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36 * \brief API for neighborhood searching for analysis.
38 * The main part of the API is the class gmx::AnalysisNeighborhood.
39 * See the class documentation for usage.
41 * The classes within this file can be used independently of the other parts
43 * The library also uses the classes internally.
45 * \author Teemu Murtola <teemu.murtola@gmail.com>
47 * \ingroup module_selection
49 #ifndef GMX_SELECTION_NBSEARCH_H
50 #define GMX_SELECTION_NBSEARCH_H
52 #include <boost/shared_ptr.hpp>
54 #include "../legacyheaders/typedefs.h"
55 #include "../utility/common.h"
56 #include "../utility/gmxassert.h"
58 #include "indexutil.h"
67 class AnalysisNeighborhoodSearchImpl;
68 class AnalysisNeighborhoodPairSearchImpl;
71 class AnalysisNeighborhoodSearch;
72 class AnalysisNeighborhoodPairSearch;
75 * Input positions for neighborhood searching.
77 * This class supports uniformly specifying sets of positions for various
78 * methods in the analysis neighborhood searching classes
79 * (AnalysisNeighborhood and AnalysisNeighborhoodSearch).
81 * Note that copies are not made: only a reference to the positions passed to
82 * the constructors are kept. The caller is responsible to ensure that those
83 * positions remain in scope as long as the neighborhood search object requires
86 * Also note that in addition to constructors here, Selection and
87 * SelectionPosition provide conversions operators to this type. It is done
88 * this way to not introduce a cyclic dependency between the selection code and
89 * the neighborhood search code, which in turn allows splitting this search
90 * code into a separate lower-level module if desired at some point.
92 * Methods in this class do not throw.
95 * \ingroup module_selection
97 class AnalysisNeighborhoodPositions
101 * Initializes positions from a single position vector.
103 * For positions initialized this way, AnalysisNeighborhoodPair always
104 * returns zero in the corresponding index.
106 * This constructor is not explicit to allow directly passing an rvec
107 * to methods that accept positions.
109 AnalysisNeighborhoodPositions(const rvec &x)
110 : count_(1), index_(-1), x_(&x)
114 * Initializes positions from an array of position vectors.
116 AnalysisNeighborhoodPositions(const rvec x[], int count)
117 : count_(count), index_(-1), x_(x)
122 * Selects a single position to use from an array.
124 * If called, a single position from the array of positions passed to
125 * the constructor is used instead of the whole array.
126 * In contrast to the AnalysisNeighborhoodPositions(const rvec &)
127 * constructor, AnalysisNeighborhoodPair objects return \p index
130 AnalysisNeighborhoodPositions &selectSingleFromArray(int index)
132 GMX_ASSERT(index >= 0 && index < count_, "Invalid position index");
142 //! To access the positions for initialization.
143 friend class internal::AnalysisNeighborhoodSearchImpl;
144 //! To access the positions for initialization.
145 friend class internal::AnalysisNeighborhoodPairSearchImpl;
149 * Neighborhood searching for analysis tools.
151 * This class implements neighborhood searching routines for analysis tools.
152 * The emphasis is in flexibility and ease of use; one main driver is to have
153 * a common implementation of grid-based searching to avoid replicating this in
154 * multiple tools (and to make more tools take advantage of the significant
155 * performance improvement this allows).
157 * To use the search, create an object of this type, call setCutoff() to
158 * initialize it, and then repeatedly call initSearch() to start a search with
159 * different sets of reference positions. For each set of reference positions,
160 * use methods in the returned AnalysisNeighborhoodSearch to find the reference
161 * positions that are within the given cutoff from a provided position.
163 * initSearch() is thread-safe and can be called from multiple threads. Each
164 * call returns a different instance of the search object that can be used
165 * independently of the others. The returned AnalysisNeighborhoodSearch
166 * objects are also thread-safe, and can be used concurrently from multiple
167 * threads. It is also possible to create multiple concurrent searches within
171 * Support for exclusions.
172 * The 4.5/4.6 C API had very low-level support for exclusions, which was not
173 * very convenient to use, and hadn't been tested much. The internal code that
174 * it used to do the exclusion during the search itself is still there, but it
175 * needs more thought on what would be a convenient way to initialize it.
176 * Can be implemented once there is need for it in some calling code.
179 * \ingroup module_selection
181 class AnalysisNeighborhood
184 //! Searching algorithm to use.
187 //! Select algorithm based on heuristic efficiency considerations.
