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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
66 #include "../legacyheaders/typedefs.h"
68 /** Stores a set of index groups. */
69 typedef struct gmx_ana_indexgrps_t gmx_ana_indexgrps_t;
72 * Specifies the type of index partition or index mapping in several contexts.
74 * \see gmx_ana_index_make_block(), gmx_ana_indexmap_init()
78 INDEX_UNKNOWN, /**< Unknown index type.*/
79 INDEX_ATOM, /**< Each atom in a separate block.*/
80 INDEX_RES, /**< Each residue in a separate block.*/
81 INDEX_MOL, /**< Each molecule in a separate block.*/
82 INDEX_ALL /**< All atoms in a single block.*/
86 * Stores a single index group.
88 typedef struct gmx_ana_index_t
90 /** Number of atoms. */
94 /** Number of items allocated for \p index. */
99 * Data structure for calculating index group mappings.
101 typedef struct gmx_ana_indexmap_t
103 /** Type of the mapping. */
106 * Current reference IDs.
108 * This array provides a mapping from the current index group (last given
109 * to gmx_ana_indexmap_update()) to the blocks in \p b, i.e., the
110 * original index group used in gmx_ana_indexmap_init().
111 * The mapping is zero-based.
112 * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), the indices
113 * for blocks not present in the current group are set to -1, otherwise
114 * they are removed completely and the \p nr field updated.
118 * Current mapped IDs.
120 * This array provides an arbitrary mapping from the current index group
121 * to the original index group. Instead of a zero-based mapping, the
122 * values from the \p orgid array are used. That is,
123 * \c mapid[i]=orgid[refid[i]].
124 * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this array
129 * Mapped block structure.
131 * A block structure that corresponds to the current index group.
132 * \c mapb.nra and \c mapb.a correspond to the last mapped index group.
137 * Arbitrary ID numbers for the blocks.
139 * This array has \p b.nr elements, each defining an ID number for a
141 * These are initialized in gmx_ana_indexmap_init() based on the type:
142 * - \ref INDEX_ATOM : the atom indices
143 * - \ref INDEX_RES : the residue numbers
144 * - \ref INDEX_MOL : the molecule numbers
146 * All the above numbers are zero-based.
147 * After gmx_ana_indexmap_init(), the user is free to change these values
148 * if the above are not appropriate.
149 * The mapped values can be read through \p mapid.
154 * Block data that defines the mapping (internal use only).
156 * The data is initialized by gmx_ana_indexmap_init() and is not changed
158 * Hence, it cannot be directly applied to the index group passed to
159 * gmx_ana_indexmap_update() unless \p bMaskOnly was specified or the
160 * index group is identical to the one provided to gmx_ana_indexmap_init().
164 * true if the current reference IDs are for the whole group (internal use only).
166 * This is used internally to optimize the evaluation such that
167 * gmx_ana_indexmap_update() does not take any time if the group is
171 } gmx_ana_indexmap_t;
174 /*! \name Functions for handling gmx_ana_indexgrps_t
177 /** Reads index groups from a file or constructs them from topology. */
179 gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
181 /** Frees memory allocated for index groups. */
183 gmx_ana_indexgrps_free(gmx_ana_indexgrps_t *g);
184 /** Returns true if the index group structure is emtpy. */
186 gmx_ana_indexgrps_is_empty(gmx_ana_indexgrps_t *g);
188 /** Returns a pointer to an index group. */
190 gmx_ana_indexgrps_get_grp(gmx_ana_indexgrps_t *g, int n);
191 /** Extracts a single index group. */
193 gmx_ana_indexgrps_extract(gmx_ana_index_t *dest, std::string *destName,
194 gmx_ana_indexgrps_t *src, int n);
195 /** Finds and extracts a single index group by name. */
197 gmx_ana_indexgrps_find(gmx_ana_index_t *dest, std::string *destName,
198 gmx_ana_indexgrps_t *src, const char *name);
200 /** Writes out a list of index groups. */
202 gmx_ana_indexgrps_print(FILE *fp, gmx_ana_indexgrps_t *g, int maxn);
