Rosetta 3.4
Public Types | Public Member Functions | Protected Attributes
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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List of all members.

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
 SelectResiduesByLayer (bool const pick_core, bool const pick_boundary, bool const pick_surface)
 value constructor
 SelectResiduesByLayer (String const pick)
 value constructor selected layer can be given by string, for example, core_surface or core_boundary_surface
 ~SelectResiduesByLayer ()
 destructor
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
void sasa_surface (Real const r, String const ss="")
 accessible surface for evaluating residues are in surface or not
void sasa_core (Real const r, String const ss="")
 accessible surface for evaluating residues are in core or not
void make_rasmol_format_file (bool const b)
 accessible surface for evaluating residues are in core or not
void exclude_aatypes_for_selection (utility::vector1< AA > const &aas)
 amino acid types excluded for selection
void restrict_aatypes_for_selection (utility::vector1< AA > const &aas)
 amino acid types restricted for selection
Real rsd_sasa (Size const i) const
 accessbile surface are of each residue
String layer (Size const i) const
 return defined layer for each residue
utility::vector1< Size > const & selected_boundary_residues () const
 selected residues on boundary
utility::vector1< Size > const & selected_core_residues () const
 selected residues in core
utility::vector1< Size > const & selected_surface_residues () const
 selected residues on surface
utility::vector1< Size > const compute (Pose const &pose, String secstruct="")
 apply

Protected Attributes

bool pick_core_
 design core ?
bool pick_boundary_
 design boundary ?
bool pick_surface_
 design surface ?
Real pore_radius_
 pore radius for calculating asa( accessible surface area )
std::map< char, Realburial_
 asa pore radius for calculating asa
std::map< char, Realsurface_
 pore radius for calculating asa
utility::vector1< AAexcluded_aatypes_for_selection_
 amino acid types excluded for selection
utility::vector1< AArestricted_aatypes_for_selection_
 amino acid types restricted for selection
utility::vector1< Sizeselected_core_residues_
 selected residues in core
utility::vector1< Sizeselected_boundary_residues_
 selected residues at boundary
utility::vector1< Sizeselected_surface_residues_
 selected residues on surface
bool make_rasmol_format_file_
 create rasmol format script for selected residues; red: surface, blue: core, green: boundary
utility::vector1< Realrsd_sasa_
 output in rasmol format
utility::vector1< Stringrsd_layer_

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 ( )

destructor


Member Function Documentation

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 
)
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_.

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

asa pore radius for calculating asa

Referenced by sasa_core().

amino acid types excluded for selection

Referenced by exclude_aatypes_for_selection().

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

Referenced by make_rasmol_format_file().

design boundary ?

Referenced by SelectResiduesByLayer(), and set_design_layer().

design core ?

Referenced by SelectResiduesByLayer(), and set_design_layer().

design surface ?

Referenced by SelectResiduesByLayer(), and set_design_layer().

pore radius for calculating asa( accessible surface area )

Referenced by pore_radius().

amino acid types restricted for selection

Referenced by restrict_aatypes_for_selection().

Referenced by layer().

output in rasmol format

asa for each residue

Referenced by rsd_sasa().

selected residues at boundary

Referenced by selected_boundary_residues().

selected residues in core

Referenced by selected_core_residues().

selected residues on surface

Referenced by selected_surface_residues().

pore radius for calculating asa

Referenced by sasa_surface().


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