#include "gmxpre.h"
#include <cctype>
#include <cstring>
#include <memory>
#include <regex>
#include <string>
#include <vector>
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
#include "gromacs/selection/selparam.h"
#include "gromacs/selection/selvalue.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "keywords.h"
#include "parsetree.h"
#include "scanner.h"
#include "selelem.h"
#include "selmethod.h"

Include dependency graph for sm_keywords.cpp:

Description

Implements internal selection methods for numeric and string keyword evaluation.

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

Classes
struct	t_methoddata_kwint
	Data structure for integer keyword expression evaluation. More...

struct	t_methoddata_kwreal
	Data structure for real keyword expression evaluation. More...

class	anonymous_namespace{sm_keywords.cpp}::StringKeywordMatchItem
	Single item in the list of strings/regular expressions to match. More...

struct	anonymous_namespace{sm_keywords.cpp}::t_methoddata_kwstr
	Data structure for string keyword expression evaluation. More...

struct	t_methoddata_kweval
	Data structure for keyword evaluation in arbitrary groups. More...

Typedefs
typedef struct t_methoddata_kwint	t_methoddata_kwint
	Data structure for integer keyword expression evaluation. More...

typedef struct t_methoddata_kwreal	t_methoddata_kwreal
	Data structure for real keyword expression evaluation. More...

Functions
static void *	init_data_kwint (int npar, gmx_ana_selparam_t *param)
	Allocates data for integer keyword evaluation. More...

static void *	init_data_kwreal (int npar, gmx_ana_selparam_t *param)
	Allocates data for real keyword evaluation. More...

static void *	init_data_kwstr (int npar, gmx_ana_selparam_t *param)
	Allocates data for string keyword evaluation. More...

static void	init_kwint (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	/brief Initializes data for integer keyword evaluation. More...

static void	init_kwreal (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes data for real keyword evaluation. More...

static void	init_kwstr (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes data for string keyword evaluation. More...

static void	free_data_kwstr (void *data)
	Frees the memory allocated for string keyword evaluation. More...

static void	evaluate_keyword_int (const gmx::SelMethodEvalContext &context, gmx_ana_index_t g, gmx_ana_selvalue_t out, void *data)
	Evaluates integer selection keywords. More...

static void	evaluate_keyword_real (const gmx::SelMethodEvalContext &context, gmx_ana_index_t g, gmx_ana_selvalue_t out, void *data)
	Evaluates real selection keywords. More...

static void	evaluate_keyword_str (const gmx::SelMethodEvalContext &context, gmx_ana_index_t g, gmx_ana_selvalue_t out, void *data)
	Evaluates string selection keywords. More...

static void	init_kweval (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes keyword evaluation for an arbitrary group. More...

static void	init_output_kweval (const gmx_mtop_t top, gmx_ana_selvalue_t out, void *data)
	Initializes output for keyword evaluation in an arbitrary group. More...

static void	free_data_kweval (void *data)
	Frees the data allocated for keyword evaluation in an arbitrary group. More...

static void	init_frame_kweval (const gmx::SelMethodEvalContext &context, void *data)
	Initializes frame evaluation for keyword evaluation in an arbitrary group. More...

static void	evaluate_kweval (const gmx::SelMethodEvalContext &context, gmx_ana_index_t g, gmx_ana_selvalue_t out, void *data)
	Evaluates keywords in an arbitrary group. More...

static void	evaluate_kweval_pos (const gmx::SelMethodEvalContext &context, gmx_ana_index_t g, gmx_ana_selvalue_t out, void *data)
	Evaluates keywords in an arbitrary set of positions. More...

void	_gmx_selelem_set_kwstr_match_type (const gmx::SelectionTreeElementPointer &sel, gmx::SelectionStringMatchType matchType)
	Sets the string match type for string keyword evaluation. More...

static gmx::SelectionTreeElementPointer	init_evaluator_group (gmx_ana_selmethod_t method, const gmx::SelectionParserParameterList &params, void scanner)
	Initializes a selection element for evaluating a keyword in a given group. More...

static gmx::SelectionTreeElementPointer	init_evaluator_pos (gmx_ana_selmethod_t method, const gmx::SelectionParserParameterList &params, void scanner)
	Initializes a selection element for evaluating a keyword in given positions. More...

gmx::SelectionTreeElementPointer	_gmx_sel_init_keyword_evaluator (gmx_ana_selmethod_t method, const gmx::SelectionTreeElementPointer &child, void scanner)
	Initializes a selection element for evaluating a keyword in a given group. More...

