src/gromacs/selection/indexutil.h

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  35 /*! \file
  36  * \brief API for handling index files and index groups.
  37  *
  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.
  50  *
  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.
  56  *
  57  * \author Teemu Murtola <teemu.murtola@gmail.com>
  58  * \inlibraryapi
  59  * \ingroup module_selection
  60  */
  61 #ifndef GMX_SELECTION_INDEXUTIL_H
  62 #define GMX_SELECTION_INDEXUTIL_H
  63
  64 #include <cstdio>
  65
  66 #include <string>
  67
  68 #include "gromacs/topology/block.h"
  69
  70 namespace gmx
  71 {
  72 class TextWriter;
  73 }
  74
  75 struct gmx_mtop_t;
  76
  77 /** Stores a set of index groups. */
  78 struct gmx_ana_indexgrps_t;
  79
  80 /*! \brief
  81  * Specifies the type of index partition or index mapping in several contexts.
  82  *
  83  * \see gmx_ana_index_make_block(), gmx_ana_indexmap_init()
  84  */
  85 typedef enum
  86 {
  87     INDEX_UNKNOWN, /**< Unknown index type.*/
  88     INDEX_ATOM,    /**< Each atom in a separate block.*/
  89     INDEX_RES,     /**< Each residue in a separate block.*/
  90     INDEX_MOL,     /**< Each molecule in a separate block.*/
  91     INDEX_ALL      /**< All atoms in a single block.*/
  92 } e_index_t;
  93
  94 /*! \brief
  95  * Stores a single index group.
  96  */
  97 struct gmx_ana_index_t
  98 {
  99     /** Number of atoms. */
 100     int                 isize;
 101     /** List of atoms. */
 102     int                *index;
 103     /** Number of items allocated for \p index. */
 104     int                 nalloc_index;
 105 };
 106
 107 /*! \brief
 108  * Data structure for calculating index group mappings.
 109  */
 110 struct gmx_ana_indexmap_t
 111 {
 112     /** Type of the mapping. */
 113     e_index_t           type;
 114     /*! \brief
 115      * Current reference IDs.
 116      *
 117      * This array provides a mapping from the current index group (last given
 118      * to gmx_ana_indexmap_update()) to the blocks in \p b, i.e., the
 119      * original index group used in gmx_ana_indexmap_init().
 120      * The mapping is zero-based.
 121      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), the indices
 122      * for blocks not present in the current group are set to -1, otherwise
 123      * they are removed completely and the \p nr field updated.
 124      */
 125     int                *refid;
 126     /*! \brief
 127      * Current mapped IDs.
 128      *
 129      * This array provides IDs for the current index group.  Instead of a
 130      * zero-based mapping that \p refid provides, the values from the \p orgid
 131      * array are used, thus allowing the mapping to be customized.
 132      * In other words, `mapid[i] = orgid[refid[i]]`.
 133      * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this array
 134      * equals \p orgid.
 135      */
 136     int                *mapid;
 137     /*! \brief
 138      * Mapped block structure.
 139      *
 140      * A block structure that corresponds to the current index group.
 141      * \c mapb.nra and \c mapb.a correspond to the last mapped index group.
 142      */
 143     t_blocka            mapb;
 144
 145     /*! \brief
 146      * Customizable ID numbers for the original blocks.
 147      *
 148      * This array has \p b.nr elements, each defining an original ID number for
 149      * a block in \p b (i.e., in the original group passed to
 150      * gmx_ana_indexmap_init()).
 151      * These are initialized in gmx_ana_indexmap_init() based on the type:
 152      *  - \ref INDEX_ATOM : the atom indices
 153      *  - \ref INDEX_RES :  the residue indices
 154      *  - \ref INDEX_MOL :  the molecule indices
 155      *
 156      * All the above numbers are zero-based.
 157      * After gmx_ana_indexmap_init(), the caller is free to change these values
 158      * if the above are not appropriate.
 159      * The mapped values can be read through \p mapid.
 160      */
 161     int                *orgid;
 162
 163     /*! \brief
 164      * Block data that defines the mapping (internal use only).
 165      *
 166      * The data is initialized by gmx_ana_indexmap_init() and is not changed
 167      * after that.
 168      * Hence, it cannot be directly applied to the index group passed to
 169      * gmx_ana_indexmap_update() unless \p bMaskOnly was specified or the
 170      * index group is identical to the one provided to gmx_ana_indexmap_init().
 171      */
 172     t_blocka            b;
 173     /*! \brief
 174      * true if the current reference IDs are for the whole group (internal use only).
 175      *
 176      * This is used internally to optimize the evaluation such that
 177      * gmx_ana_indexmap_update() does not take any time if the group is
 178      * actually static.
