include/indexutil.h

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  31 /*! \file
  32  * \brief API for handling index files and index groups.
  33  *
  34  * The API contains functions and data structures for handling index
  35  * files more conveniently than as several separate variables.
  36  * In addition to basic functions for initializing the data structures and
  37  * making copies, functions are provided for performing (most) set operations
  38  * on sorted index groups.
  39  * There is also a function for partitioning a index group based on
  40  * topology information such as residues or molecules.
  41  * Finally, there is a set of functions for constructing mappings between
  42  * an index group and its subgroups such.
  43  * These can be used with dynamic index group in calculations if one
  44  * needs to have a unique ID for each possible atom/residue/molecule in the
  45  * selection, e.g., for analysis of dynamics or for look-up tables.
  46  *
  47  * Mostly, these functions are used internally by the library and the
  48  * selection engine.
  49  * However, some of the checking functions can be useful in user code to
  50  * check the validity of input groups.
  51  * Also, the mapping functions are useful when dealing with dynamic index
  52  * groups.
  53  */
  54 #ifndef INDEXUTIL_H
  55 #define INDEXUTIL_H
  56
  57 #include <typedefs.h>
  58
  59 #ifdef __cplusplus
  60 extern "C"
  61 {
  62 #endif
  63
  64 /*! Stores a set of index groups.*/
  65 typedef struct gmx_ana_indexgrps_t gmx_ana_indexgrps_t;
  66
  67 /*! \brief
  68  * Specifies the type of index partition or index mapping in several contexts.
  69  *
  70  * \see gmx_ana_index_make_block(), gmx_ana_indexmap_init()
  71  */
  72 typedef enum
  73 {
  74     INDEX_UNKNOWN, /*!< Unknown index type.*/
  75     INDEX_ATOM,    /*!< Each atom in a separate block.*/
  76     INDEX_RES,     /*!< Each residue in a separate block.*/
  77     INDEX_MOL,     /*!< Each molecule in a separate block.*/
  78     INDEX_ALL,     /*!< All atoms in a single block.*/
  79 } e_index_t;
  80
  81 /*! \brief
  82  * Stores a single index group.
  83  */
  84 typedef struct gmx_ana_index_t
  85 {
  86     /*! Number of atoms.*/
  87     int                 isize;
  88     /*! List of atoms.*/
  89     atom_id            *index;
  90     /*! Group name.*/
  91     char               *name;
  92     /*! Number of items allocated for \p index.*/
  93     int                 nalloc_index;
  94 } gmx_ana_index_t;
  95
  96 /*! \brief
  97  * Data structure for calculating index group mappings.
  98  */
  99 typedef struct gmx_ana_indexmap_t
 100 {
 101     /*! Type of the mapping.*/
 102     e_index_t           type;
 103     /*! \brief
 104      * Current number of mapped values.
 105      *
 106      * This is the current number of values in the \p refid and \p mapid
 107      * arrays.
 108      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this
 109      * is always equal to \p b.nr, i.e., the number of blocks in the
 110      * original index group.
 111      */
 112     int                 nr;
 113     /*! \brief
 114      * Current reference IDs.
 115      *
 116      * This array provides a mapping from the current index group (last given
 117      * to gmx_ana_indexmap_update()) to the blocks in \p b, i.e., the
 118      * original index group used in gmx_ana_indexmap_init().
 119      * The mapping is zero-based.
 120      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), the indices
 121      * for blocks not present in the current group are set to -1, otherwise
 122      * they are removed completely and the \p nr field updated.
 123      */
 124     int                *refid;
 125     /*! \brief
 126      * Current mapped IDs.
 127      *
 128      * This array provides an arbitrary mapping from the current index group
 129      * to the original index group. Instead of a zero-based mapping, the
 130      * values from the \p orgid array are used. That is,
 131      * \c mapid[i]=orgid[refid[i]].
 132      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this array
 133      * equals \p orgid.
 134      */
 135     int                *mapid;
 136     /*! \brief
 137      * Mapped block structure.
 138      *
 139      * A block structure that corresponds to the current index group.
 140      */
 141     t_block             mapb;
 142
 143     /*! \brief
 144      * Arbitrary ID numbers for the blocks.
 145      *
 146      * This array has \p b.nr elements, each defining an ID number for a
 147      * block in \p b.
 148      * These are initialized in gmx_ana_indexmap_init() based on the type:
 149      *  - \ref INDEX_ATOM : the atom indices
 150      *  - \ref INDEX_RES :  the residue numbers
 151      *  - \ref INDEX_MOL :  the molecule numbers
 152      *
 153      * All the above numbers are zero-based.
 154      * After gmx_ana_indexmap_init(), the user is free to change these values
 155      * if the above are not appropriate.
 156      * The mapped values can be read through \p mapid.
