include/indexutil.h

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  38 /*! \file
  39  * \brief API for handling index files and index groups.
  40  *
  41  * The API contains functions and data structures for handling index
  42  * files more conveniently than as several separate variables.
  43  * In addition to basic functions for initializing the data structures and
  44  * making copies, functions are provided for performing (most) set operations
  45  * on sorted index groups.
  46  * There is also a function for partitioning a index group based on
  47  * topology information such as residues or molecules.
  48  * Finally, there is a set of functions for constructing mappings between
  49  * an index group and its subgroups such.
  50  * These can be used with dynamic index group in calculations if one
  51  * needs to have a unique ID for each possible atom/residue/molecule in the
  52  * selection, e.g., for analysis of dynamics or for look-up tables.
  53  *
  54  * Mostly, these functions are used internally by the library and the
  55  * selection engine.
  56  * However, some of the checking functions can be useful in user code to
  57  * check the validity of input groups.
  58  * Also, the mapping functions are useful when dealing with dynamic index
  59  * groups.
  60  */
  61 #ifndef INDEXUTIL_H
  62 #define INDEXUTIL_H
  63 #include "visibility.h"
  64 #include "typedefs.h"
  65
  66 #ifdef __cplusplus
  67 extern "C"
  68 {
  69 #endif
  70
  71 /** Stores a set of index groups. */
  72 typedef struct gmx_ana_indexgrps_t gmx_ana_indexgrps_t;
  73
  74 /*! \brief
  75  * Specifies the type of index partition or index mapping in several contexts.
  76  *
  77  * \see gmx_ana_index_make_block(), gmx_ana_indexmap_init()
  78  */
  79 typedef enum
  80 {
  81     INDEX_UNKNOWN, /**< Unknown index type.*/
  82     INDEX_ATOM,    /**< Each atom in a separate block.*/
  83     INDEX_RES,     /**< Each residue in a separate block.*/
  84     INDEX_MOL,     /**< Each molecule in a separate block.*/
  85     INDEX_ALL      /**< All atoms in a single block.*/
  86 } e_index_t;
  87
  88 /*! \brief
  89  * Stores a single index group.
  90  */
  91 typedef struct gmx_ana_index_t
  92 {
  93     /** Number of atoms. */
  94     int                 isize;
  95     /** List of atoms. */
  96     atom_id            *index;
  97     /** Group name. */
  98     char               *name;
  99     /** Number of items allocated for \p index. */
 100     int                 nalloc_index;
 101 } gmx_ana_index_t;
 102
 103 /*! \brief
 104  * Data structure for calculating index group mappings.
 105  */
 106 typedef struct gmx_ana_indexmap_t
 107 {
 108     /** Type of the mapping. */
 109     e_index_t           type;
 110     /*! \brief
 111      * Current number of mapped values.
 112      *
 113      * This is the current number of values in the \p refid and \p mapid
 114      * arrays.
 115      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this
 116      * is always equal to \p b.nr, i.e., the number of blocks in the
 117      * original index group.
 118      */
 119     int                 nr;
 120     /*! \brief
 121      * Current reference IDs.
 122      *
 123      * This array provides a mapping from the current index group (last given
 124      * to gmx_ana_indexmap_update()) to the blocks in \p b, i.e., the
 125      * original index group used in gmx_ana_indexmap_init().
 126      * The mapping is zero-based.
 127      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), the indices
 128      * for blocks not present in the current group are set to -1, otherwise
 129      * they are removed completely and the \p nr field updated.
 130      */
 131     int                *refid;
 132     /*! \brief
 133      * Current mapped IDs.
 134      *
 135      * This array provides an arbitrary mapping from the current index group
 136      * to the original index group. Instead of a zero-based mapping, the
 137      * values from the \p orgid array are used. That is,
 138      * \c mapid[i]=orgid[refid[i]].
 139      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this array
 140      * equals \p orgid.
 141      */
 142     int                *mapid;
 143     /*! \brief
 144      * Mapped block structure.
 145      *
 146      * A block structure that corresponds to the current index group.
 147      */
 148     t_block             mapb;
 149
 150     /*! \brief
 151      * Arbitrary ID numbers for the blocks.
 152      *
 153      * This array has \p b.nr elements, each defining an ID number for a
 154      * block in \p b.
 155      * These are initialized in gmx_ana_indexmap_init() based on the type:
 156      *  - \ref INDEX_ATOM : the atom indices
 157      *  - \ref INDEX_RES :  the residue numbers
 158      *  - \ref INDEX_MOL :  the molecule numbers
 159      *
 160      * All the above numbers are zero-based.
 161      * After gmx_ana_indexmap_init(), the user is free to change these values
 162      * if the above are not appropriate.
 163      * The mapped values can be read through \p mapid.
