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.

0.9.3 - Release¶

(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

(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/

(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).

(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.

(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.