#include <LayerOperations.hh>

Inheritance diagram for protocols::toolbox::task_operations::LayerOperations:

Collaboration diagram for protocols::toolbox::task_operations::LayerOperations:

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::TagPtr	TagPtr

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr	TagPtr

typedef pose::Pose	Pose

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 selected layer can be given by string, for example, core_surface or core_boundary_surface 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	~TaskOperation ()

virtual void	apply (Pose const &, PackerTask &) const =0
	Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...

virtual void	parse_tag (TagPtr)
	Used to parse an xml-like tag to load parameters and properties. More...

virtual void	parse_def (utility::lua::LuaObject const &def)

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, Real >	burial_
	asa pore radius for calculating asa More...

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

utility::vector1< Size >	selected_core_residues_
	amino acid types excluded for selection 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...

utility::vector1< Real >	rsd_sasa_
	asa for each residue More...

utility::vector1< String >	rsd_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...

Detailed Description

Definition at line 43 of file LayerOperations.hh.

Member Typedef Documentation

typedef core::pack::task::PackerTask protocols::toolbox::task_operations::LayerOperations::PackerTask

Definition at line 52 of file LayerOperations.hh.

typedef TaskOperation protocols::toolbox::task_operations::LayerOperations::parent

Definition at line 55 of file LayerOperations.hh.

typedef core::pose::Pose protocols::toolbox::task_operations::LayerOperations::Pose

Definition at line 49 of file LayerOperations.hh.

typedef core::Real protocols::toolbox::task_operations::LayerOperations::Real

Definition at line 50 of file LayerOperations.hh.

typedef core::Size protocols::toolbox::task_operations::LayerOperations::Size

Definition at line 45 of file LayerOperations.hh.

typedef std::string protocols::toolbox::task_operations::LayerOperations::String

Definition at line 47 of file LayerOperations.hh.

typedef utility::tag::TagPtr protocols::toolbox::task_operations::LayerOperations::TagPtr

Definition at line 56 of file LayerOperations.hh.

typedef core::pack::task::operation::TaskOperation protocols::toolbox::task_operations::LayerOperations::TaskOperation

Definition at line 53 of file LayerOperations.hh.

typedef core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::LayerOperations::TaskOperationOP

Definition at line 54 of file LayerOperations.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 80 of file LayerOperations.cc.

References initialize().

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

value constructor

Definition at line 92 of file LayerOperations.cc.

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

value constructor

Definition at line 103 of file LayerOperations.cc.

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

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

destructor

Definition at line 64 of file LayerOperations.cc.

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

private

copy constructor

Definition at line 127 of file LayerOperations.cc.

Member Function Documentation

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

private

return accessible surface area for each residue

Definition at line 227 of file LayerOperations.cc.

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().

core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::LayerOperations::clone ( ) const

virtual

make clone

clone

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

Definition at line 68 of file LayerOperations.cc.

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
	)

Definition at line 174 of file LayerOperations.cc.

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

Definition at line 200 of file LayerOperations.cc.

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

Definition at line 103 of file LayerOperations.hh.

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

Definition at line 92 of file LayerOperations.hh.

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

Definition at line 194 of file LayerOperations.cc.

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

Definition at line 159 of file LayerOperations.cc.

References burial_.

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

accessible surface for evaluating residues are in surface or not

Definition at line 144 of file LayerOperations.cc.

References surface_.

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

selected residues on boundary

Definition at line 206 of file LayerOperations.cc.

References selected_boundary_residues_.

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

selected residues in core

Definition at line 213 of file LayerOperations.cc.

References selected_core_residues_.

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

selected residues on surface

Definition at line 220 of file LayerOperations.cc.

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

Definition at line 84 of file LayerOperations.hh.

References pick_boundary_, pick_core_, and pick_surface_.

Member Data Documentation

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

protected

asa pore radius for calculating asa

Definition at line 162 of file LayerOperations.hh.

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

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

protected

which chain to pick

Definition at line 198 of file LayerOperations.hh.

Referenced by compute().

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

protected

design selection?

Definition at line 192 of file LayerOperations.hh.

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

protected

take chains apart, as defined by user specified jump number

Definition at line 201 of file LayerOperations.hh.

bool protocols::toolbox::task_operations::LayerOperations::make_rasmol_format_file_

protected

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

Definition at line 183 of file LayerOperations.hh.

Referenced by compute(), and make_rasmol_format_file().

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

protected

design/repack boundary ?

Definition at line 153 of file LayerOperations.hh.

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

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

protected

design/repack core ?

Definition at line 150 of file LayerOperations.hh.

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

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

protected

design surface ?

Definition at line 156 of file LayerOperations.hh.

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 )

Definition at line 159 of file LayerOperations.hh.

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

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

protected

repack the rest of the protein?

Definition at line 195 of file LayerOperations.hh.

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

protected

Definition at line 189 of file LayerOperations.hh.

Referenced by compute(), and layer().

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

protected

asa for each residue

Definition at line 186 of file LayerOperations.hh.

Referenced by compute(), and rsd_sasa().

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

protected

selected residues at boundary

Definition at line 177 of file LayerOperations.hh.

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

Definition at line 174 of file LayerOperations.hh.

Referenced by compute(), and selected_core_residues().

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

protected

selected residues on surface

Definition at line 180 of file LayerOperations.hh.

Referenced by compute(), and selected_surface_residues().

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

protected

pore radius for calculating asa

Definition at line 165 of file LayerOperations.hh.

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

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

src/protocols/toolbox/task_operations/LayerOperations.hh
src/protocols/toolbox/task_operations/LayerOperations.cc

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation