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core::select::util::SelectResiduesByLayer Class Reference

#include <SelectResiduesByLayer.hh>

Inheritance diagram for core::select::util::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 (SelectResiduesByLayer const &src)
 Copy 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...
 
 ~SelectResiduesByLayer () override
 Destructor. More...
 
SelectResiduesByLayerOP clone () const
 Clone operator. More...
 
void initialize (Real const &burial, Real const &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
 
bool is_selection_initialized ()
 whether the selection has been computed once (it could be stale) More...
 
core::Real const & dist_midpoint () const
 Midpoint of the distance falloff sigmoid. More...
 
void set_dist_midpoint (core::Real const &val)
 Set the midpoint of the distance falloff sigmoid. More...
 
core::Real const & rsd_neighbor_denominator () const
 Factor by which number of residue neighbors is divided. More...
 
void set_rsd_neighbor_denominator (core::Real const &val)
 Set the value by which the number of residue neighbors is divided. More...
 
core::Real const & angle_shift_factor () const
 Get the shift factor for the angle term. More...
 
void set_angle_shift_factor (core::Real const &val)
 Set the shift factor for the angle term. More...
 
core::Real const & angle_exponent () const
 Get the exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully. More...
 
void set_angle_exponent (core::Real const &val)
 Set the exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully. More...
 
core::Real const & dist_exponent () const
 Get the exponent for the distance term, which affects how sharp the falloff is with distance. More...
 
void set_dist_exponent (core::Real const &val)
 Set the exponent for the distance term, which affects how sharp the falloff is with distance. More...
 
utility::vector1< Size > const compute (Pose const &pose, String const &secstruct="", bool const skip_dssp=false)
 apply More...
 

Protected Attributes

bool pick_core_
 design core ? More...
 
bool pick_boundary_
 design boundary ? More...
 
bool pick_surface_
 design surface ? More...
 
bool cache_selection_
 recompute residue selection every time? 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...
 
bool use_sidechain_neighbors_
 
bool is_selection_initialized_
 has the residue selection been computed? More...
 
utility::vector1< Realrsd_sasa_
 asa for each residue More...
 
utility::vector1< Stringrsd_layer_
 
core::Real dist_midpoint_
 Midpoint for the distance falloff sigmoid. Defaults to 9.0. More...
 
core::Real rsd_neighbor_denominator_
 Divisor for the number of residue neighbours. Defaults to 1.0. More...
 
core::Real angle_shift_factor_
 Shift factor for the angle term. More...
 
core::Real angle_exponent_
 Exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully. More...
 
core::Real dist_exponent_
 Exponent for the distance term, which affects how sharp the falloff is with distance. More...
 

Private Member Functions

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

Constructor & Destructor Documentation

core::select::util::SelectResiduesByLayer::SelectResiduesByLayer ( )

Default constructor.

default constructor

References initialize().

core::select::util::SelectResiduesByLayer::SelectResiduesByLayer ( SelectResiduesByLayer const &  src)

Copy constructor.

core::select::util::SelectResiduesByLayer::SelectResiduesByLayer ( bool const  pick_core,
bool const  pick_boundary,
bool const  pick_surface 
)

Value constructor.

value constructor

References initialize().

core::select::util::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 TR().

core::select::util::SelectResiduesByLayer::~SelectResiduesByLayer ( )
overridedefault

Destructor.

destructor

Member Function Documentation

core::Real const& core::select::util::SelectResiduesByLayer::angle_exponent ( ) const
inline

Get the exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor is then added, and the resulting value is raised to the angle_exponent (default 2.0) and multiplied by the distance factor.

References angle_exponent_.

Referenced by calc_sc_neighbors().

core::Real const& core::select::util::SelectResiduesByLayer::angle_shift_factor ( ) const
inline

Get the shift factor for the angle term.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor (default 0.5) is then added, and the resulting value is raised to the angle_exponent and multiplied by the distance factor.

References angle_shift_factor_.

Referenced by calc_sc_neighbors().

utility::vector1< core::Real > const core::select::util::SelectResiduesByLayer::calc_rsd_sasa ( Pose const &  pose) const
private
utility::vector1< core::Real > const core::select::util::SelectResiduesByLayer::calc_sc_neighbors ( Pose const &  pose) const
private
SelectResiduesByLayerOP core::select::util::SelectResiduesByLayer::clone ( ) const

Clone operator.

Construct a copy of this object and return an owning pointer to the copy.

utility::vector1< core::Size > const core::select::util::SelectResiduesByLayer::compute ( Pose const &  pose,
String const &  secstruct = "",
bool const  skip_dssp = false 
)
core::Real const& core::select::util::SelectResiduesByLayer::dist_exponent ( ) const
inline

Get the exponent for the distance term, which affects how sharp the falloff is with distance.

The distance term is: 1/(1+exp(n*(d - m))), where d is the distance, n is the exponent set by this term, and m is the midpoint of the falloff. The n value sets the sharpness. Defaults to 1.0.

References dist_exponent_.

Referenced by calc_sc_neighbors().

core::Real const& core::select::util::SelectResiduesByLayer::dist_midpoint ( ) const
inline

Midpoint of the distance falloff sigmoid.

Defaults to 9.0. Only used by the sidchain_neighbors code.

References dist_midpoint_.

Referenced by calc_sc_neighbors().

void core::select::util::SelectResiduesByLayer::exclude_aatypes_for_selection ( utility::vector1< AA > const &  aas)

amino acid types excluded for selection

References excluded_aatypes_for_selection_.

void core::select::util::SelectResiduesByLayer::initialize ( Real const &  burial,
Real const &  surface 
)
bool core::select::util::SelectResiduesByLayer::is_selection_initialized ( )
inline

whether the selection has been computed once (it could be stale)

References is_selection_initialized_.

std::string core::select::util::SelectResiduesByLayer::layer ( Size const  i) const

return defined layer for each residue

References rsd_layer_.

Referenced by SelectResiduesByLayer().

void core::select::util::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 core::select::util::SelectResiduesByLayer::pore_radius ( Real const  ps)
inline

set pore radius for colculating asa

References pore_radius_.

void core::select::util::SelectResiduesByLayer::restrict_aatypes_for_selection ( utility::vector1< AA > const &  aas)

amino acid types restricted for selection

References restricted_aatypes_for_selection_.

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

core::Real const& core::select::util::SelectResiduesByLayer::rsd_neighbor_denominator ( ) const
inline

Factor by which number of residue neighbors is divided.

Defaults to 1.0. Only used by the sidchain_neighbors code.

References rsd_neighbor_denominator_.

Referenced by calc_sc_neighbors().

core::Real core::select::util::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 core::select::util::SelectResiduesByLayer::sasa_core ( Real const &  r,
String const &  ss = "" 
)

accessible surface for evaluating residues are in core or not

References burial_.

void core::select::util::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 & core::select::util::SelectResiduesByLayer::selected_boundary_residues ( ) const

selected residues on boundary

References selected_boundary_residues_.

utility::vector1< core::Size > const & core::select::util::SelectResiduesByLayer::selected_core_residues ( ) const

selected residues in core

References selected_core_residues_.

utility::vector1< core::Size > const & core::select::util::SelectResiduesByLayer::selected_surface_residues ( ) const

selected residues on surface

References selected_surface_residues_.

void core::select::util::SelectResiduesByLayer::set_angle_exponent ( core::Real const &  val)
inline

Set the exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor is then added, and the resulting value is raised to the angle_exponent (default 2.0) and multiplied by the distance factor.

References angle_exponent_, and protocols::hybridization::val.

void core::select::util::SelectResiduesByLayer::set_angle_shift_factor ( core::Real const &  val)
inline

Set the shift factor for the angle term.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor (default 0.5) is then added, and the resulting value is raised to the angle_exponent and multiplied by the distance factor.

References angle_shift_factor_, and protocols::hybridization::val.

void core::select::util::SelectResiduesByLayer::set_design_layer ( bool const  pick_core,
bool const  pick_boundary,
bool const  pick_surface 
)
inline
void core::select::util::SelectResiduesByLayer::set_dist_exponent ( core::Real const &  val)
inline

Set the exponent for the distance term, which affects how sharp the falloff is with distance.

The distance term is: 1/(1+exp(n*(d - m))), where d is the distance, n is the exponent set by this term, and m is the midpoint of the falloff. The n value sets the sharpness. Defaults to 1.0.

References dist_exponent_, and protocols::hybridization::val.

void core::select::util::SelectResiduesByLayer::set_dist_midpoint ( core::Real const &  val)
inline

Set the midpoint of the distance falloff sigmoid.

References dist_midpoint_, and protocols::hybridization::val.

void core::select::util::SelectResiduesByLayer::set_rsd_neighbor_denominator ( core::Real const &  val)
inline

Set the value by which the number of residue neighbors is divided.

References rsd_neighbor_denominator_, and protocols::hybridization::val.

void core::select::util::SelectResiduesByLayer::use_sidechain_neighbors ( bool const  b)
inline
bool core::select::util::SelectResiduesByLayer::use_sidechain_neighbors ( ) const

Member Data Documentation

core::Real core::select::util::SelectResiduesByLayer::angle_exponent_
protected

Exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor is then added, and the resulting value is raised to the angle_exponent (default 2.0) and multiplied by the distance factor.

Referenced by angle_exponent(), and set_angle_exponent().

core::Real core::select::util::SelectResiduesByLayer::angle_shift_factor_
protected

Shift factor for the angle term.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor (default 0.5) is then added, and the resulting value is raised to the angle_exponent and multiplied by the distance factor.

Referenced by angle_shift_factor(), and set_angle_shift_factor().

std::map< char, Real > core::select::util::SelectResiduesByLayer::burial_
protected

asa pore radius for calculating asa

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

bool core::select::util::SelectResiduesByLayer::cache_selection_
protected

recompute residue selection every time?

core::Real core::select::util::SelectResiduesByLayer::dist_exponent_
protected

Exponent for the distance term, which affects how sharp the falloff is with distance.

The distance term is: 1/(1+exp(n*(d - m))), where d is the distance, n is the exponent set by this term, and m is the midpoint of the falloff. The n value sets the sharpness. Defaults to 1.0.

Referenced by dist_exponent(), and set_dist_exponent().

core::Real core::select::util::SelectResiduesByLayer::dist_midpoint_
protected

Midpoint for the distance falloff sigmoid. Defaults to 9.0.

Only used by the sidechain_neighbors code.

Referenced by dist_midpoint(), and set_dist_midpoint().

utility::vector1< AA > core::select::util::SelectResiduesByLayer::excluded_aatypes_for_selection_
protected

amino acid types excluded for selection

Referenced by compute(), and exclude_aatypes_for_selection().

bool core::select::util::SelectResiduesByLayer::is_selection_initialized_
protected

has the residue selection been computed?

Referenced by compute(), and is_selection_initialized().

bool core::select::util::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 core::select::util::SelectResiduesByLayer::pick_boundary_
protected

design boundary ?

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

bool core::select::util::SelectResiduesByLayer::pick_core_
protected

design core ?

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

bool core::select::util::SelectResiduesByLayer::pick_surface_
protected

design surface ?

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

Real core::select::util::SelectResiduesByLayer::pore_radius_
protected

pore radius for calculating asa( accessible surface area )

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

utility::vector1< AA > core::select::util::SelectResiduesByLayer::restricted_aatypes_for_selection_
protected

amino acid types restricted for selection

Referenced by compute(), and restrict_aatypes_for_selection().

utility::vector1< String > core::select::util::SelectResiduesByLayer::rsd_layer_
protected

Referenced by compute(), and layer().

core::Real core::select::util::SelectResiduesByLayer::rsd_neighbor_denominator_
protected

Divisor for the number of residue neighbours. Defaults to 1.0.

Only used by the sidechain_neighbors code.

Referenced by rsd_neighbor_denominator(), and set_rsd_neighbor_denominator().

utility::vector1< Real > core::select::util::SelectResiduesByLayer::rsd_sasa_
protected

asa for each residue

Referenced by compute(), and rsd_sasa().

utility::vector1< Size > core::select::util::SelectResiduesByLayer::selected_boundary_residues_
protected

selected residues at boundary

Referenced by compute(), and selected_boundary_residues().

utility::vector1< Size > core::select::util::SelectResiduesByLayer::selected_core_residues_
protected

selected residues in core

Referenced by compute(), and selected_core_residues().

utility::vector1< Size > core::select::util::SelectResiduesByLayer::selected_surface_residues_
protected

selected residues on surface

Referenced by compute(), and selected_surface_residues().

std::map< char, Real > core::select::util::SelectResiduesByLayer::surface_
protected

pore radius for calculating asa

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

bool core::select::util::SelectResiduesByLayer::use_sidechain_neighbors_
protected

Referenced by compute(), and use_sidechain_neighbors().


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