#include <VarSolDRotamerDots.hh>

Inheritance diagram for protocols::vardist_solaccess::VarSolDistSasaCalculator:

[legend]

Public Member Functions
	VarSolDistSasaCalculator ()

VarSolDistSasaCalculatorCOP	get_self_ptr () const

VarSolDistSasaCalculatorOP	get_self_ptr ()

VarSolDistSasaCalculatorCAP	get_self_weak_ptr () const

VarSolDistSasaCalculatorAP	get_self_weak_ptr ()

core::pose::metrics::PoseMetricCalculatorOP	clone () const override

void	set_element_radii (std::string atype_name, core::Real coll_radius, core::Real int_radius, core::Size nshells)

void	set_atom_type_radii (std::string atype_name, core::Real coll_radius, core::Real int_radius, core::Size nshells)

core::id::AtomID_Map< core::Real >	calculate (const core::pose::Pose &pose)

Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
	StructureDependentCalculator ()

void	notify_structure_change () override

void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override

std::string	get (std::string const &key, Pose const &this_pose) override

Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()

virtual void	notify_energy_change ()

Protected Member Functions
void	lookup (const std::string &key, basic::MetricValueBase *valptr) const override

std::string	print (const std::string &key) const override

void	recompute (const core::pose::Pose &this_pose) override

Private Member Functions
void	initialize_sasa_arrays ()
	Initializes the pointers to the angles and masks FArrays used by sasa.cc and inits the dot sphere coordinates. More...

core::Real	interaction_radii_squared (core::Size attype1, core::Size attype2) const

Private Attributes
core::Real	probe_radius_

core::Real	wobble_

core::Real	total_sasa_

core::id::AtomID_Map< core::Real >	atom_sasa_

utility::vector1< core::Real >	residue_sasa_

utility::vector1< VarSolDRotamerDotsOP >	rotamer_dots_vec_

utility::vector1< utility::vector1< core::Real > >	radii_

utility::vector1< core::Real >	msas_radii_

utility::vector1< core::Real >	coll_radii_

utility::vector1< core::Real >	int_radii_

utility::vector1< utility::vector1< core::Real > >	int_radii_sum_

utility::vector1< utility::vector1< core::Real > >	int_radii_sum2_

core::Size const	num_bytes_

const ObjexxFCL::FArray2D_ubyte *	lg_masks_

const ObjexxFCL::FArray2D_int *	lg_angles_

core::Real	polar_expansion_radius_

bool	up_to_date

Friends
class	VarSolDRotamerDots

Constructor & Destructor Documentation

◆ VarSolDistSasaCalculator()

protocols::vardist_solaccess::VarSolDistSasaCalculator::VarSolDistSasaCalculator ( )

References initialize_sasa_arrays().

Member Function Documentation

◆ calculate()

id::AtomID_Map< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::calculate ( const core::pose::Pose & pose )

References atom_sasa_, and recompute().

◆ clone()

core::pose::metrics::PoseMetricCalculatorOP protocols::vardist_solaccess::VarSolDistSasaCalculator::clone ( ) const

overridevirtual

Implements core::pose::metrics::PoseMetricCalculator.

◆ get_self_ptr() [1/2]

VarSolDistSasaCalculatorOP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_ptr ( )

inline

◆ get_self_ptr() [2/2]

VarSolDistSasaCalculatorCOP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_ptr ( ) const

inline

Referenced by recompute().

◆ get_self_weak_ptr() [1/2]

VarSolDistSasaCalculatorAP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_weak_ptr ( )

inline

◆ get_self_weak_ptr() [2/2]

VarSolDistSasaCalculatorCAP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_weak_ptr ( ) const

inline

◆ initialize_sasa_arrays()

void protocols::vardist_solaccess::VarSolDistSasaCalculator::initialize_sasa_arrays ( )

private

Initializes the pointers to the angles and masks FArrays used by sasa.cc and inits the dot sphere coordinates.

This call should only occur once (when the first RotamerDots object get constructed) and never again.

References core::chemical::AtomType::atom_type_name(), coll_radii_, core::chemical::AtomType::element(), core::chemical::AtomType::extra_parameter(), core::chemical::FA_STANDARD, core::scoring::sasa::get_legrand_sasa_angles(), core::scoring::sasa::get_legrand_sasa_masks(), int_radii_, int_radii_sum2_, int_radii_sum_, lg_angles_, lg_masks_, protocols::mean_field::max(), msas_radii_, and radii_.

Referenced by VarSolDistSasaCalculator().

◆ interaction_radii_squared()

core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::interaction_radii_squared	(	core::Size	attype1,
		core::Size	attype2
	)		const

private

Referenced by protocols::vardist_solaccess::VarSolDRotamerDots::get_atom_overlap_masks().

◆ lookup()

void protocols::vardist_solaccess::VarSolDistSasaCalculator::lookup	(	const std::string &	key,
		basic::MetricValueBase *	valptr
	)		const

overrideprotectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References atom_sasa_, residue_sasa_, total_sasa_, and protocols::TR().

◆ print()

std::string protocols::vardist_solaccess::VarSolDistSasaCalculator::print ( const std::string & key ) const

overrideprotectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References residue_sasa_, core::id::to_string(), and total_sasa_.

◆ recompute()

void protocols::vardist_solaccess::VarSolDistSasaCalculator::recompute ( const core::pose::Pose & this_pose )

overrideprotectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References atom_sasa_, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), get_self_ptr(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), residue_sasa_, rotamer_dots_vec_, core::pose::Pose::size(), total_sasa_, and protocols::TR().

