Public Member Functions
	SimulateCryoMover ()

void	apply (core::pose::Pose pose)

void	recenter_pose_at_origin (core::pose::Pose &)

void	set_extent (core::pose::Pose const &, core::Real)

void	pose_to_xyz (core::pose::Pose const &, utility::vector1< core::Real > &all_x, utility::vector1< core::Real > &all_y, utility::vector1< core::Real > &all_z)

void	downsample_xyz (core::Real, utility::vector1< core::Real > &, utility::vector1< core::Real > &, utility::vector1< core::Real > &)

void	truncate_xyz (utility::vector1< core::Real > &, utility::vector1< core::Real > &, utility::vector1< core::Real > &, utility::vector1< core::Size > &, utility::vector1< core::Size > &, utility::vector1< core::Size > &)

void	recenter_to_img_coordinates (utility::vector1< core::Real > &, utility::vector1< core::Real > &, utility::vector1< core::Real > &)

void	add_flat_noise (ObjexxFCL::FArray3D< float > &, core::Real)

void	add_gaussian_noise (ObjexxFCL::FArray3D< float > &, core::Real, core::Real)

void	add_perlin_noise (ObjexxFCL::FArray3D< float > &, core::Real, core::Real)

ObjexxFCL::FArray3D< float >	three_projections_from_xyz (utility::vector1< core::Size > &, utility::vector1< core::Size > &, utility::vector1< core::Size > &)

ObjexxFCL::FArray3D< float >	three_fine_projections_from_xyz (utility::vector1< core::Real > &, utility::vector1< core::Real > &, utility::vector1< core::Real > &, core::Real, core::Real)

void	append_to_density (ObjexxFCL::FArray3D< float > const &, ObjexxFCL::FArray3D< float > &, int, int)

void	writeStarFile (std::string filename)

void	normalize_projections (ObjexxFCL::FArray3D< float > &)

void	offset_projections (ObjexxFCL::FArray3D< float > &, core::Real)

void	set_bfactors (core::pose::Pose pose)

void	set_image_stack (core::scoring::electron_density::ElectronDensity const &stack_in)

core::scoring::electron_density::ElectronDensity	get_image_stack ()

void	set_NR (core::Size NR)

core::Size	get_NR ()

void	set_noise_range (core::Real noise_range)

core::Real	get_noise_range ()

void	set_gauss_multiplier (core::Real gauss_multiplier)

core::Real	get_gauss_multiplier ()

void	set_gauss_offset (core::Real gauss_offset)

core::Real	get_gauss_offset ()

void	set_pixel_size (core::Real pixel_size)

core::Real	get_pixel_size ()

void	set_resolution (core::Real resolution)

core::Real	get_resolution ()

void	set_box_size_multiplier (core::Real box_size_multiplier)

core::Real	get_box_size_multiplier ()

void	set_perlin_noise_multiplier (core::Real perlin_noise_multiplier)

core::Real	get_perlin_noise_multiplier ()

void	set_perlin_noise_offset (core::Real perlin_noise_offset)

core::Real	get_perlin_noise_offset ()

void	set_integration_test (bool const integration_test)

core::Real	get_integration_test () const

Private Attributes
core::scoring::electron_density::ElectronDensity	image_stack_

numeric::xyzVector< core::Size >	extents_

core::Size	num_rotations_to_project_from_

core::Real	gauss_offset_

core::Real	gauss_multiplier_

core::Real	noise_range_

core::Real	pixel_size_

core::Real	dist_to_detector_

core::Real	resolution_

core::Real	box_size_multiplier_

core::Real	perlin_noise_multiplier_

core::Real	perlin_noise_offset_

bool	integration_test_

utility::vector1< core::Real >	bfactors_

utility::vector1< core::Real >	scatter_factors_

Constructor & Destructor Documentation

◆ SimulateCryoMover()

SimulateCryoMover::SimulateCryoMover ( )

inline

Member Function Documentation

◆ add_flat_noise()

void SimulateCryoMover::add_flat_noise	(	ObjexxFCL::FArray3D< float > &	three_projections,
		core::Real	noise_range
	)

References basic::options::OptionKeys::remodel::rg, numeric::random::rg(), ObjexxFCL::FArray3D< T >::u1(), ObjexxFCL::FArray3D< T >::u2(), ObjexxFCL::FArray3D< T >::u3(), x, predPRE::y, and predPRE::z.

