smooth_2D.m File Reference

Functions
	extended (1:bda,:)]

Variables
function	smoothed
	wr = param1(1)
	ar = param1(2)
	flagr = param1(3)
	wa = param2(1)
	aa = param2(2)
	flaga = param2(3)
filter have half size of	data [xf, yf] = meshgrid(linspace(-wr/4,wr/4,a/2), linspace(-wa/4,wa/4,b/2))
	Gaussian = exp(-(xf.^2/ar^2+yf.^2/aa^2))
	filter = Gaussian / sum(sum(Gaussian))
	bda = int8(a/4)
	bdb = int8(b/4)
else	symm = fliplr(data)
	extended = [symm(:,(b-bdb+1):b), data, symm(:,1:bdb)]

Function Documentation

extended()

extended	(	1:bda	,
		:
	)

Variable Documentation

aa

aa = param2(2)

ar

ar = param1(2)

Referenced by get_hb_info(), numeric::VoxelArray< _Float, _Value >::load(), and numeric::VoxelArray< _Float, _Value >::save().

bda

bda = int8(a/4)

bdb

bdb = int8(b/4)

data

filter have half size of data[xf, yf] = meshgrid(linspace(-wr/4,wr/4,a/2), linspace(-wa/4,wa/4,b/2))

Referenced by add_constraints(), analyze_base_pair_test(), detail::buffer< Container::value_type >::append(), RDCToolMover::apply(), InjectorMover::apply(), InterfaceStrandFinderMover::apply(), RNA_ScoreMover::apply(), bind_std_array(), bind_std_forward_list(), bind_std_stl_vector(), bind_T20_template_variadic(), ui::task::NetworkCall::call(), myspace::collect_silent(), correct_dunbrack(), correct_rama(), create_starting_template(), ui::task::Node::data_download_finished(), numeric::deserialize(), numeric::interpolation::spline::Interpolator::deserialize(), numeric::interpolation::spline::CompoundInterpolator::deserialize(), numeric::interpolation::spline::SimpleInterpolator::deserialize(), basic::mpi::DbMoverMessageListener::deserialize_data(), design_test(), do_clustering(), RDCToolMover::dump_averages(), dump_data(), dynamic_format_arg_store< Context >::emplace_arg(), evaluate_score(), utility::exit_handler(), fillPoseAndDataList(), lactamize::find_lactams(), generateRankedAlignments(), utility::thread::SharedThreadLocalData< T >::get(), get_base_steps(), Cache::get_data(), myspace::get_data_index(), utility::io::get_lines_from_file_data(), get_native_pdb_names(), SVC_Q::get_Q(), ONE_CLASS_Q::get_Q(), SVR_Q::get_Q(), get_score_terms(), get_sequence_and_secstruct_from_dssp(), basic::datacache::get_set_from_datamap(), get_torsion_list(), basic::get_usage_from_procfilesystem(), basic::datacache::WriteableCacheableMap::has(), myspace::initialize_data(), basic::datacache::WriteableCacheableMap::insert(), interp_linear(), numeric::kdtree::KDTree::KDTree(), numeric::fourier::SO3coeffs::Legendre(), numeric::nls::lm_lmdif(), numeric::nls::lmmin(), load_as_fullatom(), TNM::load_normal_modes(), main(), numeric::kdtree::make_points(), numeric::MathTensor< T >::MathTensor(), motif_scan(), my_main(), ui::widgets::PoseEditor::on_action_open_pose_triggered(), processChildren(), processChildrenIntensification(), RBSegmentRelax_test(), myspace::read_contact(), CapriTotalEnergy::read_datafile(), read_list_file(), read_list_pose_range(), read_master_pose_range(), read_patchdock_entry(), read_rama_map_file(), numeric::read_tensor_from_file(), readPoseAndData_SILENT(), basic::mpi::DbMoverMessageListener::receive(), binder::relevant_include(), myspace::DataClass::report_by_aa(), myspace::report_data(), basic::mpi::request_data_from_head_node(), RosettaJob::request_job_from_server(), rna_features_from_pose(), RunPepSpec(), myspace::scan_contact(), myspace::scan_Evalue(), basic::mpi::send_data_to_head_node(), set_secstruct_from_psipred_ss2(), setup_capri_data(), simple_opte_test(), basic::options::start_files(), utility::swap4_aligned(), Cache::swap_index(), GlycanClashCheckMover::tabulate_individual_data(), test(), test_k_square(), tf_specificity_test(), basic::Emitter::write(), myspace::write_silent(), and zf_test().

extended

extended = [symm(:,(b-bdb+1):b), data, symm(:,1:bdb)]

filter

filter = Gaussian / sum(sum(Gaussian))

Referenced by mh::filter::aa1(), mh::filter::aa2(), cen_fold(), mh::filter::coorderr(), MatchSet::cross(), doit(), mh::filter::dssp1(), mh::filter::dssp2(), DRRAFTER_util::easy_cat(), erraser_wrapper::erraser_single_res(), mh::filter::faatr(), mh::filter::faatr_or_hb(), mh::filter::faatr_or_hbbb(), mh::filter::filter(), CrystDesign::filter_and_report(), filter_frags(), mh::filter::filter_harvest(), mh::filter::filter_io(), mh::filter::hb_bb(), mh::filter::hb_bb_sc(), mh::filter::hb_sc(), InstantiateModulesBenchmark::instantiate_filters(), mh::filter::lig(), main(), mh::filter::max_seqsep(), mh::filter::maxdist2(), mh::filter::mindist2(), mh::filter::motif_type(), mh::filter::no_hb_bb(), mh::filter::nodisulf(), mh::filter::noloops(), mh::filter::not_restype(), mh::filter::not_restype_one(), mh::filter::occupancy(), mh::filter::oneloop(), mh::filter::pdb(), erraser_util::phenix_rna_validate(), mp_ddG::print_ddG_breakdown(), mp_ddG::print_score_labels_to_file(), mh::filter::restype(), mh::filter::restype1(), mh::filter::restype2(), mh::filter::restype_one(), run(), mh::filter::sasa(), mh::filter::score(), erraser_wrapper::seq_rebuild(), mh::filter::seqsep(), ui::network::BowmanModel::set_filter(), mh::filter::ss1(), mh::filter::ss2(), and mh::filter::uniformfrag().

flaga

col if flaga = param2(3)

flagr

end row if flagr = param1(3)

Gaussian

Gaussian = exp(-(xf.^2/ar^2+yf.^2/aa^2))

smoothed

function smoothed

Initial value:

= smooth_2D(data, param1, param2)
data = squeeze(data)

symm

else symm = fliplr(data)

Referenced by pointGroupHit::add_symmop(), MirrorSymmTest::apply(), ElecDensMinPackMinMover::apply(), MinTestMover::apply(), TCDock::dump_pdb(), main(), and run().

wa

wa = param2(1)

Referenced by numeric::nls::lm_qrfac(), numeric::nls::lm_qrsolv(), and prune_cb_pairs().

wr

wr = param1(1)

Referenced by numeric::statistics::w().