Parsing and Evaluation of Analysis Selections (selection)

Collaboration diagram for Parsing and Evaluation of Analysis Selections (selection):

Description

Provides functionality for initializing and evaluating selections.

The core of the selection engine is accessed through gmx::SelectionCollection, which manages a set of selections. Documentation for that class explains the general selection mechanisms.

For each selection that is parsed using a gmx::SelectionCollection, a gmx::Selection handle is returned and can be used to access information about that selection. gmx::SelectionPosition is a helper class used to access information about individual positions in a selection. These classes refer to internal state within the gmx::SelectionCollection, and their contents update automatically when the gmx::SelectionCollection is compiled or evaluated.

This module also provides gmx::SelectionOption and gmx::SelectionOptionInfo classes for declaring options that evaluate to selections (see Extensible Handling of Options (options) for general explanation of the options mechanism). These classes provide the main interface to obtain gmx::Selection objects in trajectory analysis using gmx::TrajectoryAnalysisModule. To use these classes outside the trajectory analysis framework, a gmx::SelectionOptionManager or a gmx::SelectionOptionBehavior needs to be created to serve as a bridge between the selection option classes and the gmx::SelectionCollection object. gmx::SelectionFileOption can be used to implement generic file input for selection options (done internally within gmx::SelectionOptionBehavior).

The selection module contains some lower-level functionality that is currently internal to it (centerofmass.h, indexutil.h, poscalc.h, position.h), but could possibly be useful also outside the module. It should be considered whether they should be moved somewhere else.

Author

Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Classes
class	gmx::FileNameOptionManager
	Handles interaction of file name options with global options. More...
class	gmx::AnalysisNeighborhoodPositions
	Input positions for neighborhood searching. More...
class	gmx::AnalysisNeighborhood
	Neighborhood searching for analysis tools. More...
class	gmx::AnalysisNeighborhoodPair
	Value type to represent a pair of positions found in neighborhood searching. More...
class	gmx::AnalysisNeighborhoodSearch
	Initialized neighborhood search with a fixed set of reference positions. More...
class	gmx::AnalysisNeighborhoodPairSearch
	Initialized neighborhood pair search with a fixed set of positions. More...
class	gmx::Selection
	Provides access to a single selection. More...
class	gmx::SelectionPosition
	Provides access to information about a single selected position. More...
class	gmx::SelectionCollection
	Collection of selections. More...
struct	gmx::SelectionTopologyProperties
	Describes topology properties required for selection evaluation. More...
class	gmx::SelectionFileOption
	Specifies a special option that provides selections from a file. More...
class	gmx::SelectionFileOptionInfo
	Wrapper class for accessing and modifying selection file option information. More...
class	gmx::SelectionOption
	Specifies an option that provides selection(s). More...
class	gmx::SelectionOptionInfo
	Wrapper class for accessing and modifying selection option information. More...
class	gmx::ITopologyProvider
	Provides topology information to SelectionOptionBehavior. More...
class	gmx::SelectionOptionBehavior
	Options behavior to allow using SelectionOptions. More...
class	gmx::SelectionOptionManager
	Handles interaction of selection options with other options and user input. More...

Functions
static bool	next_group_index (int atomIndex, const gmx_mtop_t *top, e_index_t type, int *id)
	Helper for splitting a sequence of atom indices into groups. More...
HelpTopicPointer	gmx::createSelectionHelpTopic ()
	*/ More...

Directories
directory	selection
	Parsing and Evaluation of Analysis Selections (selection)
directory	tests
	Unit tests for Parsing and Evaluation of Analysis Selections (selection).

Files
file	indexutil.h
	API for handling index files and index groups.
file	nbsearch.h
	API for neighborhood searching for analysis.
file	position.h
	API for handling positions.
file	selection.h
	Declares gmx::Selection and supporting classes.
file	selectioncollection.h
	Declares gmx::SelectionCollection.
file	selectionenums.h
	Declares common types used in selections.
file	selectionfileoption.h
	Declares gmx::SelectionFileOption and gmx::SelectionFileOptionInfo.
file	selectionoption.h
	Declares gmx::SelectionOption and gmx::SelectionOptionInfo.
file	selectionoptionbehavior.h
	Declares gmx::SelectionOptionBehavior.
file	selectionoptionmanager.h
	Declares gmx::SelectionOptionManager.
file	selhelp.h
	Functions for initializing online help for selections.
file	selection.h
	Public API convenience header for selection handling.

Function Documentation

HelpTopicPointer gmx::createSelectionHelpTopic

(

)

*/

Creates a help tree for selections.

Exceptions

std::bad_alloc

if out of memory.

Returns

Root topic of the created selection tree.

static bool next_group_index ( int  atomIndex, const gmx_mtop_t *  top, e_index_t  type, int *  id  )

static

Helper for splitting a sequence of atom indices into groups.

Parameters

[in]	atomIndex	Index of the next atom in the sequence.
[in]	top	Topology structure.
[in]	type	Type of group to split into.
[in,out]	id	Variable to receive the next group id.

Returns

true if atomIndex starts a new group in the sequence, i.e., if *id was changed.

*id should be initialized to -1 before first call of this function, and then each atom index in the sequence passed to the function in turn.