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37 * Implements the \p merge and \p plus selection modifiers.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
42 #include "gromacs/legacyheaders/macros.h"
43 #include "gromacs/legacyheaders/smalloc.h"
44 #include "gromacs/legacyheaders/vec.h"
46 #include "gromacs/selection/position.h"
47 #include "gromacs/selection/selmethod.h"
48 #include "gromacs/utility/exceptions.h"
51 * Data structure for the merging selection modifiers.
55 /** Input positions. */
57 /** Other input positions. */
59 /** Stride for merging (\c stride values from \c p1 for each in \c p2). */
63 /** Allocates data for the merging selection modifiers. */
65 init_data_merge(int npar, gmx_ana_selparam_t *param);
66 /** Initializes data for the merging selection modifiers. */
68 init_merge(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
69 /** Initializes output for the \p merge selection modifier. */
71 init_output_merge(t_topology *top, gmx_ana_selvalue_t *out, void *data);
72 /** Initializes output for the \p plus selection modifier. */
74 init_output_plus(t_topology *top, gmx_ana_selvalue_t *out, void *data);
75 /** Frees the memory allocated for the merging selection modifiers. */
77 free_data_merge(void *data);
78 /** Evaluates the \p merge selection modifier. */
80 evaluate_merge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
81 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
82 /** Evaluates the \p plus selection modifier. */
84 evaluate_plus(t_topology *top, t_trxframe *fr, t_pbc *pbc,
85 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
87 /** Parameters for the merging selection modifiers. */
88 static gmx_ana_selparam_t smparams_merge[] = {
89 {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
90 {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
91 {"stride", {INT_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
94 /** Help text for the merging selection modifiers. */
95 static const char *help_merge[] = {
96 "MERGING SELECTIONS[PAR]",
98 "[TT]POSEXPR merge POSEXPR [stride INT][tt][BR]",
99 "[TT]POSEXPR merge POSEXPR [merge POSEXPR ...][tt][BR]",
100 "[TT]POSEXPR plus POSEXPR [plus POSEXPR ...][tt][PAR]",
102 "Basic selection keywords can only create selections where each atom",
103 "occurs at most once. The [TT]merge[tt] and [TT]plus[tt] selection",
104 "keywords can be used to work around this limitation. Both create",
105 "a selection that contains the positions from all the given position",
106 "expressions, even if they contain duplicates.",
107 "The difference between the two is that [TT]merge[tt] expects two or more",
108 "selections with the same number of positions, and the output contains",
109 "the input positions selected from each expression in turn, i.e.,",
110 "the output is like A1 B1 A2 B2 and so on. It is also possible to merge",
111 "selections of unequal size as long as the size of the first is a",
112 "multiple of the second one. The [TT]stride[tt] parameter can be used",
113 "to explicitly provide this multiplicity.",
114 "[TT]plus[tt] simply concatenates the positions after each other, and",
115 "can work also with selections of different sizes.",
116 "These keywords are valid only at the selection level, not in any",
120 /** \internal Selection method data for the \p plus modifier. */
121 gmx_ana_selmethod_t sm_merge = {
122 "merge", POS_VALUE, SMETH_MODIFIER,
123 asize(smparams_merge), smparams_merge,
132 {"merge POSEXPR", asize(help_merge), help_merge},
135 /** \internal Selection method data for the \p plus modifier. */
136 gmx_ana_selmethod_t sm_plus = {
137 "plus", POS_VALUE, SMETH_MODIFIER,
138 asize(smparams_merge)-1, smparams_merge,
147 {"plus POSEXPR", asize(help_merge), help_merge},
151 * \param[in] npar Should be 2 for \c plus and 3 for \c merge.
152 * \param[in,out] param Method parameters (should point to a copy of
153 * \ref smparams_merge).
154 * \returns Pointer to the allocated data (\p t_methoddata_merge).
156 * Allocates memory for a \p t_methoddata_merge structure.
159 init_data_merge(int npar, gmx_ana_selparam_t *param)
161 t_methoddata_merge *data;
165 param[0].val.u.p = &data->p1;
166 param[1].val.u.p = &data->p2;
169 param[2].val.u.i = &data->stride;
175 * \param[in] top Not used.
176 * \param[in] npar Not used (should be 2 or 3).
177 * \param[in] param Method parameters (should point to \ref smparams_merge).
178 * \param[in] data Should point to a \p t_methoddata_merge.
179 * \returns 0 if everything is successful, -1 on error.
182 init_merge(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
184 t_methoddata_merge *d = (t_methoddata_merge *)data;
188 GMX_THROW(gmx::InvalidInputError("Stride for merging should be positive"));
190 /* If no stride given, deduce it from the input sizes */
193 d->stride = d->p1.nr / d->p2.nr;
195 if (d->p1.nr != d->stride*d->p2.nr)
197 GMX_THROW(gmx::InconsistentInputError("The number of positions to be merged are not compatible"));
202 * Does common initialization to all merging modifiers.
