#include <gromacs/selection/selectioncollection.h>

Description

Collection of selections.

This class is the main interface to the core of the selection engine. It is used to initialize and manage a collection of selections that share the same topology. Selections within one collection can share variables and can be optimized together. Selections from two different collections do not interact.

The constructor creates an empty selection collection object. To initialize the object, either call initOptions(), or both setReferencePosType() and setOutputPosType(). See these methods for more details on the initialization options.

After setting the default values, one or more selections can be parsed with one or more calls to parseInteractive(), parseFromStdin(), parseFromFile(), and/or parseFromString(). After all selections are parsed, the topology must be set with setTopology() unless requiresTopology() returns false (the topology can also be set earlier). setIndexGroups() must also be called if external index group references are used in the selections; it can be called at any point before compile(). Once all selections are parsed, they must be compiled all at once using compile().

After compilation, dynamic selections have the maximum number of atoms they can evaluate to, but positions have undefined values (see Selection and SelectionPosition). evaluate() can be used to update the selections for a new frame. evaluateFinal() can be called after all the frames have been processed to restore the selection values back to the ones they were after compile().

At any point, requiresTopology() can be called to see whether the information provided so far requires loading the topology. Similarly, requiresIndexGroups() tells whether external index groups are requires. printTree() can be used to print the internal representation of the selections (mostly useful for debugging).

Note that for trajectory analysis using TrajectoryAnalysisModule, the SelectionCollection object is managed by Gromacs, and Selection objects are obtained from SelectionOption.

Classes
class	Impl
	Private implemention class for SelectionCollection. More...

Public Types
enum	SelectionTypeOption { IncludeSelectionTypeOption, AlwaysAtomSelections }
	Flag for initOptions() to select how to behave with -seltype option. More...

Public Member Functions
	SelectionCollection ()
	Creates an empty selection collection. More...

void	initOptions (IOptionsContainer *options, SelectionTypeOption selectionTypeOption)
	Initializes options for setting global properties on the collection. More...

void	setReferencePosType (const char *type)
	Sets the default reference position handling for a selection collection. More...

void	setOutputPosType (const char *type)
	Sets the default reference position handling for a selection collection. More...

void	setDebugLevel (int debugLevel)
	Sets the debugging level for the selection collection. More...

SelectionTopologyProperties	requiredTopologyProperties () const
	Returns what topology information is required for evaluation. More...

bool	requiresIndexGroups () const
	Returns true if the collection requires external index groups. More...

void	setTopology (gmx_mtop_t *top, int natoms)
	Sets the topology for the collection. More...

void	setIndexGroups (gmx_ana_indexgrps_t *grps)
	Sets the external index groups to use for the selections. More...

SelectionList	parseFromStdin (int count, bool bInteractive, const std::string &context)
	Parses selection(s) from standard input. More...

SelectionList	parseInteractive (int count, TextInputStream inputStream, TextOutputStream outputStream, const std::string &context)
	Parses selection(s) interactively using provided streams. More...

SelectionList	parseFromFile (const std::string &filename)
	Parses selection(s) from a file. More...

SelectionList	parseFromString (const std::string &str)
	Parses selection(s) from a string. More...

void	compile ()
	Prepares the selections for evaluation and performs optimizations. More...

void	evaluate (t_trxframe fr, t_pbc pbc)
	Evaluates selections in the collection. More...

void	evaluateFinal (int nframes)
	Evaluates the largest possible index groups from dynamic selections. More...

void	printTree (FILE *fp, bool bValues) const
	Prints a human-readable version of the internal selection element tree. More...

void	printXvgrInfo (FILE *fp) const
	Prints the selection strings into an XVGR file as comments. More...

Friends
class	SelectionCompiler
	Needed for the compiler to freely modify the collection.

class	SelectionEvaluator
	Needed for the evaluator to freely modify the collection.

Member Enumeration Documentation

enum gmx::SelectionCollection::SelectionTypeOption

Flag for initOptions() to select how to behave with -seltype option.

Enumerator
IncludeSelectionTypeOption	Add the option for the user to select default value for setOutputPosType().
AlwaysAtomSelections	Do not add the option, selections will always select atoms by default.

