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37 * Implements functions in selmethod.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
44 #include "selmethod.h"
49 #include "gromacs/utility/arraysize.h"
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/exceptions.h"
52 #include "gromacs/utility/stringutil.h"
54 #include "selmethod-impl.h"
58 * Helper structure for defining selection methods.
62 * Name to register the method under.
64 * If NULL, use the actual name of the method.
65 * This field is used for defining synonyms.
68 /** Method data structure to register. */
69 gmx_ana_selmethod_t *method;
73 * Convenience function for reporting errors found in selection methods.
76 report_error(FILE *fp, const char *name, gmx_fmtstr const char *fmt, ...) gmx_format(printf, 3, 4);
79 report_error(FILE *fp, const char *name, gmx_fmtstr const char *fmt, ...)
85 fprintf(fp, "selection method '%s': ", name);
86 vfprintf(fp, fmt, ap);
93 * Convenience function for reporting errors found in selection method parameters.
96 report_param_error(FILE *fp, const char *mname, const char *pname,
97 gmx_fmtstr const char *fmt, ...) gmx_format(printf, 4, 5);
99 report_param_error(FILE *fp, const char *mname, const char *pname,
100 gmx_fmtstr const char *fmt, ...)
106 fprintf(fp, "selection method '%s': parameter '%s': ", mname, pname);
107 vfprintf(fp, fmt, ap);
114 * Checks the validity of parameters.
116 * \param[in] fp File handle to use for diagnostic messages
118 * \param[in] name Name of the method (used for error messages).
119 * \param[in] nparams Number of parameters in \p param.
120 * \param[in,out] param Parameter array
121 * (only the \c flags field of boolean parameters may be modified).
122 * \param[in] symtab Symbol table (used for checking overlaps).
123 * \returns true if there are no problems with the parameters,
126 * This function performs some checks common to both check_method() and
128 * The purpose of these checks is to ensure that the selection parser does not
129 * need to check for the validity of the parameters at each turn, and to
130 * report programming errors as early as possible.
131 * If you remove a check, make sure that the parameter parser can handle the
132 * resulting parameters.
135 check_params(FILE *fp, const char *name, int nparams, gmx_ana_selparam_t param[],
136 const gmx::SelectionParserSymbolTable &symtab)
141 if (nparams > 0 && !param)
143 report_error(fp, name, "error: missing parameter data");
146 if (nparams == 0 && param)
148 report_error(fp, name, "warning: parameter data unused because nparams=0");
150 /* Check each parameter */
151 for (i = 0; i < nparams; ++i)
153 /* Check that there is at most one NULL name, in the beginning */
154 if (param[i].name == nullptr && i > 0)
156 report_error(fp, name, "error: NULL parameter should be the first one");
160 /* Check for duplicates */
161 for (j = 0; j < i; ++j)
163 if (param[j].name == nullptr)
167 if (!gmx_strcasecmp(param[i].name, param[j].name))
169 report_error(fp, name, "error: duplicate parameter name '%s'", param[i].name);
175 if (param[i].flags & SPAR_SET)
177 report_param_error(fp, name, param[i].name, "warning: flag SPAR_SET is set");
178 param[i].flags &= ~SPAR_SET;
180 if (param[i].flags & SPAR_RANGES)
182 if (param[i].val.type != INT_VALUE && param[i].val.type != REAL_VALUE)
184 report_param_error(fp, name, param[i].name, "error: SPAR_RANGES cannot be set for a non-numeric parameter");
187 if (param[i].flags & SPAR_DYNAMIC)
189 report_param_error(fp, name, param[i].name, "warning: SPAR_DYNAMIC does not have effect with SPAR_RANGES");
190 param[i].flags &= ~SPAR_DYNAMIC;
192 if (!(param[i].flags & SPAR_VARNUM) && param[i].val.nr != 1)
194 report_param_error(fp, name, param[i].name, "error: range should take either one or an arbitrary number of values");
197 if (param[i].flags & SPAR_ATOMVAL)
199 report_param_error(fp, name, param[i].name, "error: SPAR_RANGES and SPAR_ATOMVAL both set");
203 if ((param[i].flags & SPAR_VARNUM) && (param[i].flags & SPAR_ATOMVAL))
205 report_param_error(fp, name, param[i].name, "error: SPAR_VARNUM and SPAR_ATOMVAL both set");
208 if (param[i].flags & SPAR_ENUMVAL)
210 if (param[i].val.type != STR_VALUE)
212 report_param_error(fp, name, param[i].name, "error: SPAR_ENUMVAL can only be set for string parameters");
215 if (param[i].val.nr != 1)
217 report_param_error(fp, name, param[i].name, "error: SPAR_ENUMVAL parameters should take exactly one value");
220 if (param[i].flags & (SPAR_DYNAMIC | SPAR_VARNUM | SPAR_ATOMVAL))
222 report_param_error(fp, name, param[i].name, "error: only SPAR_OPTIONAL supported with SPAR_ENUMVAL");
226 /* Check boolean parameters */
227 if (param[i].val.type == NO_VALUE)
229 if (param[i].val.nr != 0)
231 report_param_error(fp, name, param[i].name, "error: number of values should be zero for boolean parameters");
234 /* The boolean parameters should always be optional, so set the
235 * flag for convenience. */
236 param[i].flags |= SPAR_OPTIONAL;
237 /* Any other flags should not be specified */
238 if (param[i].flags & ~SPAR_OPTIONAL)
240 report_param_error(fp, name, param[i].name, "error: boolean parameter should not have any flags set");
245 if (param[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL))
247 if (param[i].val.nr != -1)
249 report_param_error(fp, name, param[i].name, "warning: val.nr is not -1 although SPAR_VARNUM/SPAR_ATOMVAL is set");
251 param[i].val.nr = -1;
253 else if (param[i].val.type != NO_VALUE)
255 if (param[i].val.nr <= 0)
257 report_param_error(fp, name, param[i].name, "error: val.nr <= 0");
261 /* Check that the value pointer is NULL */
262 if (param[i].nvalptr != nullptr)
264 report_param_error(fp, name, param[i].name, "warning: nvalptr is set");
266 if (param[i].val.u.ptr != nullptr && !(param[i].flags & SPAR_ENUMVAL))
268 report_param_error(fp, name, param[i].name, "warning: value pointer is set");
270 /* Check that the name contains only valid characters */
271 if (param[i].name == nullptr)
275 if (!isalpha(param[i].name[0]))
277 report_param_error(fp, name, param[i].name, "error: name does not begin with a letter");
281 for (j = 1; param[i].name[j] != 0; ++j)
283 if (param[i].name[j] != '_' && !isalnum(param[i].name[j]))
285 report_param_error(fp, name, param[i].name, "error: name contains non-alphanumeric characters");
290 if (param[i].name[j] != 0)
294 /* Check that the name does not conflict with a method */
295 if (symtab.findSymbol(param[i].name) != nullptr)
297 report_param_error(fp, name, param[i].name, "error: name conflicts with another method or a keyword");
300 } /* End of parameter loop */
301 /* Check parameters of existing methods */
302 gmx::SelectionParserSymbolIterator symbol
303 = symtab.beginIterator(gmx::SelectionParserSymbol::MethodSymbol);
304 while (symbol != symtab.endIterator())
306 gmx_ana_selmethod_t *method = symbol->methodValue();
307 gmx_ana_selparam_t *param =
308 gmx_ana_selmethod_find_param(name, method);
311 report_param_error(fp, method->name, param->name, "error: name conflicts with another method or a keyword");
320 * Checks the validity of selection method callback functions.
322 * \param[in] fp File handle to use for diagnostic messages
324 * \param[in] method The method to check.
325 * \returns true if there are no problems, false otherwise.
327 * This function performs some checks common to both check_method() and
329 * This function checks that all the required callbacks are defined, i.e.,
330 * not NULL, to find programming errors.
