kmeans_bb_dependent_rotlib Namespace Reference

Functions
def	load_centroid (fn, ncluster)
def	pbc (bin)
def	get_bb_bin_index (bb)
def	show_bb_table (bbtable)
def	get_prior (rot_bb_data, n)
def	get_prior_svd (rot_bb_data, n)

Variables
float	cutoff = 1.6
	restype = sys.argv[1]
	ncluster = int(sys.argv[2])
string	inpfile = "./split/" + restype + ".dat"
	inp = open(inpfile, 'r')
	lines = inp.readlines()
list	xyzlist = []
list	bblist = []
	dats = line.split()
	dis = float(dats[0])
	ang = float(dats[1])
	dih = float(dats[2])
	psi = float(dats[3])
	phi = float(dats[4])
	x = dis*sin(ang)*cos(dih)
	y = dis*sin(ang)*sin(dih)
	z = dis*cos(ang)
	data = vstack(xyzlist)
	cluster, find the centroid More...
	save_data = data
string	fn = "ref/" + restype
def	centroids = load_centroid(fn, ncluster)
	_
	idx
	dist
	nd = len(data)
	savend = nd
float	K0 = 0.5
list	center_int_lst = []
list	rot_bb_data_lst = []
	r = sqrt(x*x+y*y+z*z)
	t = arccos(z/r)
	p = arctan2(y,x)
	flag = i
	n = sum(flag)
	rot_bb_data = np.zeros([36,36])
	psi_bin
	phi_bin
	marginal_psi
	marginal_phi
	newN
int	nrot = 0

Function Documentation

get_bb_bin_index()

def kmeans_bb_dependent_rotlib.get_bb_bin_index

(

bb

)

References enumerate_junctions.int, and pbc().

get_prior()

def kmeans_bb_dependent_rotlib.get_prior	(		rot_bb_data,
			n
	)

get_prior_svd()

def kmeans_bb_dependent_rotlib.get_prior_svd	(		rot_bb_data,
			n
	)

References ObjexxFCL.len().

load_centroid()

def kmeans_bb_dependent_rotlib.load_centroid	(		fn,
			ncluster
	)

References run_backbone.float, and basic::database.open().

pbc()

def kmeans_bb_dependent_rotlib.pbc

(

bin

)

References enumerate_junctions.int.

Referenced by get_bb_bin_index().

show_bb_table()

def kmeans_bb_dependent_rotlib.show_bb_table

(

bbtable

)

References enumerate_junctions.int.

Variable Documentation

_

kmeans_bb_dependent_rotlib._

private

ang

kmeans_bb_dependent_rotlib.ang = float(dats[1])

bblist

list kmeans_bb_dependent_rotlib.bblist = []

center_int_lst

list kmeans_bb_dependent_rotlib.center_int_lst = []

centroids

kmeans_bb_dependent_rotlib.centroids = load_centroid(fn, ncluster)

cutoff

kmeans_bb_dependent_rotlib.cutoff = 1.6

data

kmeans_bb_dependent_rotlib.data = vstack(xyzlist)

cluster, find the centroid

dats

kmeans_bb_dependent_rotlib.dats = line.split()

dih

kmeans_bb_dependent_rotlib.dih = float(dats[2])

dis

kmeans_bb_dependent_rotlib.dis = float(dats[0])

dist

kmeans_bb_dependent_rotlib.dist

flag

kmeans_bb_dependent_rotlib.flag = i

fn

string kmeans_bb_dependent_rotlib.fn = "ref/" + restype

idx

kmeans_bb_dependent_rotlib.idx

inp

kmeans_bb_dependent_rotlib.inp = open(inpfile, 'r')

inpfile

string kmeans_bb_dependent_rotlib.inpfile = "./split/" + restype + ".dat"

K0

float kmeans_bb_dependent_rotlib.K0 = 0.5

lines

kmeans_bb_dependent_rotlib.lines = inp.readlines()

marginal_phi

kmeans_bb_dependent_rotlib.marginal_phi

marginal_psi

kmeans_bb_dependent_rotlib.marginal_psi

n

kmeans_bb_dependent_rotlib.n = sum(flag)

ncluster

kmeans_bb_dependent_rotlib.ncluster = int(sys.argv[2])

nd

kmeans_bb_dependent_rotlib.nd = len(data)

newN

kmeans_bb_dependent_rotlib.newN

Referenced by align_conformations().

nrot

int kmeans_bb_dependent_rotlib.nrot = 0

Referenced by numeric::AxisRotationSampler.AxisRotationSampler(), calc_scores(), correct_dunbrack(), CenRotSidechainMover.get_random_rotamer(), get_rotamer_type_index(), jacobi(), m_inv_gen(), main(), myspace.report_data(), and core::pack::annealer::FixbbSimAnnealer.run().

p

kmeans_bb_dependent_rotlib.p = arctan2(y,x)

phi

kmeans_bb_dependent_rotlib.phi = float(dats[4])

phi_bin

kmeans_bb_dependent_rotlib.phi_bin

psi

kmeans_bb_dependent_rotlib.psi = float(dats[3])

psi_bin

kmeans_bb_dependent_rotlib.psi_bin

r

kmeans_bb_dependent_rotlib.r = sqrt(x*x+y*y+z*z)

restype

kmeans_bb_dependent_rotlib.restype = sys.argv[1]

rot_bb_data

kmeans_bb_dependent_rotlib.rot_bb_data = np.zeros([36,36])

rot_bb_data_lst

list kmeans_bb_dependent_rotlib.rot_bb_data_lst = []

save_data

kmeans_bb_dependent_rotlib.save_data = data

savend

kmeans_bb_dependent_rotlib.savend = nd

t

kmeans_bb_dependent_rotlib.t = arccos(z/r)

x

def kmeans_bb_dependent_rotlib.x = dis*sin(ang)*cos(dih)

xyzlist

list kmeans_bb_dependent_rotlib.xyzlist = []

y

def kmeans_bb_dependent_rotlib.y = dis*sin(ang)*sin(dih)

z

def kmeans_bb_dependent_rotlib.z = dis*cos(ang)