Referenced by calculate().

◆ set_atom_type_radii()

void protocols::vardist_solaccess::VarSolDistSasaCalculator::set_atom_type_radii	(	std::string	atype_name,
		core::Real	coll_radius,
		core::Real	int_radius,
		core::Size	nshells
	)

References coll_radii_, core::chemical::FA_STANDARD, int_radii_, int_radii_sum2_, int_radii_sum_, protocols::mean_field::max(), and radii_.

Referenced by set_element_radii().

◆ set_element_radii()

void protocols::vardist_solaccess::VarSolDistSasaCalculator::set_element_radii	(	std::string	atype_name,
		core::Real	coll_radius,
		core::Real	int_radius,
		core::Size	nshells
	)

References core::chemical::FA_STANDARD, and set_atom_type_radii().

Friends And Related Function Documentation

◆ VarSolDRotamerDots

friend class VarSolDRotamerDots

friend

Member Data Documentation

◆ atom_sasa_

core::id::AtomID_Map< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::atom_sasa_

private

Referenced by calculate(), lookup(), and recompute().

◆ coll_radii_

utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::coll_radii_

private

Referenced by initialize_sasa_arrays(), and set_atom_type_radii().

◆ int_radii_

utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::int_radii_

private

Referenced by initialize_sasa_arrays(), and set_atom_type_radii().

◆ int_radii_sum2_

utility::vector1< utility::vector1< core::Real > > protocols::vardist_solaccess::VarSolDistSasaCalculator::int_radii_sum2_

private

Referenced by initialize_sasa_arrays(), protocols::vardist_solaccess::VarSolDRotamerDots::interaction_radii_squared(), and set_atom_type_radii().

◆ int_radii_sum_

utility::vector1< utility::vector1< core::Real > > protocols::vardist_solaccess::VarSolDistSasaCalculator::int_radii_sum_

private

Referenced by initialize_sasa_arrays(), and set_atom_type_radii().

◆ lg_angles_

const ObjexxFCL::FArray2D_int* protocols::vardist_solaccess::VarSolDistSasaCalculator::lg_angles_

private

Referenced by initialize_sasa_arrays().

◆ lg_masks_

const ObjexxFCL::FArray2D_ubyte* protocols::vardist_solaccess::VarSolDistSasaCalculator::lg_masks_

private

Referenced by initialize_sasa_arrays().

◆ msas_radii_

utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::msas_radii_

private

Referenced by initialize_sasa_arrays(), and protocols::vardist_solaccess::VarSolDRotamerDots::msas_for_atom().

◆ num_bytes_

core::Size const protocols::vardist_solaccess::VarSolDistSasaCalculator::num_bytes_

private

Referenced by protocols::vardist_solaccess::VarSolDRotamerDots::increment_self_overlap(), protocols::vardist_solaccess::VarSolDRotamerDots::intersect_residues(), and protocols::vardist_solaccess::VarSolDRotamerDots::overlap_atoms().

◆ polar_expansion_radius_

core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::polar_expansion_radius_

private

◆ probe_radius_

core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::probe_radius_

private

◆ radii_

utility::vector1< utility::vector1< core::Real > > protocols::vardist_solaccess::VarSolDistSasaCalculator::radii_

private

Referenced by initialize_sasa_arrays(), protocols::vardist_solaccess::VarSolDRotamerDots::overlap_atoms(), set_atom_type_radii(), and protocols::vardist_solaccess::VarSolDRotamerDots::write_dot_kinemage().

◆ residue_sasa_

utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::residue_sasa_

private

Referenced by lookup(), print(), and recompute().

◆ rotamer_dots_vec_

utility::vector1< VarSolDRotamerDotsOP > protocols::vardist_solaccess::VarSolDistSasaCalculator::rotamer_dots_vec_

private

Referenced by recompute().

◆ total_sasa_

core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::total_sasa_

private

Referenced by lookup(), print(), and recompute().

◆ up_to_date

bool protocols::vardist_solaccess::VarSolDistSasaCalculator::up_to_date

private

◆ wobble_

core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::wobble_

private

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

src/protocols/vardist_solaccess/VarSolDRotamerDots.hh
src/protocols/vardist_solaccess/VarSolDRotamerDots.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

◆ VarSolDistSasaCalculator()

Member Function Documentation

◆ calculate()

◆ clone()

◆ get_self_ptr() [1/2]

◆ get_self_ptr() [2/2]

◆ get_self_weak_ptr() [1/2]

◆ get_self_weak_ptr() [2/2]

◆ initialize_sasa_arrays()

◆ interaction_radii_squared()

◆ lookup()

◆ print()

◆ recompute()

◆ set_atom_type_radii()

◆ set_element_radii()

Friends And Related Function Documentation

◆ VarSolDRotamerDots

Member Data Documentation

◆ atom_sasa_

◆ coll_radii_

◆ int_radii_

◆ int_radii_sum2_

◆ int_radii_sum_

◆ lg_angles_

◆ lg_masks_

◆ msas_radii_

◆ num_bytes_

◆ polar_expansion_radius_

◆ probe_radius_

◆ radii_

◆ residue_sasa_

◆ rotamer_dots_vec_

◆ total_sasa_

◆ up_to_date

◆ wobble_