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37 * Declares gmx::Selection and supporting classes.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
41 * \ingroup module_selection
43 #ifndef GMX_SELECTION_SELECTION_H
44 #define GMX_SELECTION_SELECTION_H
49 #include "../legacyheaders/typedefs.h"
51 #include "../utility/arrayref.h"
52 #include "../utility/common.h"
53 #include "../utility/gmxassert.h"
56 #include "indexutil.h"
57 #include "selectionenums.h"
62 class SelectionOptionStorage;
63 class SelectionTreeElement;
65 class AnalysisNeighborhoodPositions;
67 class SelectionPosition;
69 //! Container of selections used in public selection interfaces.
70 typedef std::vector<Selection> SelectionList;
76 * Internal data for a single selection.
78 * This class is internal to the selection module, but resides in a public
79 * header because of efficiency reasons: it allows frequently used access
80 * methods in \ref Selection to be inlined.
82 * Methods in this class do not throw unless otherwise specified.
84 * \ingroup module_selection
90 * Creates a new selection object.
92 * \param[in] elem Root of the evaluation tree for this selection.
93 * \param[in] selstr String that was parsed to produce this selection.
94 * \throws std::bad_alloc if out of memory.
96 SelectionData(SelectionTreeElement *elem, const char *selstr);
99 //! Returns the name for this selection.
100 const char *name() const { return name_.c_str(); }
101 //! Returns the string that was parsed to produce this selection.
102 const char *selectionText() const { return selectionText_.c_str(); }
103 //! Returns true if the size of the selection (posCount()) is dynamic.
104 bool isDynamic() const { return bDynamic_; }
105 //! Returns the type of positions in the selection.
106 e_index_t type() const { return rawPositions_.m.type; }
108 //! Number of positions in the selection.
109 int posCount() const { return rawPositions_.nr; }
110 //! Returns the root of the evaluation tree for this selection.
111 SelectionTreeElement &rootElement() { return rootElement_; }
113 //! Returns whether the covered fraction can change between frames.
114 bool isCoveredFractionDynamic() const { return bDynamicCoveredFraction_; }
116 //! Returns true if the given flag is set.
117 bool hasFlag(SelectionFlag flag) const { return flags_.test(flag); }
118 //! Sets the flags for this selection.
119 void setFlags(SelectionFlags flags) { flags_ = flags; }
121 //! \copydoc Selection::initCoveredFraction()
122 bool initCoveredFraction(e_coverfrac_t type);
125 * Updates the name of the selection if missing.
127 * \throws std::bad_alloc if out of memory.
129 * If selections get their value from a group reference that cannot be
130 * resolved during parsing, the name is final only after group
131 * references have been resolved.
133 * This function is called by SelectionCollection::setIndexGroups().
137 * Computes total masses and charges for all selection positions.
139 * \param[in] top Topology information.
140 * \throws std::bad_alloc if out of memory.
142 * For dynamic selections, the values need to be updated after each
143 * evaluation with refreshMassesAndCharges().
144 * This is done by SelectionEvaluator.
146 * This function is called by SelectionCompiler.
148 * Strong exception safety guarantee.
150 void initializeMassesAndCharges(const t_topology *top);
152 * Updates masses and charges after dynamic selection has been
155 * \param[in] top Topology information.
157 * Called by SelectionEvaluator.
159 void refreshMassesAndCharges(const t_topology *top);
161 * Updates the covered fraction after a selection has been evaluated.
163 * Called by SelectionEvaluator.
165 void updateCoveredFractionForFrame();
167 * Computes average covered fraction after all frames have been evaluated.
169 * \param[in] nframes Number of frames that have been evaluated.
171 * \p nframes should be equal to the number of calls to
172 * updateCoveredFractionForFrame().
173 * Called by SelectionEvaluator::evaluateFinal().
175 void computeAverageCoveredFraction(int nframes);
177 * Restores position information to state it was in after compilation.
179 * \param[in] top Topology information.
181 * Depends on SelectionCompiler storing the original atoms in the
182 * \a rootElement_ object.
183 * Called by SelectionEvaluator::evaluateFinal().
185 void restoreOriginalPositions(const t_topology *top);
188 //! Name of the selection.
190 //! The actual selection string.
191 std::string selectionText_;
192 //! Low-level representation of selected positions.
193 gmx_ana_pos_t rawPositions_;
194 //! Total masses for the current positions.
195 std::vector<real> posMass_;
196 //! Total charges for the current positions.
197 std::vector<real> posCharge_;
198 SelectionFlags flags_;
199 //! Root of the selection evaluation tree.
200 SelectionTreeElement &rootElement_;
201 //! Type of the covered fraction.