205 /*! \name Functions for handling gmx_ana_index_t
208 /** Reserves memory to store an index group of size \p isize. */
210 gmx_ana_index_reserve(gmx_ana_index_t *g, int isize);
211 /** Frees any memory not necessary to hold the current contents. */
213 gmx_ana_index_squeeze(gmx_ana_index_t *g);
214 /** Initializes an empty index group. */
216 gmx_ana_index_clear(gmx_ana_index_t *g);
217 /** Constructs a \c gmx_ana_index_t from given values. */
219 gmx_ana_index_set(gmx_ana_index_t *g, int isize, atom_id *index, int nalloc);
220 /** Creates a simple index group from the first to the \p natoms'th atom. */
222 gmx_ana_index_init_simple(gmx_ana_index_t *g, int natoms);
223 /** Frees memory allocated for an index group. */
225 gmx_ana_index_deinit(gmx_ana_index_t *g);
226 /** Copies a \c gmx_ana_index_t. */
228 gmx_ana_index_copy(gmx_ana_index_t *dest, gmx_ana_index_t *src, bool bAlloc);
230 /** Writes out the contents of a index group. */
232 gmx_ana_index_dump(FILE *fp, gmx_ana_index_t *g, int maxn);
234 /** Checks whether an index group is sorted. */
236 gmx_ana_index_check_sorted(gmx_ana_index_t *g);
239 /*! \name Functions for set operations on gmx_ana_index_t
242 /** Sorts the indices within an index group. */
244 gmx_ana_index_sort(gmx_ana_index_t *g);
245 /** Checks whether two index groups are equal. */
247 gmx_ana_index_equals(gmx_ana_index_t *a, gmx_ana_index_t *b);
248 /** Checks whether a sorted index group contains another sorted index group. */
250 gmx_ana_index_contains(gmx_ana_index_t *a, gmx_ana_index_t *b);
252 /** Calculates the intersection between two sorted index groups. */
254 gmx_ana_index_intersection(gmx_ana_index_t *dest,
255 gmx_ana_index_t *a, gmx_ana_index_t *b);
256 /** Calculates the set difference between two sorted index groups. */
258 gmx_ana_index_difference(gmx_ana_index_t *dest,
259 gmx_ana_index_t *a, gmx_ana_index_t *b);
260 /** Calculates the size of the difference between two sorted index groups. */
262 gmx_ana_index_difference_size(gmx_ana_index_t *a, gmx_ana_index_t *b);
263 /** Calculates the union of two sorted index groups. */
265 gmx_ana_index_union(gmx_ana_index_t *dest,
266 gmx_ana_index_t *a, gmx_ana_index_t *b);
267 /** Merges two distinct sorted index groups. */
269 gmx_ana_index_merge(gmx_ana_index_t *dest,
270 gmx_ana_index_t *a, gmx_ana_index_t *b);
271 /** Calculates the intersection and the difference in one call. */
273 gmx_ana_index_partition(gmx_ana_index_t *dest1, gmx_ana_index_t *dest2,
274 gmx_ana_index_t *src, gmx_ana_index_t *g);
277 /*! \name Functions for handling gmx_ana_indexmap_t and related things
280 /** Partition a group based on topology information. */
282 gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
283 e_index_t type, bool bComplete);
284 /** Checks whether a group consists of full blocks. */
286 gmx_ana_index_has_full_blocks(gmx_ana_index_t *g, t_block *b);
287 /** Checks whether a group consists of full blocks. */
289 gmx_ana_index_has_full_ablocks(gmx_ana_index_t *g, t_blocka *b);
290 /** Checks whether a group consists of full residues/molecules. */
292 gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type, t_topology *top);
294 /** Initializes an empty index group mapping. */
296 gmx_ana_indexmap_clear(gmx_ana_indexmap_t *m);
297 /** Reserves memory for an index group mapping. */
299 gmx_ana_indexmap_reserve(gmx_ana_indexmap_t *m, int nr, int isize);
300 /** Initializes an index group mapping. */
302 gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
303 t_topology *top, e_index_t type);
304 /** Sets an index group mapping to be static. */
306 gmx_ana_indexmap_set_static(gmx_ana_indexmap_t *m, t_blocka *b);
307 /** Frees memory allocated for index group mapping. */
309 gmx_ana_indexmap_deinit(gmx_ana_indexmap_t *m);
310 /** Makes a deep copy of an index group mapping. */
312 gmx_ana_indexmap_copy(gmx_ana_indexmap_t *dest, gmx_ana_indexmap_t *src, bool bFirst);
313 /** Updates an index group mapping. */
315 gmx_ana_indexmap_update(gmx_ana_indexmap_t *m, gmx_ana_index_t *g, bool bMaskOnly);