gemmi::NeighborSearch Struct Reference

#include <neighbor.hpp>

Classes
struct	Mark

Public Member Functions
	NeighborSearch ()=default
	NeighborSearch (Model &model_, const UnitCell &cell, double radius)
	NeighborSearch (SmallStructure &small_st, double radius)
NeighborSearch &	populate (bool include_h_=true)
void	add_chain (const Chain &chain, bool include_h_=true)
void	add_chain_n (const Chain &chain, int n_ch)
void	add_atom (const Atom &atom, int n_ch, int n_res, int n_atom)
void	add_site (const SmallStructure::Site &site, int n)
std::vector< Mark > &	get_subcell (const Fractional &fr)
template<typename Func >
void	for_each_cell (const Position &pos, const Func &func, int k=1)
template<typename Func >
void	for_each (const Position &pos, char alt, double radius, const Func &func, int k=1)
int	sufficient_k (double r) const
std::vector< Mark * >	find_atoms (const Position &pos, char alt, double min_dist, double radius)
std::vector< Mark * >	find_neighbors (const Atom &atom, double min_dist, double max_dist)
std::vector< Mark * >	find_site_neighbors (const SmallStructure::Site &site, double min_dist, double max_dist)
std::pair< Mark *, double >	find_nearest_atom_within_k (const Position &pos, int k, double radius)
Mark *	find_nearest_atom (const Position &pos, double radius=INFINITY)
double	dist_sq (const Position &pos1, const Position &pos2) const
double	dist (const Position &pos1, const Position &pos2) const
FTransform	get_image_transformation (int image_idx) const

Public Attributes
Grid< std::vector< Mark > >	grid
double	radius_specified = 0.
Model *	model = nullptr
SmallStructure *	small_structure = nullptr
bool	use_pbc = true
bool	include_h = true

Detailed Description

Definition at line 19 of file neighbor.hpp.

Constructor & Destructor Documentation

NeighborSearch() [1/3]

gemmi::NeighborSearch::NeighborSearch ( )

default

NeighborSearch() [2/3]

gemmi::NeighborSearch::NeighborSearch ( Model &  model_, const UnitCell &  cell, double  radius  )

inline

Definition at line 63 of file neighbor.hpp.

NeighborSearch() [3/3]

gemmi::NeighborSearch::NeighborSearch ( SmallStructure &  small_st, double  radius  )

inline

Definition at line 69 of file neighbor.hpp.

Member Function Documentation

populate()

NeighborSearch & gemmi::NeighborSearch::populate ( bool  include_h_ = true )

inline

Definition at line 237 of file neighbor.hpp.

add_chain()

void gemmi::NeighborSearch::add_chain ( const Chain &  chain, bool  include_h_ = true  )

inline

Definition at line 254 of file neighbor.hpp.

add_chain_n()

void gemmi::NeighborSearch::add_chain_n ( const Chain &  chain, int  n_ch  )

inline

Definition at line 267 of file neighbor.hpp.

add_atom()

void gemmi::NeighborSearch::add_atom ( const Atom &  atom, int  n_ch, int  n_res, int  n_atom  )

inline

Definition at line 278 of file neighbor.hpp.

add_site()

void gemmi::NeighborSearch::add_site ( const SmallStructure::Site &  site, int  n  )

inline

Definition at line 301 of file neighbor.hpp.

get_subcell()

std::vector< Mark > & gemmi::NeighborSearch::get_subcell ( const Fractional &  fr )

inline

Definition at line 83 of file neighbor.hpp.

for_each_cell()

template<typename Func >

void gemmi::NeighborSearch::for_each_cell	(	const Position &	pos,
		const Func &	func,
		int	k = 1
	)

Definition at line 326 of file neighbor.hpp.

for_each()

template<typename Func >

void gemmi::NeighborSearch::for_each ( const Position &  pos, char  alt, double  radius, const Func &  func, int  k = 1  )

inline

Definition at line 93 of file neighbor.hpp.

sufficient_k()

int gemmi::NeighborSearch::sufficient_k ( double  r ) const

inline

Definition at line 106 of file neighbor.hpp.

find_atoms()

std::vector< Mark * > gemmi::NeighborSearch::find_atoms ( const Position &  pos, char  alt, double  min_dist, double  radius  )

inline

Definition at line 112 of file neighbor.hpp.

find_neighbors()

std::vector< Mark * > gemmi::NeighborSearch::find_neighbors ( const Atom &  atom, double  min_dist, double  max_dist  )

inline

Definition at line 125 of file neighbor.hpp.

find_site_neighbors()

std::vector< Mark * > gemmi::NeighborSearch::find_site_neighbors ( const SmallStructure::Site &  site, double  min_dist, double  max_dist  )

inline

Definition at line 128 of file neighbor.hpp.

find_nearest_atom_within_k()

std::pair< Mark *, double > gemmi::NeighborSearch::find_nearest_atom_within_k ( const Position &  pos, int  k, double  radius  )

inline

Definition at line 135 of file neighbor.hpp.

find_nearest_atom()

Mark * gemmi::NeighborSearch::find_nearest_atom ( const Position &  pos, double  radius = INFINITY  )

inline

Definition at line 152 of file neighbor.hpp.

dist_sq()

double gemmi::NeighborSearch::dist_sq ( const Position &  pos1, const Position &  pos2  ) const

inline

Definition at line 176 of file neighbor.hpp.

dist()

double gemmi::NeighborSearch::dist ( const Position &  pos1, const Position &  pos2  ) const

inline

Definition at line 179 of file neighbor.hpp.

get_image_transformation()

FTransform gemmi::NeighborSearch::get_image_transformation ( int  image_idx ) const

inline

Definition at line 183 of file neighbor.hpp.

Member Data Documentation

grid

Grid<std::vector<Mark> > gemmi::NeighborSearch::grid

Definition at line 54 of file neighbor.hpp.

radius_specified

double gemmi::NeighborSearch::radius_specified = 0.

Definition at line 55 of file neighbor.hpp.

model

Model* gemmi::NeighborSearch::model = nullptr

Definition at line 56 of file neighbor.hpp.

small_structure

SmallStructure* gemmi::NeighborSearch::small_structure = nullptr

Definition at line 57 of file neighbor.hpp.

use_pbc

bool gemmi::NeighborSearch::use_pbc = true

Definition at line 58 of file neighbor.hpp.

include_h

bool gemmi::NeighborSearch::include_h = true

Definition at line 59 of file neighbor.hpp.

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The documentation for this struct was generated from the following file:

• /home/wojdyr/gemmi/gemmi/include/gemmi/neighbor.hpp