core::scoring::sasa::SasaMethod Class Reference

Abstract base class for SasaMethods. Feel free to edit as needed. More...

#include <SasaMethod.hh>

Public Member Functions
	SasaMethod (Real probe_radius, SasaRadii radii_set)
virtual	~SasaMethod ()
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_use_big_polar_hydrogen (bool big_polar_h)
	Legacy option to increase polar hydrogen radii to 1.08A. Supported for now. More...

Protected Attributes
Real	probe_radius_
SasaRadii	radii_set_
bool	include_probe_radius_
bool	use_big_polar_H_

Detailed Description

Abstract base class for SasaMethods. Feel free to edit as needed.

Constructor & Destructor Documentation

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

core::scoring::sasa::SasaMethod::~SasaMethod ( )

virtual

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

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

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_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_.

Member Data Documentation

bool core::scoring::sasa::SasaMethod::include_probe_radius_

protected

Referenced by core::scoring::sasa::LeGrandSasa::calculate(), and set_include_probe_radius_in_calc().

Real core::scoring::sasa::SasaMethod::probe_radius_

protected

Referenced by core::scoring::sasa::LeGrandSasa::calculate(), and set_probe_radius().

SasaRadii core::scoring::sasa::SasaMethod::radii_set_

protected

Referenced by core::scoring::sasa::LeGrandSasa::calculate(), and set_radii_set().

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

protected

Referenced by core::scoring::sasa::LeGrandSasa::calculate(), and set_use_big_polar_hydrogen().

---

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

• src/core/scoring/sasa/SasaMethod.hh
• src/core/scoring/sasa/SasaMethod.cc