 179      */
 180     bool                bStatic;
 181 };
 182
 183
 184 /*! \name Functions for handling gmx_ana_indexgrps_t
 185  */
 186 /*@{*/
 187 /** Reads index groups from a file or constructs them from topology. */
 188 void
 189 gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, gmx_mtop_t *top,
 190                        const char *fnm);
 191 /** Frees memory allocated for index groups. */
 192 void
 193 gmx_ana_indexgrps_free(gmx_ana_indexgrps_t *g);
 194 /** Returns true if the index group structure is emtpy. */
 195 bool
 196 gmx_ana_indexgrps_is_empty(gmx_ana_indexgrps_t *g);
 197
 198 /** Returns a pointer to an index group. */
 199 gmx_ana_index_t *
 200 gmx_ana_indexgrps_get_grp(gmx_ana_indexgrps_t *g, int n);
 201 /** Extracts a single index group. */
 202 bool
 203 gmx_ana_indexgrps_extract(gmx_ana_index_t *dest, std::string *destName,
 204                           gmx_ana_indexgrps_t *src, int n);
 205 /** Finds and extracts a single index group by name. */
 206 bool
 207 gmx_ana_indexgrps_find(gmx_ana_index_t *dest, std::string *destName,
 208                        gmx_ana_indexgrps_t *src, const char *name);
 209
 210 /** Writes out a list of index groups. */
 211 void
 212 gmx_ana_indexgrps_print(gmx::TextWriter *writer, gmx_ana_indexgrps_t *g, int maxn);
 213 /*@}*/
 214
 215 /*! \name Functions for handling gmx_ana_index_t
 216  */
 217 /*@{*/
 218 /** Reserves memory to store an index group of size \p isize. */
 219 void
 220 gmx_ana_index_reserve(gmx_ana_index_t *g, int isize);
 221 /** Frees any memory not necessary to hold the current contents. */
 222 void
 223 gmx_ana_index_squeeze(gmx_ana_index_t *g);
 224 /** Initializes an empty index group. */
 225 void
 226 gmx_ana_index_clear(gmx_ana_index_t *g);
 227 /** Constructs a \c gmx_ana_index_t from given values. */
 228 void
 229 gmx_ana_index_set(gmx_ana_index_t *g, int isize, int *index, int nalloc);
 230 /** Creates a simple index group from the first to the \p natoms'th atom. */
 231 void
 232 gmx_ana_index_init_simple(gmx_ana_index_t *g, int natoms);
 233 /** Frees memory allocated for an index group. */
 234 void
 235 gmx_ana_index_deinit(gmx_ana_index_t *g);
 236 /** Copies a \c gmx_ana_index_t. */
 237 void
 238 gmx_ana_index_copy(gmx_ana_index_t *dest, gmx_ana_index_t *src, bool bAlloc);
 239
 240 /** Writes out the contents of a index group. */
 241 void
 242 gmx_ana_index_dump(gmx::TextWriter *writer, gmx_ana_index_t *g, int maxn);
 243
 244 /*! \brief
 245  * Returns maximum atom index that appears in an index group.
 246  *
 247  * \param[in]  g      Index group to query.
 248  * \returns    Largest atom index that appears in \p g, or zero if \p g is empty.
 249  */
 250 int
 251 gmx_ana_index_get_max_index(gmx_ana_index_t *g);
 252 /** Checks whether an index group is sorted. */
 253 bool
 254 gmx_ana_index_check_sorted(gmx_ana_index_t *g);
 255 /*! \brief
 256  * Checks whether an index group has atoms from a defined range.
 257  *
 258  * \param[in]  g      Index group to check.
 259  * \param[in]  natoms Largest atom number allowed.
 260  * \returns    true if all atoms in the index group are in the
 261  *     range 0 to \p natoms (i.e., no atoms over \p natoms are referenced).
 262  */
 263 bool
 264 gmx_ana_index_check_range(gmx_ana_index_t *g, int natoms);
 265 /*@}*/
 266
 267 /*! \name Functions for set operations on gmx_ana_index_t
 268  */
 269 /*@{*/
 270 /** Sorts the indices within an index group. */
 271 void
 272 gmx_ana_index_sort(gmx_ana_index_t *g);
 273 /*! \brief
 274  * Removes duplicates from a sorted index group.
 275  *
 276  * \param[in,out] g  Index group to be processed.
 277  */
 278 void
 279 gmx_ana_index_remove_duplicates(gmx_ana_index_t *g);
 280 /** Checks whether two index groups are equal. */
 281 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 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 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 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 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 void
 300 gmx_ana_index_union(gmx_ana_index_t *dest,
 301                     gmx_ana_index_t *a, gmx_ana_index_t *b);
 302 /*! \brief
 303  * Calculates the union of two index groups, where the second group may not be sorted.