333 check_callbacks(FILE *fp, gmx_ana_selmethod_t *method)
339 /* Make some checks on init_data and free */
340 if (method->nparams > 0 && !method->init_data)
342 report_error(fp, method->name, "error: init_data should be provided because the method has parameters");
345 if (method->free && !method->init_data)
347 report_error(fp, method->name, "warning: free is not used because of missing init_data");
349 /* Check presence of outinit for position-valued methods */
350 if (method->type == POS_VALUE && !method->outinit)
352 report_error(fp, method->name, "error: outinit should be provided because the method has POS_VALUE");
355 /* Check presence of outinit for variable output count methods */
356 if ((method->flags & SMETH_VARNUMVAL) && !method->outinit)
358 report_error(fp, method->name, "error: outinit should be provided because the method has SMETH_VARNUMVAL");
361 /* Warn of dynamic callbacks in static methods */
362 if (!(method->flags & SMETH_MODIFIER))
364 if (method->pupdate && !(method->flags & SMETH_DYNAMIC))
366 report_error(fp, method->name, "warning: pupdate not used because the method is static");
367 method->pupdate = nullptr;
370 /* Check that there is an evaluation function */
371 if (method->type != NO_VALUE && !method->update && !method->pupdate)
373 report_error(fp, method->name, "error: evaluation function missing");
376 /* Loop through the parameters to determine if initialization callbacks
379 for (i = 0; i < method->nparams; ++i)
381 if (method->param[i].val.type != POS_VALUE
382 && (method->param[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
387 /* Check that the callbacks required by the parameters are present */
388 if (bNeedInit && !method->init)
390 report_error(fp, method->name, "error: init should be provided");
397 * Checks the validity of a selection method.
399 * \param[in] fp File handle to use for diagnostic messages
401 * \param[in,out] method Method to check.
402 * \param[in] symtab Symbol table (used for checking overlaps).
404 * Checks the validity of the given selection method data structure
405 * that does not have \ref SMETH_MODIFIER set.
406 * If you remove a check, please make sure that the selection parser,
407 * compiler, and evaluation functions can deal with the method.
410 check_method(FILE *fp, gmx_ana_selmethod_t *method,
411 const gmx::SelectionParserSymbolTable &symtab)
416 if (method->type == NO_VALUE)
418 report_error(fp, method->name, "error: no value type specified");
421 if (method->type == STR_VALUE && method->nparams > 0)
423 report_error(fp, method->name, "error: evaluates to a string but is not a keyword");
427 if (method->type == GROUP_VALUE)
429 /* Group methods should always have SMETH_SINGLEVAL,
430 * so set it for convenience. */
431 method->flags |= SMETH_SINGLEVAL;
432 /* Check that conflicting flags are not present. */
433 if (method->flags & SMETH_VARNUMVAL)
435 report_error(fp, method->name, "error: SMETH_VARNUMVAL cannot be set for group-valued methods");
441 if ((method->flags & SMETH_SINGLEVAL)
442 && (method->flags & SMETH_VARNUMVAL))
444 report_error(fp, method->name, "error: SMETH_SINGLEVAL and SMETH_VARNUMVAL both set");
448 if ((method->flags & SMETH_CHARVAL) && method->type != STR_VALUE)
450 report_error(fp, method->name, "error: SMETH_CHARVAL can only be specified for STR_VALUE methods");
453 /* Check the parameters */
454 if (!check_params(fp, method->name, method->nparams, method->param, symtab))
458 /* Check the callback pointers */
459 if (!check_callbacks(fp, method))
468 * Checks the validity of a selection modifier method.
470 * \param[in] fp File handle to use for diagnostic messages
472 * \param[in,out] method Method to check.
473 * \param[in] symtab Symbol table (used for checking overlaps).
475 * Checks the validity of the given selection method data structure
476 * that has \ref SMETH_MODIFIER set.
477 * If you remove a check, please make sure that the selection parser,
478 * compiler, and evaluation functions can deal with the method.