Variables
static gmx_ana_selparam_t	smparams_keyword_int []
	Parameters for integer keyword evaluation. More...

static gmx_ana_selparam_t	smparams_keyword_real []
	Parameters for real keyword evaluation. More...

static gmx_ana_selparam_t	smparams_keyword_str []
	Parameters for string keyword evaluation. More...

gmx_ana_selmethod_t	sm_keyword_int
	Selection method data for integer keyword evaluation. More...

gmx_ana_selmethod_t	sm_keyword_real
	Selection method data for real keyword evaluation. More...

gmx_ana_selmethod_t	sm_keyword_str
	Selection method data for string keyword evaluation. More...

static gmx_ana_selparam_t	smparams_kweval_group []
	Parameters for keyword evaluation in an arbitrary group. More...

static gmx_ana_selparam_t	smparams_kweval_pos []
	Parameters for keyword evaluation from positions. More...

Typedef Documentation

typedef struct t_methoddata_kwint t_methoddata_kwint

Data structure for integer keyword expression evaluation.

typedef struct t_methoddata_kwreal t_methoddata_kwreal

Data structure for real keyword expression evaluation.

Function Documentation

gmx::SelectionTreeElementPointer _gmx_sel_init_keyword_evaluator	(	struct gmx_ana_selmethod_t *	method,
		const gmx::SelectionTreeElementPointer &	child,
		void *	scanner
	)

Initializes a selection element for evaluating a keyword in a given group.

Parameters

[in]	method	Keyword selection method to evaluate.
[in]	child	The group/positions to evaluate `method` in.
[in]	scanner	Scanner data structure.

Returns: Pointer to the created selection element.

Creates a SEL_EXPRESSION selection element that evaluates the keyword method given by method in the group/positions given by child.

child should be a selection tree that evaluates to GROUP_VALUE or POS_VALUE.

void _gmx_selelem_set_kwstr_match_type	(	const gmx::SelectionTreeElementPointer &	sel,
		gmx::SelectionStringMatchType	matchType
	)

Sets the string match type for string keyword evaluation.

Parameters

[in,out]	sel	Selection element to initialize.
[in]	matchType	Method to use to match string values.

Sets the string matching method for string keyword matching.

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

static

Evaluates integer selection keywords.

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

Does a binary search to find which atoms match the ranges in the t_methoddata_kwint structure for this selection. Matching atoms are stored in out->u.g.

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

static

Evaluates real selection keywords.

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

Does a binary search to find which atoms match the ranges in the t_methoddata_kwreal structure for this selection. Matching atoms are stored in out->u.g.

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

static

Evaluates string selection keywords.

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

Does a linear search to find which atoms match the strings in the t_methoddata_kwstr structure for this selection. Wildcards are allowed in the strings. Matching atoms are stored in out->u.g.

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

static

Evaluates keywords in an arbitrary group.

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

Calls the evaluation function of the wrapped keyword with the given parameters, with the exception of using t_methoddata_kweval::g for the evaluation group.

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

static

Evaluates keywords in an arbitrary set of positions.

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

Calls the evaluation function of the wrapped keyword with the given parameters, with the exception of using t_methoddata_kweval::p for the evaluation positions.

static void free_data_kweval ( void * data )

static

Frees the data allocated for keyword evaluation in an arbitrary group.

Parameters

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

Frees the memory allocated for all the members of t_methoddata_kweval.

static void free_data_kwstr ( void * data )

static

Frees the memory allocated for string keyword evaluation.

Parameters

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

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

static

Allocates data for integer keyword evaluation.

Parameters

[in]	npar	Not used.
	param	Not used.

Returns: Pointer to the allocated data (t_methoddata_kwint).

Allocates memory for a t_methoddata_kwint structure.

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

static

Allocates data for real keyword evaluation.

Parameters

[in]	npar	Not used.
	param	Not used.

Returns: Pointer to the allocated data (t_methoddata_kwreal).

Allocates memory for a t_methoddata_kwreal structure.

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

static

Allocates data for string keyword evaluation.

Parameters

[in]	npar	Not used.
	param	Not used.

Returns: Pointer to the allocated data (t_methoddata_kwstr).

Allocates memory for a t_methoddata_kwstr structure.

static gmx::SelectionTreeElementPointer init_evaluator_group	(	gmx_ana_selmethod_t *	method,
		const gmx::SelectionParserParameterList &	params,
		void *	scanner
	)

static

Initializes a selection element for evaluating a keyword in a given group.

Parameters

[in]	method	Keyword selection method to evaluate.
[in]	params	Parameters to pass to initialization (the child group).
[in]	scanner	Scanner data structure.

Returns: Pointer to the created selection element.

Implements _gmx_sel_init_keyword_evaluator() for GROUP_VALUE input selections.

static gmx::SelectionTreeElementPointer init_evaluator_pos	(	gmx_ana_selmethod_t *	method,
		const gmx::SelectionParserParameterList &	params,
		void *	scanner
	)

static

Initializes a selection element for evaluating a keyword in given positions.

