#include "gmxpre.h"
#include "selmethod.h"
#include <ctype.h>
#include <stdarg.h>
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "symrec.h"

Include dependency graph for selmethod.cpp:

Description

Implements functions in selmethod.h.

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

Classes
struct	t_register_method
	Helper structure for defining selection methods. More...

Functions
static void	report_error (FILE fp, const char name, const char *fmt,...)
	Convenience function for reporting errors found in selection methods.

static void	report_param_error (FILE fp, const char mname, const char pname, const char fmt,...)
	Convenience function for reporting errors found in selection method parameters.

static bool	check_params (FILE fp, const char name, int nparams, gmx_ana_selparam_t param[], const gmx::SelectionParserSymbolTable &symtab)
	Checks the validity of parameters. More...

static bool	check_callbacks (FILE fp, gmx_ana_selmethod_t method)
	Checks the validity of selection method callback functions. More...

static bool	check_method (FILE fp, gmx_ana_selmethod_t method, const gmx::SelectionParserSymbolTable &symtab)
	Checks the validity of a selection method. More...

static bool	check_modifier (FILE fp, gmx_ana_selmethod_t method, const gmx::SelectionParserSymbolTable &symtab)
	Checks the validity of a selection modifier method. More...

int	gmx_ana_selmethod_register (gmx::SelectionParserSymbolTable symtab, const char name, gmx_ana_selmethod_t *method)
	Registers a selection method. More...

int	gmx_ana_selmethod_register_defaults (gmx::SelectionParserSymbolTable *symtab)
	Registers all selection methods in the library. More...

gmx_ana_selparam_t *	gmx_ana_selmethod_find_param (const char name, gmx_ana_selmethod_t method)
	Finds a parameter from a selection method by name. More...

Variables
gmx_ana_selmethod_t	sm_cog
	Selection method data for the `cog` method. More...

gmx_ana_selmethod_t	sm_com
	Selection method data for the `com` method. More...

gmx_ana_selmethod_t	sm_all
	Selection method data for `all` selection keyword. More...

gmx_ana_selmethod_t	sm_none
	Selection method data for `none` selection keyword. More...

gmx_ana_selmethod_t	sm_atomnr
	Selection method data for `atomnr` selection keyword. More...

gmx_ana_selmethod_t	sm_resnr
	Selection method data for `resnr` selection keyword. More...

gmx_ana_selmethod_t	sm_resindex
	Selection method data for `resindex` selection keyword. More...

gmx_ana_selmethod_t	sm_molindex
	Selection method data for `molindex` selection keyword. More...

gmx_ana_selmethod_t	sm_atomname
	Selection method data for `atomname` selection keyword. More...

gmx_ana_selmethod_t	sm_pdbatomname
	Selection method data for `pdbatomname` selection keyword. More...

gmx_ana_selmethod_t	sm_atomtype
	Selection method data for `atomtype` selection keyword. More...

gmx_ana_selmethod_t	sm_resname
	Selection method data for `resname` selection keyword. More...

gmx_ana_selmethod_t	sm_insertcode
	Selection method data for `chain` selection keyword. More...

gmx_ana_selmethod_t	sm_chain
	Selection method data for `chain` selection keyword. More...

gmx_ana_selmethod_t	sm_mass
	Selection method data for `mass` selection keyword. More...

gmx_ana_selmethod_t	sm_charge
	Selection method data for `charge` selection keyword. More...

gmx_ana_selmethod_t	sm_altloc
	Selection method data for `chain` selection keyword. More...

gmx_ana_selmethod_t	sm_occupancy
	Selection method data for `occupancy` selection keyword. More...

gmx_ana_selmethod_t	sm_betafactor
	Selection method data for `betafactor` selection keyword. More...

gmx_ana_selmethod_t	sm_x
	Selection method data for `x` selection keyword. More...

gmx_ana_selmethod_t	sm_y
	Selection method data for `y` selection keyword. More...

gmx_ana_selmethod_t	sm_z
	Selection method data for `z` selection keyword. More...

gmx_ana_selmethod_t	sm_distance
	Selection method data for the `distance` method. More...

gmx_ana_selmethod_t	sm_mindistance
	Selection method data for the `distance` method. More...

gmx_ana_selmethod_t	sm_within
	Selection method data for the `within` method. More...

gmx_ana_selmethod_t	sm_insolidangle
	Selection method data for the `insolidangle` method. More...