Constructor & Destructor Documentation

gmx::SelectionCollection::SelectionCollection ( )

Creates an empty selection collection.

Exceptions

std::bad_alloc if out of memory.

Member Function Documentation

void gmx::SelectionCollection::compile ( )

Prepares the selections for evaluation and performs optimizations.

Exceptions

InconsistentInputError	if topology is required but not set.
InvalidInputError	if setIndexGroups() has not been called and there are index group references.
unspecified	if compilation fails (TODO: list/reduce these).

Before compilation, selections should have been added to the collection using the parseFrom*() functions. The compiled selection collection can be passed to evaluate() to evaluate the selection for a frame. Before the compiled selection is evaluated, the selections indicate the maximal set of atoms/positions to which they can be evaluated; see Selection.

If an error occurs, the collection is cleared.

The covered fraction information is initialized to CFRAC_NONE for all selections.

void gmx::SelectionCollection::evaluate	(	t_trxframe *	fr,
		t_pbc *	pbc
	)

Evaluates selections in the collection.

Parameters

[in]	fr	Frame for which the evaluation should be carried out.
[in]	pbc	PBC data, or NULL if no PBC should be used.

Exceptions

unspeficied Multiple possible exceptions to indicate evaluation failure (TODO: enumerate).

void gmx::SelectionCollection::evaluateFinal ( int nframes )

Evaluates the largest possible index groups from dynamic selections.

Parameters

[in] nframes Total number of frames.

This method restores the selections to the state they were after compile().

nframes should equal the number of times evaluate() has been called.

Does not throw.

void gmx::SelectionCollection::initOptions	(	IOptionsContainer *	options,
		SelectionTypeOption	selectionTypeOption
	)

Initializes options for setting global properties on the collection.

Parameters

[in,out]	options	Options object to initialize.
[in]	selectionTypeOption	Whether to add option to influence setOutputPosType().

Exceptions

std::bad_alloc if out of memory.

Adds options to options that can be used to set the default position types (see setReferencePosType() and setOutputPosType()) and debugging flags.

SelectionList gmx::SelectionCollection::parseFromFile ( const std::string & filename )

Parses selection(s) from a file.

Parameters

[in] filename Name of the file to parse selections from.

Returns: Vector of parsed selections.

Exceptions

std::bad_alloc	if out of memory.
InvalidInputError	if there is a parsing error.

The returned objects remain valid for the lifetime of the selection collection. Some information about the selections only becomes available once compile() has been called; see Selection.

SelectionList gmx::SelectionCollection::parseFromStdin	(	int	count,
		bool	bInteractive,
		const std::string &	context
	)

Parses selection(s) from standard input.

Parameters

[in]	count	Number of selections to parse (if -1, parse as many as provided by the user).
[in]	bInteractive	Whether the parser should behave interactively.
[in]	context	Context to print for interactive input.

Returns: Vector of parsed selections.

Exceptions

std::bad_alloc	if out of memory.
InvalidInputError	if there is a parsing error (an interactive parser only throws this if too few selections are provided and the user forced the end of input).

The returned objects remain valid for the lifetime of the selection collection. Some information about the selections only becomes available once compile() has been called; see Selection.

The string provided to context should be such that it can replace the three dots in "Specify selections ...:". It can be empty.

SelectionList gmx::SelectionCollection::parseFromString ( const std::string & str )

Parses selection(s) from a string.

Parameters

[in] str String to parse selections from.

Returns: Vector of parsed selections.

Exceptions

std::bad_alloc	if out of memory.
InvalidInputError	if there is a parsing error.

The returned objects remain valid for the lifetime of the selection collection. Some information about the selections only becomes available once compile() has been called; see Selection.

SelectionList gmx::SelectionCollection::parseInteractive	(	int	count,
		TextInputStream *	inputStream,
		TextOutputStream *	outputStream,
		const std::string &	context
	)

Parses selection(s) interactively using provided streams.

Parameters

[in]	count	Number of selections to parse (if -1, parse as many as provided by the user).
[in]	inputStream	Stream to use for input.
[in]	outputStream	Stream to use for output (if NULL, the parser runs non-interactively and does not produce any status messages).
[in]	context	Context to print for interactive input.

Returns: Vector of parsed selections.