Parameters

[in]	method	Keyword selection method to evaluate.
[in]	params	Parameters to pass to initialization (the child positions).
[in]	scanner	Scanner data structure.

Returns: Pointer to the created selection element.

Implements _gmx_sel_init_keyword_evaluator() for POS_VALUE input selections.

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

static

Initializes frame evaluation for keyword evaluation in an arbitrary group.

Parameters

[in]	context	Evaluation context.
	data	Should point to a t_methoddata_kweval.

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

static

Initializes keyword evaluation for an arbitrary group.

Parameters

[in]	top	Not used.
[in]	npar	Not used.
[in]	param	Not used.
[in]	data	Should point to t_methoddata_kweval.

Calls the initialization method of the wrapped keyword.

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

static

/brief Initializes data for integer keyword evaluation.

Parameters

[in]	top	Not used.
[in]	npar	Not used (should be 2).
[in]	param	Method parameters (should point to smparams_keyword_int).
[in]	data	Should point to t_methoddata_kwint.

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

static

Initializes data for real keyword evaluation.

Parameters

[in]	top	Not used.
[in]	npar	Not used (should be 2).
[in]	param	Method parameters (should point to smparams_keyword_real).
[in]	data	Should point to t_methoddata_kwreal.

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

static

Initializes data for string keyword evaluation.

Parameters

[in]	top	Not used.
[in]	npar	Not used (should be 2).
[in]	param	Method parameters (should point to smparams_keyword_str).
[in]	data	Should point to t_methoddata_kwstr.

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

static

Initializes output for keyword evaluation in an arbitrary group.

Parameters

[in]	top	Not used.
[in,out]	out	Pointer to output data structure.
[in,out]	data	Should point to `t_methoddata_kweval`.

Variable Documentation

gmx_ana_selmethod_t sm_keyword_int

Initial value:

= {
    "kw_int",
    GROUP_VALUE,
     8 ,
    asize(smparams_keyword_int),
    smparams_keyword_int,
    &init_data_kwint,
    nullptr,
    &init_kwint,
    nullptr,
    nullptr,
    nullptr,
    &evaluate_keyword_int,
    nullptr,
    { nullptr, nullptr, 0, nullptr },
}

Selection method data for integer keyword evaluation.

gmx_ana_selmethod_t sm_keyword_real

Initial value:

= {
    "kw_real",
    GROUP_VALUE,
     8 ,
    asize(smparams_keyword_real),
    smparams_keyword_real,
    &init_data_kwreal,
    nullptr,
    &init_kwreal,
    nullptr,
    nullptr,
    nullptr,
    &evaluate_keyword_real,
    nullptr,
    { nullptr, nullptr, 0, nullptr },
}

Selection method data for real keyword evaluation.

gmx_ana_selmethod_t sm_keyword_str

Initial value:

= {
    "kw_str",
    GROUP_VALUE,
     8 ,
    asize(smparams_keyword_str),
    smparams_keyword_str,
    &init_data_kwstr,
    nullptr,
    &init_kwstr,
    nullptr,
    &free_data_kwstr,
    nullptr,
    &evaluate_keyword_str,
    nullptr,
    { nullptr, nullptr, 0, nullptr },
}

Selection method data for string keyword evaluation.

gmx_ana_selparam_t smparams_keyword_int[]

static

Initial value:

= {
    { nullptr, { INT_VALUE, -1, { nullptr } }, nullptr,  32  },
    { nullptr, { INT_VALUE, -1, { nullptr } }, nullptr,  8  |  16  },
}

Parameters for integer keyword evaluation.

gmx_ana_selparam_t smparams_keyword_real[]

static

Initial value:

= {
    { nullptr, { REAL_VALUE, -1, { nullptr } }, nullptr,  32  |  4  },
    { nullptr, { REAL_VALUE, -1, { nullptr } }, nullptr,  8  |  16  },
}

Parameters for real keyword evaluation.

gmx_ana_selparam_t smparams_keyword_str[]

static

Initial value:

= {
    { nullptr, { STR_VALUE, -1, { nullptr } }, nullptr,  32  },
    { nullptr, { STR_VALUE, -1, { nullptr } }, nullptr,  16  },
}

Parameters for string keyword evaluation.

gmx_ana_selparam_t smparams_kweval_group[]

static

Initial value:

= {
    { nullptr, { GROUP_VALUE, 1, { nullptr } }, nullptr,  4  },
}

Parameters for keyword evaluation in an arbitrary group.

gmx_ana_selparam_t smparams_kweval_pos[]

static

Initial value:

= {
    { nullptr, { POS_VALUE, 1, { nullptr } }, nullptr,  4  },
}

Parameters for keyword evaluation from positions.

Description

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation