0.10.1

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).

Benchmark data

Benchmarks run with small molecule force field (ff) and protein ff, openff-2.0.0 and ff14SB, respectively.

Tyk2

Cdk2