Referenced by apply().

◆ add_gaussian_noise()

void SimulateCryoMover::add_gaussian_noise	(	ObjexxFCL::FArray3D< float > &	three_projections,
		core::Real	gauss_multiplier,
		core::Real	gauss_offset
	)

References numeric::random::gaussian(), ObjexxFCL::FArray3D< T >::u1(), ObjexxFCL::FArray3D< T >::u2(), ObjexxFCL::FArray3D< T >::u3(), x, predPRE::y, and predPRE::z.

Referenced by apply().

◆ add_perlin_noise()

void SimulateCryoMover::add_perlin_noise	(	ObjexxFCL::FArray3D< float > &	three_projections,
		core::Real	perlin_noise_multiplier,
		core::Real	perlin_noise_offset
	)

Add perlin noise to all pixels

References amino_acids::frequency, basic::options::option, ObjexxFCL::FArray3D< T >::u1(), ObjexxFCL::FArray3D< T >::u2(), ObjexxFCL::FArray3D< T >::u3(), x, predPRE::y, and predPRE::z.

Referenced by apply().

◆ append_to_density()

void SimulateCryoMover::append_to_density	(	ObjexxFCL::FArray3D< float > const &	three_projections,
		ObjexxFCL::FArray3D< float > &	density,
		int	offset,
		int	proj_num
	)

References score_vs_rmsd::density, offset, ObjexxFCL::FArray3D< T >::u1(), ObjexxFCL::FArray3D< T >::u2(), x, and predPRE::y.

◆ apply()

void SimulateCryoMover::apply ( core::pose::Pose pose )

References add_flat_noise(), add_gaussian_noise(), add_perlin_noise(), basic::options::OptionKeys::cryst::crystal_refine, score_vs_rmsd::density, downsample_xyz(), numeric::UniformRotationSampler::get(), create_a3b_hbs::i, create_a3b_hbs::j, normalize_projections(), numeric::UniformRotationSampler::nrots(), offset_projections(), basic::options::option, beta_nonlocal::pose, pose_to_xyz(), basic::options::OptionKeys::out::prefix, numeric::random::random_range(), recenter_pose_at_origin(), recenter_to_img_coordinates(), set_extent(), three_fine_projections_from_xyz(), basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute(), and main().

◆ downsample_xyz()

void SimulateCryoMover::downsample_xyz	(	core::Real	divisor,
		utility::vector1< core::Real > &	all_x,
		utility::vector1< core::Real > &	all_y,
		utility::vector1< core::Real > &	all_z
	)

References create_a3b_hbs::i.

Referenced by apply().

◆ get_box_size_multiplier()

core::Real SimulateCryoMover::get_box_size_multiplier ( )

inline

◆ get_gauss_multiplier()

core::Real SimulateCryoMover::get_gauss_multiplier ( )

inline

◆ get_gauss_offset()

core::Real SimulateCryoMover::get_gauss_offset ( )

inline

◆ get_image_stack()

core::scoring::electron_density::ElectronDensity SimulateCryoMover::get_image_stack ( )

inline

◆ get_integration_test()

core::Real SimulateCryoMover::get_integration_test ( ) const

inline

◆ get_noise_range()

core::Real SimulateCryoMover::get_noise_range ( )

inline

◆ get_NR()

core::Size SimulateCryoMover::get_NR ( )

inline

◆ get_perlin_noise_multiplier()

core::Real SimulateCryoMover::get_perlin_noise_multiplier ( )

inline

◆ get_perlin_noise_offset()

core::Real SimulateCryoMover::get_perlin_noise_offset ( )

inline

◆ get_pixel_size()

core::Real SimulateCryoMover::get_pixel_size ( )

inline

◆ get_resolution()

core::Real SimulateCryoMover::get_resolution ( )

inline

◆ normalize_projections()

void SimulateCryoMover::normalize_projections ( ObjexxFCL::FArray3D< float > & three_projections )

References max(), min(), ObjexxFCL::FArray3D< T >::u1(), ObjexxFCL::FArray3D< T >::u2(), ObjexxFCL::FArray3D< T >::u3(), x, predPRE::y, and predPRE::z.

Referenced by apply().