188 eSearchMode_Automatic,
189 //! Use a simple loop over all pairs.
191 //! Use grid-based searching whenever possible.
195 //! Creates an uninitialized neighborhood search.
196 AnalysisNeighborhood();
197 ~AnalysisNeighborhood();
200 * Set cutoff distance for the neighborhood searching.
202 * \param[in] cutoff Cutoff distance for the search
203 * (<=0 stands for no cutoff).
205 * Currently, can only be called before the first call to initSearch().
206 * If this method is not called, no cutoff is used in the searches.
210 void setCutoff(real cutoff);
212 * Sets the algorithm to use for searching.
214 * \param[in] mode Search mode to use.
216 * Note that if \p mode is \ref eSearchMode_Grid, it is still only a
217 * suggestion: grid-based searching may not be possible with the
218 * provided input, in which case a simple search is still used.
219 * This is mainly useful for testing purposes to force a mode.
223 void setMode(SearchMode mode);
224 //! Returns the currently active search mode.
225 SearchMode mode() const;
228 * Initializes neighborhood search for a set of positions.
230 * \param[in] pbc PBC information for the frame.
231 * \param[in] positions Set of reference positions to use.
232 * \returns Search object that can be used to find positions from
233 * \p x within the given cutoff.
234 * \throws std::bad_alloc if out of memory.
236 * Currently, the input positions cannot use
237 * AnalysisNeighborhoodPositions::selectSingleFromArray().
239 AnalysisNeighborhoodSearch
240 initSearch(const t_pbc *pbc,
241 const AnalysisNeighborhoodPositions &positions);
246 PrivateImplPointer<Impl> impl_;
250 * Value type to represent a pair of positions found in neighborhood searching.
252 * Methods in this class do not throw.
255 * \ingroup module_selection
257 class AnalysisNeighborhoodPair
260 //! Initializes an invalid pair.
261 AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0) {}
262 //! Initializes a pair object with the given data.
263 AnalysisNeighborhoodPair(int refIndex, int testIndex)
264 : refIndex_(refIndex), testIndex_(testIndex)
269 * Whether this pair is valid.
271 * If isValid() returns false, other methods should not be called.
273 bool isValid() const { return refIndex_ >= 0; }
276 * Returns the index of the reference position in the pair.
278 * This index is always the index into the position array provided to
279 * AnalysisNeighborhood::initSearch().
283 GMX_ASSERT(isValid(), "Accessing invalid object");
287 * Returns the index of the test position in the pair.
289 * The contents of this index depends on the context (method call) that
291 * If there was no array in the call, this index is zero.
293 int testIndex() const
295 GMX_ASSERT(isValid(), "Accessing invalid object");
305 * Initialized neighborhood search with a fixed set of reference positions.
307 * An instance of this class is obtained through
308 * AnalysisNeighborhood::initSearch(), and can be used to do multiple searches
309 * against the provided set of reference positions.
310 * It is possible to create concurrent pair searches (including from different
311 * threads), as well as call other methods in this class while a pair search is
314 * This class works like a pointer: copies of it point to the same search.
315 * In general, avoid creating copies, and only use the copy/assignment support
316 * for moving the variable around. With C++11, this class would best be
319 * Methods in this class do not throw unless otherwise indicated.
322 * Make it such that reset() is not necessary to call in code that repeatedly
323 * assigns the result of AnalysisNeighborhood::initSearch() to the same
324 * variable (see sm_distance.cpp).
327 * Consider merging nearestPoint() and minimumDistance() by adding the distance
328 * to AnalysisNeighborhoodPair.
331 * \ingroup module_selection
333 class AnalysisNeighborhoodSearch
337 * Internal short-hand type for a pointer to the implementation class.
339 * shared_ptr is used here to automatically keep a reference count to
340 * track whether an implementation class is still used outside the
341 * AnalysisNeighborhood object. Ownership currently always stays with
342 * AnalysisNeighborhood; it always keeps one instance of the pointer.
344 typedef boost::shared_ptr<internal::AnalysisNeighborhoodSearchImpl>
348 * Initializes an invalid search.
350 * Such an object cannot be used for searching. It needs to be
351 * assigned a value from AnalysisNeighborhood::initSearch() before it
352 * can be used. Provided to allow declaring a variable to hold the
353 * search before calling AnalysisNeighborhood::initSearch().
355 AnalysisNeighborhoodSearch();
357 * Internally initialize the search.