Exceptions

std::bad_alloc	if out of memory.
InvalidInputError	if there is a parsing error (an interactive parser only throws this if too few selections are provided and the user forced the end of input).

Works the same as parseFromStdin(), except that the caller can provide streams to use instead of stdin and stderr.

Mainly usable for unit testing interactive input.

void gmx::SelectionCollection::printTree	(	FILE *	fp,
		bool	bValues
	)		const

Prints a human-readable version of the internal selection element tree.

Parameters

[in]	fp	File handle to receive the output.
[in]	bValues	If true, the evaluated values of selection elements are printed as well.

The output is very techical, and intended for debugging purposes.

Does not throw.

void gmx::SelectionCollection::printXvgrInfo ( FILE * fp ) const

Prints the selection strings into an XVGR file as comments.

Parameters

[in] fp Output file.

Does not throw.

SelectionTopologyProperties gmx::SelectionCollection::requiredTopologyProperties ( ) const

Returns what topology information is required for evaluation.

Returns: What topology information is required for compiling and/or evaluating the selections in the collection.

Before the parser functions have been called, the return value is based just on the position types set. After parser functions have been called, the return value also takes into account the selection keywords used. After the compiler has been called, the return value is final and also considers possible force evaluation requested for the selections.

Does not throw.

bool gmx::SelectionCollection::requiresIndexGroups ( ) const

Returns true if the collection requires external index groups.

Returns: true if any selection has an unresolved index group reference.

The return value is false after setIndexGroups() has been called.

Does not throw.

void gmx::SelectionCollection::setDebugLevel ( int debugLevel )

Sets the debugging level for the selection collection.

Parameters

[in] debugLevel Debug level to set (0 = no debug information).

initOptions() creates debugging options that can also be used to set the debug level. These are normally hidden, but if this method is called before initOptions() with a non-zero debugLevel, they are made visible.

Mostly useful for debugging tools.

Does not throw.

void gmx::SelectionCollection::setIndexGroups ( gmx_ana_indexgrps_t * grps )

Sets the external index groups to use for the selections.

Parameters

[in] grps Index groups to use for the selections.

Exceptions

std::bad_alloc	if out of memory.
InconsistentInputError	if a group reference cannot be resolved.

Only the first call to this method can have a non-NULL grps. At this point, any selections that have already been provided are searched for references to external groups, and the references are replaced by the contents of the groups. If any referenced group cannot be found in grps (or if grps is NULL and there are any references), InconsistentInputError is thrown.

The selection collection keeps a reference to grps until this method is called with a NULL grps. If this method is not called before compile(), it is automatically called as setIndexGroups(NULL).

void gmx::SelectionCollection::setOutputPosType ( const char * type )

Sets the default reference position handling for a selection collection.

Parameters

[in] type Default selection output position type (one of the strings acceptable for PositionCalculationCollection::typeFromEnum()).

Exceptions

InternalError if type is invalid.

Should be called before calling the parser functions, unless initOptions() has been called. In the latter case, can still be used to override the default value (before initOptions() is called) and/or the value provided through the Options object.

Strong exception safety.

void gmx::SelectionCollection::setReferencePosType ( const char * type )

Sets the default reference position handling for a selection collection.

Parameters

[in] type Default selection reference position type (one of the strings acceptable for PositionCalculationCollection::typeFromEnum()).

Exceptions

InternalError if type is invalid.

Should be called before calling the parser functions, unless initOptions() has been called. In the latter case, can still be used to override the default value (before initOptions() is called) and/or the value provided through the Options object.

Strong exception safety.

void gmx::SelectionCollection::setTopology	(	gmx_mtop_t *	top,
		int	natoms
	)

Sets the topology for the collection.

Parameters

[in]	top	Topology data.
[in]	natoms	Number of atoms. If <=0, the number of atoms in the topology is used.

Either the topology must be provided, or natoms must be > 0.

natoms determines the largest atom index that can be selected by the selection: even if the topology contains more atoms, they will not be selected.

Does not throw currently, but this is subject to change when more underlying code is converted to C++.

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

src/gromacs/selection/selectioncollection.h
src/gromacs/selection/selectioncollection.cpp

Description

Classes

Public Types

Public Member Functions

Friends

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation