#include <SelectResiduesByLayer.hh>

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef std::string	String

typedef core::chemical::AA	AA

typedef core::pose::Pose	Pose

Public Member Functions
	SelectResiduesByLayer ()
	default constructor More...

	SelectResiduesByLayer (bool const pick_core, bool const pick_boundary, bool const pick_surface)
	value constructor More...

	SelectResiduesByLayer (String const pick)
	value constructor More...

virtual	~SelectResiduesByLayer ()
	destructor More...

void	initialize (Real burial, Real surface)

void	set_design_layer (bool const pick_core, bool const pick_boundary, bool const pick_surface)

void	pore_radius (Real const ps)
	set pore radius for colculating asa More...

void	sasa_surface (Real const r, String const ss="")
	accessible surface for evaluating residues are in surface or not More...

void	sasa_core (Real const r, String const ss="")
	accessible surface for evaluating residues are in core or not More...

void	make_rasmol_format_file (bool const b)
	accessible surface for evaluating residues are in core or not More...

void	use_sidechain_neighbors (bool const b)

void	exclude_aatypes_for_selection (utility::vector1< AA > const &aas)
	amino acid types excluded for selection More...

void	restrict_aatypes_for_selection (utility::vector1< AA > const &aas)
	amino acid types restricted for selection More...

Real	rsd_sasa (Size const i) const
	accessbile surface are of each residue More...

String	layer (Size const i) const
	return defined layer for each residue More...

utility::vector1< Size > const &	selected_boundary_residues () const
	selected residues on boundary More...

utility::vector1< Size > const &	selected_core_residues () const
	selected residues in core More...

utility::vector1< Size > const &	selected_surface_residues () const
	selected residues on surface More...

bool	use_sidechain_neighbors () const

utility::vector1< Size > const	compute (Pose const &pose, String secstruct="")
	apply More...

Protected Attributes
bool	pick_core_
	design core ? More...

bool	pick_boundary_
	design boundary ? More...

bool	pick_surface_
	design surface ? More...

Real	pore_radius_
	pore radius for calculating asa( accessible surface area ) More...

std::map< char, Real >	burial_
	asa pore radius for calculating asa More...

std::map< char, Real >	surface_
	pore radius for calculating asa More...

utility::vector1< AA >	excluded_aatypes_for_selection_
	amino acid types excluded for selection More...

utility::vector1< AA >	restricted_aatypes_for_selection_
	amino acid types restricted for selection More...

utility::vector1< Size >	selected_core_residues_
	selected residues in core More...

utility::vector1< Size >	selected_boundary_residues_
	selected residues at boundary More...

utility::vector1< Size >	selected_surface_residues_
	selected residues on surface More...

bool	make_rasmol_format_file_
	create rasmol format script for selected residues; red: surface, blue: core, green: boundary More...

bool	use_sidechain_neighbors_

utility::vector1< Real >	rsd_sasa_
	output in rasmol format More...

utility::vector1< String >	rsd_layer_

Private Member Functions
	SelectResiduesByLayer (SelectResiduesByLayer const &)
	copy constructor More...

utility::vector1< Real > const	calc_rsd_sasa (Pose const &pose) const
	return accessible surface area for each residue More...

utility::vector1< Real > const	calc_sc_neighbors (Pose const &pose) const
	return accessible surface area for each residue More...

Member Typedef Documentation

typedef core::chemical::AA protocols::toolbox::SelectResiduesByLayer::AA

typedef core::pose::Pose protocols::toolbox::SelectResiduesByLayer::Pose

typedef core::Real protocols::toolbox::SelectResiduesByLayer::Real

typedef core::Size protocols::toolbox::SelectResiduesByLayer::Size

typedef std::string protocols::toolbox::SelectResiduesByLayer::String

Constructor & Destructor Documentation

protocols::toolbox::SelectResiduesByLayer::SelectResiduesByLayer ( )

default constructor

References initialize().

protocols::toolbox::SelectResiduesByLayer::SelectResiduesByLayer	(	bool const	pick_core,
		bool const	pick_boundary,
		bool const	pick_surface
	)

value constructor

References initialize().

protocols::toolbox::SelectResiduesByLayer::SelectResiduesByLayer ( String const pick )

value constructor

selected layer can be given by string, for example, core_surface or core_boundary_surface

References initialize(), layer(), pick_boundary_, pick_core_, pick_surface_, runtime_assert, utility::string_split(), and protocols::TR.

protocols::toolbox::SelectResiduesByLayer::~SelectResiduesByLayer ( )

virtual

destructor

protocols::toolbox::SelectResiduesByLayer::SelectResiduesByLayer ( SelectResiduesByLayer const & rval )

private

copy constructor

Member Function Documentation

utility::vector1< core::Real > const protocols::toolbox::SelectResiduesByLayer::calc_rsd_sasa ( Pose const & pose ) const

private

return accessible surface area for each residue

References core::scoring::calc_per_atom_sasa(), core::pose::initialize_atomid_map(), pore_radius_, rsd_sasa(), core::id::AtomID_Map< T >::set(), and core::pose::Pose::total_residue().

Referenced by compute().

utility::vector1< core::Real > const protocols::toolbox::SelectResiduesByLayer::calc_sc_neighbors ( Pose const & pose ) const

private

return accessible surface area for each residue

References core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), numeric::xyzVector< class >::dot(), core::conformation::Residue::name3(), normalize, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::kinmatch::xyz().

Referenced by compute().

utility::vector1< core::Size > const protocols::toolbox::SelectResiduesByLayer::compute	(	Pose const &	pose,
		String	secstruct = `""`
	)

void protocols::toolbox::SelectResiduesByLayer::exclude_aatypes_for_selection ( utility::vector1< AA > const & aas )

amino acid types excluded for selection

References excluded_aatypes_for_selection_.

void protocols::toolbox::SelectResiduesByLayer::initialize	(	Real	burial,
		Real	surface
	)

References burial_, and surface_.

