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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 = new t_methoddata_merge();
163 param[0].val.u.p = &data->p1;
164 param[1].val.u.p = &data->p2;
167 param[2].val.u.i = &data->stride;
173 * \param[in] top Not used.
174 * \param[in] npar Not used (should be 2 or 3).
175 * \param[in] param Method parameters (should point to \ref smparams_merge).
176 * \param[in] data Should point to a \p t_methoddata_merge.
177 * \returns 0 if everything is successful, -1 on error.
180 init_merge(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
182 t_methoddata_merge *d = (t_methoddata_merge *)data;
186 GMX_THROW(gmx::InvalidInputError("Stride for merging should be positive"));
188 /* If no stride given, deduce it from the input sizes */
191 d->stride = d->p1.count() / d->p2.count();
193 if (d->p1.count() != d->stride*d->p2.count())
195 GMX_THROW(gmx::InconsistentInputError("The number of positions to be merged are not compatible"));
200 * Does common initialization to all merging modifiers.
202 * \param[in] top Topology data structure.
203 * \param[in,out] out Pointer to output data structure.
204 * \param[in,out] data Should point to \c t_methoddata_merge.
207 init_output_common(t_topology *top, gmx_ana_selvalue_t *out, void *data)
209 t_methoddata_merge *d = (t_methoddata_merge *)data;
211 if (d->p1.m.type != d->p2.m.type)
213 /* TODO: Maybe we could pick something else here? */
214 out->u.p->m.type = INDEX_UNKNOWN;
218 out->u.p->m.type = d->p1.m.type;
220 gmx_ana_pos_reserve_for_append(out->u.p, d->p1.count() + d->p2.count(),
221 d->p1.m.b.nra + d->p2.m.b.nra,
222 d->p1.v != NULL, d->p1.f != NULL);
223 gmx_ana_pos_empty_init(out->u.p);
227 * \param[in] top Topology data structure.
228 * \param[in,out] out Pointer to output data structure.
229 * \param[in,out] data Should point to \c t_methoddata_merge.
232 init_output_merge(t_topology *top, gmx_ana_selvalue_t *out, void *data)
234 t_methoddata_merge *d = (t_methoddata_merge *)data;
237 init_output_common(top, out, data);
238 for (i = 0; i < d->p2.count(); ++i)
240 for (j = 0; j < d->stride; ++j)
242 gmx_ana_pos_append_init(out->u.p, &d->p1, d->stride * i + j);
244 gmx_ana_pos_append_init(out->u.p, &d->p2, i);
249 * \param[in] top Topology data structure.
250 * \param[in,out] out Pointer to output data structure.
251 * \param[in,out] data Should point to \c t_methoddata_merge.
254 init_output_plus(t_topology *top, gmx_ana_selvalue_t *out, void *data)
256 t_methoddata_merge *d = (t_methoddata_merge *)data;
259 init_output_common(top, out, data);
260 for (i = 0; i < d->p1.count(); ++i)
262 gmx_ana_pos_append_init(out->u.p, &d->p1, i);
264 for (i = 0; i < d->p2.count(); ++i)
266 gmx_ana_pos_append_init(out->u.p, &d->p2, i);
271 * \param data Data to free (should point to a \p t_methoddata_merge).
273 * Frees the memory allocated for \c t_methoddata_merge.
276 free_data_merge(void *data)
278 t_methoddata_merge *d = (t_methoddata_merge *)data;
283 * \param[in] top Not used.
284 * \param[in] fr Not used.
285 * \param[in] pbc Not used.
286 * \param[in] p Positions to merge (should point to \p data->p1).
287 * \param[out] out Output data structure (\p out->u.p is used).
288 * \param[in] data Should point to a \p t_methoddata_merge.
291 evaluate_merge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
292 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
294 t_methoddata_merge *d = (t_methoddata_merge *)data;
298 if (d->p1.count() != d->stride*d->p2.count())
300 GMX_THROW(gmx::InconsistentInputError("The number of positions to be merged are not compatible"));
302 gmx_ana_pos_empty(out->u.p);
303 for (i = 0; i < d->p2.count(); ++i)
305 for (j = 0; j < d->stride; ++j)
307 refid = d->p1.m.refid[d->stride*i+j];
310 refid = (d->stride+1) * (refid / d->stride) + (refid % d->stride);
312 gmx_ana_pos_append(out->u.p, &d->p1, d->stride*i+j, refid);
314 refid = (d->stride+1)*d->p2.m.refid[i] + d->stride;
315 gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
317 gmx_ana_pos_append_finish(out->u.p);
321 * \param[in] top Not used.
322 * \param[in] fr Not used.
323 * \param[in] pbc Not used.
324 * \param[in] p Positions to merge (should point to \p data->p1).
325 * \param[out] out Output data structure (\p out->u.p is used).
326 * \param[in] data Should point to a \p t_methoddata_merge.
329 evaluate_plus(t_topology *top, t_trxframe *fr, t_pbc *pbc,
330 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
332 t_methoddata_merge *d = (t_methoddata_merge *)data;
336 gmx_ana_pos_empty(out->u.p);
337 for (i = 0; i < d->p1.count(); ++i)
339 refid = d->p1.m.refid[i];
340 gmx_ana_pos_append(out->u.p, &d->p1, i, refid);
342 for (i = 0; i < d->p2.count(); ++i)
344 refid = d->p2.m.refid[i];
347 refid += d->p1.m.b.nr;
349 gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
351 gmx_ana_pos_append_finish(out->u.p);