Release history

This section lists features and improvements of note in each release.

The full release history can be viewed at the GitHub perses releases page.

0.10.3 - Release

Bugfix release.

Enhancements

• Print perses version on startup by @mikemhenry in https://github.com/choderalab/perses/pull/1176

• Support pymbar 3 & 4 by @mikemhenry in https://github.com/choderalab/perses/pull/1173

• Store initial and final topologies for all phases – small molecule pipeline by @ijpulidos in https://github.com/choderalab/perses/pull/1210

Documentation

• Added MPI example with dipeptide mutation by @ijpulidos in https://github.com/choderalab/perses/pull/1228

• Update comments in RESTCapableHybridTopologyFactory doc string by @zhang-ivy in https://github.com/choderalab/perses/pull/1189

• Clean examples – CLI protein-ligand example for Tyk2 by @ijpulidos in https://github.com/choderalab/perses/pull/1223

Bug Fixes

• Fix spectator support by @ijpulidos in https://github.com/choderalab/perses/pull/1233

• Realtime analysis interval to default to checkpoint interval by @ijpulidos in https://github.com/choderalab/perses/pull/1227

• Correctly set cutoff for CustomNonbondedForce in HybridTopologyFactory when using a non-default cutoff distance. by @mikemhenry in

• Backport openfe fixes for context deletion by @mikemhenry in https://github.com/choderalab/perses/pull/1229

Testing/CI/Packaging

• Run CI on new 0.10.x branch by @mikemhenry in https://github.com/choderalab/perses/pull/1212

• Use python executable from env by @mikemhenry in https://github.com/choderalab/perses/pull/1174

• Remove example testing by @mikemhenry in https://github.com/choderalab/perses/pull/1214

• CI miscellaneous fixes by @ijpulidos in https://github.com/choderalab/perses/pull/1217

• Improve docker building by @mikemhenry in https://github.com/choderalab/perses/pull/1200

Full Changelog: https://github.com/choderalab/perses/compare/0.10.2…0.10.3

0.10.2 - Release

Bugfix release.

Enhancements

• Added support for reading input files (ex yaml, sdf, pdbs) from AWS, GCP, and Azure. See the documentation for [cloudpathlib](https://cloudpathlib.drivendata.org/stable/authentication/) for how to setup authentication. Currently only reading the yaml from S3 is unit tested (ie perses-cli –yaml s3://perses-testing/template_s3.yaml), but other cloud providers and input files should work. AzureBlobPath, S3Path and GSPath are supported URI endpoints. Please report any issues on our issue tracker! by @mikemhenry in https://github.com/choderalab/perses/pull/1073

• CUDA platform was hardcoded in geometry engine, generating performance issues by not clearing openmm contexts correctly. Fixed by defaulting to using the faster CPU platform (for the geometry engine) and explicitly deleting context variables after they are used. by @ijpulidos in https://github.com/choderalab/perses/pull/1091

• Set aromatic draw style to OEAromaticStyle_Circle in atom mapper rendering by @mikemhenry in https://github.com/choderalab/perses/pull/1103

• Ligands with atoms changing constrained status were not being handled by mapping proposal. Atoms in bonds that change constrained/unconstrained to unconstrained/constrained during the transformation are now _demapped_. by @ijpulidos in https://github.com/choderalab/perses/pull/1125

• Now that upstream openmmtools is storing velocities on checkpoint, the small molecule transformation pipeline does not reassign velocities on resume by default. Instead, the velocities are read from the checkpoint file. by @ijpulidos in https://github.com/choderalab/perses/pull/1133

• CLI workflow for replica exchange now uses the faster LangevinMiddleIntegrator via the LangevinDynamicsMove. Tests were updated to reflect the changes. by @ijpulidos in https://github.com/choderalab/perses/pull/1138

• Add opencontainers image-spec to Dockerfile by @SauravMaheshkar in https://github.com/choderalab/perses/pull/1139

• Updated to support openff-toolkit 0.11, which included API-breaking changes. by @jchodera in https://github.com/choderalab/perses/pull/1128

