inside_helices Namespace Reference

Variables
str	fullhelp
	parser = argparse.ArgumentParser(prog=sys.argv[0], epilog=fullhelp, formatter_class=argparse.RawDescriptionHelpFormatter)
	help
	type
	nargs
	default
	args = parser.parse_args()
	system = loos.createSystem(args.system_file)
	traj = loos.createTrajectory(args.traj_file, system)
	protein = loos.selectAtoms(system, args.protein_string)
	output_directory = args.directory
list	helices = []
	helix_centroids = loos.AtomicGroup()
	first
	last
str	helix_string = '(resid >= ' + first + ') ' + '&& (resid <= ' + last + ')'
	helix = loos.selectAtoms(protein, helix_string)
	target = loos.selectAtoms(system, args.target_string)
	chains = target.splitByResidue()
	tmp = args.zmax
	zmax
	zmin
list	slicers = []
tuple	block_size = (args.zmax - args.zmin) / args.zblocks
tuple	z1 = args.zmin + i*block_size
tuple	z2 = args.zmin + (i+1)*block_size
	ch = ConvexHull.ZSliceSelector(z1, z2)
int	frame = 0
dict	bound_lipids = {}
list	hulls = []
list	current_list = []
	centroid = helix.centroid()
	hull = ConvexHull.ConvexHull(helix_centroids)
int	atoms_inside = 0
	z = atom.coords().z()
	index = int((z-args.zmin)/block_size)
str	key = atom.segid() + ":" + str(atom.resid())
dict	frames = bound_lipids[lipid]
int	occ = float(len(frames)) / frame
	file = open(output_directory + "/" + lipid + ".dat", "w")

Detailed Description

Program to detect lipid chains that have made their way inside a membrane
protein