 164      */
 165     int                *orgid;
 166
 167     /*! \brief
 168      * Block data that defines the mapping (internal use only).
 169      *
 170      * The data is initialized by gmx_ana_indexmap_init() and is not changed
 171      * after that.
 172      * Hence, it cannot be directly applied to the index group passed to
 173      * gmx_ana_indexmap_update() unless \p bMaskOnly was specified or the
 174      * index group is identical to the one provided to gmx_ana_indexmap_init().
 175      */
 176     t_blocka            b;
 177     /*! \brief
 178      * TRUE if the current reference IDs are for the whole group (internal use only).
 179      *
 180      * This is used internally to optimize the evaluation such that
 181      * gmx_ana_indexmap_update() does not take any time if the group is
 182      * actually static.
 183      */
 184     gmx_bool                bStatic;
 185     /*! \brief
 186      * TRUE if the current mapping is for the whole group (internal use only).
 187      *
 188      * This is used internally to optimize the evaluation such that
 189      * gmx_ana_indexmap_update() does not take any time if the group is
 190      * actually static.
 191      */
 192     gmx_bool                bMapStatic;
 193 } gmx_ana_indexmap_t;
 194
 195
 196 /*! \name Functions for handling gmx_ana_indexgrps_t
 197  */
 198 /*@{*/
 199 /** Allocate memory for index groups. */
 200 void
 201 gmx_ana_indexgrps_alloc(gmx_ana_indexgrps_t **g, int ngrps);
 202 /** Initializes index groups from arrays. */
 203 void
 204 gmx_ana_indexgrps_set(gmx_ana_indexgrps_t **g, int ngrps, int *isize,
 205                       atom_id **index, char **name, gmx_bool bFree);
 206 /** Reads index groups from a file or constructs them from topology. */
 207 void
 208 gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
 209                        const char *fnm);
 210 /** Ask user to select index groups, possibly constructing groups from
 211  *  topology. */
 212 void
 213 gmx_ana_indexgrps_get(gmx_ana_indexgrps_t **g, t_topology *top,
 214                       const char *fnm, int ngrps);
 215 /** Ask user to select index groups from those specified in a file. */
 216 void
 217 gmx_ana_indexgrps_rd(gmx_ana_indexgrps_t **g, const char *fnm, int ngrps);
 218 /** Frees memory allocated for index groups. */
 219 void
 220 gmx_ana_indexgrps_free(gmx_ana_indexgrps_t *g);
 221 /** Create a deep copy of \c gmx_ana_indexgrps_t. */
 222 void
 223 gmx_ana_indexgrps_clone(gmx_ana_indexgrps_t **dest, gmx_ana_indexgrps_t *src);
 224 /** Returns TRUE if the index group structure is emtpy. */
 225 gmx_bool
 226 gmx_ana_indexgrps_is_empty(gmx_ana_indexgrps_t *g);
 227
 228 /** Returns a pointer to an index group. */
 229 gmx_ana_index_t *
 230 gmx_ana_indexgrps_get_grp(gmx_ana_indexgrps_t *g, int n);
 231 /** Extracts a single index group. */
 232 gmx_bool
 233 gmx_ana_indexgrps_extract(gmx_ana_index_t *dest, gmx_ana_indexgrps_t *src, int n);
 234 /** Finds and extracts a single index group by name. */
 235 gmx_bool
 236 gmx_ana_indexgrps_find(gmx_ana_index_t *dest, gmx_ana_indexgrps_t *src, char *name);
 237
 238 /** Writes out a list of index groups. */
 239 void
 240 gmx_ana_indexgrps_print(gmx_ana_indexgrps_t *g, int maxn);
 241 /*@}*/
 242
 243 /*! \name Functions for handling gmx_ana_index_t
 244  */
 245 /*@{*/
 246 /** Reserves memory to store an index group of size \p isize. */
 247 void
 248 gmx_ana_index_reserve(gmx_ana_index_t *g, int isize);
 249 /** Frees any memory not necessary to hold the current contents. */
 250 void
 251 gmx_ana_index_squeeze(gmx_ana_index_t *g);
 252 /** Initializes an empty index group. */
 253 void
 254 gmx_ana_index_clear(gmx_ana_index_t *g);
 255 /** Constructs a \c gmx_ana_index_t from given values. */
 256 void
 257 gmx_ana_index_set(gmx_ana_index_t *g, int isize, atom_id *index, char *name,
 258                   int nalloc);
 259 /** Creates a simple index group from the first to the \p natoms'th atom. */
 260 void
 261 gmx_ana_index_init_simple(gmx_ana_index_t *g, int natoms, char *name);
 262 /** Frees memory allocated for an index group. */
 263 void
