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core::scoring::sasa::SasaMethod Class Referenceabstract

Abstract base class for SasaMethods. Feel free to edit as needed. Virt atms are skipped as radii=0. More...

#include <SasaMethod.hh>

Inheritance diagram for core::scoring::sasa::SasaMethod:
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Public Member Functions

 SasaMethod (Real probe_radius, SasaRadii radii_set)
 
 ~SasaMethod () override
 
virtual Real calculate (const pose::Pose &pose, const id::AtomID_Map< bool > &atom_subset, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa)=0
 Calculate Sasa. Atoms not calculated have -1 sasa in AtomID_Map. This is carried over for compatability purposes. More...
 
virtual std::string get_name () const =0
 
void set_include_probe_radius_in_calc (bool include_probe_radius)
 Include the probe radius in calc. Typical for SASA. More...
 
void set_probe_radius (Real probe_radius)
 Set the probe radius. Typical value is that of water at 1.4 A. More...
 
void set_radii_set (SasaRadii radii_set)
 Set the radii type. More...
 
void set_sasa_method_hp_mode (SasaMethodHPMode const mode_in)
 Set whether we're counting all SASA (default), polar SASA, or hydrophobic SASA. More...
 
SasaMethodHPMode sasa_method_hp_mode () const
 Get whether we're counting all SASA (default), polar SASA, or hydrophobic SASA. More...
 
void set_use_big_polar_hydrogen (bool big_polar_h)
 Legacy option to increase polar hydrogen radii to 1.08A. Supported for now. More...
 

Static Public Member Functions

static SasaMethodHPMode sasa_metric_mode_from_name (std::string const &mode_name)
 Given the name of the SasaMethodHPMode, get the mode. More...
 
static std::string sasa_metric_name_from_mode (SasaMethodHPMode const mode)
 Given the SasaMethodHPMode, get the name. More...
 
static std::string list_sasa_method_hp_modes ()
 Construct a comma-separeted string listing all of the sasa metric modes. More...
 
static bool skip_atom (core::conformation::Residue const &rsd, core::Size const atom_index, SasaMethodHPMode const hp_mode)
 Given a residue, an atom index, and a SasaMethodHPMode, determine whether the atom is one to skip (returns true) or count (returns false). More...
 
static bool is_polar_atom (core::conformation::Residue const &rsd, core::Size const atom_index)
 Classify an atom on a residue as "polar" for the purposes of SASA. More...
 

Protected Attributes

Real probe_radius_
 
SasaRadii radii_set_
 
bool include_probe_radius_
 
bool use_big_polar_H_
 

Private Attributes

SasaMethodHPMode sasa_method_hp_mode_ = SasaMethodHPMode::ALL_SASA
 Are we counting all SASA (default), polar SASA, or hydrophobic SASA? More...
 

Detailed Description

Abstract base class for SasaMethods. Feel free to edit as needed. Virt atms are skipped as radii=0.

Constructor & Destructor Documentation

core::scoring::sasa::SasaMethod::SasaMethod ( Real  probe_radius,
SasaRadii  radii_set 
)
core::scoring::sasa::SasaMethod::~SasaMethod ( )
overridedefault

Member Function Documentation

virtual Real core::scoring::sasa::SasaMethod::calculate ( const pose::Pose pose,
const id::AtomID_Map< bool > &  atom_subset,
id::AtomID_Map< Real > &  atom_sasa,
utility::vector1< Real > &  rsd_sasa 
)
pure virtual

Calculate Sasa. Atoms not calculated have -1 sasa in AtomID_Map. This is carried over for compatability purposes.

Implemented in core::scoring::sasa::LeGrandSasa.

virtual std::string core::scoring::sasa::SasaMethod::get_name ( ) const
pure virtual
bool core::scoring::sasa::SasaMethod::is_polar_atom ( core::conformation::Residue const &  rsd,
core::Size const  atom_index 
)
static
std::string core::scoring::sasa::SasaMethod::list_sasa_method_hp_modes ( )
static
SasaMethodHPMode core::scoring::sasa::SasaMethod::sasa_method_hp_mode ( ) const
inline

Get whether we're counting all SASA (default), polar SASA, or hydrophobic SASA.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References sasa_method_hp_mode_.

Referenced by core::scoring::sasa::LeGrandSasa::calculate().

SasaMethodHPMode core::scoring::sasa::SasaMethod::sasa_metric_mode_from_name ( std::string const &  mode_name)
static
std::string core::scoring::sasa::SasaMethod::sasa_metric_name_from_mode ( SasaMethodHPMode const  mode)
static
void core::scoring::sasa::SasaMethod::set_include_probe_radius_in_calc ( bool  include_probe_radius)

Include the probe radius in calc. Typical for SASA.

References include_probe_radius_.

void core::scoring::sasa::SasaMethod::set_probe_radius ( Real  probe_radius)

Set the probe radius. Typical value is that of water at 1.4 A.

References probe_radius_.

void core::scoring::sasa::SasaMethod::set_radii_set ( SasaRadii  radii_set)

Set the radii type.

References radii_set_.

void core::scoring::sasa::SasaMethod::set_sasa_method_hp_mode ( SasaMethodHPMode const  mode_in)

Set whether we're counting all SASA (default), polar SASA, or hydrophobic SASA.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::scoring::sasa::END_OF_LIST, and sasa_method_hp_mode_.

void core::scoring::sasa::SasaMethod::set_use_big_polar_hydrogen ( bool  big_polar_h)

Legacy option to increase polar hydrogen radii to 1.08A. Supported for now.

References use_big_polar_H_.

bool core::scoring::sasa::SasaMethod::skip_atom ( core::conformation::Residue const &  rsd,
core::Size const  atom_index,
SasaMethodHPMode const  hp_mode 
)
static

Given a residue, an atom index, and a SasaMethodHPMode, determine whether the atom is one to skip (returns true) or count (returns false).

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::scoring::sasa::ALL_SASA, core::scoring::sasa::HYDROPHOBIC_SASA, is_polar_atom(), and core::scoring::sasa::POLAR_SASA.

Referenced by core::scoring::sasa::LeGrandSasa::calculate().

Member Data Documentation

bool core::scoring::sasa::SasaMethod::include_probe_radius_
protected
Real core::scoring::sasa::SasaMethod::probe_radius_
protected
SasaRadii core::scoring::sasa::SasaMethod::radii_set_
protected
SasaMethodHPMode core::scoring::sasa::SasaMethod::sasa_method_hp_mode_ = SasaMethodHPMode::ALL_SASA
private

Are we counting all SASA (default), polar SASA, or hydrophobic SASA?

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Referenced by sasa_method_hp_mode(), and set_sasa_method_hp_mode().

bool core::scoring::sasa::SasaMethod::use_big_polar_H_
protected

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