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33 * Implements the \p same selection method.
35 * \author Teemu Murtola <teemu.murtola@cbr.su.se>
36 * \ingroup module_selection
40 #include "gromacs/legacyheaders/macros.h"
41 #include "gromacs/legacyheaders/smalloc.h"
42 #include "gromacs/legacyheaders/string2.h"
44 #include "gromacs/selection/selmethod.h"
45 #include "gromacs/utility/exceptions.h"
48 #include "parsetree.h"
52 * Data structure for the \p same selection method.
54 * To avoid duplicate initialization code, the same data structure is used
55 * for matching both integer and string keywords; hence the unions.
59 /** Value for each atom to match. */
67 * Number of values in the \p as array.
69 * For string values, this is actually the number of values in the
70 * \p as_s_sorted array.
73 /** Values to match against. */
81 * Separate array for sorted \p as.s array.
83 * The array of strings returned as the output value of a parameter should
84 * not be messed with to avoid memory corruption (the pointers in the array
85 * may be reused for several evaluations), so we keep our own copy for
89 /** Whether simple matching can be used. */
93 /** Allocates data for the \p same selection method. */
95 init_data_same(int npar, gmx_ana_selparam_t *param);
96 /** Initializes the \p same selection method. */
98 init_same(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
99 /** Frees the data allocated for the \p same selection method. */
101 free_data_same(void *data);
102 /** Initializes the evaluation of the \p same selection method for a frame. */
104 init_frame_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
105 /** Evaluates the \p same selection method. */
107 evaluate_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc,
108 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
109 /** Initializes the evaluation of the \p same selection method for a frame. */
111 init_frame_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
112 /** Evaluates the \p same selection method. */
114 evaluate_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc,
115 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
117 /** Parameters for the \p same selection method. */
118 static gmx_ana_selparam_t smparams_same_int[] = {
119 {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_ATOMVAL},
120 {"as", {INT_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
123 /** Parameters for the \p same selection method. */
124 static gmx_ana_selparam_t smparams_same_str[] = {
125 {NULL, {STR_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_ATOMVAL},
126 {"as", {STR_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
129 /** Help text for the \p same selection method. */
130 static const char *help_same[] = {
131 "EXTENDING SELECTIONS[PAR]",
133 "[TT]same KEYWORD as ATOM_EXPR[tt][PAR]",
135 "The keyword [TT]same[tt] can be used to select all atoms for which",
136 "the given [TT]KEYWORD[tt] matches any of the atoms in [TT]ATOM_EXPR[tt].",
137 "Keywords that evaluate to integer or string values are supported.",
140 /*! \internal \brief Selection method data for the \p same method. */
141 gmx_ana_selmethod_t sm_same = {
142 "same", GROUP_VALUE, 0,
143 asize(smparams_same_int), smparams_same_int,
149 &init_frame_same_int,
152 {"same KEYWORD as ATOM_EXPR", asize(help_same), help_same},
156 * Selection method data for the \p same method.
158 * This selection method is used for matching string keywords. The parser
159 * never sees this method; _gmx_selelem_custom_init_same() replaces sm_same
160 * with this method in cases where it is required.
162 static gmx_ana_selmethod_t sm_same_str = {
163 "same", GROUP_VALUE, SMETH_SINGLEVAL,
164 asize(smparams_same_str), smparams_same_str,
170 &init_frame_same_str,
173 {"same KEYWORD as ATOM_EXPR", asize(help_same), help_same},
177 * \param[in] npar Not used (should be 2).
178 * \param[in,out] param Method parameters (should point to a copy of
179 * ::smparams_same_int or ::smparams_same_str).
180 * \returns Pointer to the allocated data (\ref t_methoddata_same).
183 init_data_same(int npar, gmx_ana_selparam_t *param)
185 t_methoddata_same *data;
188 data->as_s_sorted = NULL;
189 param[1].nvalptr = &data->nas;
194 * \param[in,out] method The method to initialize.
