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36 * \page page_module_selection_custom Custom selection methods
38 * Custom selection methods are defined by creating a new instance of
39 * \c gmx_ana_selmethod_t and filling it with the necessary data for handling
41 * The structure contains callback pointers that define the actual behavior
43 * The following sections discuss how the structure should be filled and how
44 * to implement the callbacks.
47 * \section selmethods_define \c gmx_ana_selmethod_t data structure
49 * An example \c gmx_ana_selmethod_t definition could look like this:
52 gmx_ana_selmethod_t sm_example = {
53 "example", GROUP_VALUE, 0,
54 asize(sm_params_example), sm_params_example,
63 {"example from POS_EXPR [cutoff REAL]", 0, NULL},
67 * The first value defines the name of the method.
68 * It is used mostly for informational purposes; the actual name(s) recognized
69 * by the selection parser are defined by the call to
70 * gmx_ana_selmethod_register() (see \ref selmethods_register).
72 * The second value defines the type of the value the method returns.
74 * - \ref NO_VALUE : This is allowed only for methods that have the flag
75 * \ref SMETH_MODIFIER set (see \ref selmethods_modifiers).
76 * - \ref INT_VALUE : The method returns one or more integer values.
77 * - \ref REAL_VALUE : The method returns one or more floating-point values.
78 * - \ref STR_VALUE : The method returns one or more strings.
79 * - \ref POS_VALUE : The method returns one or more 3D vectors.
80 * - \ref GROUP_VALUE : The method returns a single index group.
82 * The third value gives additional information about the method using
83 * a combination of flags.
85 * - \ref SMETH_REQTOP : If set, the topology information is always loaded
86 * and the \p top pointer passed to the callbacks is guaranteed to be
87 * non-NULL. Should be set if the method requires topology information
89 * - \ref SMETH_DYNAMIC : If set, the method can only be evaluated dynamically,
90 * i.e., it requires data from the trajectory frame.
91 * - \ref SMETH_MODIFIER : If set, the method is a selection modifier and
92 * not an actual selection method.
93 * For more details, see \ref selmethods_modifiers.
95 * There are two additional flags that specify the number of values the
96 * method returns. Only one of them can be set at a time.
97 * If neither is set, the default behavior is to evaluate a value for each
98 * input atom (except for \ref GROUP_VALUE methods, which always return a
100 * Other behaviors can be specified with these flags:
101 * - \ref SMETH_SINGLEVAL : If set, the method evaluates to a single value.
102 * This is automatically set if the type is \ref GROUP_VALUE.
103 * - \ref SMETH_VARNUMVAL : If set, the method evaluates to an arbitrary
105 * The number of values is determined based on the values given by the user
106 * to the method parameters (see \ref selmethods_params).
108 * If either of these flags is specified (and the method type is not
109 * \ref GROUP_VALUE), the group passed to the evaluation callback should not
110 * be used as it can be NULL.
111 * Currently, the above flags only work (have been tested) for \ref POS_VALUE
114 * There is one additional flag that can only be specified for \ref STR_VALUE
115 * methods: \ref SMETH_CHARVAL . It is meant for to ease implementation of
116 * methods that evaluate to strings consisting of single characters.
118 * The next two values determine the number of parameters and a pointer to
119 * the parameter array. The contents of the parameter array are described in
120 * \ref selmethods_params. If the method does not take parameters, the first
121 * value should be 0 and the second can be NULL.
122 * Currently, \ref STR_VALUE methods cannot take parameters, but this limitation
123 * should be easy to lift if required.
125 * These are followed by function callbacks that determine the
126 * actual behavior of the method. Any of these except the evaluation callback
127 * can be NULL (the evaluation callback can also be NULL if \ref NO_VALUE is
128 * specified for a selection modifier). However, the presence of parameters
129 * can require some of the callbacks to be implemented.
130 * The details are described in \ref selmethods_callbacks.
132 * Finally, there is a data structure that gives help texts for the method.
134 * The \c gmx_ana_selmethod_t variable should be declared as a global variable
135 * or it should be otherwise ensured that the structure is not freed: only a
136 * pointer to the structure is stored by the library.
139 * \section selmethods_params Defining parameters
141 * Parameters to selection methods are defined in a separate array of
142 * \c gmx_ana_selparam_t structures.
