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protocols::toolbox::SelectResiduesByLayer Class Reference

#include <SelectResiduesByLayer.hh>

Inheritance diagram for protocols::toolbox::SelectResiduesByLayer:
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Collaboration diagram for protocols::toolbox::SelectResiduesByLayer:
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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 selected layer can be given by string, for example, core_surface or core_boundary_surface 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 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...
 
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, Realburial_
 asa pore radius for calculating asa More...
 
std::map< char, Realsurface_
 pore radius for calculating asa More...
 
utility::vector1< AAexcluded_aatypes_for_selection_
 amino acid types excluded for selection More...
 
utility::vector1< AArestricted_aatypes_for_selection_
 amino acid types restricted for selection More...
 
utility::vector1< Sizeselected_core_residues_
 selected residues in core More...
 
utility::vector1< Sizeselected_boundary_residues_
 selected residues at boundary More...
 
utility::vector1< Sizeselected_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...
 
utility::vector1< Realrsd_sasa_
 output in rasmol format More...
 
utility::vector1< Stringrsd_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...
 

Member Typedef Documentation

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

value constructor

References initialize(), layer(), pick_boundary_, pick_core_, pick_surface_, 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
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 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().

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

accessible surface for evaluating residues are in core or not

References burial_.

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

accessible surface for evaluating residues are in surface or not

References 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

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().


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