 304  *
 305  * \param[out] dest Output index group (the union of \p a and \p b).
 306  * \param[in]  a    First index group (must be sorted).
 307  * \param[in]  b    Second index group.
 308  *
 309  * \p a and \p b can have common items.
 310  * \p dest can equal \p a or \p b.
 311  */
 312 void
 313 gmx_ana_index_union_unsorted(gmx_ana_index_t *dest,
 314                              gmx_ana_index_t *a, gmx_ana_index_t *b);
 315 /** Merges two distinct sorted index groups. */
 316 void
 317 gmx_ana_index_merge(gmx_ana_index_t *dest,
 318                     gmx_ana_index_t *a, gmx_ana_index_t *b);
 319 /** Calculates the intersection and the difference in one call. */
 320 void
 321 gmx_ana_index_partition(gmx_ana_index_t *dest1, gmx_ana_index_t *dest2,
 322                         gmx_ana_index_t *src, gmx_ana_index_t *g);
 323 /*@}*/
 324
 325 /*! \name Functions for handling gmx_ana_indexmap_t and related things
 326  */
 327 /*@{*/
 328 /** Partition a group based on topology information. */
 329 void
 330 gmx_ana_index_make_block(t_blocka *t, const gmx_mtop_t *top, gmx_ana_index_t *g,
 331                          e_index_t type, bool bComplete);
 332 /** Checks whether a group consists of full blocks. */
 333 bool
 334 gmx_ana_index_has_full_blocks(const gmx_ana_index_t *g, const t_block *b);
 335 /** Checks whether a group consists of full blocks. */
 336 bool
 337 gmx_ana_index_has_full_ablocks(gmx_ana_index_t *g, t_blocka *b);
 338 /** Checks whether a group consists of full residues/molecules. */
 339 bool
 340 gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type,
 341                                  const gmx_mtop_t *top);
 342
 343 /** Initializes an empty index group mapping. */
 344 void
 345 gmx_ana_indexmap_clear(gmx_ana_indexmap_t *m);
 346 /** Reserves memory for an index group mapping. */
 347 void
 348 gmx_ana_indexmap_reserve(gmx_ana_indexmap_t *m, int nr, int isize);
 349 /** Initializes an index group mapping. */
 350 void
 351 gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
 352                       const gmx_mtop_t *top, e_index_t type);
 353 /*! \brief
 354  * Initializes `orgid` entries based on topology grouping.
 355  *
 356  * \param[in,out] m     Mapping structure to use/initialize.
 357  * \param[in]     top   Topology structure
 358  *     (can be NULL if not required for \p type).
 359  * \param[in]     type  Type of groups to use.
 360  * \returns  The number of groups of type \p type that were present in \p m.
 361  * \throws   InconsistentInputError if the blocks in \p m do not have a unique
 362  *     group (e.g., contain atoms from multiple residues with `type == INDEX_RES`).
 363  *
 364  * By default, the gmx_ana_indexmap_t::orgid fields are initialized to
 365  * atom/residue/molecule indices from the topology (see documentation for the
 366  * struct for more details).
 367  * This function can be used to set the field to a zero-based group index
 368  * instead.  The first block will always get `orgid[0] = 0`, and all following
 369  * blocks that belong to the same residue/molecule (\p type) will get the same
 370  * index.  Each time a block does not belong to the same group, it will get the
 371  * next available number.
 372  * If `type == INDEX_ATOM`, the `orgid` field is initialized as 0, 1, ...,
 373  * independent of whether the blocks are single atoms or not.
 374  *
 375  * Strong exception safety guarantee.
 376  */
 377 int
 378 gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, const gmx_mtop_t *top,
 379                                   e_index_t type);
 380 /** Sets an index group mapping to be static. */
 381 void
 382 gmx_ana_indexmap_set_static(gmx_ana_indexmap_t *m, t_blocka *b);
 383 /** Frees memory allocated for index group mapping. */
 384 void
 385 gmx_ana_indexmap_deinit(gmx_ana_indexmap_t *m);
 386 /** Makes a deep copy of an index group mapping. */
 387 void
 388 gmx_ana_indexmap_copy(gmx_ana_indexmap_t *dest, gmx_ana_indexmap_t *src, bool bFirst);
 389 /** Updates an index group mapping. */
 390 void
 391 gmx_ana_indexmap_update(gmx_ana_indexmap_t *m, gmx_ana_index_t *g, bool bMaskOnly);
 392 /*@}*/
 393
 394 #endif