#include <gromacs/selection/poscalc.h>

Description

Collection of gmx_ana_poscalc_t structures for the same topology.

Calculations within one collection share the same topology, and they are optimized. Calculations in different collections do not interact. The topology for a collection can be set with setTopology(). This needs to be done before calling gmx_ana_poscalc_set_maxindex() for any calculation in the collection, unless that calculation does not require topology information.

A new calculation is created with createCalculation(). If flags need to be adjusted later, gmx_ana_poscalc_set_flags() can be used. After the flags are final, the largest possible index group for which the positions are needed has to be set with gmx_ana_poscalc_set_maxindex(). setTopology() should have been called before this function is called. After the above calls, gmx_ana_poscalc_init_pos() can be used to initialize output to a gmx_ana_pos_t structure. Several different structures can be initialized for the same calculation; the only requirement is that the structure passed later to gmx_ana_poscalc_update() has been initialized properly. The memory allocated for a calculation can be freed with gmx_ana_poscalc_free().

The position evaluation is simple: initFrame() should be called once for each frame, and gmx_ana_poscalc_update() can then be called for each calculation that is needed for that frame.

It is also possible to initialize the calculations based on a type provided as a string. The possible strings are listed in typeEnumValues, and the string can be converted to the parameters for createCalculation() using typeFromEnum(). createCalculationFromEnum() is also provided for convenience.

Classes
class	Impl
	Private implementation class for PositionCalculationCollection. More...

Public Types
enum	RequiredTopologyInfo { RequiredTopologyInfo::None, RequiredTopologyInfo::Topology, RequiredTopologyInfo::TopologyAndMasses }
	Describes what topology information is needed for position calculation. More...

Public Member Functions
	PositionCalculationCollection ()
	Creates a new position calculation collection object. More...

	~PositionCalculationCollection ()
	Destroys a position calculation collection and its calculations. More...

void	setTopology (const gmx_mtop_t *top)
	Sets the topology used for the calculations. More...

void	printTree (FILE *fp) const
	Prints information about calculations. More...

gmx_ana_poscalc_t *	createCalculation (e_poscalc_t type, int flags)
	Creates a new position calculation. More...

gmx_ana_poscalc_t *	createCalculationFromEnum (const char *post, int flags)
	Creates a new position calculation based on an enum value. More...

void	getRequiredAtoms (gmx_ana_index_t *out) const
	Computes the atoms required to evaluate this collection. More...

void	initEvaluation ()
	Initializes evaluation for a position calculation collection. More...

void	initFrame (const t_trxframe *fr)
	Initializes a position calculation collection for a new frame. More...

Static Public Member Functions
static void	typeFromEnum (const char post, e_poscalc_t type, int *flags)
	Converts a string to parameters for createCalculationFromEnum(). More...

static RequiredTopologyInfo	requiredTopologyInfoForType (const char *post, bool forces)
	Returns what information is needed for position evaluation. More...

Static Public Attributes
static const char *const	typeEnumValues []
	Array of strings acceptable for position calculation type enum. More...

Friends
struct	::gmx_ana_poscalc_t
	Needed to access the implementation class from the C code.

Member Enumeration Documentation

enum gmx::PositionCalculationCollection::RequiredTopologyInfo

strong

Describes what topology information is needed for position calculation.

Enumerator
None	No topology is needed.
Topology	Topology is needed (residue/molecule info).
TopologyAndMasses	Masses are needed.

Constructor & Destructor Documentation

gmx::PositionCalculationCollection::PositionCalculationCollection ( )

Creates a new position calculation collection object.

Exceptions

std::bad_alloc if out of memory.

gmx::PositionCalculationCollection::~PositionCalculationCollection ( )

Destroys a position calculation collection and its calculations.

Any calculations in the collection are also freed, even if references to them are left.

Member Function Documentation

gmx_ana_poscalc_t * gmx::PositionCalculationCollection::createCalculation	(	e_poscalc_t	type,
		int	flags
	)

Creates a new position calculation.

Parameters

[in]	type	Type of calculation.
[in]	flags	Flags for setting calculation options (see documentation of the flags).