• Make solute-only trajectory writing optional. This option is controlled by the atom_selection option in the yaml file. The syntax uses the MDTraj selection syntax, e.g. not water @mikemhenry in https://github.com/choderalab/perses/pull/1185

• Users can now specify solvent model for simulations using the solvent_model field in the input YAML file. Supported values are ‘tip3p’, ‘spce’, ‘tip4pew’, ‘tip5p’, and ‘swm4ndp’ (polarizable) by @ijpulidos in https://github.com/choderalab/perses/pull/1202

Documentation

• Document setting ionic_strength in examples/new-cli/template.yaml by @mikemhenry in https://github.com/choderalab/perses/pull/1104

• Add reproducible version of COVID Moonshot example anyone can run as an example by @jchodera in https://github.com/choderalab/perses/pull/1145

• Speed up RTD env generation by @mikemhenry in https://github.com/choderalab/perses/pull/1105

• Fix documentation string for ProteinMutationExecutor, using False for reassign_velocities parameter. by @ijpulidos in https://github.com/choderalab/perses/pull/1169

• Document how to control the log level in the CLI by @mikemhenry in https://github.com/choderalab/perses/pull/1198

Bug Fixes

• Fixes bug where if a : was in a key, we could not override the argument in our perses-cli. @mikemhenry in https://github.com/choderalab/perses/pull/1062

• Resolves #1157 objects serialized with utils.data.serialize now will be compressed with bzip2 or gzip depending on file name (.gz and .bz2, respectively) by @mikemhenry in https://github.com/choderalab/perses/pull/1163

• Fixes for new openmmtools 0.23.0 by @mikemhenry in https://github.com/choderalab/perses/pull/1203

Testing/CI/Packaging

• add python 3.10 to CI by @mikemhenry in https://github.com/choderalab/perses/pull/1080

• skip broken tests by @mikemhenry in https://github.com/choderalab/perses/pull/1074

• Feat/fix ssl gpu error by @mikemhenry in https://github.com/choderalab/perses/pull/1095

• Previously the keyword argument save_freq in validate_endstate_energies_md was not functional and the value of 250 steps was hard coded. Now, save_freq works and has a default value of 250 steps. by @mikemhenry in https://github.com/choderalab/perses/pull/1101

• fix issue with test asset name by @mikemhenry in https://github.com/choderalab/perses/pull/1102

• Examples and benchmarks template input files now run vacuum, solvent and complex phases in order. by @ijpulidos in https://github.com/choderalab/perses/pull/1122

• Add openmm 8 to testing matrix by @mikemhenry in https://github.com/choderalab/perses/pull/1124

• Fix resume tests to use new CLI (resolves issue #1150) by @mikemhenry in https://github.com/choderalab/perses/pull/1151

• Avoid testing non-examples in CI by @ijpulidos in https://github.com/choderalab/perses/pull/1164

• only run dev with newest python version by @mikemhenry in https://github.com/choderalab/perses/pull/1165

• remove outdated recipe by @mikemhenry in https://github.com/choderalab/perses/pull/1159

• update release process by @mikemhenry in https://github.com/choderalab/perses/pull/1162

• add env caching to CI by @mikemhenry in https://github.com/choderalab/perses/pull/1178

• Skip failing openmm 8 tests by @mikemhenry in https://github.com/choderalab/perses/pull/1186

• Add small molecule repex consistency tests by @zhang-ivy in https://github.com/choderalab/perses/pull/1065

• Fix RESTTopologyFactory test by @zhang-ivy in https://github.com/choderalab/perses/pull/1188

• enable merge queue by @mikemhenry in https://github.com/choderalab/perses/pull/1206

• Using default online analysis interval in GPU repex tests by @ijpulidos in https://github.com/choderalab/perses/pull/1207

New Contributors

• @SauravMaheshkar made their first contribution in https://github.com/choderalab/perses/pull/1139

Full Changelog: https://github.com/choderalab/perses/compare/0.10.1…0.10.2

0.10.1 - Release

Bugfix release.

