Despite the large number of lines changed, the changes consist essentially of

1. move classes and function from scripts to the library (hence so many lines changed), for example move class PrepareReceptor from wk_prepare_receptor.py to waterkit/receptor_prep.py
2. add methods to read and write strings, instead of files, for example PrepareReceptor.write_pdbqt_string and Molecule.from_pdbqt_string
3. add the new function that wraps the default waterkit workflow

Here's an example usage:

from waterkit import run_waterkit_and_gist

run_waterkit_and_gist(
    "rec42.pdb",
    output_prefix = "watah/rec42",
    box_center = (71.8, 74.5, 242.7),
    box_size = (13, 16, 16),
    autogrid_exec_path="/path/to/autogrid4",
    ignore_gaps = True,
    n_frames=108,
)

This writes the following files:

watah/rec42_prepared.pdb
watah/rec42-wk_gist-gO.dx
watah/rec42-wk_gist-Eww-dens.dx
watah/rec42-wk_gist-Esw-dens.dx
watah/rec42-wk_gist-dTStrans-dens.dx
watah/rec42-wk_gist-dTSorient-dens.dx