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37 * Implements functions in selmethod.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
47 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/selection/selmethod.h"
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/exceptions.h"
56 * These global variables cannot be const because gmx_ana_selmethod_register()
57 * modifies them to set some defaults. This is a small price to pay for the
58 * convenience of not having to remember exactly how the selection compiler
59 * expects the structures to be filled, and even more so if the expectations
60 * change. Also, even if the gmx_ana_selmethod_t structures were made const,
61 * the parameters could not be without typecasts somewhere, because the param
62 * field in gmx_ana_selmethod_t cannot be declared const.
64 * Even though the variables may be modified, this should be thread-safe as
65 * modifications are done only in gmx_ana_selmethod_register(), and it should
66 * work even if called more than once for the same structure, and even if
67 * called concurrently from multiple threads (as long as the selection
68 * collection is not the same).
70 * All of these problems should go away if/when the selection methods are
71 * implemented as C++ classes.
75 extern gmx_ana_selmethod_t sm_cog;
76 extern gmx_ana_selmethod_t sm_com;
77 /* From sm_simple.c */
78 extern gmx_ana_selmethod_t sm_all;
79 extern gmx_ana_selmethod_t sm_none;
80 extern gmx_ana_selmethod_t sm_atomnr;
81 extern gmx_ana_selmethod_t sm_resnr;
82 extern gmx_ana_selmethod_t sm_resindex;
83 extern gmx_ana_selmethod_t sm_molindex;
84 extern gmx_ana_selmethod_t sm_atomname;
85 extern gmx_ana_selmethod_t sm_pdbatomname;
86 extern gmx_ana_selmethod_t sm_atomtype;
87 extern gmx_ana_selmethod_t sm_resname;
88 extern gmx_ana_selmethod_t sm_insertcode;
89 extern gmx_ana_selmethod_t sm_chain;
90 extern gmx_ana_selmethod_t sm_mass;
91 extern gmx_ana_selmethod_t sm_charge;
92 extern gmx_ana_selmethod_t sm_altloc;
93 extern gmx_ana_selmethod_t sm_occupancy;
94 extern gmx_ana_selmethod_t sm_betafactor;
95 extern gmx_ana_selmethod_t sm_x;
96 extern gmx_ana_selmethod_t sm_y;
97 extern gmx_ana_selmethod_t sm_z;
98 /* From sm_distance.c */
99 extern gmx_ana_selmethod_t sm_distance;
100 extern gmx_ana_selmethod_t sm_mindistance;
101 extern gmx_ana_selmethod_t sm_within;
102 /* From sm_insolidangle.c */
103 extern gmx_ana_selmethod_t sm_insolidangle;
105 extern gmx_ana_selmethod_t sm_same;
107 /* From sm_merge.c */
108 extern gmx_ana_selmethod_t sm_merge;
109 extern gmx_ana_selmethod_t sm_plus;
110 /* From sm_permute.c */
111 extern gmx_ana_selmethod_t sm_permute;
114 * Helper structure for defining selection methods.
118 * Name to register the method under.
120 * If NULL, use the actual name of the method.
121 * This field is used for defining synonyms.
124 /** Method data structure to register. */
125 gmx_ana_selmethod_t *method;
128 /** Array of selection methods defined in the library. */
129 static const t_register_method smtable_def[] = {
137 {"resid", &sm_resnr},
138 {NULL, &sm_resindex},
139 {"residue", &sm_resindex},
140 {NULL, &sm_molindex},
141 {"mol", &sm_molindex},
142 {"molecule", &sm_molindex},
143 {NULL, &sm_atomname},
144 {"name", &sm_atomname},
145 {NULL, &sm_pdbatomname},
146 {"pdbname", &sm_pdbatomname},
147 {NULL, &sm_atomtype},
148 {"type", &sm_atomtype},
150 {NULL, &sm_insertcode},
155 {NULL, &sm_occupancy},
156 {NULL, &sm_betafactor},
161 {NULL, &sm_distance},
162 {NULL, &sm_mindistance},
164 {NULL, &sm_insolidangle},
173 * Convenience function for reporting errors found in selection methods.
176 report_error(FILE *fp, const char *name, const char *fmt, ...)
182 fprintf(fp, "selection method '%s': ", name);
183 vfprintf(fp, fmt, ap);
190 * Convenience function for reporting errors found in selection method parameters.
193 report_param_error(FILE *fp, const char *mname, const char *pname,
194 const char *fmt, ...)
200 fprintf(fp, "selection method '%s': parameter '%s': ", mname, pname);
201 vfprintf(fp, fmt, ap);
208 * Checks the validity of parameters.
