#include <gromacs/selection/selelem.h>

Collaboration diagram for gmx::SelectionTreeElement:

Description

Represents an element of a selection expression.

Public Member Functions
	SelectionTreeElement (e_selelem_t type, const SelectionLocation &location)
	Allocates memory and performs common initialization. More...

void	freeValues ()
	Frees the memory allocated for the v union.

void	freeExpressionData ()
	Frees the memory allocated for the u union.

void	freeCompilerData ()
	Frees the memory allocated for the selection compiler. More...

void	mempoolReserve (int count)
	Reserves memory for value from a memory pool. More...

void	mempoolRelease ()
	Releases memory pool used for value. More...

const std::string &	name () const
	Returns the name of the element.

const SelectionLocation &	location () const
	Returns the location of the element.

void	setName (const char *name)
	Sets the name of the element. More...

void	setName (const std::string &name)
	Sets the name of the element. More...

void	fillNameIfMissing (const char *selectionText)
	Sets the name of a root element if it is missing. More...

SelectionTopologyProperties	requiredTopologyProperties () const
	Returns which topology properties the selection element subtree requires for evaluation. More...

void	checkUnsortedAtoms (bool bUnsortedAllowed, ExceptionInitializer *errors) const
	Checks that this element and its children do not contain unsupported elements with unsorted atoms. More...

bool	requiresIndexGroups () const
	Checks whether the element or its children have unresolved index group references. More...

void	resolveIndexGroupReference (gmx_ana_indexgrps_t *grps, int natoms)
	Resolves an unresolved reference to an index group. More...

void	checkIndexGroup (int natoms)
	Checks that an index group has valid atom indices. More...

Public Attributes
e_selelem_t	type
	Type of the element.

gmx_ana_selvalue_t	v
	Value storage of the element. More...

sel_evalfunc	evaluate
	Evaluation function for the element. More...

int	flags
	Information flags about the element. More...

union {
gmx_ana_index_t cgrp
	Index group data for several element types. More...

struct {
struct gmx_ana_selmethod_t * method
	Pointer the method used in this expression.

void * mdata
	Pointer to the data allocated by the method's `init_data` (see sel_datafunc()).

struct gmx_ana_pos_t * pos
	Pointer to the position data passed to the method.

struct gmx_ana_poscalc_t * pc
	Pointer to the evaluation data for `pos`.

} expr
	Data for SEL_EXPRESSION and SEL_MODIFIER elements.

e_boolean_t boolt
	Operation type for SEL_BOOLEAN elements.

struct {
e_arithmetic_t type
	Operation type.

char * opstr
	String representation.

} arith
	Operation type for SEL_ARITHMETIC elements.

struct gmx_ana_selparam_t * param
	Associated selection parameter for SEL_SUBEXPRREF elements.

struct {
char * name
	Name of the referenced external group.

int id
	If name is NULL, the index number of the referenced group.

} gref
	The string/number used to reference the group.

}	u
	Data required by the evaluation function.

struct gmx_sel_mempool_t *	mempool
	Memory pool to use for values, or NULL if standard memory handling.

t_compiler_data *	cdata
	Internal data for the selection compiler.

SelectionTreeElementPointer	child
	The first child element. More...

SelectionTreeElementPointer	next
	The next sibling element.

Constructor & Destructor Documentation

gmx::SelectionTreeElement::SelectionTreeElement	(	e_selelem_t	type,
		const SelectionLocation &	location
	)

Allocates memory and performs common initialization.

Parameters

[in]	type	Type of selection element to create.
[in]	location	Location of the element.

type is set to type, v::type is set to GROUP_VALUE for boolean and comparison expressions and NO_VALUE for others, and SEL_ALLOCVAL is set for non-root elements (SEL_ALLOCDATA is also set for SEL_BOOLEAN elements). All the pointers are set to NULL.

Member Function Documentation

void gmx::SelectionTreeElement::checkIndexGroup ( int natoms )

Checks that an index group has valid atom indices.

