Gromacs
2016.4
|
API for handling selection methods.
There should be no need to use the data structures or call the functions in this file directly unless implementing a custom selection method.
Instructions for implementing custom selection methods can be found on a separate page: Custom selection methods
Classes | |
struct | gmx_ana_selmethod_help_t |
Help information for a selection method. More... | |
struct | gmx_ana_selmethod_t |
Describes a selection method. More... | |
Macros | |
Selection method flags | |
#define | SMETH_REQTOP 1 |
If set, the method requires topology information. | |
#define | SMETH_DYNAMIC 2 |
If set, the method can only be evaluated dynamically. | |
#define | SMETH_SINGLEVAL 4 |
If set, the method evaluates to a single value. More... | |
#define | SMETH_VARNUMVAL 8 |
If set, the method evaluates to an arbitrary number of values. More... | |
#define | SMETH_CHARVAL 64 |
If set, the method evaluates to single-character strings. More... | |
#define | SMETH_ALLOW_UNSORTED 128 |
If set, the method accepts unsorted atoms in its input parameters. More... | |
#define | SMETH_MODIFIER 256 |
If set, the method is a selection modifier. More... | |
Typedefs | |
typedef void *(* | sel_datafunc )(int npar, gmx_ana_selparam_t *param) |
Allocates and initializes internal data and parameter values. More... | |
typedef void(* | sel_posfunc )(gmx::PositionCalculationCollection *pcc, void *data) |
Sets the position calculation collection for the method. More... | |
typedef void(* | sel_initfunc )(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data) |
Does initialization based on topology and/or parameter values. More... | |
typedef void(* | sel_outinitfunc )(t_topology *top, gmx_ana_selvalue_t *out, void *data) |
Initializes output data structure. More... | |
typedef void(* | sel_freefunc )(void *data) |
Frees the internal data. More... | |
typedef void(* | sel_framefunc )(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data) |
Initializes the evaluation for a new frame. More... | |
typedef void(* | sel_updatefunc )(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data) |
Evaluates a selection method. More... | |
typedef void(* | sel_updatefunc_pos )(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data) |
Evaluates a selection method using positions. More... | |
Functions | |
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... | |
#define SMETH_ALLOW_UNSORTED 128 |
If set, the method accepts unsorted atoms in its input parameters.
Currently, the support for this functionality is fairly limited, and only static index group references can actually contain unsorted atoms. But to make this single case work, the position evaluation must support unsorted atoms as well.
#define SMETH_CHARVAL 64 |
If set, the method evaluates to single-character strings.
This flag can only be set for STR_VALUE methods. If it is set, the selection engine automatically allocates and frees the required strings. The evaluation function should store the character values as the first character in the strings in the output data structure and should not change the string pointers.
#define SMETH_MODIFIER 256 |
If set, the method is a selection modifier.
The method type should be GROUP_VALUE or NO_VALUE . Cannot be combined with SMETH_SINGLEVAL or SMETH_VARNUMVAL .
#define SMETH_SINGLEVAL 4 |
If set, the method evaluates to a single value.
The default is that the method evaluates to a value for each input atom. Cannot be combined with SMETH_VARNUMVAL.
#define SMETH_VARNUMVAL 8 |
If set, the method evaluates to an arbitrary number of values.
The default is that the method evaluates to a value for each input atom. Cannot be combined with SMETH_SINGLEVAL or with GROUP_VALUE.
typedef void*(* sel_datafunc)(int npar, gmx_ana_selparam_t *param) |
Allocates and initializes internal data and parameter values.
[in] | npar | Number of parameters in param . |
[in,out] | param | Pointer to (a copy of) the method's gmx_ana_selmethod_t::param . |
unspecified | Any errors should be indicated by throwing an exception. |
Should allocate and initialize any internal data required by the method. Should also initialize the value pointers (gmx_ana_selparam_t::val
) in param
to point to variables within the internal data structure, with the exception of parameters that specify the SPAR_VARNUM or the SPAR_ATOMVAL flag (these should be handled in sel_initfunc()). However, parameters with a position value should be initialized. It is also possible to initialize SPAR_ENUMVAL statically outside this function (see SPAR_ENUMVAL). The gmx_ana_selparam_t::nvalptr
should also be initialized for non-position-valued parameters that have both SPAR_VARNUM and SPAR_DYNAMIC set (it can also be initialized for other parameters if desired, but the same information will be available through other means). For optional parameters, the default values can (and should) be initialized here, as the parameter values are not changed if the parameter is not provided.
For boolean parameters (type equals NO_VALUE), the default value should be set here. The user can override the value by giving the parameter either as 'NAME'/'noNAME', or as 'NAME on/off/yes/no'.
If the method takes any parameters, this function must be provided.
typedef void(* sel_framefunc)(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data) |
Initializes the evaluation for a new frame.
[in] | top | Topology structure (can be NULL if SMETH_REQTOP is not set). |
[in] | fr | Current frame. |
[in] | pbc | Initialized periodic boundary condition structure, or NULL if PBC should not be used. |
data | Internal data structure from sel_datafunc(). |
This function should be implemented if the selection method needs to do some preprocessing for each frame, and the preprocessing does not depend on the evaluation group. Because sel_updatefunc_*
can be called more than once for a frame, it is inefficient do the preprocessing there. It is ensured that this function will be called before sel_updatefunc_*
for each frame, and that it will be called at most once for each frame. For static methods, it is called once, with fr
and pbc
set to NULL.
typedef void(* sel_freefunc)(void *data) |
Frees the internal data.
[in] | data | Internal data structure from sel_datafunc(). |
This function should be provided if the internal data structure contains dynamically allocated data, and should free any such data. The data structure itself should also be freed. For convenience, if there is no dynamically allocated data within the structure and the structure is allocated using malloc()/snew(), this function is not needed: the selection engine automatically frees the structure using sfree(). Any memory pointers received as values of parameters are managed externally, and should not be freed. Pointers set as the value pointer of SPAR_ENUMVAL parameters should not be freed.
typedef void(* sel_initfunc)(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data) |
Does initialization based on topology and/or parameter values.
[in] | top | Topology structure (can be NULL if SMETH_REQTOP is not set). |
[in] | npar | Number of parameters in param . |
[in] | param | Pointer to (an initialized copy of) the method's gmx_ana_selmethod_t::param . |
data | Internal data structure from sel_datafunc(). |
This function is called after the parameters have been processed: the values of the parameters are stored at the locations set in sel_datafunc(). The flags SPAR_DYNAMIC and SPAR_ATOMVAL are cleared before calling the function if the value is static or single-valued, respectively. If a parameter had the SPAR_VARNUM or SPAR_ATOMVAL flag (and is not POS_VALUE), a pointer to the memory allocated for the values is found in gmx_ana_selparam_t::val
. The pointer should be stored by this function, otherwise the values cannot be accessed. For SPAR_VARNUM parameters, the number of values can be accessed through gmx_ana_selparam_t::val
. For parameters with SPAR_DYNAMIC, the number is the maximum number of values (the actual number can be accessed in sel_framefunc() and in the update callback through the value pointed by gmx_ana_selparam_t::nvalptr
). For SPAR_ATOMVAL parameters, gmx_ana_selparam_t::val::nr
is set to 1 if a single value was provided, otherwise it is set to the maximum number of values possibly passed to the method. The value pointed by gmx_ana_selparam_t::nvalptr
always contains the same value as gmx_ana_selparam_t::val::nr
.
For dynamic GROUP_VALUE parameters (SPAR_DYNAMIC set), the value will be the largest possible selection that may occur during the evaluation. For other types of dynamic parameters, the values are undefined.
If the method takes any parameters with the SPAR_VARNUM or SPAR_ATOMVAL flags, this function must be provided, except if these parameters all have POS_VALUE.