210 * \param[in] fp File handle to use for diagnostic messages
212 * \param[in] name Name of the method (used for error messages).
213 * \param[in] nparams Number of parameters in \p param.
214 * \param[in,out] param Parameter array
215 * (only the \c flags field of boolean parameters may be modified).
216 * \param[in] symtab Symbol table (used for checking overlaps).
217 * \returns true if there are no problems with the parameters,
220 * This function performs some checks common to both check_method() and
222 * The purpose of these checks is to ensure that the selection parser does not
223 * need to check for the validity of the parameters at each turn, and to
224 * report programming errors as early as possible.
225 * If you remove a check, make sure that the parameter parser can handle the
226 * resulting parameters.
229 check_params(FILE *fp, const char *name, int nparams, gmx_ana_selparam_t param[],
230 const gmx::SelectionParserSymbolTable &symtab)
235 if (nparams > 0 && !param)
237 report_error(fp, name, "error: missing parameter data");
240 if (nparams == 0 && param)
242 report_error(fp, name, "warning: parameter data unused because nparams=0");
244 /* Check each parameter */
245 for (i = 0; i < nparams; ++i)
247 /* Check that there is at most one NULL name, in the beginning */
248 if (param[i].name == NULL && i > 0)
250 report_error(fp, name, "error: NULL parameter should be the first one");
254 /* Check for duplicates */
255 for (j = 0; j < i; ++j)
257 if (param[j].name == NULL)
261 if (!gmx_strcasecmp(param[i].name, param[j].name))
263 report_error(fp, name, "error: duplicate parameter name '%s'", param[i].name);
269 if (param[i].flags & SPAR_SET)
271 report_param_error(fp, name, param[i].name, "warning: flag SPAR_SET is set");
272 param[i].flags &= ~SPAR_SET;
274 if (param[i].flags & SPAR_RANGES)
276 if (param[i].val.type != INT_VALUE && param[i].val.type != REAL_VALUE)
278 report_param_error(fp, name, param[i].name, "error: SPAR_RANGES cannot be set for a non-numeric parameter");
281 if (param[i].flags & SPAR_DYNAMIC)
283 report_param_error(fp, name, param[i].name, "warning: SPAR_DYNAMIC does not have effect with SPAR_RANGES");
284 param[i].flags &= ~SPAR_DYNAMIC;
286 if (!(param[i].flags & SPAR_VARNUM) && param[i].val.nr != 1)
288 report_param_error(fp, name, param[i].name, "error: range should take either one or an arbitrary number of values");
291 if (param[i].flags & SPAR_ATOMVAL)
293 report_param_error(fp, name, param[i].name, "error: SPAR_RANGES and SPAR_ATOMVAL both set");
297 if ((param[i].flags & SPAR_VARNUM) && (param[i].flags & SPAR_ATOMVAL))
299 report_param_error(fp, name, param[i].name, "error: SPAR_VARNUM and SPAR_ATOMVAL both set");
302 if (param[i].flags & SPAR_ENUMVAL)
304 if (param[i].val.type != STR_VALUE)
306 report_param_error(fp, name, param[i].name, "error: SPAR_ENUMVAL can only be set for string parameters");
309 if (param[i].val.nr != 1)
311 report_param_error(fp, name, param[i].name, "error: SPAR_ENUMVAL parameters should take exactly one value");
314 if (param[i].flags & (SPAR_DYNAMIC | SPAR_VARNUM | SPAR_ATOMVAL))
316 report_param_error(fp, name, param[i].name, "error: only SPAR_OPTIONAL supported with SPAR_ENUMVAL");
320 /* Check boolean parameters */
321 if (param[i].val.type == NO_VALUE)
323 if (param[i].val.nr != 0)
325 report_param_error(fp, name, param[i].name, "error: number of values should be zero for boolean parameters");
328 /* The boolean parameters should always be optional, so set the
329 * flag for convenience. */
330 param[i].flags |= SPAR_OPTIONAL;
331 /* Any other flags should not be specified */
332 if (param[i].flags & ~SPAR_OPTIONAL)
334 report_param_error(fp, name, param[i].name, "error: boolean parameter should not have any flags set");
339 if (param[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL))
341 if (param[i].val.nr != -1)
343 report_param_error(fp, name, param[i].name, "warning: val.nr is not -1 although SPAR_VARNUM/SPAR_ATOMVAL is set");
345 param[i].val.nr = -1;
347 else if (param[i].val.type != NO_VALUE)
349 if (param[i].val.nr <= 0)
351 report_param_error(fp, name, param[i].name, "error: val.nr <= 0");