195 * \param[in,out] params Pointer to the first parameter.
196 * \param[in] scanner Scanner data structure.
197 * \returns 0 on success, a non-zero error code on error.
199 * If \p *method is not a \c same method, this function returns zero
203 _gmx_selelem_custom_init_same(gmx_ana_selmethod_t **method,
204 const gmx::SelectionParserParameterListPointer ¶ms,
208 /* Do nothing if this is not a same method. */
209 if (!*method || (*method)->name != sm_same.name || params->empty())
214 const gmx::SelectionParserValueList &kwvalues = params->front().values();
215 if (kwvalues.size() != 1 || !kwvalues.front().hasExpressionValue()
216 || kwvalues.front().expr->type != SEL_EXPRESSION)
218 _gmx_selparser_error(scanner, "'same' should be followed by a single keyword");
221 gmx_ana_selmethod_t *kwmethod = kwvalues.front().expr->u.expr.method;
222 if (kwmethod->type == STR_VALUE)
224 *method = &sm_same_str;
227 /* We do custom processing for the "as" parameter. */
228 gmx::SelectionParserParameterList::iterator asparam = ++params->begin();
229 if (asparam != params->end() && asparam->name() == sm_same.param[1].name)
231 gmx::SelectionParserParameterList kwparams;
232 gmx::SelectionParserValueListPointer values(
233 new gmx::SelectionParserValueList(asparam->values()));
235 gmx::SelectionParserParameter::create(NULL, move(values)));
237 /* Create a second keyword evaluation element for the keyword given as
238 * the first parameter, evaluating the keyword in the group given by the
239 * second parameter. */
240 gmx::SelectionTreeElementPointer kwelem
241 = _gmx_sel_init_keyword_evaluator(kwmethod, kwparams, scanner);
242 // FIXME: Use exceptions.
247 /* Replace the second parameter with one with a value from \p kwelem. */
248 std::string pname = asparam->name();
249 *asparam = gmx::SelectionParserParameter::createFromExpression(pname, kwelem);
255 * \param top Not used.
256 * \param npar Not used (should be 2).
257 * \param param Initialized method parameters (should point to a copy of
258 * ::smparams_same_int or ::smparams_same_str).
259 * \param data Pointer to \ref t_methoddata_same to initialize.
260 * \returns 0 on success, -1 on failure.
263 init_same(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
265 t_methoddata_same *d = (t_methoddata_same *)data;
267 d->val.ptr = param[0].val.u.ptr;
268 d->as.ptr = param[1].val.u.ptr;
269 if (param[1].val.type == STR_VALUE)
271 snew(d->as_s_sorted, d->nas);
273 if (!(param[0].flags & SPAR_ATOMVAL))
275 GMX_THROW(gmx::InvalidInputError(
276 "The 'same' selection keyword combined with a "
277 "non-keyword does not make sense"));
282 * \param data Data to free (should point to a \ref t_methoddata_same).
285 free_data_same(void *data)
287 t_methoddata_same *d = (t_methoddata_same *)data;
289 sfree(d->as_s_sorted);
294 * Helper function for comparison of two integers.
297 cmp_int(const void *a, const void *b)
299 if (*(int *)a < *(int *)b)
303 if (*(int *)a > *(int *)b)
311 * \param[in] top Not used.
312 * \param[in] fr Current frame.
313 * \param[in] pbc PBC structure.
314 * \param data Should point to a \ref t_methoddata_same.
316 * Sorts the \c data->as.i array and removes identical values for faster and
320 init_frame_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
322 t_methoddata_same *d = (t_methoddata_same *)data;
325 /* Collapse adjacent values, and check whether the array is sorted. */
327 for (i = 1, j = 0; i < d->nas; ++i)
329 if (d->as.i[i] != d->as.i[j])
331 if (d->as.i[i] < d->as.i[j])
336 d->as.i[j] = d->as.i[i];
343 qsort(d->as.i, d->nas, sizeof(d->as.i[0]), &cmp_int);
344 /* More identical values may become adjacent after sorting. */
345 for (i = 1, j = 0; i < d->nas; ++i)
347 if (d->as.i[i] != d->as.i[j])
350 d->as.i[j] = d->as.i[i];
358 * See sel_updatefunc() for description of the parameters.