◆ offset_projections()

void SimulateCryoMover::offset_projections	(	ObjexxFCL::FArray3D< float > &	three_projections,
		core::Real	particle_offset
	)

References ObjexxFCL::FArray3D< T >::u1(), ObjexxFCL::FArray3D< T >::u2(), ObjexxFCL::FArray3D< T >::u3(), x, predPRE::y, and predPRE::z.

Referenced by apply().

◆ pose_to_xyz()

void SimulateCryoMover::pose_to_xyz	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	all_x,
		utility::vector1< core::Real > &	all_y,
		utility::vector1< core::Real > &	all_z
	)

References predPRE::chain, detail::find(), basic::options::option, beta_nonlocal::pose, cal_NBR_radius::res_num, basic::options::OptionKeys::inout::dbms::user, and x.

Referenced by apply().

◆ recenter_pose_at_origin()

void SimulateCryoMover::recenter_pose_at_origin ( core::pose::Pose & pose )

References val2thr::atom, beta_nonlocal::pose, and cal_NBR_radius::res_num.

Referenced by apply().

◆ recenter_to_img_coordinates()

void SimulateCryoMover::recenter_to_img_coordinates	(	utility::vector1< core::Real > &	all_x,
		utility::vector1< core::Real > &	all_y,
		utility::vector1< core::Real > &	all_z
	)

References center, and create_a3b_hbs::i.

Referenced by apply().

◆ set_bfactors()

void SimulateCryoMover::set_bfactors ( core::pose::Pose pose )

References predPRE::chain, detail::find(), basic::options::option, beta_nonlocal::pose, cal_NBR_radius::res_num, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and x.

◆ set_box_size_multiplier()

void SimulateCryoMover::set_box_size_multiplier ( core::Real box_size_multiplier )

inline

Referenced by set_options().

◆ set_extent()

void SimulateCryoMover::set_extent	(	core::pose::Pose const &	pose,
		core::Real	pixel_size
	)

References max(), beta_nonlocal::pose, cal_NBR_radius::res_num, round(), subloop_histogram::ymax, and subloop_histogram::ymin.

Referenced by apply().

◆ set_gauss_multiplier()

void SimulateCryoMover::set_gauss_multiplier ( core::Real gauss_multiplier )

inline

Referenced by set_options().

◆ set_gauss_offset()

void SimulateCryoMover::set_gauss_offset ( core::Real gauss_offset )

inline

Referenced by set_options().

◆ set_image_stack()

void SimulateCryoMover::set_image_stack ( core::scoring::electron_density::ElectronDensity const & stack_in )

inline

◆ set_integration_test()

void SimulateCryoMover::set_integration_test ( bool const integration_test )

inline

References basic::options::OptionKeys::magnesium::integration_test.

Referenced by set_options().

◆ set_noise_range()

void SimulateCryoMover::set_noise_range ( core::Real noise_range )

inline

Referenced by set_options().

◆ set_NR()

void SimulateCryoMover::set_NR ( core::Size NR )

inline

Referenced by set_options().

◆ set_perlin_noise_multiplier()

void SimulateCryoMover::set_perlin_noise_multiplier ( core::Real perlin_noise_multiplier )

inline

Referenced by set_options().

◆ set_perlin_noise_offset()

void SimulateCryoMover::set_perlin_noise_offset ( core::Real perlin_noise_offset )

inline

Referenced by set_options().

◆ set_pixel_size()

void SimulateCryoMover::set_pixel_size ( core::Real pixel_size )

inline

Referenced by set_options().

◆ set_resolution()

void SimulateCryoMover::set_resolution ( core::Real resolution )

inline

Referenced by set_options().

◆ three_fine_projections_from_xyz()

ObjexxFCL::FArray3D< float > SimulateCryoMover::three_fine_projections_from_xyz	(	utility::vector1< core::Real > &	all_x,
		utility::vector1< core::Real > &	all_y,
		utility::vector1< core::Real > &	all_z,
		core::Real	resolution,
		core::Real	pixel_size
	)

References ObjexxFCL::FArray3D< T >::contains(), basic::options::OptionKeys::cryst::crystal_refine, ObjexxFCL::FArray3D< T >::dimension(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, build_jacobian::distance, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::mp::mp, basic::options::option, numeric::constants::d::pi, ObjexxFCL::pow(), basic::options::OptionKeys::remodel::rg, numeric::random::rg(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::sigma, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and basic::Tracer::Warning.

Referenced by apply().

