#include "gmxpre.h"
#include <cstdlib>
#include <cstring>
#include <list>
#include <string>
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/selparam.h"
#include "gromacs/selection/selvalue.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "keywords.h"
#include "parsetree.h"
#include "selelem.h"
#include "selmethod.h"
#include "selmethod_impl.h"

Include dependency graph for sm_same.cpp:

Description

Implements the same selection method.

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

Classes
struct	t_methoddata_same
	Data structure for the `same` selection method. More...

Functions
static void *	init_data_same (int npar, gmx_ana_selparam_t *param)
	Allocates data for the `same` selection method. More...

static void	init_same (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes the `same` selection method. More...

static void	free_data_same (void *data)
	Frees the data allocated for the `same` selection method. More...

static void	init_frame_same_int (const gmx::SelMethodEvalContext &context, void *data)
	Initializes the evaluation of the `same` selection method for a frame. More...

static void	evaluate_same_int (const gmx::SelMethodEvalContext &context, gmx_ana_index_t g, gmx_ana_selvalue_t out, void *data)
	Evaluates the `same` selection method. More...

static void	init_frame_same_str (const gmx::SelMethodEvalContext &context, void *data)
	Initializes the evaluation of the `same` selection method for a frame. More...

static void	evaluate_same_str (const gmx::SelMethodEvalContext &context, gmx_ana_index_t g, gmx_ana_selvalue_t out, void *data)
	Evaluates the `same` selection method. More...

void	_gmx_selelem_custom_init_same (gmx_ana_selmethod_t *method, const gmx::SelectionParserParameterListPointer &params, void scanner)
	Does custom processing for parameters of the `same` selection method. More...

static int	cmp_int (const void a, const void b)
	Helper function for comparison of two integers.

static int	cmp_str (const void a, const void b)
	Helper function for comparison of two strings.

Variables
static gmx_ana_selparam_t	smparams_same_int []
	Parameters for the `same` selection method. More...

static gmx_ana_selparam_t	smparams_same_str []
	Parameters for the `same` selection method. More...

static const char *const	help_same []
	Help text for the `same` selection method. More...

gmx_ana_selmethod_t	sm_same
	Selection method data for the `same` method. More...

static gmx_ana_selmethod_t	sm_same_str
	Selection method data for the `same` method. More...

Function Documentation

void _gmx_selelem_custom_init_same	(	gmx_ana_selmethod_t **	method,
		const gmx::SelectionParserParameterListPointer &	params,
		void *	scanner
	)

Does custom processing for parameters of the same selection method.

Parameters

[in,out]	method	The method to initialize.
[in,out]	params	Pointer to the first parameter.
[in]	scanner	Scanner data structure.

If *method is not a same method, this function returns immediately.

static void evaluate_same_int	(	const gmx::SelMethodEvalContext &	context,
		gmx_ana_index_t *	g,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Evaluates the same selection method.

See sel_updatefunc() for description of the parameters. data should point to a t_methoddata_same.

Calculates which values in data->val.i can be found in data->as.i (assumed sorted), and writes the corresponding atoms to output. If data->val is sorted, uses a linear scan of both arrays, otherwise a binary search of data->as is performed for each block of values in data->val.

static void evaluate_same_str	(	const gmx::SelMethodEvalContext &	context,
		gmx_ana_index_t *	g,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Evaluates the same selection method.

See sel_updatefunc() for description of the parameters. data should point to a t_methoddata_same.

Calculates which strings in data->val.s can be found in data->as.s (assumed sorted), and writes the corresponding atoms to output. A binary search of data->as is performed for each block of values in data->val.

static void free_data_same ( void * data )

static

Frees the data allocated for the same selection method.

Parameters

data	Data to free (should point to a t_methoddata_same).

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

static

Allocates data for the same selection method.

Parameters

[in]	npar	Not used (should be 2).
[in,out]	param	Method parameters (should point to a copy of smparams_same_int or smparams_same_str).

Returns: Pointer to the allocated data (t_methoddata_same).

static void init_frame_same_int	(	const gmx::SelMethodEvalContext &	context,
		void *	data
	)

static

Initializes the evaluation of the same selection method for a frame.

Parameters

[in]	context	Not used.
	data	Should point to a t_methoddata_same.

Sorts the data->as.i array and removes identical values for faster and simpler lookup.

static void init_frame_same_str	(	const gmx::SelMethodEvalContext &	context,
		void *	data
	)

static

Initializes the evaluation of the same selection method for a frame.

Parameters

[in]	context	Not used.
	data	Should point to a t_methoddata_same.

Sorts the data->as.s array and removes identical values for faster and simpler lookup.

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

static

Initializes the same selection method.

Parameters

top	Not used.
npar	Not used (should be 2).
param	Initialized method parameters (should point to a copy of smparams_same_int or smparams_same_str).
data	Pointer to t_methoddata_same to initialize.

Returns: 0 on success, -1 on failure.

Variable Documentation

const char* const help_same[]

static

Initial value:

= {
    "::",
    "",
    "  same KEYWORD as ATOM_EXPR",
    "",
    "The keyword [TT]same[tt] can be used to select all atoms for which",
    "the given [TT]KEYWORD[tt] matches any of the atoms in [TT]ATOM_EXPR[tt].",
    "Keywords that evaluate to integer or string values are supported.",
}

Help text for the same selection method.

gmx_ana_selmethod_t sm_same

Initial value:

= {
    "same",
    GROUP_VALUE,
    0,
    asize(smparams_same_int),
    smparams_same_int,
    &init_data_same,
    nullptr,
    &init_same,
    nullptr,
    &free_data_same,
    &init_frame_same_int,
    &evaluate_same_int,
    nullptr,
    { "same KEYWORD as ATOM_EXPR", "Extending selections", asize(help_same), help_same },
}

Selection method data for the same method.

gmx_ana_selmethod_t sm_same_str

static

Initial value:

= {
    "same",
    GROUP_VALUE,
     8 ,
    asize(smparams_same_str),
    smparams_same_str,
    &init_data_same,
    nullptr,
    &init_same,
    nullptr,
    &free_data_same,
    &init_frame_same_str,
    &evaluate_same_str,
    nullptr,
    { nullptr, nullptr, 0, nullptr },
}

Selection method data for the same method.

This selection method is used for matching string keywords. The parser never sees this method; _gmx_selelem_custom_init_same() replaces sm_same with this method in cases where it is required.

gmx_ana_selparam_t smparams_same_int[]

static

Initial value:

= {
    { nullptr, { INT_VALUE, -1, { nullptr } }, nullptr,  4  |  32  },
    { "as", { INT_VALUE, -1, { nullptr } }, nullptr,  4  |  16  },
}

Parameters for the same selection method.

gmx_ana_selparam_t smparams_same_str[]

static

Initial value:

= {
    { nullptr, { STR_VALUE, -1, { nullptr } }, nullptr,  4  |  32  },
    { "as", { STR_VALUE, -1, { nullptr } }, nullptr,  4  |  16  },
}

Parameters for the same selection method.

Description

Classes

Functions

Variables

Function Documentation

Variable Documentation