protocols::vardist_solaccess::VarSolDistSasaCalculator Class Reference

#include <VarSolDRotamerDots.hh>

Inheritance diagram for protocols::vardist_solaccess::VarSolDistSasaCalculator:

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

protocols::vardist_solaccess::VarSolDistSasaCalculator::VarSolDistSasaCalculator

(

)

References initialize_sasa_arrays().

Member Function Documentation

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

(

const core::pose::Pose &

pose

)

References atom_sasa_, and recompute().

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

overridevirtual

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

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

inline

Referenced by recompute().

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

inline

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

inline

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

inline

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().

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().

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().

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_.

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::conformation::Residue::natoms(), core::pose::Pose::residue(), residue_sasa_, rotamer_dots_vec_, core::pose::Pose::size(), total_sasa_, and protocols::TR().

Referenced by calculate().

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().

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

friend class VarSolDRotamerDots

friend

Member Data Documentation

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

private

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

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

private

Referenced by initialize_sasa_arrays(), and set_atom_type_radii().

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

private

Referenced by initialize_sasa_arrays(), and set_atom_type_radii().

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().

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

private

Referenced by initialize_sasa_arrays(), and set_atom_type_radii().

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

private

Referenced by initialize_sasa_arrays().

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

private

Referenced by initialize_sasa_arrays().

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

private

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

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().

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

private

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

private

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().

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

private

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

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

private

Referenced by recompute().

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

private

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

bool protocols::vardist_solaccess::VarSolDistSasaCalculator::up_to_date

private

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

private

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

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