gmx::SelectionPosition Class Reference

#include <gromacs/selection/selection.h>

Description

Provides access to information about a single selected position.

Each position has associated coordinates, and possibly velocities and forces if they have been requested and are available. It also has a set of atoms associated with it; typically the coordinates are the center-of-mass or center-of-geometry coordinates for that set of atoms. It is possible that there are not atoms associated if the selection has been provided as a fixed position.

After the selection has been compiled, but not yet evaluated, the contents of the coordinate, velocity and force vectors are undefined.

Default copy constructor and assignment operators are used, and work as intended: the copy references the same position and works identically.

Methods in this class do not throw.

See Also

Selection

Examples:

template.cpp.

Public Member Functions
	SelectionPosition (const internal::SelectionData &sel, int index)
	Constructs a wrapper object for given selection position. More...
e_index_t	type () const
	Returns type of this position. More...
const rvec &	x () const
	Returns coordinates for this position.
const rvec &	v () const
	Returns velocity for this position. More...
const rvec &	f () const
	Returns force for this position. More...
real	mass () const
	Returns total mass for this position. More...
real	charge () const
	Returns total charge for this position. More...
int	atomCount () const
	Returns the number of atoms that make up this position.
ArrayRef< const int >	atomIndices () const
	Return atom indices that make up this position.
bool	selected () const
	Returns whether this position is selected in the current frame. More...
int	refId () const
	Returns reference ID for this position. More...
int	mappedId () const
	Returns mapped ID for this position. More...
	operator AnalysisNeighborhoodPositions () const
	Allows passing a selection position directly to neighborhood searching. More...

Constructor & Destructor Documentation

gmx::SelectionPosition::SelectionPosition ( const internal::SelectionData &  sel, int  index  )

inline

Constructs a wrapper object for given selection position.

Parameters

[in]	sel	Selection from which the position is wrapped.
[in]	index	Zero-based index of the position to wrap.

Asserts if index is out of range.

Only for internal use of the library. To obtain a SelectionPosition object in other code, use Selection::position().

Member Function Documentation

real gmx::SelectionPosition::charge ( ) const

inline

Returns total charge for this position.

Returns the sum of charges of atoms that make up this position. If there are no atoms associated or charges are not available, returns zero.

const rvec& gmx::SelectionPosition::f ( ) const

inline

Returns force for this position.

Must not be called if Selection::hasForces() returns false.

int gmx::SelectionPosition::mappedId ( ) const

inline

Returns mapped ID for this position.

Returns ID of the position that corresponds to that set with Selection::setOriginalId().

If for an array id, setOriginalId(i, id[i]) has been called for each i, then it always holds that mappedId()==id[refId()].

Selection::setOriginalId() has not been called, the default values are dependent on type():

• INDEX_ATOM: atom indices
• INDEX_RES: residue indices
• INDEX_MOL: molecule indices

All the default values are zero-based.

real gmx::SelectionPosition::mass ( ) const

inline

Returns total mass for this position.

Returns the total mass of atoms that make up this position. If there are no atoms associated or masses are not available, returns unity.

gmx::SelectionPosition::operator AnalysisNeighborhoodPositions

(

)

const

Allows passing a selection position directly to neighborhood searching.

When initialized this way, AnalysisNeighborhoodPair objects return the index that can be used to access this position using Selection::position().

Works exactly like if AnalysisNeighborhoodPositions had a constructor taking a SelectionPosition object as a parameter. See AnalysisNeighborhoodPositions for rationale and additional discussion.

int gmx::SelectionPosition::refId ( ) const

inline

Returns reference ID for this position.

For dynamic selections, this provides means to associate positions across frames. After compilation, these IDs are consequently numbered starting from zero. For each frame, the ID then reflects the location of the position in the original array of positions. If SelectionOption::dynamicMask() has been set for the parent selection, the IDs for positions not present in the current selection are set to -1, otherwise they are removed completely.

Example: If a dynamic selection consists of at most three positions, after compilation refId() will return 0, 1, 2 for them, respectively. If for a particular frame, only the first and the third are present, refId() will return 0, 2. If SelectionOption::dynamicMask() has been set, all three positions can be accessed also for that frame and refId() will return 0, -1, 2.

bool gmx::SelectionPosition::selected ( ) const

inline

Returns whether this position is selected in the current frame.

The return value is equivalent to refid() == -1. Returns always true if SelectionOption::dynamicMask() has not been set.

See Also

refId()

e_index_t gmx::SelectionPosition::type ( ) const

inline

Returns type of this position.

Currently always returns the same as Selection::type().

const rvec& gmx::SelectionPosition::v ( ) const

inline

Returns velocity for this position.

Must not be called if Selection::hasVelocities() returns false.

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

• api/legacy/include/gromacs/selection/selection.h
• src/gromacs/selection/selection.cpp