scattering Namespace Reference

Classes
class	FullHelp

Functions
	fullhelp ()
	deduceAtomicNumber (system)

Variables
str	header = " ".join(sys.argv)
	parser = argparse.ArgumentParser(description="Compute X-ray scattering")
	help
	action
	default
	type
	args = parser.parse_args()
	q_min = args.qmin
	q_max = args.qmax
	num_qvals = args.nq
	system = loos.createSystem(args.system_file)
	traj
	subset = loos.selectAtoms(system, args.selection)
	formFactors = loos.FormFactorSet()
	total = np.zeros([num_qvals])
	q_vals = np.arange(q_min, q_max, (q_max - q_min)/num_qvals)
float	rgyr = 0.0
float	qrg = q_vals * rgyr
float	kratky = qrg * qrg * total
	out_file

Detailed Description

Compute X-ray scattering using the spherical scattering approximation. Performs
both regular intensity and Kratky.

Structure factors from Szalóki, I. Empirical Equations for Atomic Form Factor
and Incoherent Scattering Functions. X Ray Spectrom 1996, 25 (1), 21–28

Function Documentation

deduceAtomicNumber()

scattering.deduceAtomicNumber

(

system

)

Given an AtomicGroup system, guess the atomic number based on the atom's
name. NOT a particularly robust method, but useable if your system file
doesn't give you the element.
Only knows hydrogen, carbon, nitrogen, oxygen, sulfur. This covers
protein, nuclei acid, and lipid, but will probably fail on salt (calcium and
sodium will probably clash)

Variable Documentation

traj

scattering.traj

Initial value:

=  loos.pyloos.Trajectory(args.traj_file, system,
                                  skip=args.skip, stride=args.stride)