Referenced by protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), and SelectResiduesByLayer().

std::string protocols::toolbox::SelectResiduesByLayer::layer ( Size const i ) const

return defined layer for each residue

References rsd_layer_.

Referenced by SelectResiduesByLayer().

void protocols::toolbox::SelectResiduesByLayer::make_rasmol_format_file ( bool const b )

inline

accessible surface for evaluating residues are in core or not

References protocols::match::upstream::b, and make_rasmol_format_file_.

void protocols::toolbox::SelectResiduesByLayer::pore_radius ( Real const ps )

inline

set pore radius for colculating asa

References pore_radius_.

void protocols::toolbox::SelectResiduesByLayer::restrict_aatypes_for_selection ( utility::vector1< AA > const & aas )

amino acid types restricted for selection

References restricted_aatypes_for_selection_.

Referenced by protocols::simple_filters::RotamerBoltzmannWeight::compute().

core::Real protocols::toolbox::SelectResiduesByLayer::rsd_sasa ( Size const i ) const

accessbile surface are of each residue

References rsd_sasa_.

Referenced by calc_rsd_sasa(), and protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute().

void protocols::toolbox::SelectResiduesByLayer::sasa_core	(	Real const	r,
		String const	ss = `""`
	)

accessible surface for evaluating residues are in core or not

References burial_, and runtime_assert.

void protocols::toolbox::SelectResiduesByLayer::sasa_surface	(	Real const	r,
		String const	ss = `""`
	)

accessible surface for evaluating residues are in surface or not

References runtime_assert, and surface_.

utility::vector1< core::Size > const & protocols::toolbox::SelectResiduesByLayer::selected_boundary_residues ( ) const

selected residues on boundary

References selected_boundary_residues_.

utility::vector1< core::Size > const & protocols::toolbox::SelectResiduesByLayer::selected_core_residues ( ) const

selected residues in core

References selected_core_residues_.

utility::vector1< core::Size > const & protocols::toolbox::SelectResiduesByLayer::selected_surface_residues ( ) const

selected residues on surface

References selected_surface_residues_.

void protocols::toolbox::SelectResiduesByLayer::set_design_layer	(	bool const	pick_core,
		bool const	pick_boundary,
		bool const	pick_surface
	)

inline

References pick_boundary_, pick_core_, and pick_surface_.

void protocols::toolbox::SelectResiduesByLayer::use_sidechain_neighbors ( bool const b )

inline

References protocols::match::upstream::b, and use_sidechain_neighbors_.

bool protocols::toolbox::SelectResiduesByLayer::use_sidechain_neighbors ( ) const

References use_sidechain_neighbors_.

Member Data Documentation

std::map< char, Real > protocols::toolbox::SelectResiduesByLayer::burial_

protected

asa pore radius for calculating asa

Referenced by compute(), initialize(), and sasa_core().

utility::vector1< AA > protocols::toolbox::SelectResiduesByLayer::excluded_aatypes_for_selection_

protected

amino acid types excluded for selection

Referenced by compute(), and exclude_aatypes_for_selection().

bool protocols::toolbox::SelectResiduesByLayer::make_rasmol_format_file_

protected

create rasmol format script for selected residues; red: surface, blue: core, green: boundary

Referenced by compute(), and make_rasmol_format_file().

bool protocols::toolbox::SelectResiduesByLayer::pick_boundary_

protected

design boundary ?

Referenced by compute(), SelectResiduesByLayer(), and set_design_layer().

bool protocols::toolbox::SelectResiduesByLayer::pick_core_

protected

design core ?

Referenced by compute(), SelectResiduesByLayer(), and set_design_layer().

bool protocols::toolbox::SelectResiduesByLayer::pick_surface_

protected

design surface ?

Referenced by compute(), SelectResiduesByLayer(), and set_design_layer().

Real protocols::toolbox::SelectResiduesByLayer::pore_radius_

protected

pore radius for calculating asa( accessible surface area )

Referenced by calc_rsd_sasa(), compute(), and pore_radius().

utility::vector1< AA > protocols::toolbox::SelectResiduesByLayer::restricted_aatypes_for_selection_

protected

amino acid types restricted for selection

Referenced by compute(), and restrict_aatypes_for_selection().

utility::vector1< String > protocols::toolbox::SelectResiduesByLayer::rsd_layer_

protected

Referenced by compute(), and layer().

utility::vector1< Real > protocols::toolbox::SelectResiduesByLayer::rsd_sasa_

protected

output in rasmol format

asa for each residue

Referenced by compute(), and rsd_sasa().

utility::vector1< Size > protocols::toolbox::SelectResiduesByLayer::selected_boundary_residues_

protected

selected residues at boundary

Referenced by compute(), and selected_boundary_residues().

utility::vector1< Size > protocols::toolbox::SelectResiduesByLayer::selected_core_residues_

protected

selected residues in core

Referenced by compute(), and selected_core_residues().

utility::vector1< Size > protocols::toolbox::SelectResiduesByLayer::selected_surface_residues_

protected

selected residues on surface

Referenced by compute(), and selected_surface_residues().

std::map< char, Real > protocols::toolbox::SelectResiduesByLayer::surface_

protected

pore radius for calculating asa

Referenced by compute(), initialize(), and sasa_surface().

bool protocols::toolbox::SelectResiduesByLayer::use_sidechain_neighbors_

protected

Referenced by compute(), and use_sidechain_neighbors().

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

src/protocols/toolbox/SelectResiduesByLayer.hh
src/protocols/toolbox/SelectResiduesByLayer.cc

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation