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.
0.10.0 - 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
: whentopology_index_map
, which contains the atom indices involved in a particular torsion, is None – fixed by not trying to add that torsion whentopology_index_map
isNone
. (#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 ofopenff-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
usingclick
. 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. Formerperses-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¶
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¶
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 anAtomMapping
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.