Release History
Releases follow the major.minor.micro scheme recommended by
PEP440, where
majorincrements denote a change that may break API compatibility with previousmajorreleasesminorincrements add features but do not break API compatibilitymicroincrements represent bugfix releases or improvements in documentation
Current development
PR #588: Updates the default OpenMM simulation protocol to use
openmm.LangevinMiddleIntegratorinstead ofopenmmtools.integrators.LangevinIntegrator.
0.4.10 - October 3, 2024
PR #577: Fixes a bug in which target mole fractions, not the simulated mole fractions, were used when calculating mixture properties.
PR #574: Unconditionally use the new
pydantic.v1import path for more consistent access to the v1 API.PR #569: Fixes a bug in which molecular weights were not scaled by Avogadro’s number.
PR #562: Updates for Pint 0.21 and newer (likely through 0.23).
0.4.9 - August 30, 2024
PR #555: More gracefully handle Packmol failures.
0.4.8 - January 30, 2024
0.4.7 - October 16, 2023
0.4.6 - October 12, 2023
PR #532: Changes
BaseEnergyMinimisation.toleranceto use units of force.
0.4.5 - July 24, 2023
PR #517: Adds support for Foyer forcefields.
0.4.4 - July 24, 2023
This release drops support for Python 3.8, adds support for Python 3.10, and removed protocols based on Yank.
0.4.3
This release adds support for OpenMM 8. Support for OpenMM 7 will be removed in a future release.
Bugfixes
Documentation
PR #499: Updates tutorials for upstream changes.
0.4.2
New Features
PR #479: Improves compatibility with pymbar 3 and 4.
Bugfixes
PR #489: Properly creates Amber-style systems involving multiple molecules.
Behavior Changes
PR #490: Deprecates Yank protocols.
0.4.1
New Features
PR #475: Tests compatibility with pymbar 3 and 4.
0.4.0
Behavior Changes
This release is intended to be compatible with OpenFF Toolkit version 0.11.0 and newer and is not compatible with older versions. To use OpenFF Evaluator in environments with older versions of the toolkit (0.10.x and older) please use the 0.3.x release line.
The simtk namespace is no longer supported. It is recommended to use OpenMM 7.6 or newer.
Two other version constraints have been added: pymbar >=4.0.0 and mdtraj =1.9.3,1.9.4. A
future release should fix compatibility with newer versions of MDTraj.
Unit-bearing quantities are now handled by openff-units instead of the openmm.units units
module. See the openff-units Documentation for more information, including OpenMM interoperability.
The use of CMILES has been replaced with equivalent behavior using the OpenFF Toolkit as CMILES is no longer actively maintained.
New Features
PR #465: Adds support for AMD GPUs via OpenCL.
Documentation
0.3.11
Bugfixes
PR #445: Fix OpenMM unit utils API regression
0.3.10
Bugfixes
PR #444: Fix labelling molecules with virtual sites
0.3.9
Bugfixes
PR #402: Fix importing full ThermoML archive
Behavior Changes
The way that ThermoML archive files are served was changed in 2021 so that individual journal archives are no longer
made available. Instead, now only the full ThermoML archive can be downloaded. Because of this, the ImportThermoMLDataSchema
schema no longer allows users to select which journal to pull data from.
0.3.8
Bugfixes
PR #390: Fix excluding v-sites from OpenMM positions
0.3.7
Bugfixes
PR #389: Fix v-site positions not set by OpenMM
0.3.6
Bugfixes
New Features
0.3.5
Bugfixes
New Features
0.3.4
A patch release which adds the option (and enables it by default) to remove working files, such as simulated trajectories, when they are no longer needed.
Behavior Changes
PR #349: Working files are deleted by default after an estimation batch completes.
0.3.3
This release facilitates the migration of the openff-evaluator package from omnia to conda-forge. This mainly involves changes which update the package to use the new namespaces introduced in the openff-tookit package, rather than the old and now deprecated openforcefield namespaces.
Bugfixes
PR #346: Remove the unsupported encoding json kwarg.
