contact_distance Namespace Reference

Variables
str	fullhelp
	lo = options.LoosOptions("Compute distance matrix using contacts", fullhelp)
	default
	type
	help
	action
	args = lo.parse_args()
	system = loos.createSystem(args.model)
	chain = loos.selectAtoms(system, args.selection)
	residues = chain.splitByResidue()
	num_residues = len(residues)
	t
	traj = loos.pyloos.VirtualTrajectory(t)
int	num_pairs = len(residues) * (len(residues)-1) // 2
	contacts = numpy.zeros((len(traj), num_pairs), float)
	default_box = loos.GCoord(10000., 10000., 10000.)
int	frame_number = 0
	box = frame.periodicBox()
int	index = 0
	r1 = residues[i]
	contact
	dists = pdist(contacts, 'euclidean')
	square_dists = squareform(dists)
	outfile = open(args.outfile, "w")
	frame_boundaries = traj.frameBoundaries()
list	traj_header = [" traj start end filename"]
list	s = ["0", "0", str(len(traj)-1), args.traj]
int	i = len(args.traj) - 1
str	header = "\n".join(str(x) for x in [lo.header(), traj_header])

Detailed Description

From a trajectory, create an all-to-all distance matrix analogous to rmsds, but
working in the space of residue-residue contacts

Variable Documentation

contact

contact_distance.contact

Initial value:

=  r1.logisticContact(residues[j],
                                         args.radius,
                                         args.sigma,
                                         box)

t

contact_distance.t

Initial value:

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