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
andColvars
format.Refactoring of the
AMBER
simulation wrapper code and expanded to include wrappers forGROMACS
andNAMD
.Namespace refactoring for the
align
,dummy
, andtleap
modules (now underpaprika.build
).Namespace refactoring for the OpenFF-Evaluator related modules (now under
paprika.evaluator
).Enhancements to the
tleap
class, which includes a wrapper aroundInterMol
for convertingAMBER
files to other MD formats and support for solvating with theBind3P
water model.Migrate continuous integration (CI) to Github Actions (GHA).
Minor bug fixes.
v1.0.4¶
(08/18/2020)
Refactor codes for
setup.py
andanalysis.py
modules to allow a smoother integration with OpenFF-EvaluatorOpenMM restraints code is now decoupled from
setup.py
and placed in a separate filerestraints/openmm.py
Updated install requirements to Ambertools v20
Added hydrogen mass repartitioning option to
TLeap
API moduleMinor 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
andpaprika.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.