New Features
0.3.2
This release exposes the option to disable caching of simulation data by an evaluator server. The performance of the local storage backend is currently poor when dealing with large amounts of cached data and hence it may be preferable to disable caching in such cases.
New Features
PR #337: Expose server option to dis/enable data caching.
0.3.1
This release fixes a bug introduced in version 0.3.0 of this framework, whereby the default workflows for computing excess properties could in rare cases be incorrectly merged leading to downstream protocols taking their inputs from the wrong upstream protocol outputs.
While this bug should not affect most calculations, it is recommended that any production calculations performed using version 0.3.0 of this framework be repeated using version 0.3.1.
Bugfixes
PR #331: Fixes merging excess properties.
0.3.0
The main feature of this release is the overhauling of how the framework computes the gradients of observables with respect to force field parameters.
In particular, from this release onwards all gradients will be computed using the fluctuation formula (also referred to as the thermodynamic gradient), rather than calculation be the re-weighted finite difference approach (PR #280). In general the two methods produce gradients which are numerically indistinguishable, and so this should not markedly change any scientific output of this framework.
The change was made to, in future, enable better integration with automatic differentiation libraries such as jax, and differentiable simulation engines such as timemachine which readily and rapidly give access to \(\mathrm{d} U / \mathrm{d} \theta_i\).
Additionally, as of version 0.3.0 ‘known’ charges (i.e. those assigned to TIP3P water and ions) are no longer
automatically applied when using a SMIRNOFF based force field. This feature was originally included in the framework as
the OpenFF toolkit did not support defining charges on specific molecules in the force field itself. This is now fully
supported through the LibraryCharges section of a SMIRNOFF force field and hence this workaround is no longer
required. From now on all ion and water charges must be specified in the SMIRNOFF force field.
Finally, this release includes beta support for computing host-guest binding affinities using the
attach-pull-release (APR) method through integration with the pAPRika and
taproom packages. This support was largely facilitated by the
efforts of the paprika authors - David R. Slochower and
Jeffry Setiadi.
Bugfixes
New Features
PR #262: Initial host-guest binding affinity support via
paprikaandtaproom.PR #280: Switch to computing thermodynamic gradients.
PR #309: Add a date to the timestamp logging output.
PR #311: Initial solvation free energy gradient support.
PR #312: Support caching free energy data.
PR #324: Adds new miscellaneous
DummyProtocolprotocol.
Behavior Changes
Breaking Changes
The
StatisticsArrayarray has been completely removed and replaced with a new set of observable (Observable,ObservableArray,ObservableFrameobjects (#279, #286).The following protocol inputs / outputs have been renamed:
SolvationYankProtocol.solvent_X_system->SolvationYankProtocol.solution_X_systemSolvationYankProtocol.solvent_X_coordinates->SolvationYankProtocol.solution_X_coordinatesSolvationYankProtocol.estimated_free_energy->SolvationYankProtocol.free_energy_difference
The following classes have been renamed:
OpenMMReducedPotentials->OpenMMEvaluateEnergies.AveragePropertyProtocol->BaseAverageObservable,ExtractAverageStatistic->AverageObservable,ExtractUncorrelatedData->BaseDecorrelateProtocol,ExtractUncorrelatedTrajectoryData->DecorrelateTrajectory,ExtractUncorrelatedStatisticsData->DecorrelateObservablesConcatenateStatistics->ConcatenateObservables,BaseReducedPotentials->BaseEvaluateEnergies,ReweightStatistics -> ReweightObservable
The following classes have been removed:
OpenMMGradientPotentials,BaseGradientPotentials,CentralDifferenceGradient
The final value estimated by a workflow must now be an
Observableobject which contains any gradient information to return. (#296).
0.2.2
This release adds documentation for how physical properties are computed within the framework (both for this, and for previous releases.
Documentation
PR #281: Initial pass at physical property documentation.
0.2.1
A patch release offering minor bug fixes and quality of life improvements.