Bugfixes

• Bug when trying to use the new RESTCapableHybridTopologyFactory in the small molecule pipeline – fixed by not specifying a protocol, hence allowing the HybridCompatibilityMixin object to automatically handle it. Issue #1039 (PR #1045)

• Bug in create_endstates_from_real_systems() – fixed by setting the global parameters for valence forces to the appropriate endstate. Also added tyk2 transformation test. Issue #1041 (PR #1050).

• Bug in the RESTCapableHybridTopologyFactory lifting expression – fixed by separating the cutoff distance from the lifting distance. (PR #1046)

• Fix bug in RelativeFEPSetup that prevents user from controlling the padding when solvating for solvent phase calculations. (PR #1053)

• Bug in test_unsampled_endstate_energies_GPU and test_RESTCapableHybridTopologyFactory_energies_GPU – fixed by removing unit-less rest_radius argument and using default instead. (PR #1057)

Enhancements

• Add flag transform_waters_into_ions_for_charge_changes for disabling the introduction of a counterion for charge changing transformations. Issue #1004 (PR #1030)

• Perses output yaml file now adds timestamp and ligands names information (for old and new ligands). Issue #998 (PR #1052).

• Protein mutation repex internal consistency tests to ensure convergence. So far only testing neutral transformations. Issue #1044 (PR #1054).

0.10.0 - Release

New command line interface (CLI), many enhancements for the API (especially the PointMutationExecutor) and improved testing.

Bugfixes

• Bug in geometry engine’s _determine_extra_torsions: when topology_index_map, which contains the atom indices involved in a particular torsion, is None – fixed by not trying to add that torsion when topology_index_map is None. (#855)

• Bug generated by changes upstream in the openmm package – default method for calculating solvent padding changed, which resulted in smaller boxes. Fixed by adding more padding to the simulation box, it is now 1.1 nm. Openmm issue #3502. Perses issue #949 (#953)

• Fixed energy bookkeeping in test of HybridTopologyFactory when a ring amino acid is involved in transformation. (#969)

• Avoid changing the global context cache behavior on module imports. Issue #968 (#977).

• Benchmark free energy plots now shift data to experimental mean. (#981)

• Skip introduction of counterion for charge changing mutations in vacuum and fix typo in the phase name in test_resume_protein_mutation_no_checkpoint (#991).

• Recovered logging capabilities respecting the LOGLEVEL environment variable. Issue #1018 (#1032).

Enhancements

• Improved continuous integration (CI) performance. (#961)

• PointMutationExecutor now accepts both solute and solvated PDBs (previously only accepted solute PDBs). (#967)

• Tests and examples are now using openff-2.0.0 force field instead of openff-1.0.0. (#971)

• Use names (instead of indices) for fetching the force components of a system, avoiding issues with force reordering upstream in openmm. Issue #993 (#976 and #1007)

• Increase stability of simulations by decreasing the default hydrogen mass to 3 amu in the PointMutationExecutor. Issue #982 (#983).

• Improved CI tests on both CPU and GPU. Better handling of temporary directories, closing opened reporter files when tests are finished, and using same environments for CPU and GPU (#985 #989 #1012)

• Performance increase when retrieving the old or new positions from the hybrid positions. Issue #1005 (#1020)

• Use of unique names for force components in HybridTopologyFactory (#1022).

• New function create_endstates_from_real_systems() for creating unsampled endstates for currently supported hybrid topology factories (#1023).

• Improve the readability and usability of PointMutationExecutor and updates how parameters are specified for solvation (#1024).

New features

• Introduce RESTCapableHybridTopologyFactory. Hybrid factory that allows for REST scaling, alchemical scaling, and 4th dimension softcore. So far, only working for protein mutations (#848 #992).

• New perses command line interface (CLI) perses-cli using click. Allowing a more friendly interface for users. It tests the running environment, sets the platform for the simulation and allows interactive overriding arbitrary options in the input YAML file. Former perses-relative CLI entry point is now deprecated (#972 #1021 #1027).

• Support for handling charge changes (by transforming a water into a counterion) for both protein mutations and ligands transformations. #862 (#973).

• Hybrid topology factory class name can now be specified using the hybrid_topology_factory parameter in the input YAML file (#988).