 264 gmx_ana_index_deinit(gmx_ana_index_t *g);
 265 /** Copies a \c gmx_ana_index_t. */
 266 void
 267 gmx_ana_index_copy(gmx_ana_index_t *dest, gmx_ana_index_t *src, gmx_bool bAlloc);
 268
 269 /** Writes out the contents of a index group. */
 270 void
 271 gmx_ana_index_dump(gmx_ana_index_t *g, int i, int maxn);
 272
 273 /** Checks whether all indices are between 0 and \p natoms. */
 274 void
 275 gmx_ana_index_check(gmx_ana_index_t *g, int natoms);
 276 /** Checks whether an index group is sorted. */
 277 gmx_bool
 278 gmx_ana_index_check_sorted(gmx_ana_index_t *g);
 279 /*@}*/
 280
 281 /*! \name Functions for set operations on gmx_ana_index_t
 282  */
 283 /*@{*/
 284 /** Sorts the indices within an index group. */
 285 void
 286 gmx_ana_index_sort(gmx_ana_index_t *g);
 287 /** Checks whether two index groups are equal. */
 288 gmx_bool
 289 gmx_ana_index_equals(gmx_ana_index_t *a, gmx_ana_index_t *b);
 290 /** Checks whether a sorted index group contains another sorted index group. */
 291 gmx_bool
 292 gmx_ana_index_contains(gmx_ana_index_t *a, gmx_ana_index_t *b);
 293
 294 /** Calculates the intersection between two sorted index groups. */
 295 void
 296 gmx_ana_index_intersection(gmx_ana_index_t *dest,
 297                            gmx_ana_index_t *a, gmx_ana_index_t *b);
 298 /** Calculates the set difference between two sorted index groups. */
 299 void
 300 gmx_ana_index_difference(gmx_ana_index_t *dest,
 301                          gmx_ana_index_t *a, gmx_ana_index_t *b);
 302 /** Calculates the size of the difference between two sorted index groups. */
 303 int
 304 gmx_ana_index_difference_size(gmx_ana_index_t *a, gmx_ana_index_t *b);
 305 /** Calculates the union of two sorted index groups. */
 306 void
 307 gmx_ana_index_union(gmx_ana_index_t *dest,
 308                     gmx_ana_index_t *a, gmx_ana_index_t *b);
 309 /** Merges two distinct sorted index groups. */
 310 void
 311 gmx_ana_index_merge(gmx_ana_index_t *dest,
 312                     gmx_ana_index_t *a, gmx_ana_index_t *b);
 313 /** Calculates the intersection and the difference in one call. */
 314 void
 315 gmx_ana_index_partition(gmx_ana_index_t *dest1, gmx_ana_index_t *dest2,
 316                         gmx_ana_index_t *src, gmx_ana_index_t *g);
 317 /*@}*/
 318
 319 /*! \name Functions for handling gmx_ana_indexmap_t and related things
 320  */
 321 /*@{*/
 322 /** Partition a group based on topology information. */
 323 void
 324 gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
 325                          e_index_t type, gmx_bool bComplete);
 326 /** Checks whether a group consists of full blocks. */
 327 gmx_bool
 328 gmx_ana_index_has_full_blocks(gmx_ana_index_t *g, t_block *b);
 329 /** Checks whether a group consists of full blocks. */
 330 gmx_bool
 331 gmx_ana_index_has_full_ablocks(gmx_ana_index_t *g, t_blocka *b);
 332 /** Checks whether a group consists of full residues/molecules. */
 333 gmx_bool
 334 gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type, t_topology *top);
 335
 336 /** Initializes an empty index group mapping. */
 337 void
 338 gmx_ana_indexmap_clear(gmx_ana_indexmap_t *m);
 339 /** Reserves memory for an index group mapping. */
 340 void
 341 gmx_ana_indexmap_reserve(gmx_ana_indexmap_t *m, int nr, int isize);
 342 /** Initializes an index group mapping. */
 343 GMX_LIBGMX_EXPORT
 344 void
 345 gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
 346                       t_topology *top, e_index_t type);
 347 /** Sets an index group mapping to be static. */
 348 void
 349 gmx_ana_indexmap_set_static(gmx_ana_indexmap_t *m, t_blocka *b);
 350 /** Frees memory allocated for index group mapping. */
 351 void
 352 gmx_ana_indexmap_deinit(gmx_ana_indexmap_t *m);
 353 /** Makes a deep copy of an index group mapping. */
 354 void
 355 gmx_ana_indexmap_copy(gmx_ana_indexmap_t *dest, gmx_ana_indexmap_t *src, gmx_bool bFirst);
 356 /** Updates an index group mapping. */
 357 GMX_LIBGMX_EXPORT
 358 void
 359 gmx_ana_indexmap_update(gmx_ana_indexmap_t *m, gmx_ana_index_t *g, gmx_bool bMaskOnly);
 360 /*@}*/
 361
 362 #ifdef __cplusplus
 363 }
 364 #endif
 365
 366 #endif