359 * Used to implement AnalysisNeighborhood::initSearch().
360 * Cannot be called from user code.
362 explicit AnalysisNeighborhoodSearch(const ImplPointer &impl);
365 * Clears this search.
367 * Equivalent to \c "*this = AnalysisNeighborhoodSearch();".
368 * Currently, this is necessary to avoid unnecessary memory allocation
369 * if the previous search variable is still in scope when you want to
370 * call AnalysisNeighborhood::initSearch() again.
375 * Returns the searching algorithm that this search is using.
377 * The return value is never AnalysisNeighborhood::eSearchMode_Automatic.
379 AnalysisNeighborhood::SearchMode mode() const;
382 * Check whether a point is within a neighborhood.
384 * \param[in] positions Set of test positions to use.
385 * \returns true if any of the test positions is within the cutoff of
386 * any reference position.
388 bool isWithin(const AnalysisNeighborhoodPositions &positions) const;
390 * Calculates the minimum distance from the reference points.
392 * \param[in] positions Set of test positions to use.
393 * \returns The distance to the nearest reference position, or the
394 * cutoff value if there are no reference positions within the
397 real minimumDistance(const AnalysisNeighborhoodPositions &positions) const;
399 * Finds the closest reference point.
401 * \param[in] positions Set of test positions to use.
402 * \returns The reference index identifies the reference position
403 * that is closest to the test positions.
404 * The test index identifies the test position that is closest to
405 * the provided test position. The returned pair is invalid if
406 * no reference position is within the cutoff.
408 AnalysisNeighborhoodPair
409 nearestPoint(const AnalysisNeighborhoodPositions &positions) const;
412 * Start a search to find reference positions within a cutoff.
414 * \param[in] positions Set of test positions to use.
415 * \returns Initialized search object to loop through all reference
416 * positions within the configured cutoff.
417 * \throws std::bad_alloc if out of memory.
419 AnalysisNeighborhoodPairSearch
420 startPairSearch(const AnalysisNeighborhoodPositions &positions) const;
423 typedef internal::AnalysisNeighborhoodSearchImpl Impl;
429 * Initialized neighborhood pair search with a fixed set of positions.
431 * This class is used to loop through pairs of neighbors within the cutoff
432 * provided to AnalysisNeighborhood. The following code demonstrates its use:
434 gmx::AnalysisNeighborhood nb;
435 nb.setCutoff(cutoff);
436 gmx::AnalysisNeighborhoodPositions refPos(xref, nref);
437 gmx::AnalysisNeighborhoodSearch search = nb.initSearch(pbc, refPos);
438 gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(selection);
439 gmx::AnalysisNeighborhoodPair pair;
440 while (pairSearch.findNextPair(&pair))
442 // <do something for each found pair the information in pair>
446 * It is not possible to use a single search object from multiple threads
449 * This class works like a pointer: copies of it point to the same search.
450 * In general, avoid creating copies, and only use the copy/assignment support
451 * for moving the variable around. With C++11, this class would best be
454 * Methods in this class do not throw.
457 * \ingroup module_selection
459 class AnalysisNeighborhoodPairSearch
463 * Internal short-hand type for a pointer to the implementation class.
465 * See AnalysisNeighborhoodSearch::ImplPointer for rationale of using
466 * shared_ptr and ownership semantics.
468 typedef boost::shared_ptr<internal::AnalysisNeighborhoodPairSearchImpl>
472 * Internally initialize the search.
474 * Used to implement AnalysisNeighborhoodSearch::startPairSearch().
475 * Cannot be called from user code.
477 explicit AnalysisNeighborhoodPairSearch(const ImplPointer &impl);
480 * Finds the next pair within the cutoff.
482 * \param[out] pair Information about the found pair.
483 * \returns false if there were no more pairs.
485 * If the method returns false, \p pair will be invalid.
487 * \see AnalysisNeighborhoodPair
488 * \see AnalysisNeighborhoodSearch::startPairSearch()
490 bool findNextPair(AnalysisNeighborhoodPair *pair);
492 * Skip remaining pairs for a test position in the search.
494 * When called after findNextPair(), makes subsequent calls to
495 * findNextPair() skip any pairs that have the same test position as
496 * that previously returned.
497 * This is useful if the caller wants to search whether any reference
498 * position within the cutoff satisfies some condition. This method
499 * can be used to skip remaining pairs after the first such position
500 * has been found if the remaining pairs would not have an effect on
503 void skipRemainingPairsForTestPosition();