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37 * Implements the \p same selection method.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
44 #include "gromacs/legacyheaders/macros.h"
46 #include "gromacs/selection/selmethod.h"
47 #include "gromacs/utility/exceptions.h"
48 #include "gromacs/utility/smalloc.h"
51 #include "parsetree.h"
56 * Data structure for the \p same selection method.
58 * To avoid duplicate initialization code, the same data structure is used
59 * for matching both integer and string keywords; hence the unions.
61 * \ingroup module_selection
65 /** Value for each atom to match. */
73 * Number of values in the \p as array.
75 * For string values, this is actually the number of values in the
76 * \p as_s_sorted array.
79 /** Values to match against. */
87 * Separate array for sorted \p as.s array.
89 * The array of strings returned as the output value of a parameter should
90 * not be messed with to avoid memory corruption (the pointers in the array
91 * may be reused for several evaluations), so we keep our own copy for
95 /** Whether simple matching can be used. */
100 * Allocates data for the \p same selection method.
102 * \param[in] npar Not used (should be 2).
103 * \param[in,out] param Method parameters (should point to a copy of
104 * ::smparams_same_int or ::smparams_same_str).
105 * \returns Pointer to the allocated data (\ref t_methoddata_same).
108 init_data_same(int npar, gmx_ana_selparam_t *param);
110 * Initializes the \p same selection method.
112 * \param top Not used.
113 * \param npar Not used (should be 2).
114 * \param param Initialized method parameters (should point to a copy of
115 * ::smparams_same_int or ::smparams_same_str).
116 * \param data Pointer to \ref t_methoddata_same to initialize.
117 * \returns 0 on success, -1 on failure.
120 init_same(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
121 /** Frees the data allocated for the \p same selection method. */
123 free_data_same(void *data);
125 * Initializes the evaluation of the \p same selection method for a frame.
127 * \param[in] top Not used.
128 * \param[in] fr Current frame.
129 * \param[in] pbc PBC structure.
130 * \param data Should point to a \ref t_methoddata_same.
132 * Sorts the \c data->as.i array and removes identical values for faster and
136 init_frame_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
137 /** Evaluates the \p same selection method. */
139 evaluate_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
140 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
142 * Initializes the evaluation of the \p same selection method for a frame.
144 * \param[in] top Not used.
145 * \param[in] fr Current frame.
146 * \param[in] pbc PBC structure.
147 * \param data Should point to a \ref t_methoddata_same.
149 * Sorts the \c data->as.s array and removes identical values for faster and
153 init_frame_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
154 /** Evaluates the \p same selection method. */
156 evaluate_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
157 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
159 /** Parameters for the \p same selection method. */
160 static gmx_ana_selparam_t smparams_same_int[] = {
161 {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_ATOMVAL},
162 {"as", {INT_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
165 /** Parameters for the \p same selection method. */
166 static gmx_ana_selparam_t smparams_same_str[] = {
167 {NULL, {STR_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_ATOMVAL},
168 {"as", {STR_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
171 /** Help text for the \p same selection method. */
172 static const char *help_same[] = {
173 "EXTENDING SELECTIONS[PAR]",
175 "[TT]same KEYWORD as ATOM_EXPR[tt][PAR]",
177 "The keyword [TT]same[tt] can be used to select all atoms for which",
178 "the given [TT]KEYWORD[tt] matches any of the atoms in [TT]ATOM_EXPR[tt].",
179 "Keywords that evaluate to integer or string values are supported.",
182 /*! \internal \brief Selection method data for the \p same method. */
183 gmx_ana_selmethod_t sm_same = {
184 "same", GROUP_VALUE, 0,
185 asize(smparams_same_int), smparams_same_int,
191 &init_frame_same_int,
194 {"same KEYWORD as ATOM_EXPR", asize(help_same), help_same},
198 * Selection method data for the \p same method.