Does not throw currently, but may throw std::bad_alloc in the future.

gmx_ana_poscalc_t * gmx::PositionCalculationCollection::createCalculationFromEnum	(	const char *	post,
		int	flags
	)

Creates a new position calculation based on an enum value.

Parameters

[in]	post	One of the strings acceptable for typeFromEnum().
[in]	flags	Flags for setting calculation options (see documentation of the flags).

Exceptions

InternalError if post is not recognized.

This is a convenience wrapper for createCalculation(). flags sets the default calculation options if not overridden by post; see typeFromEnum().

May also throw std::bad_alloc in the future.

See Also: createCalculation(), typeFromEnum()

void gmx::PositionCalculationCollection::getRequiredAtoms ( gmx_ana_index_t * out ) const

Computes the atoms required to evaluate this collection.

Parameters

[out] out Maximal group of atoms required to evaluate the positions.

Does not throw.

void gmx::PositionCalculationCollection::initEvaluation ( )

Initializes evaluation for a position calculation collection.

This function does some final initialization of the data structures in the collection to prepare them for evaluation. After this function has been called, it is no longer possible to add new calculations to the collection.

Multiple calls to the function are ignored.

Does not throw currently, but may throw std::bad_alloc in the future.

void gmx::PositionCalculationCollection::initFrame ( const t_trxframe * fr )

Initializes a position calculation collection for a new frame.

Parameters

[in] fr Frame to initialize evaluation for.

Should be called for each frame before calling gmx_ana_poscalc_update().

This function calls initEvaluation() automatically if it has not been called earlier.

Does not currently throw, but may throw std::bad_alloc in the future.

void gmx::PositionCalculationCollection::printTree ( FILE * fp ) const

Prints information about calculations.

Parameters

[in] fp File handle to receive the output.

The output is very technical, making this function mainly useful for debugging purposes.

Does not throw.

PositionCalculationCollection::RequiredTopologyInfo gmx::PositionCalculationCollection::requiredTopologyInfoForType	(	const char *	post,
		bool	forces
	)

static

Returns what information is needed for position evaluation.

Parameters

[in]	post	Position type (see typeFromEnum()).
[in]	forces	Whether forces are needed.

Returns: What topology information is required for initializing and/or evaluating the positions.

void gmx::PositionCalculationCollection::setTopology ( const gmx_mtop_t * top )

Sets the topology used for the calculations.

Parameters

[in] top Topology data structure.

This function should be called to set the topology before using gmx_ana_poscalc_set_maxindex() for any calculation that requires topology information.

Does not throw.

void gmx::PositionCalculationCollection::typeFromEnum	(	const char *	post,
		e_poscalc_t *	type,
		int *	flags
	)

static

Converts a string to parameters for createCalculationFromEnum().

Parameters

[in]	post	String (typically an enum argument). Allowed values: 'atom', 'res_com', 'res_cog', 'mol_com', 'mol_cog', or one of the last four prepended by 'whole_', 'part_', or 'dyn_'.
[out]	type	`e_poscalc_t` corresponding to `post`.
[in,out]	flags	Flags corresponding to `post`. On input, the flags should contain the default flags. On exit, the flags POS_MASS, POS_COMPLMAX and POS_COMPLWHOLE have been set according to `post` (the completion flags are left at the default values if no completion prefix is given).

Exceptions

InternalError if post is not recognized.

Attention: Checking is not complete, and other values than those listed above may be accepted for post, but the results are undefined.

See Also: typeEnumValues

Member Data Documentation

const char *const gmx::PositionCalculationCollection::typeEnumValues

static

Initial value:

= {
    "atom",          "res_com",       "res_cog",       "mol_com",       "mol_cog",
    "whole_res_com", "whole_res_cog", "whole_mol_com", "whole_mol_cog", "part_res_com",
    "part_res_cog",  "part_mol_com",  "part_mol_cog",  "dyn_res_com",   "dyn_res_cog",
    "dyn_mol_com",   "dyn_mol_cog",   nullptr,
}

Array of strings acceptable for position calculation type enum.

This array contains the acceptable values for typeFromEnum() and createCalculationFromEnum(). The array contains a NULL pointer after the last item to indicate the end of the list.

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

src/gromacs/selection/poscalc.h
src/gromacs/selection/poscalc.cpp

Description

Classes

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Friends

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation