Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Attributes | Private Member Functions | List of all members
protocols::toolbox::task_operations::LayerOperations Class Reference

#include <LayerOperations.hh>

Public Types

typedef core::Size Size
 
typedef std::string String
 
typedef core::pose::Pose Pose
 
typedef core::Real Real
 
typedef
core::pack::task::PackerTask 
PackerTask
 
typedef
core::pack::task::operation::TaskOperation 
TaskOperation
 
typedef
core::pack::task::operation::TaskOperationOP 
TaskOperationOP
 
typedef TaskOperation parent
 
typedef utility::tag::TagCOP TagCOP
 

Public Member Functions

 LayerOperations ()
 default constructor More...
 
 LayerOperations (bool const pick_core, bool const pick_boundary, bool const pick_surface)
 value constructor More...
 
 LayerOperations (String const pick)
 value constructor More...
 
 ~LayerOperations ()
 destructor More...
 
virtual TaskOperationOP clone () const
 make clone 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...
 
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)
 apply More...
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual void apply (Pose const &, PackerTask &) const =0
 

Protected Attributes

bool pick_core_
 design/repack core ? More...
 
bool pick_boundary_
 design/repack 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< Sizeselected_core_residues_
 amino acid types excluded for selection 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_
 asa for each residue More...
 
utility::vector1< Stringrsd_layer_
 
bool design_
 design selection? More...
 
bool repack_rest_
 repack the rest of the protein? More...
 
core::Size chain_
 which chain to pick More...
 
core::Size jump_
 take chains apart, as defined by user specified jump number More...
 

Private Member Functions

 LayerOperations (LayerOperations 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::task_operations::LayerOperations::LayerOperations ( )

default constructor

References initialize().

protocols::toolbox::task_operations::LayerOperations::LayerOperations ( bool const  pick_core,
bool const  pick_boundary,
bool const  pick_surface 
)

value constructor

References initialize().

protocols::toolbox::task_operations::LayerOperations::LayerOperations ( 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::toolbox::task_operations::TR.

protocols::toolbox::task_operations::LayerOperations::~LayerOperations ( )

destructor

protocols::toolbox::task_operations::LayerOperations::LayerOperations ( LayerOperations const &  rval)
private

copy constructor

Member Function Documentation

utility::vector1< core::Real > const protocols::toolbox::task_operations::LayerOperations::calc_rsd_sasa ( Pose const &  pose) const
private
core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::LayerOperations::clone ( ) const
virtual

make clone

clone

Implements core::pack::task::operation::TaskOperation.

utility::vector1< core::Size > const protocols::toolbox::task_operations::LayerOperations::compute ( Pose const &  pose)
void protocols::toolbox::task_operations::LayerOperations::initialize ( Real  burial,
Real  surface 
)

References burial_, and surface_.

Referenced by LayerOperations().

std::string protocols::toolbox::task_operations::LayerOperations::layer ( Size const  i) const

return defined layer for each residue

References rsd_layer_.

Referenced by LayerOperations().

void protocols::toolbox::task_operations::LayerOperations::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::task_operations::LayerOperations::pore_radius ( Real const  ps)
inline

set pore radius for colculating asa

References pore_radius_.

core::Real protocols::toolbox::task_operations::LayerOperations::rsd_sasa ( Size const  i) const

accessbile surface are of each residue

amino acid types excluded for selection

accessbile surface are of each residue

References rsd_sasa_.

Referenced by calc_rsd_sasa().

void protocols::toolbox::task_operations::LayerOperations::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::task_operations::LayerOperations::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::task_operations::LayerOperations::selected_boundary_residues ( ) const

selected residues on boundary

References selected_boundary_residues_.

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

selected residues in core

References selected_core_residues_.

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

selected residues on surface

References selected_surface_residues_.

void protocols::toolbox::task_operations::LayerOperations::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::task_operations::LayerOperations::burial_
protected

asa pore radius for calculating asa

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

core::Size protocols::toolbox::task_operations::LayerOperations::chain_
protected

which chain to pick

Referenced by compute().

bool protocols::toolbox::task_operations::LayerOperations::design_
protected

design selection?

core::Size protocols::toolbox::task_operations::LayerOperations::jump_
protected

take chains apart, as defined by user specified jump number

bool protocols::toolbox::task_operations::LayerOperations::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::task_operations::LayerOperations::pick_boundary_
protected

design/repack boundary ?

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

bool protocols::toolbox::task_operations::LayerOperations::pick_core_
protected

design/repack core ?

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

bool protocols::toolbox::task_operations::LayerOperations::pick_surface_
protected

design surface ?

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

Real protocols::toolbox::task_operations::LayerOperations::pore_radius_
protected

pore radius for calculating asa( accessible surface area )

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

bool protocols::toolbox::task_operations::LayerOperations::repack_rest_
protected

repack the rest of the protein?

utility::vector1< String > protocols::toolbox::task_operations::LayerOperations::rsd_layer_
protected

Referenced by compute(), and layer().

utility::vector1< Real > protocols::toolbox::task_operations::LayerOperations::rsd_sasa_
protected

asa for each residue

Referenced by compute(), and rsd_sasa().

utility::vector1< Size > protocols::toolbox::task_operations::LayerOperations::selected_boundary_residues_
protected

selected residues at boundary

Referenced by compute(), and selected_boundary_residues().

utility::vector1< Size > protocols::toolbox::task_operations::LayerOperations::selected_core_residues_
protected

amino acid types excluded for selection

amino acid types restricted for selection selected residues in core

Referenced by compute(), and selected_core_residues().

utility::vector1< Size > protocols::toolbox::task_operations::LayerOperations::selected_surface_residues_
protected

selected residues on surface

Referenced by compute(), and selected_surface_residues().

std::map< char, Real > protocols::toolbox::task_operations::LayerOperations::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: