core::scoring::power_diagram Namespace Reference

Classes
class	PDinter
class	SAnode
class	PDsphere
class	PDvertex
class	PowerDiagram

Typedefs
typedef utility::pointer::shared_ptr< PDsphere >	PDsphereOP
typedef utility::pointer::shared_ptr< PDsphere const >	PDsphereCOP
typedef utility::pointer::shared_ptr< PDvertex >	PDvertexOP
typedef utility::pointer::shared_ptr< PDvertex const >	PDvertexCOP
typedef utility::pointer::shared_ptr< PDinter >	PDinterOP
typedef utility::pointer::shared_ptr< PDinter const >	PDinterCOP
typedef utility::pointer::shared_ptr< PowerDiagram >	PowerDiagramOP
typedef utility::pointer::shared_ptr< PowerDiagram const >	PowerDiagramCOP
typedef numeric::xyzVector< core::Real >	Vector
typedef numeric::xyzMatrix< core::Real >	Matrix

Functions
bool	matches_ptr (PDvertexOP elem, PDvertex *test)
Real	power_distance (Vector const &pt, PDsphere const *sph)
void	find_intersections (PDsphere const *psph, PDvertex const *vrt1, PDvertex const *vrt2, Vector const &start_pt, Vector const &dir, Real const max_extent, std::list< PDinterOP > &intersections)
bool	find_intersections (PDsphereCOP psph, Vector const &start_pt, Vector const &dir, Real const max_extent)
void	find_common_intersection_atoms (PDinterOP inter)
utility::vector1< utility::vector1< SAnode > >	get_cycles_from_intersections (std::list< PDinterOP > &inters, PDsphere const *this_sph)
Real	get_sasa_from_cycles (utility::vector1< utility::vector1< SAnode > > &cycles, PDsphere *this_sph)
void	get_derivs_from_cycles (utility::vector1< utility::vector1< SAnode > > &cycles, PDsphere *this_atom, PDsphere *check_atom, Vector &f1, Vector &f2)
void	get_derivs_from_cycle (utility::vector1< SAnode > &cycle, PDsphere *this_atom, PDsphere *check_atom, Vector &f1, Vector &f2)
bool	share_axis_atoms (PDinter const *v1, PDsphere const *a1, PDsphere const *a2)
Real	get_area_from_cycle (PDsphere *this_atom, utility::vector1< SAnode > &cycle)
Vector	vertex_xyz_from_generators (PDsphere const *a1, PDsphere const *a2, PDsphere const *a3, PDsphere const *a4)
Vector	vertex_xyz_from_generators (utility::vector1< PDsphere * > const &gen)
void	print_points (std::list< PDinterOP > &inters)
void	print_partners (PDvertexCOP vrt)
void	print_generators (PDvertexCOP vrt)
void	print_vertices (std::list< PDvertexOP > &fv, std::list< PDvertexOP > &iv)
void	print_vertices (std::list< PDvertexOP > &v)
PDvertex *	find_next_vertex_with_smallest_dist (PDvertex *srch_vrt, PDsphereOP &new_sph, Real &this_dist)
void	link_vertex_to_generators (PDvertexOP vrt)

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< core::Real > core::scoring::power_diagram::Matrix

PDinterCOP

typedef utility::pointer::shared_ptr< PDinter const > core::scoring::power_diagram::PDinterCOP

PDinterOP

typedef utility::pointer::shared_ptr< PDinter > core::scoring::power_diagram::PDinterOP

PDsphereCOP

typedef utility::pointer::shared_ptr< PDsphere const > core::scoring::power_diagram::PDsphereCOP

PDsphereOP

typedef utility::pointer::shared_ptr< PDsphere > core::scoring::power_diagram::PDsphereOP

PDvertexCOP

typedef utility::pointer::shared_ptr< PDvertex const > core::scoring::power_diagram::PDvertexCOP

PDvertexOP

typedef utility::pointer::shared_ptr< PDvertex > core::scoring::power_diagram::PDvertexOP

PowerDiagramCOP

typedef utility::pointer::shared_ptr< PowerDiagram const > core::scoring::power_diagram::PowerDiagramCOP

PowerDiagramOP

typedef utility::pointer::shared_ptr< PowerDiagram > core::scoring::power_diagram::PowerDiagramOP

Vector

typedef numeric::xyzVector< core::Real > core::scoring::power_diagram::Vector

Function Documentation

find_common_intersection_atoms()

void core::scoring::power_diagram::find_common_intersection_atoms

(

PDinterOP

inter

)

References core::scoring::power_diagram::PDvertex::generators().

Referenced by core::scoring::power_diagram::PowerDiagram::construct_from_pose().

find_intersections() [1/2]

void core::scoring::power_diagram::find_intersections	(	PDsphere const *	psph,
		PDvertex const *	vrt1,
		PDvertex const *	vrt2,
		Vector const &	start_pt,
		Vector const &	dir,
		Real const	max_extent,
		std::list< PDinterOP > &	intersections
	)

References core::scoring::power_diagram::PDsphere::rad2(), and core::scoring::power_diagram::PDsphere::xyz().

find_intersections() [2/2]

bool core::scoring::power_diagram::find_intersections	(	PDsphereCOP	psph,
		Vector const &	start_pt,
		Vector const &	dir,
		Real const	max_extent
	)

Referenced by core::scoring::power_diagram::PowerDiagram::get_intersections_for_atom().

find_next_vertex_with_smallest_dist()

PDvertex * core::scoring::power_diagram::find_next_vertex_with_smallest_dist	(	PDvertex *	srch_vrt,
		PDsphereOP &	new_sph,
		Real &	this_dist
	)

References core::scoring::power_diagram::PDvertex::partners(), and power_distance().

