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36 * \brief API for handling index files and index groups.
38 * The API contains functions and data structures for handling index
39 * files more conveniently than as several separate variables.
40 * In addition to basic functions for initializing the data structures and
41 * making copies, functions are provided for performing (most) set operations
42 * on sorted index groups.
43 * There is also a function for partitioning a index group based on
44 * topology information such as residues or molecules.
45 * Finally, there is a set of functions for constructing mappings between
46 * an index group and its subgroups such.
47 * These can be used with dynamic index group in calculations if one
48 * needs to have a unique ID for each possible atom/residue/molecule in the
49 * selection, e.g., for analysis of dynamics or for look-up tables.
51 * Mostly, these functions are used internally by the selection engine, but
52 * it is necessary to use some of these functions in order to provide external
53 * index groups to a gmx::SelectionCollection.
54 * Some of the checking functions can be useful outside the selection engine to
55 * check the validity of input groups.
57 * \author Teemu Murtola <teemu.murtola@gmail.com>
59 * \ingroup module_selection
61 #ifndef GMX_SELECTION_INDEXUTIL_H
62 #define GMX_SELECTION_INDEXUTIL_H
68 #include "gromacs/legacyheaders/types/simple.h"
69 #include "gromacs/topology/block.h"
73 /** Stores a set of index groups. */
74 struct gmx_ana_indexgrps_t;
77 * Specifies the type of index partition or index mapping in several contexts.
79 * \see gmx_ana_index_make_block(), gmx_ana_indexmap_init()
83 INDEX_UNKNOWN, /**< Unknown index type.*/
84 INDEX_ATOM, /**< Each atom in a separate block.*/
85 INDEX_RES, /**< Each residue in a separate block.*/
86 INDEX_MOL, /**< Each molecule in a separate block.*/
87 INDEX_ALL /**< All atoms in a single block.*/
91 * Stores a single index group.
93 struct gmx_ana_index_t
95 /** Number of atoms. */
99 /** Number of items allocated for \p index. */
104 * Data structure for calculating index group mappings.
106 struct gmx_ana_indexmap_t
108 /** Type of the mapping. */
111 * Current reference IDs.
113 * This array provides a mapping from the current index group (last given
114 * to gmx_ana_indexmap_update()) to the blocks in \p b, i.e., the
115 * original index group used in gmx_ana_indexmap_init().
116 * The mapping is zero-based.
117 * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), the indices
118 * for blocks not present in the current group are set to -1, otherwise
119 * they are removed completely and the \p nr field updated.
123 * Current mapped IDs.
125 * This array provides IDs for the current index group. Instead of a
126 * zero-based mapping that \p refid provides, the values from the \p orgid
127 * array are used, thus allowing the mapping to be customized.
128 * In other words, `mapid[i] = orgid[refid[i]]`.
129 * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this array
134 * Mapped block structure.
136 * A block structure that corresponds to the current index group.
137 * \c mapb.nra and \c mapb.a correspond to the last mapped index group.
142 * Customizable ID numbers for the original blocks.
144 * This array has \p b.nr elements, each defining an original ID number for
145 * a block in \p b (i.e., in the original group passed to
146 * gmx_ana_indexmap_init()).
147 * These are initialized in gmx_ana_indexmap_init() based on the type:
148 * - \ref INDEX_ATOM : the atom indices
149 * - \ref INDEX_RES : the residue indices
150 * - \ref INDEX_MOL : the molecule indices
152 * All the above numbers are zero-based.
153 * After gmx_ana_indexmap_init(), the caller is free to change these values
154 * if the above are not appropriate.
155 * The mapped values can be read through \p mapid.
160 * Block data that defines the mapping (internal use only).
162 * The data is initialized by gmx_ana_indexmap_init() and is not changed
164 * Hence, it cannot be directly applied to the index group passed to
165 * gmx_ana_indexmap_update() unless \p bMaskOnly was specified or the
166 * index group is identical to the one provided to gmx_ana_indexmap_init().