359 * \p data should point to a \c t_methoddata_same.
361 * Calculates which values in \c data->val.i can be found in \c data->as.i
362 * (assumed sorted), and writes the corresponding atoms to output.
363 * If \c data->val is sorted, uses a linear scan of both arrays, otherwise a
364 * binary search of \c data->as is performed for each block of values in
368 evaluate_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc,
369 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
371 t_methoddata_same *d = (t_methoddata_same *)data;
380 /* If we are sorted, we can do a simple linear scan. */
381 while (i < d->nas && d->as.i[i] < d->val.i[j]) ++i;
385 /* If not, we must do a binary search of all the values. */
392 int itry = (i1 + i2) / 2;
393 if (d->as.i[itry] <= d->val.i[j])
402 i = (d->as.i[i1] == d->val.i[j] ? i1 : d->nas);
404 /* Check whether the value was found in the as list. */
405 if (i == d->nas || d->as.i[i] != d->val.i[j])
407 /* If not, skip all atoms with the same value. */
408 int tmpval = d->val.i[j];
410 while (j < g->isize && d->val.i[j] == tmpval) ++j;
414 /* Copy all the atoms with this value to the output. */
415 while (j < g->isize && d->val.i[j] == d->as.i[i])
417 out->u.g->index[out->u.g->isize++] = g->index[j];
421 if (j < g->isize && d->val.i[j] < d->val.i[j - 1])
429 * Helper function for comparison of two strings.
432 cmp_str(const void *a, const void *b)
434 return strcmp(*(char **)a, *(char **)b);
438 * \param[in] top Not used.
439 * \param[in] fr Current frame.
440 * \param[in] pbc PBC structure.
441 * \param data Should point to a \ref t_methoddata_same.
443 * Sorts the \c data->as.s array and removes identical values for faster and
447 init_frame_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
449 t_methoddata_same *d = (t_methoddata_same *)data;
452 /* Collapse adjacent values.
453 * For strings, it's unlikely that the values would be sorted originally,
454 * so set bSorted always to false. */
456 d->as_s_sorted[0] = d->as.s[0];
457 for (i = 1, j = 0; i < d->nas; ++i)
459 if (strcmp(d->as.s[i], d->as_s_sorted[j]) != 0)
462 d->as_s_sorted[j] = d->as.s[i];
467 qsort(d->as_s_sorted, d->nas, sizeof(d->as_s_sorted[0]), &cmp_str);
468 /* More identical values may become adjacent after sorting. */
469 for (i = 1, j = 0; i < d->nas; ++i)
471 if (strcmp(d->as_s_sorted[i], d->as_s_sorted[j]) != 0)
474 d->as_s_sorted[j] = d->as_s_sorted[i];
481 * See sel_updatefunc() for description of the parameters.
482 * \p data should point to a \c t_methoddata_same.
484 * Calculates which strings in \c data->val.s can be found in \c data->as.s
485 * (assumed sorted), and writes the corresponding atoms to output.
486 * A binary search of \c data->as is performed for each block of values in
490 evaluate_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc,
491 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
493 t_methoddata_same *d = (t_methoddata_same *)data;
500 /* Do a binary search of the strings. */
502 ptr = bsearch(&d->val.s[j], d->as_s_sorted, d->nas,
503 sizeof(d->as_s_sorted[0]), &cmp_str);
504 /* Check whether the value was found in the as list. */
507 /* If not, skip all atoms with the same value. */
508 const char *tmpval = d->val.s[j];
510 while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0) ++j;
514 const char *tmpval = d->val.s[j];
515 /* Copy all the atoms with this value to the output. */
516 while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0)
518 out->u.g->index[out->u.g->isize++] = g->index[j];