ambertools v20

  • Added hydrogen mass repartitioning option to TLeap API module

  • Minor bug fixes

v1.0.3

(12/04/2019)

Fixed API compatibility with the new pymbar v3.0.5 and the I/O for ref_structure in the static_DAT_restraint function

v1.0.2

(11/24/2019)

Fix parsing of CUDA_VISIBLE_DEVICES class property. This bugfix was intended to go into the v1.0.1 release but was accidentally excluded.

v1.0.1

(11/24/2019)

Provides a more robust method to supply a random number seed to the compute_free_energy method.

v1.0.0

(11/04/2019)

  • The API for paprika.setup and paprika.analyze are now converged.

  • OpenMM support is proved by PropertyEstimator.

  • The documentation has (mostly) been updated and expanded.

v0.1.1

(07/30/2019)

Minor code cleanup and fix reference values for test cases that were failing in the v0.1.0 release.

v0.1.0

(07/27/2019)

This release enables paprika to work with propertyestimator of the Open Force Field Toolkit, and taproom to setup host-guest calculations with either GAFF or SMIRNOFF-based force fields using AMBER or OpenMM as simulation backends.

v0.0.4

(02/19/2019)

Updates after merging Cookiecutter for Computational Molecular Sciences (CMS) Python Packages and updating tests to pass.

v0.0.3

(05/16/2018)

Initial code and was used to run SAMPLing.