spectral_cluster_kmeans_adaptive_kernel_density_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	ksr (dx, kappa)
def	correct_pbc (dat)

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

Function Documentation

correct_pbc()

def spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.correct_pbc

(

dat

)

References ObjexxFCL.len().

get_bb_bin_index()

def spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.get_bb_bin_index

(

bb

)

References enumerate_junctions.int, and pbc().

ksr()

def spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.ksr	(		dx,
			kappa
	)

load_centroid()

def spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.load_centroid	(		fn,
			ncluster
	)

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

pbc()

def spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.pbc

(

bin

)

References enumerate_junctions.int.

Referenced by get_bb_bin_index().

show_bb_table()

def spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.show_bb_table

(

bbtable

)

References enumerate_junctions.int.

Variable Documentation

A

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.A = np.exp(-Y/scale)

Referenced by PickBAB.apply(), IAMover.apply(), CrystFFTDock.apply(), numeric::geometry::hashing::SixDCoordinateBinner.bin_index(), bind_T01_enum(), bind_T02_function(), bind_T05_default(), bind_T10_inheritance(), bind_T12_insertion_operator(), bind_T15_inner_class_1(), bind_T15_inner_class_2(), bind_T30_include_incl_a_include(), bind_T31_include_for_class_incl_a_include(), bind_T33_buffer_protocol(), bind_T60_custom_shared(), bind_T70_module_local(), bind_T71_module_local(), numeric::kinematic_closure::radians.bridge_objects(), numeric::kinematic_closure.bridgeObjects(), numeric::kinematic_closure.build_dixon_matrices(), calc_B_values(), cl_score(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.compute_in_place(), numeric::kinematic_closure.dixon_eig(), numeric::kinematic_closure.dixon_sturm(), numeric::kinematic_closure.dixonResultant(), find_disulfides(), ObjexxFCL::FArray2< T >.is_identity(), main(), numeric::model_quality.MatrixMult(), mg_hires_pdbstats_from_pose(), numeric::linear_algebra.minimum_bounding_ellipse(), ObjexxFCL::FArray2< T >.operator*=(), output_chi_stats(), output_constraints(), output_residue_struct(), output_sugar_internal_dof(), numeric::kinematic_closure.point_value16(), numeric::kinematic_closure.point_value2(), numeric::kinematic_closure.point_value4(), numeric::kinematic_closure.point_value8(), numeric::kinematic_closure.polyProduct12x4(), numeric::kinematic_closure.polyProduct2x2(), numeric::kinematic_closure.polyProduct4sq(), numeric::kinematic_closure.polyProduct4x2(), numeric::kinematic_closure.polyProduct4x4(), numeric::kinematic_closure.polyProduct6x6(), numeric::kinematic_closure.polyProduct8sq(), numeric::kinematic_closure.polyProduct8x8(), predict_chem_map_test(), apps::pilot::momeara::HBondConformation.relax_pose_around_hbond(), report_and_dump(), ObjexxFCL::FArray2< T >.right_multiply_by_transpose(), basic::svd::SVD_Solver.run_score_svd_on_matrix(), ObjexxFCL::FArray2< T >.set_diagonal(), basic::svd::SVD_Solver.set_matrix_A(), utility::options::OptionCollection.show_help_hier(), utility::options::OptionCollection.show_option_help_hier(), simulate_ERMS(), SpacegroupHit.SpacegroupHit(), ObjexxFCL::FArray2< T >.symmetric(), numeric::kinematic_closure.test_dixon(), test_PCA_eigen(), numeric::kinematic_closure.test_point_value2(), numeric::kinematic_closure.test_polyProduct2x2(), numeric::kinematic_closure.test_polyProduct4sq(), numeric::kinematic_closure.test_polyProduct4x2(), numeric::kinematic_closure.test_polyProduct4x4(), numeric::kinematic_closure.test_polyProduct6x6(), numeric::kinematic_closure.test_triaxialCoefficients(), ObjexxFCL::FArray2< T >.to_diag(), ObjexxFCL::FArray2< T >.to_identity(), ObjexxFCL::FArray2< T >.transpose(), numeric::kinematic_closure::radians.triaxialCoefficients(), and numeric::kinematic_closure.vectorDiff().

ang

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.ang = float(dats[1])

bblist

list spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.bblist = []

cutoff

float spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.cutoff = 1.6

D

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.D = np.zeros([Nd, Nd])