355 /* Check that the value pointer is NULL */
356 if (param[i].nvalptr != NULL)
358 report_param_error(fp, name, param[i].name, "warning: nvalptr is set");
360 if (param[i].val.u.ptr != NULL && !(param[i].flags & SPAR_ENUMVAL))
362 report_param_error(fp, name, param[i].name, "warning: value pointer is set");
364 /* Check that the name contains only valid characters */
365 if (param[i].name == NULL)
369 if (!isalpha(param[i].name[0]))
371 report_param_error(fp, name, param[i].name, "error: name does not begin with a letter");
375 for (j = 1; param[i].name[j] != 0; ++j)
377 if (param[i].name[j] != '_' && !isalnum(param[i].name[j]))
379 report_param_error(fp, name, param[i].name, "error: name contains non-alphanumeric characters");
384 if (param[i].name[j] != 0)
388 /* Check that the name does not conflict with a method */
389 if (symtab.findSymbol(param[i].name, true))
391 report_param_error(fp, name, param[i].name, "error: name conflicts with another method or a keyword");
394 } /* End of parameter loop */
395 /* Check parameters of existing methods */
396 gmx::SelectionParserSymbolIterator symbol
397 = symtab.beginIterator(gmx::SelectionParserSymbol::MethodSymbol);
398 while (symbol != symtab.endIterator())
400 gmx_ana_selmethod_t *method = symbol->methodValue();
401 gmx_ana_selparam_t *param =
402 gmx_ana_selmethod_find_param(name, method);
405 report_param_error(fp, method->name, param->name, "error: name conflicts with another method or a keyword");
414 * Checks the validity of selection method callback functions.
416 * \param[in] fp File handle to use for diagnostic messages
418 * \param[in] method The method to check.
419 * \returns true if there are no problems, false otherwise.
421 * This function performs some checks common to both check_method() and
423 * This function checks that all the required callbacks are defined, i.e.,
424 * not NULL, to find programming errors.
427 check_callbacks(FILE *fp, gmx_ana_selmethod_t *method)
433 /* Make some checks on init_data and free */
434 if (method->nparams > 0 && !method->init_data)
436 report_error(fp, method->name, "error: init_data should be provided because the method has parameters");
439 if (method->free && !method->init_data)
441 report_error(fp, method->name, "warning: free is not used because of missing init_data");
443 /* Check presence of outinit for position-valued methods */
444 if (method->type == POS_VALUE && !method->outinit)
446 report_error(fp, method->name, "error: outinit should be provided because the method has POS_VALUE");
449 /* Check presence of outinit for variable output count methods */
450 if ((method->flags & SMETH_VARNUMVAL) && !method->outinit)
452 report_error(fp, method->name, "error: outinit should be provided because the method has SMETH_VARNUMVAL");
455 /* Warn of dynamic callbacks in static methods */
456 if (!(method->flags & SMETH_MODIFIER))
458 if (method->pupdate && !(method->flags & SMETH_DYNAMIC))
460 report_error(fp, method->name, "warning: pupdate not used because the method is static");
461 method->pupdate = NULL;
464 /* Check that there is an evaluation function */
465 if (method->type != NO_VALUE && !method->update && !method->pupdate)
467 report_error(fp, method->name, "error: evaluation function missing");
470 /* Loop through the parameters to determine if initialization callbacks
473 for (i = 0; i < method->nparams; ++i)
475 if (method->param[i].val.type != POS_VALUE
476 && (method->param[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
481 /* Check that the callbacks required by the parameters are present */
482 if (bNeedInit && !method->init)
484 report_error(fp, method->name, "error: init should be provided");
491 * Checks the validity of a selection method.
493 * \param[in] fp File handle to use for diagnostic messages
495 * \param[in,out] method Method to check.
496 * \param[in] symtab Symbol table (used for checking overlaps).
498 * Checks the validity of the given selection method data structure
499 * that does not have \ref SMETH_MODIFIER set.
500 * If you remove a check, please make sure that the selection parser,
501 * compiler, and evaluation functions can deal with the method.
