core::scoring::power_diagram::PowerDiagram Class Reference

#include <PowerDiagram.hh>

Public Member Functions
	PowerDiagram ()
	default constructor More...
	PowerDiagram (core::pose::Pose &pose)
	power diagram from pose More...
	PowerDiagram (PowerDiagram const &)
	copy constructor More...
	~PowerDiagram ()
	default destructor More...
PowerDiagram &	operator= (PowerDiagram const &pd)
	copy assignment More...
PDsphereOP	make_new_sphere (core::pose::Pose &p, Size ires, Size iatm)
PDsphereOP	make_new_sphere (Vector &pos, Real rad)
void	construct_from_pose (core::pose::Pose &p)
void	make_initial_power_diagram ()
void	add_single_atom_to_power_diagram (PDsphereOP &new_atm)
void	store_new_sphere (PDsphereOP new_sph)
std::list< PDinterOP >	get_intersections_for_atom (Size ires, Size iatm)
std::list< PDinterOP >	get_intersections_for_atom (PDsphere *patom)
PDsphere *	sphere_lookup (Size ires, Size iatm)
core::Real	extract_sasa_for_atom (Size ires, Size iatm)
void	clear ()
	Clear all data from power diagram. More...
Size const &	vertex_count ()

Private Attributes
Size	vertex_count_
utility::vector1< PDsphereOP >	spheres_
std::list< PDvertexOP >	finite_vertices_
std::list< PDvertexOP >	infinite_vertices_
utility::vector1< utility::vector1< PDsphere * > >	sphere_lookup_

Constructor & Destructor Documentation

PowerDiagram() [1/3]

core::scoring::power_diagram::PowerDiagram::PowerDiagram ( )

inline

default constructor

Warning

no initialization of corners for speed, make sure you reset()

or otherwise set corners before adding points

PowerDiagram() [2/3]

core::scoring::power_diagram::PowerDiagram::PowerDiagram

(

core::pose::Pose &

pose

)

power diagram from pose

PowerDiagram() [3/3]

core::scoring::power_diagram::PowerDiagram::PowerDiagram ( PowerDiagram const &  )

inline

copy constructor

References finite_vertices_, infinite_vertices_, sphere_lookup_, and spheres_.

~PowerDiagram()

core::scoring::power_diagram::PowerDiagram::~PowerDiagram ( )

inline

default destructor

Member Function Documentation

add_single_atom_to_power_diagram()

void core::scoring::power_diagram::PowerDiagram::add_single_atom_to_power_diagram

(

PDsphereOP &

new_atm

)

References core::scoring::power_diagram::find_next_vertex_with_smallest_dist(), core::scoring::power_diagram::PDvertex::finite(), core::scoring::power_diagram::link_vertex_to_generators(), core::scoring::power_diagram::PDvertex::my_itr(), core::scoring::power_diagram::PDvertex::nonconst_generators(), core::scoring::power_diagram::PDvertex::nonconst_partners(), core::scoring::power_diagram::PDvertex::partners(), core::scoring::power_diagram::PDvertex::power(), core::scoring::power_diagram::power_distance(), protocols::forge::methods::replace(), core::scoring::power_diagram::PDvertex::set_live(), TR(), core::scoring::power_diagram::vertex_xyz_from_generators(), core::scoring::power_diagram::PDvertex::xyz(), and protocols::kinmatch::xyz().

clear()

void core::scoring::power_diagram::PowerDiagram::clear

(

)

Clear all data from power diagram.

construct_from_pose()

void core::scoring::power_diagram::PowerDiagram::construct_from_pose

(

core::pose::Pose &

p

)

References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_set(), core::chemical::AtomType::extra_parameter(), core::chemical::AtomTypeSet::extra_parameter_index(), core::scoring::power_diagram::find_common_intersection_atoms(), core::scoring::power_diagram::get_cycles_from_intersections(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

extract_sasa_for_atom()

Real core::scoring::power_diagram::PowerDiagram::extract_sasa_for_atom	(	Size	ires,
		Size	iatm
	)

References core::scoring::power_diagram::PDsphere::cycles(), and core::scoring::power_diagram::get_sasa_from_cycles().

get_intersections_for_atom() [1/2]

std::list< PDinterOP > core::scoring::power_diagram::PowerDiagram::get_intersections_for_atom

(

PDsphere *

patom

)

References core::scoring::power_diagram::find_intersections(), core::scoring::power_diagram::PDvertex::nonconst_generators(), core::conformation::membrane::normal, core::scoring::power_diagram::PDsphere::rad(), core::scoring::power_diagram::PDsphere::vertices(), and core::scoring::power_diagram::PDsphere::xyz().

get_intersections_for_atom() [2/2]

std::list< PDinterOP > core::scoring::power_diagram::PowerDiagram::get_intersections_for_atom	(	Size	ires,
		Size	iatm
	)

make_initial_power_diagram()

void core::scoring::power_diagram::PowerDiagram::make_initial_power_diagram

(

)

References core::scoring::power_diagram::link_vertex_to_generators(), core::scoring::power_diagram::power_distance(), TR(), core::scoring::power_diagram::vertex_xyz_from_generators(), and protocols::kinmatch::xyz().

make_new_sphere() [1/2]

PDsphereOP core::scoring::power_diagram::PowerDiagram::make_new_sphere	(	core::pose::Pose &	p,
		Size	ires,
		Size	iatm
	)

References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_set(), core::chemical::AtomType::extra_parameter(), core::chemical::AtomTypeSet::extra_parameter_index(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

make_new_sphere() [2/2]

PDsphereOP core::scoring::power_diagram::PowerDiagram::make_new_sphere	(	Vector &	pos,
		Real	rad
	)

operator=()

PowerDiagram& core::scoring::power_diagram::PowerDiagram::operator= ( PowerDiagram const &  pd )

inline

copy assignment

References finite_vertices_, infinite_vertices_, sphere_lookup_, and spheres_.

sphere_lookup()

PDsphere* core::scoring::power_diagram::PowerDiagram::sphere_lookup ( Size  ires, Size  iatm  )

inline

References sphere_lookup_.

store_new_sphere()

void core::scoring::power_diagram::PowerDiagram::store_new_sphere ( PDsphereOP  new_sph )

inline

References sphere_lookup_, and spheres_.

vertex_count()

Size const& core::scoring::power_diagram::PowerDiagram::vertex_count ( )

inline

References vertex_count_.

Member Data Documentation

finite_vertices_

std::list< PDvertexOP > core::scoring::power_diagram::PowerDiagram::finite_vertices_

private

Referenced by operator=(), and PowerDiagram().

infinite_vertices_

std::list< PDvertexOP > core::scoring::power_diagram::PowerDiagram::infinite_vertices_

private

Referenced by operator=(), and PowerDiagram().

sphere_lookup_

utility::vector1< utility::vector1< PDsphere* > > core::scoring::power_diagram::PowerDiagram::sphere_lookup_

private

Referenced by operator=(), PowerDiagram(), sphere_lookup(), and store_new_sphere().

spheres_

utility::vector1< PDsphereOP > core::scoring::power_diagram::PowerDiagram::spheres_

private

Referenced by operator=(), PowerDiagram(), and store_new_sphere().

vertex_count_

Size core::scoring::power_diagram::PowerDiagram::vertex_count_

private

Referenced by vertex_count().

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

• src/core/scoring/power_diagram/PowerDiagram.hh
• src/core/scoring/power_diagram/PowerDiagram.cc