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:

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

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

bool core::scoring::sasa::SasaMethod::is_polar_atom	(	core::conformation::Residue const &	rsd,
		core::Size const	atom_index
	)

static

Classify an atom on a residue as "polar" for the purposes of SASA.

References core::chemical::ResidueType::atom_is_polar_hydrogen(), core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), core::chemical::ResidueType::heavyatom_is_an_acceptor(), and core::conformation::Residue::type().

Referenced by skip_atom().

std::string core::scoring::sasa::SasaMethod::list_sasa_method_hp_modes ( )

static

Construct a comma-separeted string listing all of the sasa metric modes.

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.

Referenced by core::simple_metrics::metrics::SasaMetric::provide_xml_schema(), and core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::provide_xml_schema().

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

Given the name of the SasaMethodHPMode, get the mode.

Returns: SasaMethodHPMode::INVALID_MODE if the string can't be parsed; the correct SasaMethodHPMode if it can.

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, core::scoring::sasa::INVALID_MODE, and sasa_metric_name_from_mode().

Referenced by core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::set_mode(), and core::simple_metrics::metrics::SasaMetric::set_sasa_metric_mode().

std::string core::scoring::sasa::SasaMethod::sasa_metric_name_from_mode ( SasaMethodHPMode const mode )

static

Given the SasaMethodHPMode, get the name.

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, and core::scoring::sasa::POLAR_SASA.

Referenced by sasa_metric_mode_from_name().

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
	)