 157      */
 158     int                *orgid;
 159
 160     /*! \brief
 161      * Block data that defines the mapping (internal use only).
 162      *
 163      * The data is initialized by gmx_ana_indexmap_init() and is not changed
 164      * after that.
 165      * Hence, it cannot be directly applied to the index group passed to
 166      * gmx_ana_indexmap_update() unless \p bMaskOnly was specified or the
 167      * index group is identical to the one provided to gmx_ana_indexmap_init().
 168      */
 169     t_blocka            b;
 170     /*! \brief
 171      * TRUE if the current reference IDs are for the whole group (internal use only).
 172      *
 173      * This is used internally to optimize the evaluation such that
 174      * gmx_ana_indexmap_update() does not take any time if the group is
 175      * actually static.
 176      */
 177     bool                bStatic;
 178     /*! \brief
 179      * TRUE if the current mapping is for the whole group (internal use only).
 180      *
 181      * This is used internally to optimize the evaluation such that
 182      * gmx_ana_indexmap_update() does not take any time if the group is
 183      * actually static.
 184      */
 185     bool                bMapStatic;
 186 } gmx_ana_indexmap_t;
 187
 188
 189 /*! \name Functions for handling gmx_ana_indexgrps_t
 190  */
 191 /*@{*/
 192 /*! Allocate memory for index groups.*/
 193 extern void
 194 gmx_ana_indexgrps_alloc(gmx_ana_indexgrps_t **g, int ngrps);
 195 /*! Initializes index groups from arrays.*/
 196 extern void
 197 gmx_ana_indexgrps_set(gmx_ana_indexgrps_t **g, int ngrps, int *isize,
 198                       atom_id **index, char **name, bool bFree);
 199 /*! Reads index groups from a file or constructs them from topology.*/
 200 extern void
 201 gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
 202                        const char *fnm);
 203 /*! Ask user to select index groups, possibly constructing groups from
 204     topology.*/
 205 extern void
 206 gmx_ana_indexgrps_get(gmx_ana_indexgrps_t **g, t_topology *top,
 207                       const char *fnm, int ngrps);
 208 /*! Ask user to select index groups from those specified in a file.*/
 209 extern void
 210 gmx_ana_indexgrps_rd(gmx_ana_indexgrps_t **g, const char *fnm, int ngrps);
 211 /*! Frees memory allocated for index groups.*/
 212 extern void
 213 gmx_ana_indexgrps_free(gmx_ana_indexgrps_t *g);
 214 /*! Create a deep copy of \c gmx_ana_indexgrps_t.*/
 215 extern void
 216 gmx_ana_indexgrps_clone(gmx_ana_indexgrps_t **dest, gmx_ana_indexgrps_t *src);
 217 /*! Returns TRUE if the index group structure is emtpy.*/
 218 extern bool
 219 gmx_ana_indexgrps_is_empty(gmx_ana_indexgrps_t *g);
 220
 221 /*! Returns a pointer to an index group.*/
 222 extern gmx_ana_index_t *
 223 gmx_ana_indexgrps_get_grp(gmx_ana_indexgrps_t *g, int n);
 224 /*! Extracts a single index group.*/
 225 extern bool
 226 gmx_ana_indexgrps_extract(gmx_ana_index_t *dest, gmx_ana_indexgrps_t *src, int n);
 227 /*! Finds and extracts a single index group by name.*/
 228 extern bool
 229 gmx_ana_indexgrps_find(gmx_ana_index_t *dest, gmx_ana_indexgrps_t *src, char *name);
 230
 231 /*! Writes out the contents of index groups.*/
 232 extern void
 233 gmx_ana_indexgrps_dump(gmx_ana_indexgrps_t *g);
 234 /*@}*/
 235
 236 /*! \name Functions for handling gmx_ana_index_t
 237  */
 238 /*@{*/
 239 /*! Reserves memory to store an index group of size \p isize.*/
 240 extern void
 241 gmx_ana_index_reserve(gmx_ana_index_t *g, int isize);
 242 /*! Frees any memory not necessary to hold the current contents.*/
 243 extern void
 244 gmx_ana_index_squeeze(gmx_ana_index_t *g);
 245 /*! Initializes an empty index group.*/
 246 extern void
 247 gmx_ana_index_clear(gmx_ana_index_t *g);
 248 /*! Constructs a \c gmx_ana_index_t from given values.*/
 249 extern void
 250 gmx_ana_index_set(gmx_ana_index_t *g, int isize, atom_id *index, char *name,
 251                   int nalloc);
 252 /*! Creates a simple index group from the first to the \p natoms'th atom.*/
 253 extern void
 254 gmx_ana_index_init_simple(gmx_ana_index_t *g, int natoms, char *name);