202 e_coverfrac_t coveredFractionType_;
203 //! Covered fraction of the selection for the current frame.
204 real coveredFraction_;
205 //! The average covered fraction (over the trajectory).
206 real averageCoveredFraction_;
207 //! true if the value can change as a function of time.
209 //! true if the covered fraction depends on the frame.
210 bool bDynamicCoveredFraction_;
213 * Needed to wrap access to information.
215 friend class gmx::Selection;
217 * Needed for proper access to position information.
219 friend class gmx::SelectionPosition;
221 GMX_DISALLOW_COPY_AND_ASSIGN(SelectionData);
224 } // namespace internal
227 * Provides access to a single selection.
229 * This class provides a public interface for accessing selection information.
230 * General information about the selection can be accessed with methods name(),
231 * selectionText(), isDynamic(), and type(). The first three can be accessed
232 * any time after the selection has been parsed, and type() can be accessed
233 * after the selection has been compiled.
235 * There are a few methods that can be used to change the behavior of the
236 * selection. setEvaluateVelocities() and setEvaluateForces() can be called
237 * before the selection is compiled to request evaluation of velocities and/or
238 * forces in addition to coordinates.
240 * Each selection is made of a set of positions. Each position has associated
241 * coordinates, and possibly velocities and forces if they have been requested
242 * and are available. It also has a set of atoms associated with it; typically
243 * the coordinates are the center-of-mass or center-of-geometry coordinates for
244 * that set of atoms. To access the number of positions in the selection, use
245 * posCount(). To access individual positions, use position().
246 * See SelectionPosition for details of how to use individual positions.
247 * setOriginalId() can be used to adjust the return value of
248 * SelectionPosition::mappedId(); see that method for details.
250 * It is also possible to access the list of atoms that make up all the
251 * positions directly: atomCount() returns the total number of atoms in the
252 * selection and atomIndices() an array of their indices.
253 * Similarly, it is possible to access the coordinates and other properties
254 * of the positions as continuous arrays through coordinates(), velocities(),
255 * forces(), masses(), charges(), refIds(), and mappedIds().
257 * Both positions and atoms can be accessed after the selection has been
258 * compiled. For dynamic selections, the return values of these methods change
259 * after each evaluation to reflect the situation for the current frame.
260 * Before any frame has been evaluated, these methods return the maximal set
261 * to which the selection can evaluate.
263 * There are two possible modes for how positions for dynamic selections are
264 * handled. In the default mode, posCount() can change, and for each frame,
265 * only the positions that are selected in that frame can be accessed. In a
266 * masked mode, posCount() remains constant, i.e., the positions are always
267 * evaluated for the maximal set, and SelectionPosition::selected() is used to
268 * determine whether a position is selected for a frame. The masked mode can
269 * be requested with SelectionOption::dynamicMask().
271 * The class also provides methods for printing out information: printInfo()
272 * and printDebugInfo(). These are mainly for internal use by Gromacs.
274 * This class works like a pointer type: copying and assignment is lightweight,
275 * and all copies work interchangeably, accessing the same internal data.
277 * Methods in this class do not throw.
279 * \see SelectionPosition
282 * \ingroup module_selection
288 * Creates a selection wrapper that has no associated selection.
290 * Any attempt to call methods in the object before a selection is
291 * assigned results in undefined behavior.
293 Selection() : sel_(NULL) {}
295 * Creates a new selection object.
297 * \param sel Selection data to wrap.
299 * Only for internal use by the selection module.
301 explicit Selection(internal::SelectionData *sel) : sel_(sel) {}
303 //! Returns the name of the selection.
304 const char *name() const { return data().name(); }
305 //! Returns the string that was parsed to produce this selection.
306 const char *selectionText() const { return data().selectionText(); }
307 //! Returns true if the size of the selection (posCount()) is dynamic.
308 bool isDynamic() const { return data().isDynamic(); }
309 //! Returns the type of positions in the selection.
310 e_index_t type() const { return data().type(); }
312 //! Total number of atoms in the selection.
313 int atomCount() const
315 return data().rawPositions_.g != NULL ? data().rawPositions_.g->isize : 0;
317 //! Returns atom indices of all atoms in the selection.
318 ConstArrayRef<int> atomIndices() const
320 if (data().rawPositions_.g == NULL)
322 return ConstArrayRef<int>();
324 return ConstArrayRef<int>(data().rawPositions_.g->index,
325 data().rawPositions_.g->isize);
327 //! Number of positions in the selection.
328 int posCount() const { return data().posCount(); }
329 //! Access a single position.
330 SelectionPosition position(int i) const;
331 //! Returns coordinates for this selection as a continuous array.