170 * true if the current reference IDs are for the whole group (internal use only).
172 * This is used internally to optimize the evaluation such that
173 * gmx_ana_indexmap_update() does not take any time if the group is
180 /*! \name Functions for handling gmx_ana_indexgrps_t
183 /** Reads index groups from a file or constructs them from topology. */
185 gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
187 /** Frees memory allocated for index groups. */
189 gmx_ana_indexgrps_free(gmx_ana_indexgrps_t *g);
190 /** Returns true if the index group structure is emtpy. */
192 gmx_ana_indexgrps_is_empty(gmx_ana_indexgrps_t *g);
194 /** Returns a pointer to an index group. */
196 gmx_ana_indexgrps_get_grp(gmx_ana_indexgrps_t *g, int n);
197 /** Extracts a single index group. */
199 gmx_ana_indexgrps_extract(gmx_ana_index_t *dest, std::string *destName,
200 gmx_ana_indexgrps_t *src, int n);
201 /** Finds and extracts a single index group by name. */
203 gmx_ana_indexgrps_find(gmx_ana_index_t *dest, std::string *destName,
204 gmx_ana_indexgrps_t *src, const char *name);
206 /** Writes out a list of index groups. */
208 gmx_ana_indexgrps_print(FILE *fp, gmx_ana_indexgrps_t *g, int maxn);
211 /*! \name Functions for handling gmx_ana_index_t
214 /** Reserves memory to store an index group of size \p isize. */
216 gmx_ana_index_reserve(gmx_ana_index_t *g, int isize);
217 /** Frees any memory not necessary to hold the current contents. */
219 gmx_ana_index_squeeze(gmx_ana_index_t *g);
220 /** Initializes an empty index group. */
222 gmx_ana_index_clear(gmx_ana_index_t *g);
223 /** Constructs a \c gmx_ana_index_t from given values. */
225 gmx_ana_index_set(gmx_ana_index_t *g, int isize, atom_id *index, int nalloc);
226 /** Creates a simple index group from the first to the \p natoms'th atom. */
228 gmx_ana_index_init_simple(gmx_ana_index_t *g, int natoms);
229 /** Frees memory allocated for an index group. */
231 gmx_ana_index_deinit(gmx_ana_index_t *g);
232 /** Copies a \c gmx_ana_index_t. */
234 gmx_ana_index_copy(gmx_ana_index_t *dest, gmx_ana_index_t *src, bool bAlloc);
236 /** Writes out the contents of a index group. */
238 gmx_ana_index_dump(FILE *fp, gmx_ana_index_t *g, int maxn);
241 * Returns maximum atom index that appears in an index group.
243 * \param[in] g Index group to query.
244 * \returns Largest atom index that appears in \p g, or zero if \p g is empty.
247 gmx_ana_index_get_max_index(gmx_ana_index_t *g);
248 /** Checks whether an index group is sorted. */
250 gmx_ana_index_check_sorted(gmx_ana_index_t *g);
252 * Checks whether an index group has atoms from a defined range.
254 * \param[in] g Index group to check.
255 * \param[in] natoms Largest atom number allowed.
256 * \returns true if all atoms in the index group are in the
257 * range 0 to \p natoms (i.e., no atoms over \p natoms are referenced).
