spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.py File Reference

Namespaces
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib

Functions
def	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.load_centroid (fn, ncluster)
def	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.pbc (bin)
def	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.get_bb_bin_index (bb)
def	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.show_bb_table (bbtable)
def	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.ksr (dx, kappa)
def	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.correct_pbc (dat)

Variables
bool	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.draw = False
	main More...
float	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.cutoff = 1.6
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.restype = sys.argv[1]
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.sigma = float(sys.argv[2])
float	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.scale = 2.0*sigma*sigma
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.ndata = int(sys.argv[3])
string	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.inpfile = "./split/" + restype + ".dat"
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.inp = open(inpfile, 'r')
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.lines = inp.readlines()
list	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.xyzlist = []
list	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.intlist = []
list	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.bblist = []
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.Nd = len(lines)
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.prob = float(ndata)/Nd
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.pr = random()
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.dats = line.split()
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.dis = float(dats[0])
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.ang = float(dats[1])
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.dih = float(dats[2])
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.psi = float(dats[3])
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.phi = float(dats[4])
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.x = dis*sin(ang)*cos(dih)
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.y = dis*sin(ang)*sin(dih)
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.z = dis*cos(ang)
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.data = vstack(xyzlist)
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.save_data = data
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.Y = sp.squareform(sp.pdist(data, 'sqeuclidean'))
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.A = np.exp(-Y/scale)
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.D = np.zeros([Nd, Nd])
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.D_inv_sqr = np.zeros([Nd, Nd])
tuple	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.L = ( D_inv_sqr.dot(A) ).dot( D_inv_sqr )
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.eig_vals
	spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.eig_vecs = eig_vecs[eig_vals.argsort()]