Variables
str	fullhelp

	lo

	default

	help

	type

	action

	args = lo.parse_args()

	header = lo.header()

	system = loos.createSystem(args.model)

list	all_trajs = []

list	out_names = []

	num_trajs = len(args.traj)

	traj = loos.pyloos.Trajectory(t, system)

	t_base = basename(t)

	core

	ext

	no_hydrogens = loos.selectAtoms(system, "!hydrogen")

	target = loos.selectAtoms(no_hydrogens, args.selection)

	residues = target.splitByResidue()

	num_res = len(residues)

int	total_frames = 0

	num_pairs = int((num_res * (num_res-1))/2)

	frac_contacts_frame

	symm_indexer = SymmMatrix(num_res)

	frac_contacts

int	current_frame = 0

	index = symm_indexer.toFlat(i, j)

	average = np.add.reduce(frac_contacts, axis=2)

	out_file

	pca = decomposition.PCA(n_components=args.ncomp)

	labels = np.arange(pca.n_components)

	fmt

	i

	j

Detailed Description

Track a set of contacts through a trajectory.  Intended for use with a protein
or RNA, to track all residue-residue contacts within the trajectory.

Variable Documentation

all_contacts.frac_contacts

Initial value:

1= np.zeros([len(residues), len(residues), num_trajs],

2 np.float64)

all_contacts.frac_contacts_frame

Initial value:

1= np.zeros([num_pairs, total_frames],

2 np.float64)

all_contacts.lo

Initial value:

1= options.LoosOptions("Compute probability of residue-residue contacts",

2 fullhelp)