Rosetta: protocols::magnesium::SampleGrid Class Reference

#include <SampleGrid.hh>

Inheritance diagram for protocols::magnesium::SampleGrid:

Inheritance graph

Public Member Functions
	SampleGrid (core::pose::Pose const &pose)

	~SampleGrid () override

utility::vector1< core::Vector >	get_mg_positions (core::pose::Pose const &pose)

void	set_input_scan_res (utility::vector1< core::Size > const &setting)

utility::vector1< core::Size >	input_scan_res () const

void	set_tether_to_closest_res (bool const &setting)

bool	tether_to_closest_res () const

void	set_xyz_step (core::Real const &setting)

core::Real	xyz_step () const

core::Real	xmin () const

core::Real	xmax () const

core::Real	ymin () const

core::Real	ymax () const

core::Real	zmin () const

core::Real	zmax () const

Private Member Functions
void	figure_out_box_bounds (core::pose::Pose const &pose)

void	create_grid ()

utility::vector1< core::Size >	figure_out_scan_res (utility::vector1< core::Size > const &input_scan_res, core::pose::Pose const &pose)

void	define_bins (core::Real const x, core::Real const subgrid_radius, core::Real const xmin, core::Size const xgridsize, core::Real const xyz_increment, core::Size &xbinmin, core::Size &xbinmax) const

core::Real	get_position (core::Size const xbin, core::Real const xmin, core::Real const xyz_increment) const

Private Attributes
bool	tether_to_closest_res_

core::Real	xyz_step_

core::Real	xmax_

core::Real	xmin_

core::Real	ymax_

core::Real	ymin_

core::Real	zmax_

core::Real	zmin_

utility::vector1< core::Size >	input_scan_res_

utility::vector1< core::Size >	scan_res_

ObjexxFCL::FArray3D< core::Real >	min_distance_grid_

Constructor & Destructor Documentation

protocols::magnesium::SampleGrid::SampleGrid ( core::pose::Pose const & pose )

protocols::magnesium::SampleGrid::~SampleGrid ( )

overridedefault

Member Function Documentation

void protocols::magnesium::SampleGrid::create_grid ( )

private

void protocols::magnesium::SampleGrid::define_bins	(	core::Real const	x,
		core::Real const	subgrid_radius,
		core::Real const	xmin,
		core::Size const	xgridsize,
		core::Real const	xyz_increment,
		core::Size &	xbinmin,
		core::Size &	xbinmax
	)		const

private

References protocols::mean_field::max(), and protocols::mean_field::min().

void protocols::magnesium::SampleGrid::figure_out_box_bounds ( core::pose::Pose const & pose )

private

References core::init::init(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

utility::vector1< core::Size > protocols::magnesium::SampleGrid::figure_out_scan_res	(	utility::vector1< core::Size > const &	input_scan_res,
		core::pose::Pose const &	pose
	)

private

References core::conformation::Residue::nbr_atom_xyz(), core::chemical::rings::q, core::pose::Pose::residue(), and core::pose::Pose::size().

utility::vector1< Vector > protocols::magnesium::SampleGrid::get_mg_positions ( core::pose::Pose const & pose )

References core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_mg_calculation(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::is_virtual(), core::chemical::rings::q, core::pose::Pose::residue(), core::scoring::rna::rna_scoring_info_from_pose(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

Real protocols::magnesium::SampleGrid::get_position	(	core::Size const	xbin,
		core::Real const	xmin,
		core::Real const	xyz_increment
	)		const

private

utility::vector1< core::Size > protocols::magnesium::SampleGrid::input_scan_res ( ) const

inline

References input_scan_res_.

void protocols::magnesium::SampleGrid::set_input_scan_res ( utility::vector1< core::Size > const & setting )

inline

References input_scan_res_.

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

void protocols::magnesium::SampleGrid::set_tether_to_closest_res ( bool const & setting )

inline

References tether_to_closest_res_.

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

void protocols::magnesium::SampleGrid::set_xyz_step ( core::Real const & setting )

inline

References xyz_step_.

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

bool protocols::magnesium::SampleGrid::tether_to_closest_res ( ) const

inline

References tether_to_closest_res_.

core::Real protocols::magnesium::SampleGrid::xmax ( ) const

inline

References xmax_.

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

core::Real protocols::magnesium::SampleGrid::xmin ( ) const

inline

References xmin_.

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

core::Real protocols::magnesium::SampleGrid::xyz_step ( ) const

inline

References xyz_step_.

core::Real protocols::magnesium::SampleGrid::ymax ( ) const

inline

References ymax_.

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

core::Real protocols::magnesium::SampleGrid::ymin ( ) const

inline

References ymin_.

core::Real protocols::magnesium::SampleGrid::zmax ( ) const

inline

References zmax_.

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

core::Real protocols::magnesium::SampleGrid::zmin ( ) const

inline

References zmin_.

Member Data Documentation

utility::vector1< core::Size > protocols::magnesium::SampleGrid::input_scan_res_

private

Referenced by input_scan_res(), and set_input_scan_res().

ObjexxFCL::FArray3D< core::Real > protocols::magnesium::SampleGrid::min_distance_grid_

private

utility::vector1< core::Size > protocols::magnesium::SampleGrid::scan_res_

private

bool protocols::magnesium::SampleGrid::tether_to_closest_res_

private

Referenced by set_tether_to_closest_res(), and tether_to_closest_res().

core::Real protocols::magnesium::SampleGrid::xmax_

private

Referenced by xmax().

core::Real protocols::magnesium::SampleGrid::xmin_

private

Referenced by xmin().

core::Real protocols::magnesium::SampleGrid::xyz_step_

private

Referenced by set_xyz_step(), and xyz_step().

core::Real protocols::magnesium::SampleGrid::ymax_

private

Referenced by ymax().

core::Real protocols::magnesium::SampleGrid::ymin_

private

Referenced by ymin().

core::Real protocols::magnesium::SampleGrid::zmax_

private

Referenced by zmax().

core::Real protocols::magnesium::SampleGrid::zmin_

private

Referenced by zmin().

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

src/protocols/magnesium/SampleGrid.hh
src/protocols/magnesium/SampleGrid.cc