481 check_modifier(FILE *fp, gmx_ana_selmethod_t *method,
482 const gmx::SelectionParserSymbolTable &symtab)
487 if (method->type != NO_VALUE && method->type != POS_VALUE)
489 report_error(fp, method->name, "error: modifier should have type POS_VALUE or NO_VALUE");
493 if (method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
495 report_error(fp, method->name, "error: modifier should not have SMETH_SINGLEVAL or SMETH_VARNUMVAL set");
498 /* Check the parameters */
499 /* The first parameter is skipped */
500 if (!check_params(fp, method->name, method->nparams-1, method->param+1, symtab))
504 /* Check the callback pointers */
505 if (!check_callbacks(fp, method))
511 report_error(fp, method->name, "error: modifier should not have update");
514 if (method->type == POS_VALUE && !method->pupdate)
516 report_error(fp, method->name, "error: evaluation function missing");
524 * \param[in,out] symtab Symbol table to register the method to.
525 * \param[in] name Name under which the method should be registered.
526 * \param[in] method Method to register.
527 * \returns 0 on success, -1 if there was something wrong with the
530 * \p name does not need to match the name of the method, and the same
531 * method can be registered multiple times under different names.
532 * If \p name equals some previously registered name,
533 * an error message is printed and the method is not registered.
535 * The function also performs some sanity checking on the input method,
536 * and refuses to register it if there are problems.
537 * Some problems only generate warnings.
538 * All problems are described to \p stderr.
541 gmx_ana_selmethod_register(gmx::SelectionParserSymbolTable *symtab,
542 const char *name, gmx_ana_selmethod_t *method)
546 /* Check the method */
547 if (method->flags & SMETH_MODIFIER)
549 bOk = check_modifier(stderr, method, *symtab);
553 bOk = check_method(stderr, method, *symtab);
555 /* Try to register the method if everything is ok */
560 symtab->addMethod(name, method);
562 catch (const gmx::APIError &ex)
564 report_error(stderr, name, "%s", ex.what());
570 report_error(stderr, name, "warning: not registered");
577 * \param[in,out] symtab Symbol table to register the methods to.
578 * \returns 0 on success, -1 if any of the default methods could not be
582 gmx_ana_selmethod_register_defaults(gmx::SelectionParserSymbolTable *symtab)
584 /* Array of selection methods defined in the library. */
585 const t_register_method smtable_def[] = {
591 {nullptr, &sm_atomnr},
592 {nullptr, &sm_resnr},
593 {"resid", &sm_resnr},
594 {nullptr, &sm_resindex},
595 {"residue", &sm_resindex},
596 {nullptr, &sm_molindex},
597 {"mol", &sm_molindex},
598 {"molecule", &sm_molindex},
599 {nullptr, &sm_atomname},
600 {"name", &sm_atomname},
601 {nullptr, &sm_pdbatomname},
602 {"pdbname", &sm_pdbatomname},
603 {nullptr, &sm_atomtype},
604 {"type", &sm_atomtype},
605 {nullptr, &sm_resname},
606 {nullptr, &sm_insertcode},
607 {nullptr, &sm_chain},
609 {nullptr, &sm_charge},
610 {nullptr, &sm_altloc},
611 {nullptr, &sm_occupancy},
612 {nullptr, &sm_betafactor},
613 {"beta", &sm_betafactor},
618 {nullptr, &sm_distance},
619 {"dist", &sm_distance},
620 {nullptr, &sm_mindistance},
621 {"mindist", &sm_mindistance},
622 {nullptr, &sm_within},
623 {nullptr, &sm_insolidangle},
626 {nullptr, &sm_merge},
628 {nullptr, &sm_permute},
636 for (i = 0; i < asize(smtable_def); ++i)
638 gmx_ana_selmethod_t *method = smtable_def[i].method;
640 if (smtable_def[i].name == nullptr)
642 rc = gmx_ana_selmethod_register(symtab, method->name, method);
646 rc = gmx_ana_selmethod_register(symtab, smtable_def[i].name, method);
657 * \param[in] name Name of the parameter to search.
658 * \param[in] method Method to search for the parameter.
659 * \returns Pointer to the parameter in the
660 * \ref gmx_ana_selmethod_t::param "method->param" array,
661 * or NULL if no parameter with name \p name was found.
663 * This is a simple wrapper for gmx_ana_selparam_find().
666 gmx_ana_selmethod_find_param(const char *name, gmx_ana_selmethod_t *method)
668 return gmx_ana_selparam_find(name, method->nparams, method->param);