#include "gmxpre.h"
#include "gromacs/math/vec.h"
#include "gromacs/selection/position.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "selmethod.h"

Include dependency graph for sm_merge.cpp:

Description

Implements the merge and plus selection modifiers.

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

Classes
struct	t_methoddata_merge
	Data structure for the merging selection modifiers. More...

Functions
static void *	init_data_merge (int npar, gmx_ana_selparam_t *param)
	Allocates data for the merging selection modifiers. More...

static void	init_merge (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes data for the merging selection modifiers. More...

static void	init_output_merge (const gmx_mtop_t top, gmx_ana_selvalue_t out, void *data)
	Initializes output for the `merge` selection modifier. More...

static void	init_output_plus (const gmx_mtop_t top, gmx_ana_selvalue_t out, void *data)
	Initializes output for the `plus` selection modifier. More...

static void	free_data_merge (void *data)
	Frees the memory allocated for the merging selection modifiers. More...

static void	evaluate_merge (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t p, gmx_ana_selvalue_t out, void *data)
	Evaluates the `merge` selection modifier. More...

static void	evaluate_plus (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t p, gmx_ana_selvalue_t out, void *data)
	Evaluates the `plus` selection modifier. More...

static void	init_output_common (const gmx_mtop_t top, gmx_ana_selvalue_t out, void *data)
	Does common initialization to all merging modifiers. More...

Variables
static gmx_ana_selparam_t	smparams_merge []
	Parameters for the merging selection modifiers. More...

static const char	helptitle_merge [] = "Merging selections"
	Help title for the merging selection modifiers.

static const char *const	help_merge []
	Help text for the merging selection modifiers. More...

gmx_ana_selmethod_t	sm_merge
	Selection method data for the `plus` modifier. More...

gmx_ana_selmethod_t	sm_plus
	Selection method data for the `plus` modifier. More...

Function Documentation

static void evaluate_merge	(	const gmx::SelMethodEvalContext &	context,
		gmx_ana_pos_t *	p,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Evaluates the merge selection modifier.

Parameters

[in]	context	Not used.
[in]	p	Positions to merge (should point to `data->p1`).
[out]	out	Output data structure (`out->u.p` is used).
[in]	data	Should point to a `t_methoddata_merge`.

static void evaluate_plus	(	const gmx::SelMethodEvalContext &	context,
		gmx_ana_pos_t *	p,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Evaluates the plus selection modifier.

Parameters

[in]	context	Not used.
[in]	p	Positions to merge (should point to `data->p1`).
[out]	out	Output data structure (`out->u.p` is used).
[in]	data	Should point to a `t_methoddata_merge`.

static void free_data_merge ( void * data )

static

Frees the memory allocated for the merging selection modifiers.

Parameters

data	Data to free (should point to a `t_methoddata_merge`).

Frees the memory allocated for t_methoddata_merge.

static void * init_data_merge	(	int	npar,
		gmx_ana_selparam_t *	param
	)

static

Allocates data for the merging selection modifiers.

Parameters

[in]	npar	Should be 2 for `plus` and 3 for `merge`.
[in,out]	param	Method parameters (should point to a copy of smparams_merge).

Returns: Pointer to the allocated data (t_methoddata_merge).

Allocates memory for a t_methoddata_merge structure.

static void init_merge	(	const gmx_mtop_t *	top,
		int	npar,
		gmx_ana_selparam_t *	param,
		void *	data
	)

static

Initializes data for the merging selection modifiers.

Parameters

[in]	top	Not used.
[in]	npar	Not used (should be 2 or 3).
[in]	param	Method parameters (should point to smparams_merge).
[in]	data	Should point to a `t_methoddata_merge`.

Returns: 0 if everything is successful, -1 on error.

static void init_output_common	(	const gmx_mtop_t *	top,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Does common initialization to all merging modifiers.

Parameters

[in]	top	Topology data structure.
[in,out]	out	Pointer to output data structure.
[in,out]	data	Should point to `t_methoddata_merge`.

static void init_output_merge	(	const gmx_mtop_t *	top,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Initializes output for the merge selection modifier.

Parameters

[in]	top	Topology data structure.
[in,out]	out	Pointer to output data structure.
[in,out]	data	Should point to `t_methoddata_merge`.

static void init_output_plus	(	const gmx_mtop_t *	top,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Initializes output for the plus selection modifier.

Parameters

[in]	top	Topology data structure.
[in,out]	out	Pointer to output data structure.
[in,out]	data	Should point to `t_methoddata_merge`.

Variable Documentation

const char* const help_merge[]

static

Initial value:

= {
    "::",
    "",
    "  POSEXPR merge POSEXPR [stride INT]",
    "  POSEXPR merge POSEXPR [merge POSEXPR ...]",
    "  POSEXPR plus POSEXPR [plus POSEXPR ...]",
    "",
    "Basic selection keywords can only create selections where each atom",
    "occurs at most once. The [TT]merge[tt] and [TT]plus[tt] selection",
    "keywords can be used to work around this limitation. Both create",
    "a selection that contains the positions from all the given position",
    "expressions, even if they contain duplicates.",
    "The difference between the two is that [TT]merge[tt] expects two or more",
    "selections with the same number of positions, and the output contains",
    "the input positions selected from each expression in turn, i.e.,",
    "the output is like A1 B1 A2 B2 and so on. It is also possible to merge",
    "selections of unequal size as long as the size of the first is a",
    "multiple of the second one. The [TT]stride[tt] parameter can be used",
    "to explicitly provide this multiplicity.",
    "[TT]plus[tt] simply concatenates the positions after each other, and",
    "can work also with selections of different sizes.",
    "These keywords are valid only at the selection level, not in any",
    "subexpressions.",
}

Help text for the merging selection modifiers.

gmx_ana_selmethod_t sm_merge

Initial value:

= {
    "merge", POS_VALUE,  256 ,
    ((int)(sizeof( smparams_merge )/sizeof(( smparams_merge )[0]))), smparams_merge,
    &init_data_merge,
    nullptr,
    &init_merge,
    &init_output_merge,
    &free_data_merge,
    nullptr,
    nullptr,
    &evaluate_merge,
    {"merge POSEXPR", helptitle_merge, ((int)(sizeof( help_merge )/sizeof(( help_merge )[0]))), help_merge},
}

Selection method data for the plus modifier.

gmx_ana_selmethod_t sm_plus

Initial value:

= {
    "plus", POS_VALUE,  256 ,
    ((int)(sizeof( smparams_merge )/sizeof(( smparams_merge )[0])))-1, smparams_merge,
    &init_data_merge,
    nullptr,
    &init_merge,
    &init_output_plus,
    &free_data_merge,
    nullptr,
    nullptr,
    &evaluate_plus,
    {"plus POSEXPR", helptitle_merge, ((int)(sizeof( help_merge )/sizeof(( help_merge )[0]))), help_merge},
}

Selection method data for the plus modifier.

gmx_ana_selparam_t smparams_merge[]

static

Initial value:

= {
    {nullptr,       {POS_VALUE, -1, {nullptr}}, nullptr,  4  |  16 },
    {nullptr,       {POS_VALUE, -1, {nullptr}}, nullptr,  4  |  16 },
    {"stride",   {INT_VALUE,  1, {nullptr}}, nullptr,  2 },
}

Parameters for the merging selection modifiers.

Description

Classes

Functions

Variables

Function Documentation

Variable Documentation