143 * The order of the parameters does not matter (except possibly for callback
144 * implementation), with one important exception:
145 * If the method evaluates to a \ref POS_VALUE, the first parameter should
146 * have \ref GROUP_VALUE and be the one that is used to calculate the
149 * An example parameter definition:
151 static gmx_ana_selparam_t sm_params_example[] = {
152 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
153 {"from", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
157 * The first value gives the name of the parameter.
158 * The first parameter can have a NULL name, which means that the value should
159 * immediately follow the method name. This can be used to specify methods
160 * of the type 'within 5 of ...'.
162 * The second value specifies the type of the value that the parameter accepts.
163 * \ref NO_VALUE can be used to specify a boolean parameter, other possibilities
164 * are the same as for the selection method type.
166 * The third value gives the number of values that the parameter accepts.
167 * For boolean parameters (\ref NO_VALUE), it should be 0.
168 * For parameters with \ref SPAR_VARNUM of \ref SPAR_ATOMVAL, it should be set
169 * to -1 for consistency (it is not used).
170 * If \ref SPAR_RANGES is specified, it should be either 1 (to accept a single
171 * continuous range) or -1 (if combined with \ref SPAR_VARNUM).
172 * In all other cases, it should be a positive integer; in most cases, it
175 * The nest two pointers should always be NULL (they should be initialized in
176 * the callbacks), except the first pointer in the case of \ref SPAR_ENUMVAL
179 * The final value gives additional information about the acceptable values
180 * for the parameter using a combination of flags.
181 * The possible flags are:
182 * - \ref SPAR_OPTIONAL : If set, the user does not need to provide a value
183 * for the parameter. If not set, an error is reported if the parameter
184 * is not specified by the user.
185 * - \ref SPAR_DYNAMIC : If set, the method can handle dynamic values for
186 * the parameter, i.e., the value(s) can be given by an expression that
187 * evaluates to different values for different frames.
188 * - \ref SPAR_RANGES : Can be set only for \ref INT_VALUE and
189 * \ref REAL_VALUE parameters,
190 * and cannot be combined with \ref SPAR_DYNAMIC.
191 * If set, the parameter accepts ranges of values.
192 * The ranges are automatically sorted and compacted such that a minimum
193 * amount of non-overlapping ranges are given for the method.
194 * - \ref SPAR_VARNUM : If set, the parameter can have a variable number
195 * of values. These can be provided by the user as a list of values, or
196 * using a single \ref SMETH_VARNUMVAL (or a single \ref SMETH_SINGLEVAL)
198 * - \ref SPAR_ATOMVAL : If set, the parameter accepts either a single value
199 * or an expression that evaluates to a value for each input atom.
200 * The single input value is treated as if the same value was returned for
202 * Cannot be combined with \ref SPAR_RANGES or \ref SPAR_VARNUM.
203 * - \ref SPAR_ENUMVAL : Can only be set for \ref STR_VALUE parameters that
204 * take a single value, and cannot be combined with any other flag than
205 * \ref SPAR_OPTIONAL. If set, the parameter only accepts one of predefined
206 * string values. See \ref SPAR_ENUMVAL documentation for details on how
207 * to specify the acceptable values.
210 * \section selmethods_callbacks Implementing callbacks
212 * There are eight differen callback functions that can be implemented for
213 * selection methods: sel_datafunc(), sel_posfunc(), sel_initfunc(),
214 * sel_outinitfunc(), sel_freefunc(), sel_framefunc(), and two update functions.
215 * They are in this order in the \c gmx_ana_selmethod_t data structure.
216 * In general, any of the callbacks can be NULL, but the presence of
217 * parameters or other callbacks imposes some restrictions:
218 * - sel_datafunc() should be provided if the method takes parameters.
219 * - sel_initfunc() should be provided if the method takes
220 * any parameters with the \ref SPAR_VARNUM or \ref SPAR_ATOMVAL flags,
221 * except if those parameters have a \ref POS_VALUE.
222 * - sel_outinitfunc() should be provided for \ref POS_VALUE methods
223 * and \ref SMETH_VARNUMVAL methods.
224 * - sel_freefunc() should be provided if sel_datafunc() and/or
225 * sel_initfunc() allocate any dynamic memory in addition to the data
226 * structure itself (or allocates the data structure using some other means
228 * - sel_updatefunc_pos() only makes sense for methods with \ref SMETH_DYNAMIC
230 * - At least one update function should be provided unless the method type is
233 * The documentations for the function pointer types provide more information
234 * about how the callbacks should be implemented.
237 * \section selmethods_modifiers Selection modifiers
239 * Selection modifiers are a special kind of selection methods that can be
240 * appended to the end of a selection. They are specified by adding the
241 * \ref SMETH_MODIFIER flag to the \c gmx_ana_selmethod_t.
242 * They can have two different types:
243 * - \ref POS_VALUE : These modifiers are given the final positions
244 * as an input, and they can make modifications to the selection that are
245 * not possible otherwise (e.g., permute the atoms).
246 * The modifier should implement sel_updatefunc_pos() and also have
247 * one NULL parameter in the beginning of the parameter list that takes
248 * \ref POS_VALUE and is used to give the input positions.
249 * - \ref NO_VALUE : These modifiers do not modify the final selection, but
250 * can be used to implement per-selection options for analysis tools
251 * or to control the default behavior of the selection engine
252 * (currently, such a framework is not implemented, but should be easy to
253 * implement if required).
255 * In addition to restricting the type of the method, selection modifiers
256 * do not allow the flags \ref SMETH_SINGLEVAL and \ref SMETH_VARNUMVAL
257 * (they would not make sense).
259 * Parameters and callbacks should be implemented as with normal selection
260 * method, but beware that very little of the functionality has been tested.
263 * The modifier handling could be made more flexible and more generic;
264 * the current implementation does not allow many things which would be
265 * possible with slight changes in the internals of the library.
268 * \section selmethods_register Registering the method
270 * After defining the method with \c gmx_ana_selmethod_t, it should be
271 * registered with the selection engine.
272 * In analysis programs, this can be done by calling
273 * gmx_ana_selmethod_register().
274 * If adding the method to the library, you should add a pointer to the new
275 * method structure into the \c smtable_def array (in selmethod.cpp), and it is
276 * registered automatically.
277 * In both cases, gmx_ana_selmethod_register() does several checks on the
278 * structure and reports any errors or inconsistencies it finds.
281 * \brief API for handling selection methods.
283 * There should be no need to use the data structures or call the
284 * functions in this file directly unless implementing a custom selection
287 * Instructions for implementing custom selection methods can be found
288 * on a separate page: \ref page_module_selection_custom
290 * \author Teemu Murtola <teemu.murtola@gmail.com>
291 * \ingroup module_selection
293 #ifndef GMX_SELECTION_SELMETHOD_H
294 #define GMX_SELECTION_SELMETHOD_H
296 #include "../legacyheaders/typedefs.h"
298 #include "indexutil.h"
299 #include "selparam.h"
300 #include "selvalue.h"
304 class PositionCalculationCollection;
305 class SelectionParserSymbolTable;
308 struct gmx_ana_pos_t;
309 struct gmx_ana_selcollection_t;
311 /*! \name Selection method flags
312 * \anchor selmethod_flags
316 * If set, the method requires topology information.
318 #define SMETH_REQTOP 1
320 * If set, the method can only be evaluated dynamically.
322 #define SMETH_DYNAMIC 2
324 * If set, the method evaluates to a single value.
326 * The default is that the method evaluates to a value for each input atom.
327 * Cannot be combined with \ref SMETH_VARNUMVAL.
329 #define SMETH_SINGLEVAL 4
331 * If set, the method evaluates to an arbitrary number of values.
333 * The default is that the method evaluates to a value for each input atom.
334 * Cannot be combined with \ref SMETH_SINGLEVAL or with \ref GROUP_VALUE.
336 #define SMETH_VARNUMVAL 8
338 * If set, the method evaluates to single-character strings.
340 * This flag can only be set for \ref STR_VALUE methods. If it is set, the
341 * selection engine automatically allocates and frees the required strings.
342 * The evaluation function should store the character values as the first
343 * character in the strings in the output data structure and should not change
344 * the string pointers.
346 #define SMETH_CHARVAL 64
348 * If set, the method is a selection modifier.
350 * The method type should be \ref GROUP_VALUE or \ref NO_VALUE .
351 * Cannot be combined with \ref SMETH_SINGLEVAL or \ref SMETH_VARNUMVAL .
353 #define SMETH_MODIFIER 256
357 * Allocates and initializes internal data and parameter values.
359 * \param[in] npar Number of parameters in \p param.
360 * \param[in,out] param Pointer to (a copy of) the method's
361 * \c gmx_ana_selmethod_t::param.
362 * \returns Pointer to method-specific data structure.
363 * This pointer will be passed as the last parameter of all other function
365 * \throws unspecified Any errors should be indicated by throwing an
368 * Should allocate and initialize any internal data required by the method.
369 * Should also initialize the value pointers (\c gmx_ana_selparam_t::val) in
370 * \p param to point to variables within the internal data structure,
371 * with the exception of parameters that specify the \ref SPAR_VARNUM or
372 * the \ref SPAR_ATOMVAL flag (these should be handled in sel_initfunc()).
373 * However, parameters with a position value should be initialized.
374 * It is also possible to initialize \ref SPAR_ENUMVAL statically outside
375 * this function (see \ref SPAR_ENUMVAL).
376 * The \c gmx_ana_selparam_t::nvalptr should also be initialized for
377 * non-position-valued parameters that have both \ref SPAR_VARNUM and
378 * \ref SPAR_DYNAMIC set (it can also be initialized for other parameters if
379 * desired, but the same information will be available through other means).
380 * For optional parameters, the default values can (and should) be initialized
381 * here, as the parameter values are not changed if the parameter is not
384 * For boolean parameters (type equals \ref NO_VALUE), the default value
385 * should be set here. The user can override the value by giving the parameter
386 * either as 'NAME'/'noNAME', or as 'NAME on/off/yes/no'.
388 * If the method takes any parameters, this function must be provided.
390 typedef void *(*sel_datafunc)(int npar, gmx_ana_selparam_t *param);
392 * Sets the position calculation collection for the method.
394 * \param[in] pcc Position calculation collection that the method should use
395 * for position calculations.
396 * \param data Internal data structure from sel_datafunc().
398 * This function should be provided if the method uses the routines from
399 * poscalc.h for calculating positions.
400 * The pointer \p pcc should then be stored and used for initialization for
401 * any position calculation structures.
403 typedef void (*sel_posfunc)(gmx::PositionCalculationCollection *pcc, void *data);
405 * Does initialization based on topology and/or parameter values.
407 * \param[in] top Topology structure
408 * (can be NULL if \ref SMETH_REQTOP is not set).
409 * \param[in] npar Number of parameters in \p param.
410 * \param[in] param Pointer to (an initialized copy of) the method's
411 * \c gmx_ana_selmethod_t::param.
412 * \param data Internal data structure from sel_datafunc().
413 * \returns 0 on success, a non-zero error code on failure.
415 * This function is called after the parameters have been processed:
416 * the values of the parameters are stored at the locations set in
418 * The flags \ref SPAR_DYNAMIC and \ref SPAR_ATOMVAL are cleared before
419 * calling the function if the value is static or single-valued, respectively.
420 * If a parameter had the \ref SPAR_VARNUM or \ref SPAR_ATOMVAL flag (and
421 * is not \ref POS_VALUE), a pointer to the memory allocated for the values is
422 * found in \c gmx_ana_selparam_t::val.
423 * The pointer should be stored by this function, otherwise the values
424 * cannot be accessed.
425 * For \ref SPAR_VARNUM parameters, the number of values can be accessed
426 * through \c gmx_ana_selparam_t::val. For parameters with \ref SPAR_DYNAMIC,
427 * the number is the maximum number of values (the actual number can be
428 * accessed in sel_framefunc() and in the update callback through the value
429 * pointed by \c gmx_ana_selparam_t::nvalptr).
430 * For \ref SPAR_ATOMVAL parameters, \c gmx_ana_selparam_t::val::nr is set to
431 * 1 if a single value was provided, otherwise it is set to the maximum number
432 * of values possibly passed to the method.
433 * The value pointed by \c gmx_ana_selparam_t::nvalptr always contains the same
434 * value as \c gmx_ana_selparam_t::val::nr.
