packing_score_per_res Namespace Reference

Classes
class	FullHelp

Functions
	fullhelp ()

Variables
str	header = "#" + " ".join(sys.argv)
	parser = argparse.ArgumentParser(description="Compute per-residue packing score for small molecules")
	help
	nargs
	type
	default
	action
	args = parser.parse_args()
	system = loos.createSystem(args.system_file)
	protein = loos.selectAtoms(system, args.protein_selection)
	probe = loos.selectAtoms(system, args.probe_selection)
	residues = protein.splitByResidue()
	probes = probe.splitByMolecule()
int	frame_index = 0
	traj
	vtraj = loos.pyloos.VirtualTrajectory(traj)
	scores = numpy.zeros([len(residues), len(probes), len(vtraj)], float)
	box = frame.periodicBox()
	s = residues[r].packingScore(probes[p], box, False)
	fmt
	ave = numpy.add.reduce(scores, axis=0)
	resids = numpy.arange(1, len(residues)+1)
	pca = decomposition.PCA()

Detailed Description

Compute packing score between each residue of a protein and a number of
small molecules in solution.

Alan Grossfield, University of Rochester Medical Center

Variable Documentation

traj

packing_score_per_res.traj

Initial value:

=  loos.pyloos.Trajectory(args.traj[0],
                              system,
                              skip=args.skip,
                              stride=args.stride)