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

gmx_ana_selmethod_t	sm_permute
	Selection method data for the `permute` modifier. More...

static const t_register_method	smtable_def []
	Array of selection methods defined in the library. More...

Function Documentation

static bool check_callbacks	(	FILE *	fp,
		gmx_ana_selmethod_t *	method
	)

static

Checks the validity of selection method callback functions.

Parameters

[in]	fp	File handle to use for diagnostic messages (can be NULL).
[in]	method	The method to check.

Returns: true if there are no problems, false otherwise.

This function performs some checks common to both check_method() and check_modifier(). This function checks that all the required callbacks are defined, i.e., not NULL, to find programming errors.

static bool check_method	(	FILE *	fp,
		gmx_ana_selmethod_t *	method,
		const gmx::SelectionParserSymbolTable &	symtab
	)

static

Checks the validity of a selection method.

Parameters

[in]	fp	File handle to use for diagnostic messages (can be NULL).
[in,out]	method	Method to check.
[in]	symtab	Symbol table (used for checking overlaps).

Checks the validity of the given selection method data structure that does not have SMETH_MODIFIER set. If you remove a check, please make sure that the selection parser, compiler, and evaluation functions can deal with the method.

static bool check_modifier	(	FILE *	fp,
		gmx_ana_selmethod_t *	method,
		const gmx::SelectionParserSymbolTable &	symtab
	)

static

Checks the validity of a selection modifier method.

Parameters

[in]	fp	File handle to use for diagnostic messages (can be NULL).
[in,out]	method	Method to check.
[in]	symtab	Symbol table (used for checking overlaps).

Checks the validity of the given selection method data structure that has SMETH_MODIFIER set. If you remove a check, please make sure that the selection parser, compiler, and evaluation functions can deal with the method.

static bool check_params	(	FILE *	fp,
		const char *	name,
		int	nparams,
		gmx_ana_selparam_t	param[],
		const gmx::SelectionParserSymbolTable &	symtab
	)

static

Checks the validity of parameters.

Parameters

[in]	fp	File handle to use for diagnostic messages (can be NULL).
[in]	name	Name of the method (used for error messages).
[in]	nparams	Number of parameters in `param`.
[in,out]	param	Parameter array (only the `flags` field of boolean parameters may be modified).
[in]	symtab	Symbol table (used for checking overlaps).

Returns: true if there are no problems with the parameters, false otherwise.

This function performs some checks common to both check_method() and check_modifier(). The purpose of these checks is to ensure that the selection parser does not need to check for the validity of the parameters at each turn, and to report programming errors as early as possible. If you remove a check, make sure that the parameter parser can handle the resulting parameters.

gmx_ana_selparam_t* gmx_ana_selmethod_find_param	(	const char *	name,
		gmx_ana_selmethod_t *	method
	)

Finds a parameter from a selection method by name.

Parameters

[in]	name	Name of the parameter to search.
[in]	method	Method to search for the parameter.

Returns: Pointer to the parameter in the method->param array, or NULL if no parameter with name name was found.

This is a simple wrapper for gmx_ana_selparam_find().

int gmx_ana_selmethod_register	(	gmx::SelectionParserSymbolTable *	symtab,
		const char *	name,
		gmx_ana_selmethod_t *	method
	)

Registers a selection method.

Parameters

[in,out]	symtab	Symbol table to register the method to.
[in]	name	Name under which the method should be registered.
[in]	method	Method to register.

Returns: 0 on success, EINVAL if there was something wrong with the method.

name does not need to match the name of the method, and the same method can be registered multiple times under different names. If name equals some previously registered name, an error message is printed and the method is not registered.

The function also performs some sanity checking on the input method, and refuses to register it if there are problems. Some problems only generate warnings. All problems are described to stderr.

int gmx_ana_selmethod_register_defaults ( gmx::SelectionParserSymbolTable * symtab )

Registers all selection methods in the library.

Parameters

[in,out] symtab Symbol table to register the methods to.