#include <SelectResiduesByLayer.hh>
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 @detail 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, bool const asu_only=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, Real > | burial_ |
| asa pore radius for calculating asa More... | |
| std::map< char, Real > | surface_ |
| pore radius for calculating asa More... | |
| utility::vector1< AA > | excluded_aatypes_for_selection_ |
| amino acid types excluded for selection More... | |
| utility::vector1< AA > | restricted_aatypes_for_selection_ |
| amino acid types restricted for selection More... | |
| utility::vector1< Size > | selected_core_residues_ |
| selected residues in core 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... | |
| bool | use_sidechain_neighbors_ |
| bool | is_selection_initialized_ |
| has the residue selection been computed? More... | |
| utility::vector1< Real > | rsd_sasa_ |
| asa for each residue More... | |
| utility::vector1< String > | rsd_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... | |
Member Typedef Documentation
◆ AA
◆ Pose
◆ Real
◆ Size
◆ String
| typedef std::string core::select::util::SelectResiduesByLayer::String |
Constructor & Destructor Documentation
◆ SelectResiduesByLayer() [1/4]
| core::select::util::SelectResiduesByLayer::SelectResiduesByLayer | ( | ) |
◆ SelectResiduesByLayer() [2/4]
| core::select::util::SelectResiduesByLayer::SelectResiduesByLayer | ( | SelectResiduesByLayer const & | src | ) |
Copy constructor.
◆ SelectResiduesByLayer() [3/4]
| core::select::util::SelectResiduesByLayer::SelectResiduesByLayer | ( | bool const | pick_core, |
| bool const | pick_boundary, | ||
| bool const | pick_surface | ||
| ) |
◆ SelectResiduesByLayer() [4/4]
| core::select::util::SelectResiduesByLayer::SelectResiduesByLayer | ( | String const & | pick | ) |
Value constructor @detail 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().
◆ ~SelectResiduesByLayer()
|
overridedefault |
Destructor.
destructor
Member Function Documentation
◆ angle_exponent()
|
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 compute().
◆ angle_shift_factor()
|
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 compute().
◆ calc_rsd_sasa()
|
private |
return accessible surface area for each residue
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::size().
Referenced by compute().
◆ clone()
| SelectResiduesByLayerOP core::select::util::SelectResiduesByLayer::clone | ( | ) | const |
Clone operator.
Construct a copy of this object and return an owning pointer to the copy.
◆ compute()
| utility::vector1< core::Size > const core::select::util::SelectResiduesByLayer::compute | ( | Pose const & | pose, |
| String const & | secstruct = "", |
||
| bool const | skip_dssp = false, |
||
| bool const | asu_only = false |
||
| ) |
apply
References core::pose::Pose::aa(), angle_exponent(), angle_shift_factor(), burial_, calc_rsd_sasa(), core::select::util::calc_sc_neighbors(), dist_exponent(), dist_midpoint(), protocols::simple_filters::dssp(), excluded_aatypes_for_selection_, is_selection_initialized_, core::pose::symmetry::is_symmetric(), make_rasmol_format_file_, core::conformation::membrane::out, pick_boundary_, pick_core_, pick_surface_, pore_radius_, restricted_aatypes_for_selection_, rsd_layer_, rsd_neighbor_denominator(), rsd_sasa_, selected_boundary_residues_, selected_core_residues_, selected_surface_residues_, core::pose::Pose::size(), surface_, core::pose::symmetry::symmetry_info(), TR(), and use_sidechain_neighbors_.
Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), and protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute().
◆ dist_exponent()
|
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 compute().
◆ dist_midpoint()
|
inline |
Midpoint of the distance falloff sigmoid.
Defaults to 9.0. Only used by the sidchain_neighbors code.
References dist_midpoint_.
Referenced by compute().
◆ exclude_aatypes_for_selection()
| 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_.
◆ initialize()
| void core::select::util::SelectResiduesByLayer::initialize | ( | Real const & | burial, |
| Real const & | surface | ||
| ) |
References core::scoring::burial, burial_, core::scoring::surface, and surface_.
Referenced by protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), and SelectResiduesByLayer().
◆ is_selection_initialized()
|
inline |
whether the selection has been computed once (it could be stale)
References is_selection_initialized_.
◆ layer()
| std::string core::select::util::SelectResiduesByLayer::layer | ( | Size const | i | ) | const |
◆ make_rasmol_format_file()
|
inline |
accessible surface for evaluating residues are in core or not
References protocols::match::upstream::b, and make_rasmol_format_file_.
◆ pore_radius()
|
inline |
set pore radius for colculating asa
References pore_radius_.
◆ restrict_aatypes_for_selection()
| 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().
◆ rsd_neighbor_denominator()
|
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 compute().
◆ rsd_sasa()
| 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().
◆ sasa_core()
| 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_.
◆ sasa_surface()
| 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_.
◆ selected_boundary_residues()
| utility::vector1< core::Size > const & core::select::util::SelectResiduesByLayer::selected_boundary_residues | ( | ) | const |
selected residues on boundary
References selected_boundary_residues_.
◆ selected_core_residues()
| utility::vector1< core::Size > const & core::select::util::SelectResiduesByLayer::selected_core_residues | ( | ) | const |
selected residues in core
References selected_core_residues_.
◆ selected_surface_residues()
| utility::vector1< core::Size > const & core::select::util::SelectResiduesByLayer::selected_surface_residues | ( | ) | const |
selected residues on surface
References selected_surface_residues_.
◆ set_angle_exponent()
|
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.
◆ set_angle_shift_factor()
|
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.
◆ set_design_layer()
|
inline |
References pick_boundary_, pick_core_, and pick_surface_.
◆ set_dist_exponent()
|
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.
◆ set_dist_midpoint()
|
inline |
Set the midpoint of the distance falloff sigmoid.
References dist_midpoint_, and protocols::hybridization::val.
◆ set_rsd_neighbor_denominator()
|
inline |
Set the value by which the number of residue neighbors is divided.
References rsd_neighbor_denominator_, and protocols::hybridization::val.
◆ use_sidechain_neighbors() [1/2]
| bool core::select::util::SelectResiduesByLayer::use_sidechain_neighbors | ( | ) | const |
References use_sidechain_neighbors_.
◆ use_sidechain_neighbors() [2/2]
|
inline |
References protocols::match::upstream::b, and use_sidechain_neighbors_.
Member Data Documentation
◆ 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().
◆ 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().
◆ burial_
|
protected |
asa pore radius for calculating asa
Referenced by compute(), initialize(), and sasa_core().
◆ cache_selection_
|
protected |
recompute residue selection every time?
◆ 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().
◆ 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().
◆ excluded_aatypes_for_selection_
|
protected |
amino acid types excluded for selection
Referenced by compute(), and exclude_aatypes_for_selection().
◆ is_selection_initialized_
|
protected |
has the residue selection been computed?
Referenced by compute(), and is_selection_initialized().
◆ 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().
◆ pick_boundary_
|
protected |
design boundary ?
Referenced by compute(), SelectResiduesByLayer(), and set_design_layer().
◆ pick_core_
|
protected |
design core ?
Referenced by compute(), SelectResiduesByLayer(), and set_design_layer().
◆ pick_surface_
|
protected |
design surface ?
Referenced by compute(), SelectResiduesByLayer(), and set_design_layer().
◆ pore_radius_
|
protected |
pore radius for calculating asa( accessible surface area )
Referenced by calc_rsd_sasa(), compute(), and pore_radius().
◆ restricted_aatypes_for_selection_
|
protected |
amino acid types restricted for selection
Referenced by compute(), and restrict_aatypes_for_selection().
◆ rsd_layer_
|
protected |
◆ 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().
◆ rsd_sasa_
|
protected |
asa for each residue
Referenced by compute(), and rsd_sasa().
◆ selected_boundary_residues_
|
protected |
selected residues at boundary
Referenced by compute(), and selected_boundary_residues().
◆ selected_core_residues_
|
protected |
selected residues in core
Referenced by compute(), and selected_core_residues().
◆ selected_surface_residues_
|
protected |
selected residues on surface
Referenced by compute(), and selected_surface_residues().
◆ surface_
|
protected |
pore radius for calculating asa
Referenced by compute(), initialize(), and sasa_surface().
◆ use_sidechain_neighbors_
|
protected |
Referenced by compute(), and use_sidechain_neighbors().
The documentation for this class was generated from the following files:
- src/core/select/util/SelectResiduesByLayer.hh
- src/core/select/util/SelectResiduesByLayer.cc