Bugfixes
New Features
0.2.0
This release overhauls the frameworks data curation abilities. In particular, it adds
a significant amount of data filters, including to filter by state, substance composition and chemical functionalities.
and components to
easily import all of the ThermoML and FreeSolv archives.
convert between property types (currently density <-> excess molar volume).
select data points close to a set of target states, and substances which contain specific functionalities (i.e. select only data points measured for ketones, alcohols or alkanes).
More information about the new curation abilities can be found in the documentation here.
New Features
Breaking Changes
All of the
PhysicalPropertyDataSet.filter_by_XXXfunctions have now been removed in favor of the new curation components. See the documentation for information about the newly available filters and more.
0.1.2
A patch release offering minor bug fixes and quality of life improvements.
Bugfixes
0.1.1
A patch release offering minor bug fixes and quality of life improvements.
Bugfixes
Documentation
PR #252: Use conda-forge for ambertools installation.
0.1.0 - OpenFF Evaluator
Introducing the OpenFF Evaluator! The release marks a significant milestone in the development of this project, and constitutes an almost full redesign of the framework with a focus on stability and ease of use.
Note: because of the extensive changes made throughout the entire framework, this release should almost be considered as an entirely new package. No files produced by previous versions of this will work with this new release.
Clearer Branding
First and foremost, this release marks the complete rebranding from the
previously named propertyestimator to the new openff-evaluator
package. This change is accompanied by the introduction of a new
openff namespace for the package, signifying it’s position in the
larger Open Force Field infrastructure and piplelines.
What was previously:
import propertyestimator
now becomes:
import openff.evaluator
The rebranded package is now shipped on conda under the new name of
openff-evaluator:
conda install -c conda-forge -c omnia openff-evaluator
Markedly Improved Documentation
In addition, the release includes for the first time a significant amount of documentation for using the `framework and it's features`_ as well as a collection of user focused tutorials which can be ran directly in the browser.
Support for RDKit
This release almost entirely removes the dependence on OpenEye thanks to support for RDKit almost universally across the framework.
The only remaining instance where OpenEye is still required is for host-guest binding affinity calculations where it is used to perform docking.
Model Validation
Starting with this release almost all models, range from
PhysicalProperty entries to ProtocolSchema objects, are now
heavily validated to help catch any typos or errors early on.
Batching of Similar Properties
The EvaluatorServer now more intelligently attempts to batch
properties which may be computed using the same simulations into a
single batch to be estimated. While the behaviour was already supported
for pure properties in previous, this has now been significantly
expanded to work well with mixture properties.
0.0.9 - Multi-state Reweighting Fix
This release implements a fix for calculating the gradients of properties being estimated by reweighting data cached from multiple independant simulations.
Bugfixes
PR #143: Fix for multi-state gradient calculations.
0.0.8 - ThermoML Improvements
This release is centered around cleaning up the ThermoML data set utilities. The main change is that ThermoML archive files can now be loaded even if they don’t contain measurement uncertainties.
New Features
PR #142: ThermoML archives without uncertainties can now be loaded.
Breaking Changes
PR #142: All ThermoMLXXX classes other than ThermoMLDataSet are now private.
0.0.7 - Bug Quick Fixes
This release aims to fix a number of minor bugs.
Bugfixes
0.0.6 - Solvation Free Energies
This release centers around two key changes -
a general refactoring of the protocol classes to be much cleaner and extensible through the removal of the old stub functions and the addition of cleaner descriptors.
the addition of workflows to estimate solvation free energies via the new
SolvationYankProtocolandSolvationFreeEnergyclasses.
The implemented free energy workflow is still rather basic, and does not yet support calculating parameter gradients or estimation from cached simulation data through reweighting.
A new table has been added to the documentation to make clear which built-in properties support which features.
New Features
PR #110: Cleanup and refactor of protocol classes.
PR #125: Support for PBS based HPC clusters.
PR #127: Adds a basic workflow for estimating solvation free energies with YANK.
PR #130: Adds a cleaner mechanism for restarting simulations from checkpoints.