 255 /*! Frees memory allocated for an index group.*/
 256 extern void
 257 gmx_ana_index_deinit(gmx_ana_index_t *g);
 258 /*! Copies a \c gmx_ana_index_t.*/
 259 extern void
 260 gmx_ana_index_copy(gmx_ana_index_t *dest, gmx_ana_index_t *src, bool bAlloc);
 261
 262 /*! Writes out the contents of a index group.*/
 263 extern void
 264 gmx_ana_index_dump(gmx_ana_index_t *g, int i);
 265
 266 /*! Checks whether all indices are between 0 and \p natoms.*/
 267 extern void
 268 gmx_ana_index_check(gmx_ana_index_t *g, int natoms);
 269 /*! Checks whether an index group is sorted.*/
 270 extern bool
 271 gmx_ana_index_check_sorted(gmx_ana_index_t *g);
 272 /*@}*/
 273
 274 /*! \name Functions for set operations on gmx_ana_index_t
 275  */
 276 /*@{*/
 277 /*! Sorts the indices within an index group.*/
 278 extern void
 279 gmx_ana_index_sort(gmx_ana_index_t *g);
 280 /*! Checks whether two index groups are equal.*/
 281 extern bool
 282 gmx_ana_index_equals(gmx_ana_index_t *a, gmx_ana_index_t *b);
 283 /*! Checks whether a sorted index group contains another sorted index group.*/
 284 extern bool
 285 gmx_ana_index_contains(gmx_ana_index_t *a, gmx_ana_index_t *b);
 286
 287 /*! Calculates the intersection between two sorted index groups.*/
 288 extern void
 289 gmx_ana_index_intersection(gmx_ana_index_t *dest,
 290                            gmx_ana_index_t *a, gmx_ana_index_t *b);
 291 /*! Calculates the set difference between two sorted index groups.*/
 292 extern void
 293 gmx_ana_index_difference(gmx_ana_index_t *dest,
 294                          gmx_ana_index_t *a, gmx_ana_index_t *b);
 295 /*! Calculates the size of the difference between two sorted index groups.*/
 296 extern int
 297 gmx_ana_index_difference_size(gmx_ana_index_t *a, gmx_ana_index_t *b);
 298 /*! Calculates the union of two sorted index groups.*/
 299 extern void
 300 gmx_ana_index_union(gmx_ana_index_t *dest,
 301                     gmx_ana_index_t *a, gmx_ana_index_t *b);
 302 /*! Merges two distinct sorted index groups.*/
 303 extern void
 304 gmx_ana_index_merge(gmx_ana_index_t *dest,
 305                     gmx_ana_index_t *a, gmx_ana_index_t *b);
 306 /*! Calculates the intersection and the difference in one call.*/
 307 extern void
 308 gmx_ana_index_partition(gmx_ana_index_t *dest1, gmx_ana_index_t *dest2,
 309                         gmx_ana_index_t *src, gmx_ana_index_t *g);
 310 /*@}*/
 311
 312 /*! \name Functions for handling gmx_ana_indexmap_t and related things
 313  */
 314 /*@{*/
 315 /*! Partition a group based on topology information.*/
 316 extern void
 317 gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
 318                          e_index_t type, bool bComplete);
 319 /*! Checks whether a group consists of full blocks.*/
 320 extern bool
 321 gmx_ana_index_has_full_blocks(gmx_ana_index_t *g, t_block *b);
 322 /*! Checks whether a group consists of full blocks.*/
 323 extern bool
 324 gmx_ana_index_has_full_ablocks(gmx_ana_index_t *g, t_blocka *b);
 325 /*! Checks whether a group consists of full residues/molecules.*/
 326 extern bool
 327 gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type, t_topology *top);
 328
 329 /*! Initializes an empty index group mapping.*/
 330 extern void
 331 gmx_ana_indexmap_clear(gmx_ana_indexmap_t *m);
 332 /*! Reserves memory for an index group mapping.*/
 333 extern void
 334 gmx_ana_indexmap_reserve(gmx_ana_indexmap_t *m, int nr, int isize);
 335 /*! Initialize index group mapping.*/
 336 extern void
 337 gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
 338                       t_topology *top, e_index_t type);
 339 /*! Frees memory allocated for index group mapping.*/
 340 extern void
 341 gmx_ana_indexmap_deinit(gmx_ana_indexmap_t *m);
 342 /*! Makes a deep copy of an index group mapping.*/
 343 extern void
 344 gmx_ana_indexmap_copy(gmx_ana_indexmap_t *dest, gmx_ana_indexmap_t *src, bool bFirst);
 345 /*! Updates an index group mapping.*/
 346 extern void
 347 gmx_ana_indexmap_update(gmx_ana_indexmap_t *m, gmx_ana_index_t *g, bool bMaskOnly);
 348 /*@}*/
 349
 350 #ifdef __cplusplus
 351 }
 352 #endif
 353
 354 #endif