Referenced by core::scoring::power_diagram::PowerDiagram::add_single_atom_to_power_diagram().

get_area_from_cycle()

core::Real core::scoring::power_diagram::get_area_from_cycle	(	PDsphere *	this_atom,
		utility::vector1< SAnode > &	cycle
	)

References core::scoring::power_diagram::PDsphere::rad(), core::scoring::power_diagram::PDsphere::rad2(), and core::scoring::power_diagram::PDsphere::xyz().

Referenced by get_sasa_from_cycles().

get_cycles_from_intersections()

utility::vector1< utility::vector1< SAnode > > core::scoring::power_diagram::get_cycles_from_intersections	(	std::list< PDinterOP > &	inters,
		PDsphere const *	this_sph
	)

References core::scoring::power_diagram::PDsphere::rad(), core::scoring::power_diagram::PDsphere::rad2(), share_axis_atoms(), and core::scoring::power_diagram::PDsphere::xyz().

Referenced by core::scoring::power_diagram::PowerDiagram::construct_from_pose().

get_derivs_from_cycle()

void core::scoring::power_diagram::get_derivs_from_cycle	(	utility::vector1< SAnode > &	cycle,
		PDsphere *	this_atom,
		PDsphere *	check_atom,
		Vector &	f1,
		Vector &	f2
	)

References core::scoring::power_diagram::PDsphere::rad(), TR(), and core::scoring::power_diagram::PDsphere::xyz().

Referenced by get_derivs_from_cycles().

get_derivs_from_cycles()

void core::scoring::power_diagram::get_derivs_from_cycles	(	utility::vector1< utility::vector1< SAnode > > &	cycles,
		PDsphere *	this_atom,
		PDsphere *	check_atom,
		Vector &	f1,
		Vector &	f2
	)

References get_derivs_from_cycle().

Referenced by core::scoring::SASAPotential::eval_residue_pair_derivatives().

get_sasa_from_cycles()

core::Real core::scoring::power_diagram::get_sasa_from_cycles	(	utility::vector1< utility::vector1< SAnode > > &	cycles,
		PDsphere *	this_sph
	)

References get_area_from_cycle(), and core::scoring::power_diagram::PDsphere::rad2().

Referenced by core::scoring::power_diagram::PowerDiagram::extract_sasa_for_atom().

link_vertex_to_generators()

void core::scoring::power_diagram::link_vertex_to_generators ( PDvertexOP  vrt )

inline

Referenced by core::scoring::power_diagram::PowerDiagram::add_single_atom_to_power_diagram(), and core::scoring::power_diagram::PowerDiagram::make_initial_power_diagram().

matches_ptr()

bool core::scoring::power_diagram::matches_ptr	(	PDvertexOP	elem,
		PDvertex *	test
	)

power_distance()

Real core::scoring::power_diagram::power_distance	(	Vector const &	pt,
		PDsphere const *	sph
	)

References core::scoring::power_diagram::PDsphere::rad2(), and core::scoring::power_diagram::PDsphere::xyz().

Referenced by core::scoring::power_diagram::PowerDiagram::add_single_atom_to_power_diagram(), find_next_vertex_with_smallest_dist(), and core::scoring::power_diagram::PowerDiagram::make_initial_power_diagram().

print_generators()

void core::scoring::power_diagram::print_generators

(

PDvertexCOP

vrt

)

References TR().

Referenced by print_vertices().

print_partners()

void core::scoring::power_diagram::print_partners

(

PDvertexCOP

vrt

)

References TR().

Referenced by print_vertices().

print_points()

void core::scoring::power_diagram::print_points

(

std::list< PDinterOP > &

inters

)

References core::chemical::element::F, core::chemical::element::I, and TR().

print_vertices() [1/2]

void core::scoring::power_diagram::print_vertices	(	std::list< PDvertexOP > &	fv,
		std::list< PDvertexOP > &	iv
	)

References core::chemical::element::F, core::chemical::element::I, TR(), and core::scoring::power_diagram::PDvertex::xyz().

print_vertices() [2/2]

void core::scoring::power_diagram::print_vertices

(

std::list< PDvertexOP > &

v

)

References core::chemical::element::F, core::chemical::element::I, print_generators(), print_partners(), TR(), and core::scoring::power_diagram::PDvertex::xyz().

share_axis_atoms()

bool core::scoring::power_diagram::share_axis_atoms	(	PDinter const *	v1,
		PDsphere const *	a1,
		PDsphere const *	a2
	)

References core::scoring::power_diagram::PDinter::atoms().

Referenced by get_cycles_from_intersections().

vertex_xyz_from_generators() [1/2]

Vector core::scoring::power_diagram::vertex_xyz_from_generators	(	PDsphere const *	a1,
		PDsphere const *	a2,
		PDsphere const *	a3,
		PDsphere const *	a4
	)

References core::scoring::power_diagram::PDsphere::rad2(), and core::scoring::power_diagram::PDsphere::xyz().

vertex_xyz_from_generators() [2/2]

Vector core::scoring::power_diagram::vertex_xyz_from_generators

(

utility::vector1< PDsphere * > const &

gen

)

Referenced by core::scoring::power_diagram::PowerDiagram::add_single_atom_to_power_diagram(), and core::scoring::power_diagram::PowerDiagram::make_initial_power_diagram().