◆ three_projections_from_xyz()

ObjexxFCL::FArray3D< float > SimulateCryoMover::three_projections_from_xyz	(	utility::vector1< core::Size > &	all_x,
		utility::vector1< core::Size > &	all_y,
		utility::vector1< core::Size > &	all_z
	)

References ObjexxFCL::FArray3D< T >::dimension(), and create_a3b_hbs::i.

◆ truncate_xyz()

void SimulateCryoMover::truncate_xyz	(	utility::vector1< core::Real > &	all_x,
		utility::vector1< core::Real > &	all_y,
		utility::vector1< core::Real > &	all_z,
		utility::vector1< core::Size > &	all_x_rnd,
		utility::vector1< core::Size > &	all_y_rnd,
		utility::vector1< core::Size > &	all_z_rnd
	)

References create_a3b_hbs::i, and round().

◆ writeStarFile()

void SimulateCryoMover::writeStarFile ( std::string filename )

References lactamize::filename, create_a3b_hbs::i, create_a3b_hbs::j, and numeric::interpolation::to_string().

Member Data Documentation

◆ bfactors_

utility::vector1< core::Real > SimulateCryoMover::bfactors_

private

◆ box_size_multiplier_

core::Real SimulateCryoMover::box_size_multiplier_

private

◆ dist_to_detector_

core::Real SimulateCryoMover::dist_to_detector_

private

◆ extents_

numeric::xyzVector< core::Size > SimulateCryoMover::extents_

private

◆ gauss_multiplier_

core::Real SimulateCryoMover::gauss_multiplier_

private

◆ gauss_offset_

core::Real SimulateCryoMover::gauss_offset_

private

◆ image_stack_

core::scoring::electron_density::ElectronDensity SimulateCryoMover::image_stack_

private

◆ integration_test_

bool SimulateCryoMover::integration_test_

private

◆ noise_range_

core::Real SimulateCryoMover::noise_range_

private

◆ num_rotations_to_project_from_

core::Size SimulateCryoMover::num_rotations_to_project_from_

private

◆ perlin_noise_multiplier_

core::Real SimulateCryoMover::perlin_noise_multiplier_

private

◆ perlin_noise_offset_

core::Real SimulateCryoMover::perlin_noise_offset_

private

◆ pixel_size_

core::Real SimulateCryoMover::pixel_size_

private

◆ resolution_

core::Real SimulateCryoMover::resolution_

private

◆ scatter_factors_

utility::vector1< core::Real > SimulateCryoMover::scatter_factors_

private

The documentation for this class was generated from the following file:

src/apps/public/electron_density/sim_cryo.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ SimulateCryoMover()

Member Function Documentation

◆ add_flat_noise()

◆ add_gaussian_noise()

◆ add_perlin_noise()

◆ append_to_density()

◆ apply()

◆ downsample_xyz()

◆ get_box_size_multiplier()

◆ get_gauss_multiplier()

◆ get_gauss_offset()

◆ get_image_stack()

◆ get_integration_test()

◆ get_noise_range()

◆ get_NR()

◆ get_perlin_noise_multiplier()

◆ get_perlin_noise_offset()

◆ get_pixel_size()

◆ get_resolution()

◆ normalize_projections()

◆ offset_projections()

◆ pose_to_xyz()

◆ recenter_pose_at_origin()

◆ recenter_to_img_coordinates()

◆ set_bfactors()

◆ set_box_size_multiplier()

◆ set_extent()

◆ set_gauss_multiplier()

◆ set_gauss_offset()

◆ set_image_stack()

◆ set_integration_test()

◆ set_noise_range()

◆ set_NR()

◆ set_perlin_noise_multiplier()

◆ set_perlin_noise_offset()

◆ set_pixel_size()

◆ set_resolution()

◆ three_fine_projections_from_xyz()

◆ three_projections_from_xyz()

◆ truncate_xyz()

◆ writeStarFile()

Member Data Documentation

◆ bfactors_

◆ box_size_multiplier_

◆ dist_to_detector_

◆ extents_

◆ gauss_multiplier_

◆ gauss_offset_

◆ image_stack_

◆ integration_test_

◆ noise_range_

◆ num_rotations_to_project_from_

◆ perlin_noise_multiplier_

◆ perlin_noise_offset_

◆ pixel_size_

◆ resolution_

◆ scatter_factors_