protons-0.0.1a7

Many script updates, new features including refactoring of the neutralization ion code, importance sampling, support for tautomers and miscellaneous changes to ligand parametrization code.

Includes changes from
#136 , #137, #138 and #139

protons-0.0.1a6

Hotfix

Pins openmm version to < 7.3 due to precision bug.

protons-0.0.1a5

Notable new features

• Carboxylic acid MC sampling for dummy atoms
• Single proton asp and glu residues ASH, and GLH (as opposed to GL4 and AS4)
• Implicit solvent force field xml files (OBC2)
• Updated SAMS implementation with 4 stages, and more internal tracking of variables for analysis
• Updated analysis functions that handle multiple netCDF4 files
• Merging of the Calibration and Simulation class
• Script for parameterizing a ligand based on Epik calculations
• Script for preparing a constant-pH simulation/calibration
• Script for running sequential constant-pH simulations/calibrations

protons-0.0.1a4

This release adds a bugfix for a potentially breaking bug in NCMC protocols that use counter ions.

Incorporates #126

protons-0.0.1a3

This release contains extensions to protons.app.ligands, and additions and bugfixes for tests of the ligands module.

protons-0.0.1a2

This prerelease contains:

• several bugfixes for NCMC protocols that use saltswap
• Improved internal bookkeeping utilities for debugging and data retrieval purposes
• Additional features for netCDF reporters

protons-0.0.1a1

First alpha release of protons-0.0.1. Cutting a release to make protons conda installable.