504 check_method(FILE *fp, gmx_ana_selmethod_t *method,
505 const gmx::SelectionParserSymbolTable &symtab)
510 if (method->type == NO_VALUE)
512 report_error(fp, method->name, "error: no value type specified");
515 if (method->type == STR_VALUE && method->nparams > 0)
517 report_error(fp, method->name, "error: evaluates to a string but is not a keyword");
521 if (method->type == GROUP_VALUE)
523 /* Group methods should always have SMETH_SINGLEVAL,
524 * so set it for convenience. */
525 method->flags |= SMETH_SINGLEVAL;
526 /* Check that conflicting flags are not present. */
527 if (method->flags & SMETH_VARNUMVAL)
529 report_error(fp, method->name, "error: SMETH_VARNUMVAL cannot be set for group-valued methods");
535 if ((method->flags & SMETH_SINGLEVAL)
536 && (method->flags & SMETH_VARNUMVAL))
538 report_error(fp, method->name, "error: SMETH_SINGLEVAL and SMETH_VARNUMVAL both set");
542 if ((method->flags & SMETH_CHARVAL) && method->type != STR_VALUE)
544 report_error(fp, method->name, "error: SMETH_CHARVAL can only be specified for STR_VALUE methods");
547 /* Check the parameters */
548 if (!check_params(fp, method->name, method->nparams, method->param, symtab))
552 /* Check the callback pointers */
553 if (!check_callbacks(fp, method))
562 * Checks the validity of a selection modifier method.
564 * \param[in] fp File handle to use for diagnostic messages
566 * \param[in,out] method Method to check.
567 * \param[in] symtab Symbol table (used for checking overlaps).
569 * Checks the validity of the given selection method data structure
570 * that has \ref SMETH_MODIFIER set.
571 * If you remove a check, please make sure that the selection parser,
572 * compiler, and evaluation functions can deal with the method.
575 check_modifier(FILE *fp, gmx_ana_selmethod_t *method,
576 const gmx::SelectionParserSymbolTable &symtab)
581 if (method->type != NO_VALUE && method->type != POS_VALUE)
583 report_error(fp, method->name, "error: modifier should have type POS_VALUE or NO_VALUE");
587 if (method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
589 report_error(fp, method->name, "error: modifier should not have SMETH_SINGLEVAL or SMETH_VARNUMVAL set");
592 /* Check the parameters */
593 /* The first parameter is skipped */
594 if (!check_params(fp, method->name, method->nparams-1, method->param+1, symtab))
598 /* Check the callback pointers */
599 if (!check_callbacks(fp, method))
605 report_error(fp, method->name, "error: modifier should not have update");
608 if (method->type == POS_VALUE && !method->pupdate)
610 report_error(fp, method->name, "error: evaluation function missing");
618 * \param[in,out] symtab Symbol table to register the method to.
619 * \param[in] name Name under which the method should be registered.
620 * \param[in] method Method to register.
621 * \returns 0 on success, EINVAL if there was something wrong with the
624 * \p name does not need to match the name of the method, and the same
625 * method can be registered multiple times under different names.
626 * If \p name equals some previously registered name,
627 * an error message is printed and the method is not registered.
629 * The function also performs some sanity checking on the input method,
630 * and refuses to register it if there are problems.
631 * Some problems only generate warnings.
632 * All problems are described to \p stderr.
635 gmx_ana_selmethod_register(gmx::SelectionParserSymbolTable *symtab,
636 const char *name, gmx_ana_selmethod_t *method)
640 /* Check the method */
641 if (method->flags & SMETH_MODIFIER)
643 bOk = check_modifier(stderr, method, *symtab);
647 bOk = check_method(stderr, method, *symtab);
649 /* Try to register the method if everything is ok */
654 symtab->addMethod(name, method);
656 catch (const gmx::APIError &ex)
658 report_error(stderr, name, ex.what());
664 report_error(stderr, name, "warning: not registered");
671 * \param[in,out] symtab Symbol table to register the methods to.
672 * \returns 0 on success, -1 if any of the default methods could not be
676 gmx_ana_selmethod_register_defaults(gmx::SelectionParserSymbolTable *symtab)
683 for (i = 0; i < asize(smtable_def); ++i)
685 gmx_ana_selmethod_t *method = smtable_def[i].method;
687 if (smtable_def[i].name == NULL)
689 rc = gmx_ana_selmethod_register(symtab, method->name, method);
693 rc = gmx_ana_selmethod_register(symtab, smtable_def[i].name, method);
704 * \param[in] name Name of the parameter to search.
705 * \param[in] method Method to search for the parameter.
706 * \returns Pointer to the parameter in the
707 * \ref gmx_ana_selmethod_t::param "method->param" array,
708 * or NULL if no parameter with name \p name was found.
710 * This is a simple wrapper for gmx_ana_selparam_find().
713 gmx_ana_selmethod_find_param(const char *name, gmx_ana_selmethod_t *method)
715 return gmx_ana_selparam_find(name, method->nparams, method->param);