This function may be called multiple times for the same method if the method takes parameters with SPAR_ATOMVAL set.
typedef void(* sel_outinitfunc)(t_topology *top, gmx_ana_selvalue_t *out, void *data) |
Initializes output data structure.
[in] | top | Topology structure (can be NULL if SMETH_REQTOP is not set). |
[in,out] | out | Output data structure. |
[in] | data | Internal data structure from sel_datafunc(). |
This function is called immediately after sel_initfunc().
If the method evaluates to a position (POS_VALUE), this function should be provided, and it should initialize the gmx_ana_pos_t
data structure pointed by out.p
(the pointer is guaranteed to be non-NULL). The out.p->g
pointer should be initialized to the group that is used to evaluate positions in sel_updatefunc() or sel_updatefunc_pos().
The function should also be provided for non-position-valued SMETH_VARNUMVAL methods. For these methods, it suffices to set the out->nr
field to reflect the maximum number of values returned by the method.
Currently, this function is not needed for other types of methods.
This function may be called multiple times for the same method if the method takes parameters with SPAR_ATOMVAL set.
typedef void(* sel_posfunc)(gmx::PositionCalculationCollection *pcc, void *data) |
Sets the position calculation collection for the method.
[in] | pcc | Position calculation collection that the method should use for position calculations. |
data | Internal data structure from sel_datafunc(). |
This function should be provided if the method uses the routines from poscalc.h for calculating positions. The pointer pcc
should then be stored and used for initialization for any position calculation structures.
typedef void(* sel_updatefunc)(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data) |
Evaluates a selection method.
[in] | top | Topology structure (can be NULL if SMETH_REQTOP is not set). |
[in] | fr | Current frame. |
[in] | pbc | Initialized periodic boundary condition structure, or NULL if PBC should not be used. |
[in] | g | Index group for which the method should be evaluated. |
[out] | out | Output data structure. |
data | Internal data structure from sel_datafunc(). |
This function should evaluate the method for each atom included in g
, and write the output to out
. The pointer in the union out->u
that corresponds to the type of the method should be used. Enough memory has been allocated to store the output values. The number of values in out
should also be updated if necessary. However, POS_VALUE or GROUP_VALUE methods should not touch out->nr
(it should be 1 anyways).
For STR_VALUE methods, the pointers stored in out->s
are discarded without freeing; it is the responsibility of this function to provide pointers that can be discarded without memory leaks.
If the method accesses fr
outside the index group specified in g
or what it receives from its parameters, it must check that fr
actually contains such an atom in case the fr
has been loaded from a trajectory that only contains a subset of the system.
typedef void(* sel_updatefunc_pos)(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data) |
Evaluates a selection method using positions.
[in] | top | Topology structure (can be NULL if SMETH_REQTOP is not set). |
[in] | fr | Current frame. |
[in] | pbc | Initialized periodic boundary condition structure, or NULL if PBC should not be used. |
[in] | pos | Positions for which the method should be evaluated. |
[out] | out | Output data structure. |
data | Internal data structure from sel_datafunc(). |
This function should evaluate the method for each position in pos
, and write the output values to out
. The pointer in the union out->u
that corresponds to the type of the method should be used. Enough memory has been allocated to store the output values. The number of values in out
should also be updated if necessary. POS_VALUE or GROUP_VALUE methods should not touch out->nr
(it should be 1 anyways). For other types of methods, the number of output values should equal the number of positions in pos
.
For STR_VALUE methods, the pointers stored in out->s
are discarded without freeing; it is the responsibility of this function to provide pointers that can be discarded without memory leaks.
If the method accesses fr
outside the atoms referenced in pos
or what it receives from its parameters, it must check that fr
actually contains such an atom in case the fr
has been loaded from a trajectory that only contains a subset of the system.
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.
[in] | name | Name of the parameter to search. |
[in] | method | Method to search for the parameter. |
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.
[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. |
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.
[in,out] | symtab | Symbol table to register the methods to. |