PR #134: Update to a more stable dask version.
Bugfixes
Breaking Changes
PR #130: The
RunOpenMMSimulation.stepsinput has now been split into thesteps_per_iterationandtotal_number_of_iterationsinputs.
Migration Guide
This release contained several public API breaking changes. For the most part, these can be remedied by the follow steps:
Replace all instances of
run_openmm_simulation_protocol.stepstorun_openmm_simulation_protocol.steps_per_iteration
0.0.5 - Fix For Merging of Estimation Requests
This release implements a fix for a major bug which caused incorrect results to be returned when submitting multiple estimation requests at the same time - namely, the returned results became jumbled between the different requests. As an example, if a request was made to estimate a data set using the smirnoff99frosst force field, and then straight after with the gaff 1.81 force field, the results of the smirnoff99frosst request may contain some properties estimated with gaff 1.81 and vice versa.
This issue does not affect cases where only a single request was made and completed at a time (i.e the results of the previous request completed before the next estimation request was made).
Bugfixes
0.0.4 - Initial Support for Non-SMIRNOFF FFs
This release adds initial support for estimating property data sets using force fields
not based on the SMIRNOFF specification. In particular, initial AMBER force field support
has been added, along with a protocol which applies said force fields using tleap.
New Features
PR #96: Adds a mechanism for specifying force fields not in the
SMIRNOFFspec.PR #99: Adds support for applying
AMBERforce field parameters throughtleapPR #111: Protocols now stream trajectories from disk, rather than pre-load the whole thing.
PR #112: Specific types of protocols can now be easily be replaced using
WorkflowOptions.PR #117: Adds support for converting
PhysicalPropertyDataSetobjects topandas.DataFrame.
Bugfixes
Breaking Changes
PR #96: The
PropertyEstimatorClient.request_estimate(force_field=...argument has been renamed toforce_field_source.
Migration Guide
This release contained several public API breaking changes. For the most part, these can be remedied by the follow steps:
Change all instances of
PropertyEstimatorClient.request_estimate(force_field=...)toPropertyEstimatorClient.request_estimate(force_field_source=...)
0.0.3 - ExcessMolarVolume and Typing Improvements
This release implements a number of bug fixes and adds two key new features, namely built in support for estimating excess molar volume measurements, and improved type checking for protocol inputs and outputs.
New Features
Bugfixes
PR #94: Fixes exception when testing equality of
ProtocolPathobjects.PR #100: Fixes precision issues when ensuring mole fractions are <= 1.0.
PR #102: Fixes replicated input for children of replicated protocols.
PR #105: Fixes excess properties weighting by the wrong mole fractions.
PR #107: Fixes excess properties being converged to the wrong uncertainty.
PR #108: Fixes calculating MBAR gradients of reweighted properties.
Breaking Changes
PR #98:
Substance.get_amountrenamed toSubstance.get_amountsand now returns an immutablefrozensetofAmountobjects, rather than a singleAmount.PR #104: The
DivideGradientByScalar,MultiplyGradientByScalar,AddGradients,SubtractGradientsandWeightGradientByMoleFractionprotocols have been removed. TheWeightQuantityByMoleFractionprotocol has been renamed toWeightByMoleFraction.
Migration Guide
This release contained several public API breaking changes. For the most part, these can be remedied by the follow steps:
Change all instances of
Substance.get_amounttoSubstance.get_amountsand handle the newly returned frozenset of amounts, rather than the previously returned single amount.Replace the now removed protocols as follows:
DivideGradientByScalar->DivideValueMultiplyGradientByScalar->MultiplyValueAddGradients->AddValuesSubtractGradients->SubtractValuesWeightGradientByMoleFraction->WeightByMoleFractionWeightQuantityByMoleFraction->WeightByMoleFraction
0.0.2 - Replicator Quick Fixes
A minor release to fix a number of minor bugs related to replicating protocols.
Bugfixes
0.0.1 - Initial Release
The initial pre-alpha release of the framework.