200 * This selection method is used for matching string keywords. The parser
201 * never sees this method; _gmx_selelem_custom_init_same() replaces sm_same
202 * with this method in cases where it is required.
204 static gmx_ana_selmethod_t sm_same_str = {
205 "same", GROUP_VALUE, SMETH_SINGLEVAL,
206 asize(smparams_same_str), smparams_same_str,
212 &init_frame_same_str,
215 {"same KEYWORD as ATOM_EXPR", asize(help_same), help_same},
219 init_data_same(int /* npar */, gmx_ana_selparam_t *param)
221 t_methoddata_same *data;
224 data->as_s_sorted = NULL;
225 param[1].nvalptr = &data->nas;
230 * \param[in,out] method The method to initialize.
231 * \param[in,out] params Pointer to the first parameter.
232 * \param[in] scanner Scanner data structure.
233 * \returns 0 on success, a non-zero error code on error.
235 * If \p *method is not a \c same method, this function returns zero
239 _gmx_selelem_custom_init_same(gmx_ana_selmethod_t **method,
240 const gmx::SelectionParserParameterListPointer ¶ms,
244 /* Do nothing if this is not a same method. */
245 if (!*method || (*method)->name != sm_same.name || params->empty())
250 const gmx::SelectionParserValueList &kwvalues = params->front().values();
251 if (kwvalues.size() != 1 || !kwvalues.front().hasExpressionValue()
252 || kwvalues.front().expr->type != SEL_EXPRESSION)
254 _gmx_selparser_error(scanner, "'same' should be followed by a single keyword");
257 gmx_ana_selmethod_t *kwmethod = kwvalues.front().expr->u.expr.method;
258 if (kwmethod->type == STR_VALUE)
260 *method = &sm_same_str;
263 /* We do custom processing for the "as" parameter. */
264 gmx::SelectionParserParameterList::iterator asparam = ++params->begin();
265 if (asparam != params->end() && asparam->name() == sm_same.param[1].name)
267 gmx::SelectionParserParameterList kwparams;
268 gmx::SelectionParserValueListPointer values(
269 new gmx::SelectionParserValueList(asparam->values()));
271 gmx::SelectionParserParameter::create(NULL, move(values)));
273 /* Create a second keyword evaluation element for the keyword given as
274 * the first parameter, evaluating the keyword in the group given by the
275 * second parameter. */
276 gmx::SelectionTreeElementPointer kwelem
277 = _gmx_sel_init_keyword_evaluator(kwmethod, kwparams, scanner);
278 // FIXME: Use exceptions.
283 /* Replace the second parameter with one with a value from \p kwelem. */
284 std::string pname = asparam->name();
285 *asparam = gmx::SelectionParserParameter::createFromExpression(pname, kwelem);
291 init_same(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
293 t_methoddata_same *d = (t_methoddata_same *)data;
295 d->val.ptr = param[0].val.u.ptr;
296 d->as.ptr = param[1].val.u.ptr;
297 if (param[1].val.type == STR_VALUE)
299 snew(d->as_s_sorted, d->nas);
301 if (!(param[0].flags & SPAR_ATOMVAL))
303 GMX_THROW(gmx::InvalidInputError(
304 "The 'same' selection keyword combined with a "
305 "non-keyword does not make sense"));
310 * \param data Data to free (should point to a \ref t_methoddata_same).
313 free_data_same(void *data)
315 t_methoddata_same *d = (t_methoddata_same *)data;
317 sfree(d->as_s_sorted);
322 * Helper function for comparison of two integers.