204 * \param[in] top Topology data structure.
205 * \param[in,out] out Pointer to output data structure.
206 * \param[in,out] data Should point to \c t_methoddata_merge.
209 init_output_common(t_topology *top, gmx_ana_selvalue_t *out, void *data)
211 t_methoddata_merge *d = (t_methoddata_merge *)data;
213 if (d->p1.m.type != d->p2.m.type)
215 /* TODO: Maybe we could pick something else here? */
216 out->u.p->m.type = INDEX_UNKNOWN;
220 out->u.p->m.type = d->p1.m.type;
222 gmx_ana_pos_reserve_for_append(out->u.p, d->p1.nr + d->p2.nr,
223 d->p1.m.b.nra + d->p2.m.b.nra,
224 d->p1.v != NULL, d->p1.f != NULL);
225 gmx_ana_pos_empty_init(out->u.p);
229 * \param[in] top Topology data structure.
230 * \param[in,out] out Pointer to output data structure.
231 * \param[in,out] data Should point to \c t_methoddata_merge.
234 init_output_merge(t_topology *top, gmx_ana_selvalue_t *out, void *data)
236 t_methoddata_merge *d = (t_methoddata_merge *)data;
239 init_output_common(top, out, data);
240 for (i = 0; i < d->p2.nr; ++i)
242 for (j = 0; j < d->stride; ++j)
244 gmx_ana_pos_append_init(out->u.p, &d->p1, d->stride * i + j);
246 gmx_ana_pos_append_init(out->u.p, &d->p2, i);
251 * \param[in] top Topology data structure.
252 * \param[in,out] out Pointer to output data structure.
253 * \param[in,out] data Should point to \c t_methoddata_merge.
256 init_output_plus(t_topology *top, gmx_ana_selvalue_t *out, void *data)
258 t_methoddata_merge *d = (t_methoddata_merge *)data;
261 init_output_common(top, out, data);
262 for (i = 0; i < d->p1.nr; ++i)
264 gmx_ana_pos_append_init(out->u.p, &d->p1, i);
266 for (i = 0; i < d->p2.nr; ++i)
268 gmx_ana_pos_append_init(out->u.p, &d->p2, i);
273 * \param data Data to free (should point to a \p t_methoddata_merge).
275 * Frees the memory allocated for \c t_methoddata_merge.
278 free_data_merge(void *data)
280 t_methoddata_merge *d = (t_methoddata_merge *)data;
286 * \param[in] top Not used.
287 * \param[in] fr Not used.
288 * \param[in] pbc Not used.
289 * \param[in] p Positions to merge (should point to \p data->p1).
290 * \param[out] out Output data structure (\p out->u.p is used).
291 * \param[in] data Should point to a \p t_methoddata_merge.
294 evaluate_merge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
295 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
297 t_methoddata_merge *d = (t_methoddata_merge *)data;
301 if (d->p1.nr != d->stride*d->p2.nr)
303 GMX_THROW(gmx::InconsistentInputError("The number of positions to be merged are not compatible"));
305 gmx_ana_pos_empty(out->u.p);
306 for (i = 0; i < d->p2.nr; ++i)
308 for (j = 0; j < d->stride; ++j)
310 refid = d->p1.m.refid[d->stride*i+j];
313 refid = (d->stride+1) * (refid / d->stride) + (refid % d->stride);
315 gmx_ana_pos_append(out->u.p, &d->p1, d->stride*i+j, refid);
317 refid = (d->stride+1)*d->p2.m.refid[i] + d->stride;
318 gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
320 gmx_ana_pos_append_finish(out->u.p);
324 * \param[in] top Not used.
325 * \param[in] fr Not used.
326 * \param[in] pbc Not used.
327 * \param[in] p Positions to merge (should point to \p data->p1).
328 * \param[out] out Output data structure (\p out->u.p is used).
329 * \param[in] data Should point to a \p t_methoddata_merge.
332 evaluate_plus(t_topology *top, t_trxframe *fr, t_pbc *pbc,
333 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
335 t_methoddata_merge *d = (t_methoddata_merge *)data;
339 gmx_ana_pos_empty(out->u.p);
340 for (i = 0; i < d->p1.nr; ++i)
342 refid = d->p1.m.refid[i];
343 gmx_ana_pos_append(out->u.p, &d->p1, i, refid);
345 for (i = 0; i < d->p2.nr; ++i)
347 refid = d->p2.m.refid[i];
350 refid += d->p1.m.b.nr;
352 gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
354 gmx_ana_pos_append_finish(out->u.p);