Parameters

[in] natoms Maximum number of atoms the selections can evaluate to.

Exceptions

std::bad_alloc	if out of memory.
InconsistentInputError	if there are invalid atom indices.

void gmx::SelectionTreeElement::checkUnsortedAtoms	(	bool	bUnsortedAllowed,
		ExceptionInitializer *	errors
	)		const

Checks that this element and its children do not contain unsupported elements with unsorted atoms.

Parameters

[in]	bUnsortedAllowed	Whether this element's parents allow it to have unsorted atoms.
	errors	Object for reporting any error messages.

Exceptions

std::bad_alloc if out of memory.

Errors are reported as nested exceptions in errors.

void gmx::SelectionTreeElement::fillNameIfMissing ( const char * selectionText )

Sets the name of a root element if it is missing.

Parameters

[in] selectionText Full selection text to use as a fallback.

Exceptions

std::bad_alloc if out of memory.

If index groups have not yet been set and the selection is a result of a group reference, the name may still be empty after this call.

Strong exception safety guarantee.

void gmx::SelectionTreeElement::freeCompilerData ( )

Frees the memory allocated for the selection compiler.

This function only frees the data for the given selection, not its children. It is safe to call the function when compiler data has not been allocated or has already been freed; in such a case, nothing is done.

void gmx::SelectionTreeElement::mempoolRelease ( )

Releases memory pool used for value.

Releases the memory allocated for the values of this element from the mempool memory pool. If no memory pool is set, nothing is done.

void gmx::SelectionTreeElement::mempoolReserve ( int count )

Reserves memory for value from a memory pool.

Parameters

[in] count Number of values to reserve memory for.

Reserves memory for the values of this element from the mempool memory pool. If no memory pool is set, nothing is done.

SelectionTopologyProperties gmx::SelectionTreeElement::requiredTopologyProperties ( ) const

Returns which topology properties the selection element subtree requires for evaluation.

Returns: List of topology properties required for evaluation.

bool gmx::SelectionTreeElement::requiresIndexGroups ( ) const

Checks whether the element or its children have unresolved index group references.

Does not throw.

void gmx::SelectionTreeElement::resolveIndexGroupReference	(	gmx_ana_indexgrps_t *	grps,
		int	natoms
	)

Resolves an unresolved reference to an index group.

Parameters

[in]	grps	Index groups to use to resolve the reference.
[in]	natoms	Maximum number of atoms the selections can evaluate to (zero if the topology/atom count is not set yet).

Exceptions

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

void gmx::SelectionTreeElement::setName ( const char * name )

inline

Sets the name of the element.

Parameters

[in] name Name to set (can be NULL).

Exceptions

std::bad_alloc if out of memory.

void gmx::SelectionTreeElement::setName ( const std::string & name )

inline

Sets the name of the element.

Parameters

[in] name Name to set (can be NULL).

Exceptions

std::bad_alloc if out of memory.

Member Data Documentation

gmx_ana_index_t gmx::SelectionTreeElement::cgrp

Index group data for several element types.

SEL_CONST : if the value type is GROUP_VALUE, this field holds the unprocessed group value.
SEL_ROOT : holds the group value for which the selection subtree should be evaluated.
SEL_SUBEXPR : holds the group for which the subexpression has been evaluated.

SelectionTreeElementPointer gmx::SelectionTreeElement::child

The first child element.

Other children can be accessed through the next field of child.

sel_evalfunc gmx::SelectionTreeElement::evaluate

Evaluation function for the element.

Can be either NULL (if the expression is a constant and does not require evaluation) or point to one of the functions defined in evaluate.h.

int gmx::SelectionTreeElement::flags

Information flags about the element.

Allowed flags are listed here: flags for gmx::SelectionTreeElement.

gmx_ana_selvalue_t gmx::SelectionTreeElement::v

Value storage of the element.

This field contains the evaluated value of the element, as well as the output value type.

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

src/gromacs/selection/selelem.h
src/gromacs/selection/compiler.cpp
src/gromacs/selection/selelem.cpp

Description

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation