protocols::magnesium::SampleGrid Class Reference

#include <SampleGrid.hh>

Inheritance diagram for protocols::magnesium::SampleGrid:

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

SampleGrid()

protocols::magnesium::SampleGrid::SampleGrid

(

core::pose::Pose const &

pose

)

~SampleGrid()

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

overridedefault

Member Function Documentation

create_grid()

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

private

define_bins()

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().

figure_out_box_bounds()

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::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

figure_out_scan_res()

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().

get_mg_positions()

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().

get_position()

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

private

input_scan_res()

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

inline

References input_scan_res_.

set_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().

set_tether_to_closest_res()

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().

set_xyz_step()

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

inline

References xyz_step_.

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

tether_to_closest_res()

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

inline

References tether_to_closest_res_.

xmax()

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

inline

References xmax_.

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

xmin()

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

inline

References xmin_.

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

xyz_step()

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

inline

References xyz_step_.

ymax()

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

inline

References ymax_.

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

ymin()

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

inline

References ymin_.

zmax()

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

inline

References zmax_.

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

zmin()

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

inline

References zmin_.

Member Data Documentation

input_scan_res_

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

private

Referenced by input_scan_res(), and set_input_scan_res().

min_distance_grid_

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

private

scan_res_

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

private

tether_to_closest_res_

bool protocols::magnesium::SampleGrid::tether_to_closest_res_

private

Referenced by set_tether_to_closest_res(), and tether_to_closest_res().

xmax_

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

private

Referenced by xmax().

xmin_

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

private

Referenced by xmin().

xyz_step_

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

private

Referenced by set_xyz_step(), and xyz_step().

ymax_

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

private

Referenced by ymax().

ymin_

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

private

Referenced by ymin().

zmax_

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

private

Referenced by zmax().

zmin_

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