hydrate_spheres - Add Hydration Layer to a Sphere Model

Add hydration shell of spheres around an existing sphere model read from a SCT format sphere file.

Useage:

Run using the command:

hydrate_spheres.py [-h] -i [INPUT_FILENAME] -o [OUTPUT_FILENAME]
                   [-p [PARAMETER_FILE]] [-n [HYDRATION_NO]]
                   [-c [CUTOFF]]

Arguments:

  -h, --help            show this help message and exit
  -i [INPUT_FILENAME], --input_filename [INPUT_FILENAME]
                        Path to the input file
  -o [OUTPUT_FILENAME], --output_filename [OUTPUT_FILENAME]
                        Path to the output file
  -p [PARAMETER_FILE], --parameter_file [PARAMETER_FILE]
                        Path to YAML format SCT parameter file
  -n [HYDRATION_NO], --hydration_no [HYDRATION_NO]
                        No. spheres to add as a hydration shell (1-26)
  -c [CUTOFF], --cutoff [CUTOFF]
                        Cutoff used to reduce the number of water spheres

Notes:

:qIf a parameter file is used it is prioritized over any parameters passed via command line flags.

Defaults:

• hydration_no = 26
• cutoff = 5

Output:

Hydrated Model: Output as four column - x, y and z coordinates and sphere radius (floating point numbers string formatted using 10.2f from Python).