436 * For dynamic \ref GROUP_VALUE parameters (\ref SPAR_DYNAMIC set), the value
437 * will be the largest possible selection that may occur during the
438 * evaluation. For other types of dynamic parameters, the values are
441 * If the method takes any parameters with the \ref SPAR_VARNUM or
442 * \ref SPAR_ATOMVAL flags, this function must be provided, except if these
443 * parameters all have \ref POS_VALUE.
445 * This function may be called multiple times for the same method if the
446 * method takes parameters with \ref SPAR_ATOMVAL set.
448 typedef void (*sel_initfunc)(t_topology *top, int npar,
449 gmx_ana_selparam_t *param, void *data);
451 * Initializes output data structure.
453 * \param[in] top Topology structure
454 * (can be NULL if \ref SMETH_REQTOP is not set).
455 * \param[in,out] out Output data structure.
456 * \param[in] data Internal data structure from sel_datafunc().
457 * \returns 0 on success, an error code on error.
459 * This function is called immediately after sel_initfunc().
461 * If the method evaluates to a position (\ref POS_VALUE), this function
462 * should be provided, and it should initialize the \c gmx_ana_pos_t data
463 * structure pointed by \p out.p (the pointer is guaranteed to be non-NULL).
464 * The \p out.p->g pointer should be initialized to the group that is used
465 * to evaluate positions in sel_updatefunc() or sel_updatefunc_pos().
467 * The function should also be provided for non-position-valued
468 * \ref SMETH_VARNUMVAL methods. For these methods, it suffices to set the
469 * \p out->nr field to reflect the maximum number of values returned by the
472 * Currently, this function is not needed for other types of methods.
474 * This function may be called multiple times for the same method if the
475 * method takes parameters with \ref SPAR_ATOMVAL set.
477 typedef void (*sel_outinitfunc)(t_topology *top, gmx_ana_selvalue_t *out,
480 * Frees the internal data.
482 * \param[in] data Internal data structure from sel_datafunc().
484 * This function should be provided if the internal data structure contains
485 * dynamically allocated data, and should free any such data.
486 * The data structure itself should also be freed.
487 * For convenience, if there is no dynamically allocated data within the
488 * structure and the structure is allocated using malloc()/snew(), this
489 * function is not needed: the selection engine automatically frees the
490 * structure using sfree().
491 * Any memory pointers received as values of parameters are managed externally,
492 * and should not be freed.
493 * Pointers set as the value pointer of \ref SPAR_ENUMVAL parameters should not
496 typedef void (*sel_freefunc)(void *data);
499 * Initializes the evaluation for a new frame.
501 * \param[in] top Topology structure
502 * (can be NULL if \ref SMETH_REQTOP is not set).
503 * \param[in] fr Current frame.
504 * \param[in] pbc Initialized periodic boundary condition structure,
505 * or NULL if PBC should not be used.
506 * \param data Internal data structure from sel_datafunc().
507 * \returns 0 on success, a non-zero error code on failure.
509 * This function should be implemented if the selection method needs to
510 * do some preprocessing for each frame, and the preprocessing does not
511 * depend on the evaluation group.
512 * Because \p sel_updatefunc_* can be called more than once for a frame,
513 * it is inefficient do the preprocessing there.
514 * It is ensured that this function will be called before
515 * \p sel_updatefunc_* for each frame, and that it will be called at most
516 * once for each frame.
517 * For static methods, it is called once, with \p fr and \p pbc set to
520 typedef void (*sel_framefunc)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
523 * Evaluates a selection method.
525 * \param[in] top Topology structure
526 * (can be NULL if \ref SMETH_REQTOP is not set).
527 * \param[in] fr Current frame.
528 * \param[in] pbc Initialized periodic boundary condition structure,
529 * or NULL if PBC should not be used.
530 * \param[in] g Index group for which the method should be evaluated.
531 * \param[out] out Output data structure.
532 * \param data Internal data structure from sel_datafunc().
533 * \returns 0 on success, a non-zero error code on error.
535 * This function should evaluate the method for each atom included in \p g,
536 * and write the output to \p out. The pointer in the union \p out->u that
537 * corresponds to the type of the method should be used.
538 * Enough memory has been allocated to store the output values.
