calculate_curve - Calculate Scattering Curve from a Sphere Model

Calculate scattering curve from sphere model

Useage:

Run using the command:

calculate_curve.py [-h] -i [INPUT_FILENAME] [-o [OUTPUT_FILENAME]]
                   [-p [PARAMETER_FILE]] [-q [Q_MAX]] [-r [RADIUS]]
                   [-b [N_BINS]] [-n [N_POINTS]] [-s] [-e [SPREAD]]
                   [-w [WAVELENGTH]] [-d [DIVERGENCE]]

Arguments:

  -h, --help            show this help message and exit
  -i [INPUT_FILENAME], --input_filename [INPUT_FILENAME]
                        Path to the input PDB 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
  -q [Q_MAX], --q_max [Q_MAX]
                        Maximum q value in output curve
  -r [RADIUS], --radius [RADIUS]
                        Sphere radius
  -b [N_BINS], --n_bins [N_BINS]
                        No. bins to use in histogram of sphere separation
  -n [N_POINTS], --n_points [N_POINTS]
                        No. points in output curve
  -s, --smear           Apply smearing to curve
  -e [SPREAD], --spread [SPREAD]
                        Wavelength spread used to calculate smearing
  -w [WAVELENGTH], --wavelength [WAVELENGTH]
                        Wavelength used to calculate smearing
  -d [DIVERGENCE], --divergence [DIVERGENCE]
                        Beam divergence used to calculate smearing

Notes:

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

Defaults:

• q_max = 0.16
• radius = 3.77
• n_bins = 400
• n_points = 100
• spread = 0.1
• wavelength = 6.0
• divergence = 0.016

Output:

Two column text file - with Q and I/I(0) columns (floating point numbers as strings formatted using 7.4f in Python).

$Q$ units are Angstrom$^{-1}$.