0.8.1

Adding yaml file options to remove constraints
Testing for FAH generator

Fix protein mutations

• Update protein mutations API
• Add protein mutations to fah generator

bug fix with atom mapping strategies

Minor bug-fix release for atom mapping strategies

Adding Geometry-based single topology mapping

This release allows for the 'geometry' keyword criteria which fixes the bug whereby ligands were being modelled into the site with the incorrect binding mode. Solves issue #688

FAH pipeline

Major change in this release is the addition of the fah_perses_generator.py, which prepares files necessary for deployment on FAH.

The repo is now pinned to the newest version of openmm, 7.4.2.

Protein mutations and atom mapping

Added protein mutation functionality

Better and faster validation checks with CUDA-double precision

Improved analysis code

Functional simulation start

bugfix release to allow setup_relative_simulation.py to be run programmatically

More flexible atom mapping

Adding yaml options for atom and bond mappings for more flexibility

Separating AtomMapper function from SmallMoleculeSetProposal engine to allow for faster testing of ideas, demonstrated in atom-mapping example

Added perses-relative entry point for setup_relative_calculation.py

Perses-lite and sMC

This release:

• Restructuring of package
• Improvements to pairwise relative free energy calculations using REPEX
• New SequentialMonteCarlo class and algorithms for performing non-equilibrium switching
• Parallelisms for dask, trailblazing, and resampling capabilities

perses-0.4.0.zip
perses-0.4.0.tar.gz

New examples and fixes to hybrid factory

This release includes:

• New examples involving transdimensional nonequilibrium switching
• Fixes to the CDK2 example
• A new PremappedSmallMoleculeSetProposalEngine
• Fixes and updates to other parts of the code