539 * The number of values in \p out should also be updated if necessary.
540 * However, \ref POS_VALUE or \ref GROUP_VALUE methods should not touch
541 * \p out->nr (it should be 1 anyways).
543 * For \ref STR_VALUE methods, the pointers stored in \p out->s are discarded
544 * without freeing; it is the responsibility of this function to provide
545 * pointers that can be discarded without memory leaks.
547 typedef void (*sel_updatefunc)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
548 gmx_ana_index_t *g, gmx_ana_selvalue_t *out,
551 * Evaluates a selection method using positions.
553 * \param[in] top Topology structure
554 * (can be NULL if \ref SMETH_REQTOP is not set).
555 * \param[in] fr Current frame.
556 * \param[in] pbc Initialized periodic boundary condition structure,
557 * or NULL if PBC should not be used.
558 * \param[in] pos Positions for which the method should be evaluated.
559 * \param[out] out Output data structure.
560 * \param data Internal data structure from sel_datafunc().
561 * \returns 0 on success, a non-zero error code on error.
563 * This function should evaluate the method for each position in \p g,
564 * and write the output values to \p out. The pointer in the union \p out->u
565 * that corresponds to the type of the method should be used.
566 * Enough memory has been allocated to store the output values.
567 * The number of values in \p out should also be updated if necessary.
568 * However, \ref POS_VALUE or \ref GROUP_VALUE methods should not touch
569 * \p out->nr (it should be 1 anyways).
571 * For \ref STR_VALUE methods, the pointers stored in \p out->s are discarded
572 * without freeing; it is the responsibility of this function to provide
573 * pointers that can be discarded without memory leaks.
575 typedef void (*sel_updatefunc_pos)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
576 struct gmx_ana_pos_t *pos,
577 gmx_ana_selvalue_t *out,
581 * Help information for a selection method.
583 * If some information is not available, the corresponding field can be set to
586 typedef struct gmx_ana_selmethod_help_t
589 * One-line description of the syntax of the method.
591 * If NULL, the name of the method is used.
595 * Number of strings in \p help.
597 * Set to 0 if \p help is NULL.
601 * Detailed help for the method.
603 * If there is no help available in addition to \p syntax, this can be set
607 } gmx_ana_selmethod_help_t;
611 * Describes a selection method.
613 * Any of the function pointers except the update call can be NULL if the
614 * operation is not required or not supported. In this case,
615 * corresponding function calls are skipped.
617 * See the function pointer type documentation for details of how the
618 * functions should be implemented.
619 * More details on implementing new selection methods can be found on a
620 * separate page: \ref page_module_selection_custom.
622 typedef struct gmx_ana_selmethod_t
624 /** Name of the method. */
626 /** Type which the method returns. */
629 * Flags to specify how the method should be handled.
631 * See \ref selmethod_flags for allowed values.
634 /** Number of parameters the method takes. */
636 /** Pointer to the array of parameter descriptions. */
637 gmx_ana_selparam_t *param;
639 /** Function for allocating and initializing internal data and parameters. */
640 sel_datafunc init_data;
641 /** Function to set the position calculation collection. */
642 sel_posfunc set_poscoll;
643 /** Function to do initialization based on topology and/or parameter values. */
645 /** Function to initialize output data structure. */
646 sel_outinitfunc outinit;
647 /** Function to free the internal data. */
650 /** Function to initialize the calculation for a new frame. */
651 sel_framefunc init_frame;
652 /** Function to evaluate the value. */
653 sel_updatefunc update;
654 /** Function to evaluate the value using positions. */
655 sel_updatefunc_pos pupdate;
657 /** Help data for the method. */
658 gmx_ana_selmethod_help_t help;
659 } gmx_ana_selmethod_t;
661 /** Registers a selection method. */
663 gmx_ana_selmethod_register(gmx::SelectionParserSymbolTable *symtab,
664 const char *name, gmx_ana_selmethod_t *method);
665 /** Registers all selection methods in the library. */
667 gmx_ana_selmethod_register_defaults(gmx::SelectionParserSymbolTable *symtab);
669 /** Finds a parameter from a selection method by name. */
671 gmx_ana_selmethod_find_param(const char *name, gmx_ana_selmethod_t *method);