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gmx::AnalysisNeighborhoodSearch Class Reference

#include <gromacs/selection/nbsearch.h>

Description

Initialized neighborhood search with a fixed set of reference positions.

An instance of this class is obtained through AnalysisNeighborhood::initSearch(), and can be used to do multiple searches against the provided set of reference positions. It is possible to create concurrent pair searches (including from different threads), as well as call other methods in this class while a pair search is in progress.

This class works like a pointer: copies of it point to the same search. In general, avoid creating copies, and only use the copy/assignment support for moving the variable around. With C++11, this class would best be movable.

Methods in this class do not throw unless otherwise indicated.

Todo:
Make it such that reset() is not necessary to call in code that repeatedly assigns the result of AnalysisNeighborhood::initSearch() to the same variable (see sm_distance.cpp).
Todo:
Consider merging nearestPoint() and minimumDistance() by adding the distance to AnalysisNeighborhoodPair.
Examples:
template.cpp.

Public Types

typedef std::shared_ptr
< internal::AnalysisNeighborhoodSearchImpl > 
ImplPointer
 Internal short-hand type for a pointer to the implementation class. More...
 

Public Member Functions

 AnalysisNeighborhoodSearch ()
 Initializes an invalid search. More...
 
 AnalysisNeighborhoodSearch (const ImplPointer &impl)
 Internally initialize the search. More...
 
void reset ()
 Clears this search. More...
 
AnalysisNeighborhood::SearchMode mode () const
 Returns the searching algorithm that this search is using. More...
 
bool isWithin (const AnalysisNeighborhoodPositions &positions) const
 Check whether a point is within a neighborhood. More...
 
real minimumDistance (const AnalysisNeighborhoodPositions &positions) const
 Calculates the minimum distance from the reference points. More...
 
AnalysisNeighborhoodPair nearestPoint (const AnalysisNeighborhoodPositions &positions) const
 Finds the closest reference point. More...
 
AnalysisNeighborhoodPairSearch startPairSearch (const AnalysisNeighborhoodPositions &positions) const
 Start a search to find reference positions within a cutoff. More...
 

Member Typedef Documentation

typedef std::shared_ptr<internal::AnalysisNeighborhoodSearchImpl> gmx::AnalysisNeighborhoodSearch::ImplPointer

Internal short-hand type for a pointer to the implementation class.

shared_ptr is used here to automatically keep a reference count to track whether an implementation class is still used outside the AnalysisNeighborhood object. Ownership currently always stays with AnalysisNeighborhood; it always keeps one instance of the pointer.

Constructor & Destructor Documentation

gmx::AnalysisNeighborhoodSearch::AnalysisNeighborhoodSearch ( )

Initializes an invalid search.

Such an object cannot be used for searching. It needs to be assigned a value from AnalysisNeighborhood::initSearch() before it can be used. Provided to allow declaring a variable to hold the search before calling AnalysisNeighborhood::initSearch().

gmx::AnalysisNeighborhoodSearch::AnalysisNeighborhoodSearch ( const ImplPointer impl)
explicit

Internally initialize the search.

Used to implement AnalysisNeighborhood::initSearch(). Cannot be called from user code.

Member Function Documentation

bool gmx::AnalysisNeighborhoodSearch::isWithin ( const AnalysisNeighborhoodPositions positions) const

Check whether a point is within a neighborhood.

Parameters
[in]positionsSet of test positions to use.
Returns
true if any of the test positions is within the cutoff of any reference position.
real gmx::AnalysisNeighborhoodSearch::minimumDistance ( const AnalysisNeighborhoodPositions positions) const

Calculates the minimum distance from the reference points.

Parameters
[in]positionsSet of test positions to use.
Returns
The distance to the nearest reference position, or the cutoff value if there are no reference positions within the cutoff.
Examples:
template.cpp.
AnalysisNeighborhood::SearchMode gmx::AnalysisNeighborhoodSearch::mode ( ) const

Returns the searching algorithm that this search is using.

The return value is never AnalysisNeighborhood::eSearchMode_Automatic.

AnalysisNeighborhoodPair gmx::AnalysisNeighborhoodSearch::nearestPoint ( const AnalysisNeighborhoodPositions positions) const

Finds the closest reference point.

Parameters
[in]positionsSet of test positions to use.
Returns
The reference index identifies the reference position that is closest to the test positions. The test index identifies the test position that is closest to the provided test position. The returned pair is invalid if no reference position is within the cutoff.
void gmx::AnalysisNeighborhoodSearch::reset ( )

Clears this search.

Equivalent to "*this = AnalysisNeighborhoodSearch();". Currently, this is necessary to avoid unnecessary memory allocation if the previous search variable is still in scope when you want to call AnalysisNeighborhood::initSearch() again.

AnalysisNeighborhoodPairSearch gmx::AnalysisNeighborhoodSearch::startPairSearch ( const AnalysisNeighborhoodPositions positions) const

Start a search to find reference positions within a cutoff.

Parameters
[in]positionsSet of test positions to use.
Returns
Initialized search object to loop through all reference positions within the configured cutoff.
Exceptions
std::bad_allocif out of memory.

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