260 gmx_ana_index_check_range(gmx_ana_index_t *g, int natoms);
263 /*! \name Functions for set operations on gmx_ana_index_t
266 /** Sorts the indices within an index group. */
268 gmx_ana_index_sort(gmx_ana_index_t *g);
269 /** Checks whether two index groups are equal. */
271 gmx_ana_index_equals(gmx_ana_index_t *a, gmx_ana_index_t *b);
272 /** Checks whether a sorted index group contains another sorted index group. */
274 gmx_ana_index_contains(gmx_ana_index_t *a, gmx_ana_index_t *b);
276 /** Calculates the intersection between two sorted index groups. */
278 gmx_ana_index_intersection(gmx_ana_index_t *dest,
279 gmx_ana_index_t *a, gmx_ana_index_t *b);
280 /** Calculates the set difference between two sorted index groups. */
282 gmx_ana_index_difference(gmx_ana_index_t *dest,
283 gmx_ana_index_t *a, gmx_ana_index_t *b);
284 /** Calculates the size of the difference between two sorted index groups. */
286 gmx_ana_index_difference_size(gmx_ana_index_t *a, gmx_ana_index_t *b);
287 /** Calculates the union of two sorted index groups. */
289 gmx_ana_index_union(gmx_ana_index_t *dest,
290 gmx_ana_index_t *a, gmx_ana_index_t *b);
291 /** Merges two distinct sorted index groups. */
293 gmx_ana_index_merge(gmx_ana_index_t *dest,
294 gmx_ana_index_t *a, gmx_ana_index_t *b);
295 /** Calculates the intersection and the difference in one call. */
297 gmx_ana_index_partition(gmx_ana_index_t *dest1, gmx_ana_index_t *dest2,
298 gmx_ana_index_t *src, gmx_ana_index_t *g);
301 /*! \name Functions for handling gmx_ana_indexmap_t and related things
304 /** Partition a group based on topology information. */
306 gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
307 e_index_t type, bool bComplete);
308 /** Checks whether a group consists of full blocks. */
310 gmx_ana_index_has_full_blocks(gmx_ana_index_t *g, t_block *b);
311 /** Checks whether a group consists of full blocks. */
313 gmx_ana_index_has_full_ablocks(gmx_ana_index_t *g, t_blocka *b);
314 /** Checks whether a group consists of full residues/molecules. */
316 gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type, t_topology *top);
318 /** Initializes an empty index group mapping. */
320 gmx_ana_indexmap_clear(gmx_ana_indexmap_t *m);
321 /** Reserves memory for an index group mapping. */
323 gmx_ana_indexmap_reserve(gmx_ana_indexmap_t *m, int nr, int isize);
324 /** Initializes an index group mapping. */
326 gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
327 t_topology *top, e_index_t type);
329 * Initializes `orgid` entries based on topology grouping.
331 * \param[in,out] m Mapping structure to use/initialize.
332 * \param[in] top Topology structure
333 * (can be NULL if not required for \p type).
334 * \param[in] type Type of groups to use.
335 * \returns The number of groups of type \p type that were present in \p m.
336 * \throws InconsistentInputError if the blocks in \p m do not have a unique
337 * group (e.g., contain atoms from multiple residues with `type == INDEX_RES`).
339 * By default, the gmx_ana_indexmap_t::orgid fields are initialized to
340 * atom/residue/molecule indices from the topology (see documentation for the
341 * struct for more details).
342 * This function can be used to set the field to a zero-based group index
343 * instead. The first block will always get `orgid[0] = 0`, and all following
344 * blocks that belong to the same residue/molecule (\p type) will get the same
345 * index. Each time a block does not belong to the same group, it will get the
346 * next available number.
347 * If `type == INDEX_ATOM`, the `orgid` field is initialized as 0, 1, ...,
348 * independent of whether the blocks are single atoms or not.
350 * Strong exception safety guarantee.
353 gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, t_topology *top,
355 /** Sets an index group mapping to be static. */
357 gmx_ana_indexmap_set_static(gmx_ana_indexmap_t *m, t_blocka *b);
358 /** Frees memory allocated for index group mapping. */
360 gmx_ana_indexmap_deinit(gmx_ana_indexmap_t *m);
361 /** Makes a deep copy of an index group mapping. */
363 gmx_ana_indexmap_copy(gmx_ana_indexmap_t *dest, gmx_ana_indexmap_t *src, bool bFirst);
364 /** Updates an index group mapping. */
366 gmx_ana_indexmap_update(gmx_ana_indexmap_t *m, gmx_ana_index_t *g, bool bMaskOnly);