Referenced by binder::IncludeSet.add_decl(), binder.add_relevant_include_for_decl(), MirrorSymmTest.apply(), ElecDensMinPackMinMover.apply(), MinTestMover.apply(), MinCenrotMover.apply(), CenRotRelaxMover.apply(), OutputCenrotIntCoord.apply(), RepackMinCenrotMover.apply(), CenRotSidechainMover.apply(), numeric::kinematic_closure::radians.bridge_objects(), numeric::kinematic_closure.bridgeObjects(), numeric::kinematic_closure.build_dixon_matrices(), compute_chi(), numeric::statistics.Dawson(), ObjexxFCL::FArray2D< T >.diag(), ObjexxFCL::KeyFArray2D< T >.diag(), numeric::kinematic_closure.dixon_eig(), numeric::kinematic_closure.dixon_sturm(), numeric::kinematic_closure.dixonResultant(), dock(), dump_hbond_pdb(), fit_centroid_to_the_best_rot(), generate_disulfide_conformations(), basic::datacache::DataCache< Data >.get(), myspace.get_movemap(), basic::datacache::DataCache< Data >.get_raw_const_ptr(), basic::datacache::DataCache< Data >.get_raw_ptr(), ObjexxFCL::FArray2D< T >.identity(), ObjexxFCL::KeyFArray2D< T >.identity(), ik_his_clamp(), numeric::xyzMatrix< T >.inverse(), binder.is_banned_symbol(), line_cone_intersection(), main(), output_sugar_internal_dof(), print_tree(), process_the_pose(), apps::pilot::momeara::HBondConformation.relax_pose_around_hbond(), replace_torsion_angles(), reroot_restype(), run(), run_hh(), myspace::Scheduler.run_md(), run_zn2his(), simple_hbond_test(), numeric::kinematic_closure.test_dixon(), numeric::kinematic_closure.test_triaxialCoefficients(), numeric::kinematic_closure::radians.triaxialCoefficients(), numeric::kinematic_closure.triaxialCoefficients(), tweak_coords(), vary_bond_length(), vary_geometry_backbone(), and vary_geometry_sidechains().

D_inv_sqr

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.D_inv_sqr = np.zeros([Nd, Nd])

data

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.data = vstack(xyzlist)

dats

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.dats = line.split()

dih

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.dih = float(dats[2])

dis

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.dis = float(dats[0])

draw

bool spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.draw = False

main

eig_vals

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.eig_vals

eig_vecs

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.eig_vecs = eig_vecs[eig_vals.argsort()]

inp

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

inpfile

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

intlist

list spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.intlist = []

L

tuple spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.L = ( D_inv_sqr.dot(A) ).dot( D_inv_sqr )

Referenced by utility.argsort(), utility::small_vectorL< T, L, BUFFER_SIZE >.at(), numeric::kinematic_closure.cross(), numeric::kinematic_closure::radians.cross(), rosetta_binders.fixedsizearray_add_on_binder(), detail.format_str_quoted(), numeric::xyzTransform< T >.intersect3D_2Planes(), intersecting_bpy_axes(), intersecting_disulfide_axes(), main(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_has_insertion_operator(), printf_arg_formatter< OutputIt, Char >.operator()(), utility::small_vectorL< T, L, BUFFER_SIZE >.operator[](), numeric::kinematic_closure.test_cross(), to_wstring(), numeric::kinematic_closure::radians.triaxialCoefficients(), numeric::kinematic_closure.triaxialCoefficients(), vprint(), and printf_arg_formatter< OutputIt, Char >.write_null_pointer().

lines

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.lines = inp.readlines()

Nd

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.Nd = len(lines)

ndata

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.ndata = int(sys.argv[3])

Referenced by myspace.report_data(), and utility.swap4_aligned().

phi

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.phi = float(dats[4])

pr

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.pr = random()

Referenced by main(), output_packstat(), output_packstat_pdb(), sheffler_voids(), basic::TracerImpl::TracerProxyImpl.t_flush(), test(), and test_known_value().

prob

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.prob = float(ndata)/Nd

Referenced by CountContact.apply(), PairDistance.apply(), CenRotCanonicalMover.apply(), get_boltzmann_probabilities(), main(), motif_scan(), my_main(), ONE_CLASS_Q.ONE_CLASS_Q(), read_rama_map_file(), single_position_motif_scan(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), SVC_Q.SVC_Q(), svm_binary_svc_probability(), svm_check_parameter(), svm_cross_validation(), svm_group_classes(), svm_svr_probability(), svm_train(), svm_train_one(), SVR_Q.SVR_Q(), and myspace.test_bbgauss().

psi

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.psi = float(dats[3])

restype

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.restype = sys.argv[1]

save_data

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.save_data = data

scale

float spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.scale = 2.0*sigma*sigma

Referenced by TCDock.__dock_base__(), correct_dunbrack(), correct_rama(), MatchSet.cross(), numeric::fourier::SHT.forwardS2(), main(), make_bonded_rna_move(), myspace.project(), sample_rna_dofs_new(), myspace::Scheduler.set_pertscale(), numeric::fourier::SHT.setup_Weights(), basic::svd::SVD_Solver.svdcmp(), numeric::linear_algebra.svdcmp(), and myspace.test_NMrelaxer().

sigma

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.sigma = float(sys.argv[2])

Referenced by get_angles(), main(), basic::sampling::orientations.pind(), sigmoid_train(), numeric.sign_transfered(), and SimulateCryoMover.three_fine_projections_from_xyz().

x

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.x = dis*sin(ang)*cos(dih)

xyzlist

list spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.xyzlist = []

y

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.y = dis*sin(ang)*sin(dih)

Y

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.Y = sp.squareform(sp.pdist(data, 'sqeuclidean'))

Referenced by numeric::interpolation.bilinearly_interpolated(), bind_T10_inheritance(), numeric::interpolation::Histogram< X, Y >.derivative_linear(), numeric::xyzTransform< T >.from_quaternion(), numeric::MathVector< T >.MakeVector(), numeric.MakeVector(), and ObjexxFCL.sign().

z

spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.z = dis*cos(ang)