v2.02

Amendment to Jupyter Notebook included in zip file.

ChargePlacer archived with Zenodo

2.01

Update README.md with citation

ChargePlacer with examples and auxillary MD scripts

This is a command line script to determine a reasonably energy minimised proton sequence for an input PDB file (input) for a given charge state (charge). See Basic Usage. A search algorithm is used to sample proton permutations across chargeable side-chains and termini represented as point charges. The algorithm is inspired by the method described by refs 1–3, it produces a reproducible output proton sequence in far fewer steps than required for sampling all permutations.

Initial Release

:zap: Make release ready

Arguments have been updated for full command line access and output
saving commands have been adapted to give full all useful information.
A new output file `energies.txt` will be created when `-a` is used, this
contains the energies of each alanine scan. The format of all output
files is now tab-separated, with blank places indicated with '--' to
ensure compatibility with most text parsing tools. The README has been
updated to include usage guidance and some references for the algorithm.
A full description of the algorithm is nto included at this stage.