325 cmp_int(const void *a, const void *b)
327 if (*(int *)a < *(int *)b)
331 if (*(int *)a > *(int *)b)
339 init_frame_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */, void *data)
341 t_methoddata_same *d = (t_methoddata_same *)data;
344 /* Collapse adjacent values, and check whether the array is sorted. */
346 for (i = 1, j = 0; i < d->nas; ++i)
348 if (d->as.i[i] != d->as.i[j])
350 if (d->as.i[i] < d->as.i[j])
355 d->as.i[j] = d->as.i[i];
362 qsort(d->as.i, d->nas, sizeof(d->as.i[0]), &cmp_int);
363 /* More identical values may become adjacent after sorting. */
364 for (i = 1, j = 0; i < d->nas; ++i)
366 if (d->as.i[i] != d->as.i[j])
369 d->as.i[j] = d->as.i[i];
377 * See sel_updatefunc() for description of the parameters.
378 * \p data should point to a \c t_methoddata_same.
380 * Calculates which values in \c data->val.i can be found in \c data->as.i
381 * (assumed sorted), and writes the corresponding atoms to output.
382 * If \c data->val is sorted, uses a linear scan of both arrays, otherwise a
383 * binary search of \c data->as is performed for each block of values in
387 evaluate_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
388 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
390 t_methoddata_same *d = (t_methoddata_same *)data;
399 /* If we are sorted, we can do a simple linear scan. */
400 while (i < d->nas && d->as.i[i] < d->val.i[j])
407 /* If not, we must do a binary search of all the values. */
414 int itry = (i1 + i2) / 2;
415 if (d->as.i[itry] <= d->val.i[j])
424 i = (d->as.i[i1] == d->val.i[j] ? i1 : d->nas);
426 /* Check whether the value was found in the as list. */
427 if (i == d->nas || d->as.i[i] != d->val.i[j])
429 /* If not, skip all atoms with the same value. */
430 int tmpval = d->val.i[j];
432 while (j < g->isize && d->val.i[j] == tmpval)
439 /* Copy all the atoms with this value to the output. */
440 while (j < g->isize && d->val.i[j] == d->as.i[i])
442 out->u.g->index[out->u.g->isize++] = g->index[j];
446 if (j < g->isize && d->val.i[j] < d->val.i[j - 1])
454 * Helper function for comparison of two strings.
457 cmp_str(const void *a, const void *b)
459 return strcmp(*(char **)a, *(char **)b);
463 init_frame_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */, void *data)
465 t_methoddata_same *d = (t_methoddata_same *)data;
468 /* Collapse adjacent values.
469 * For strings, it's unlikely that the values would be sorted originally,
470 * so set bSorted always to false. */
472 d->as_s_sorted[0] = d->as.s[0];
473 for (i = 1, j = 0; i < d->nas; ++i)
475 if (strcmp(d->as.s[i], d->as_s_sorted[j]) != 0)
478 d->as_s_sorted[j] = d->as.s[i];
483 qsort(d->as_s_sorted, d->nas, sizeof(d->as_s_sorted[0]), &cmp_str);
484 /* More identical values may become adjacent after sorting. */
485 for (i = 1, j = 0; i < d->nas; ++i)
487 if (strcmp(d->as_s_sorted[i], d->as_s_sorted[j]) != 0)
490 d->as_s_sorted[j] = d->as_s_sorted[i];
497 * See sel_updatefunc() for description of the parameters.
498 * \p data should point to a \c t_methoddata_same.
500 * Calculates which strings in \c data->val.s can be found in \c data->as.s
501 * (assumed sorted), and writes the corresponding atoms to output.
502 * A binary search of \c data->as is performed for each block of values in
506 evaluate_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
507 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
509 t_methoddata_same *d = (t_methoddata_same *)data;
516 /* Do a binary search of the strings. */
518 ptr = bsearch(&d->val.s[j], d->as_s_sorted, d->nas,
519 sizeof(d->as_s_sorted[0]), &cmp_str);
520 /* Check whether the value was found in the as list. */
523 /* If not, skip all atoms with the same value. */
524 const char *tmpval = d->val.s[j];
526 while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0)
533 const char *tmpval = d->val.s[j];
534 /* Copy all the atoms with this value to the output. */
535 while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0)
537 out->u.g->index[out->u.g->isize++] = g->index[j];