• Introduce unsampled_endstates boolean option in input YAML file, which enables/disables creation of unsampled endstates with long-range sterics correction. Issue #1033 (#1037).

0.9.5 - Release

Enhancements

• (PR #948 & PR #952) Add citation file, which should enhance the citation generated by Zenodo.

0.9.4 - Release

Performance optimizations:

• (PR #938) Separate ContextCache objects are now created for propagation and energy computation in replica exchange calculations to avoid periodic cycling behavior.

Bugfixes

• (PR #938) Mixed precision and deterministic forces are used by default.

• (PR #938) Velocities are refreshed from the Maxwell-Boltzmann distribution each iteration to avoid sudden cooling when simulations are resumed.

• (PR #944) Fixes to visualization module.

Enhancements

• (PR #909) Overhaul of Folding@home setup pipeline

• (PR #909) use_given_geometries is now True by default

• (PR #934) Preview of new CLI tool perses-cli that takes in a yaml file and creates dummy output. Work in progress. CLI/API still subject to changes.

0.9.3 - Release

Bugfixes

• (PR #894) Remove unused argument ‘implicitSolvent’ from SystemGenerator in tests.

• (PR #893) Add installation instructions to readme.

• (PR #892) Allow generate_dipeptide_top_pos_sys to accept demap_CBs.

• (PR #878) Fix stochastic failures in RepartitionedHybridTopologyFactory test.

• (PR #877) Fix naked charge padding (sigmas for hydroxyl hydrogens are changed from 1.0 nm to 0.06 nm).

• (PR #874) Added readme instructions on how to run perses examples using the docker container with GPUs/CUDA.

• (PR #866) Fix endstate validation handling in PointMutationExecutor.

• (PR #860) Simplify _construct_atom_map for protein mutations.

• Various CI fixes * PR #787 * PR #850 * PR #858 * PR #868 * PR #871 * PR #880 * PR #887 * PR #898

New features

• (PR #896) Drop support for older OpenMM versions. We now only support versions >= 7.6.0.

• (PR #924) Command line utility to automatically run and analyze benchmarks using the data set found in https://github.com/openforcefield/protein-ligand-benchmark/

0.9.2 - Bugfix release

Bugfixes

• (PR #835) Write out YAML file after all options are parsed and set. Saved as YAML original file name + date + time. Resolves #817.

• (PR #840) Minor improvements to point mutation executor. Make sure reverse geometry proposal is directly after forward proposal. Fixes formatting problem for complex positions.

• (PR #841) Minor improvements to PolymerProposalEngine.

• (PR #844) Minimal examples of amino acid (small molecule), protein-ligand and ligand mutations, with automated testing.

• (PR #849) Use an instance of ContextCache instead of the default global instance. More info at #613 (comment).

New features

• (PR #708) Create visualization module for generating PyMOL movies.

• (PR #834) Enable protein mutation transformations involving nonstandard amino acids, specifically: ASH, GLH, HID, HIE, HIP, LYN.

• (PR #838) Official Docker image hosted on docker hub docker pull choderalab/perses:0.9.2. Resolves #832.

0.9.1 - Bugfix release

Bugfixes

• (PR #830) Added limited support for resuming simulations from the CLI. Assumes simulations are only going to be resumed from the production step and not equilibration step. To extend the simulation, change n_cycles to a larger number and re-run the CLI tool. LOGLEVEL can now be set with an environmental variable when using the CLI tool.

• (PR #821) Added tests for the resume simulation functionality.

• (PR #828) Addresses (issue #815) by checking the potential energy of the proposed positions before generating the RepartitonedHybridTopologyFactory.

• (PR #809) The atom mapping facility was overhauled to address a bug in mapping rings (#805). Atom mapping is now handled via an AtomMapper factory that generates an AtomMapping class that localizes all relevant functionality.

• (PR #824) The default timestep is now 4 fs (was 1 fs) and the minimum openMM version is now 7.5.0

• (PR #812) Automatically set package version by git tag using versioneer

• (PR #804) Set the default temperature back to 300 K for relative_point_mutation_setup.py.

• (PR #796) Removed defunct atom_map argument from FEP constructor.