332 ConstArrayRef<rvec> coordinates() const
334 return ConstArrayRef<rvec>(data().rawPositions_.x, posCount());
336 //! Returns whether velocities are available for this selection.
337 bool hasVelocities() const { return data().rawPositions_.v != NULL; }
339 * Returns velocities for this selection as a continuous array.
341 * Must not be called if hasVelocities() returns false.
343 ConstArrayRef<rvec> velocities() const
345 GMX_ASSERT(hasVelocities(), "Velocities accessed, but unavailable");
346 return ConstArrayRef<rvec>(data().rawPositions_.v, posCount());
348 //! Returns whether forces are available for this selection.
349 bool hasForces() const { return sel_->rawPositions_.f != NULL; }
351 * Returns forces for this selection as a continuous array.
353 * Must not be called if hasForces() returns false.
355 ConstArrayRef<rvec> forces() const
357 GMX_ASSERT(hasForces(), "Forces accessed, but unavailable");
358 return ConstArrayRef<rvec>(data().rawPositions_.f, posCount());
360 //! Returns masses for this selection as a continuous array.
361 ConstArrayRef<real> masses() const
363 // posMass_ may have more entries than posCount() in the case of
364 // dynamic selections that don't have a topology
365 // (and thus the masses and charges are fixed).
366 GMX_ASSERT(data().posMass_.size() >= static_cast<size_t>(posCount()),
367 "Internal inconsistency");
368 return ConstArrayRef<real>(data().posMass_.begin(),
369 data().posMass_.begin() + posCount());
371 //! Returns charges for this selection as a continuous array.
372 ConstArrayRef<real> charges() const
374 // posCharge_ may have more entries than posCount() in the case of
375 // dynamic selections that don't have a topology
376 // (and thus the masses and charges are fixed).
377 GMX_ASSERT(data().posCharge_.size() >= static_cast<size_t>(posCount()),
378 "Internal inconsistency");
379 return ConstArrayRef<real>(data().posCharge_.begin(),
380 data().posCharge_.begin() + posCount());
383 * Returns reference IDs for this selection as a continuous array.
385 * \see SelectionPosition::refId()
387 ConstArrayRef<int> refIds() const
389 return ConstArrayRef<int>(data().rawPositions_.m.refid, posCount());
392 * Returns mapped IDs for this selection as a continuous array.
394 * \see SelectionPosition::mappedId()
396 ConstArrayRef<int> mappedIds() const
398 return ConstArrayRef<int>(data().rawPositions_.m.mapid, posCount());
401 //! Returns whether the covered fraction can change between frames.
402 bool isCoveredFractionDynamic() const { return data().isCoveredFractionDynamic(); }
403 //! Returns the covered fraction for the current frame.
404 real coveredFraction() const { return data().coveredFraction_; }
407 * Allows passing a selection directly to neighborhood searching.
409 * When initialized this way, AnalysisNeighborhoodPair objects return
410 * indices that can be used to index the selection positions with
413 * Works exactly like if AnalysisNeighborhoodPositions had a
414 * constructor taking a Selection object as a parameter.
415 * See AnalysisNeighborhoodPositions for rationale and additional
418 operator AnalysisNeighborhoodPositions() const;
421 * Initializes information about covered fractions.
423 * \param[in] type Type of covered fraction required.
424 * \returns true if the covered fraction can be calculated for the
427 bool initCoveredFraction(e_coverfrac_t type)
429 return data().initCoveredFraction(type);
432 * Sets whether this selection evaluates velocities for positions.
434 * \param[in] bEnabled If true, velocities are evaluated.
436 * If you request the evaluation, but then evaluate the selection for
437 * a frame that does not contain velocity information, results are
441 * Implement it such that in the above case, hasVelocities() will
442 * return false for such frames.
446 void setEvaluateVelocities(bool bEnabled)
448 data().flags_.set(efSelection_EvaluateVelocities, bEnabled);
451 * Sets whether this selection evaluates forces for positions.
453 * \param[in] bEnabled If true, forces are evaluated.
455 * If you request the evaluation, but then evaluate the selection for
456 * a frame that does not contain force information, results are
461 void setEvaluateForces(bool bEnabled)
463 data().flags_.set(efSelection_EvaluateForces, bEnabled);
467 * Sets the ID for the \p i'th position for use with
468 * SelectionPosition::mappedId().
470 * \param[in] i Zero-based index
471 * \param[in] id Identifier to set.
473 * This method is not part of SelectionPosition because that interface
474 * only provides access to const data by design.
476 * This method can only be called after compilation, before the
477 * selection has been evaluated for any frame.
479 * \see SelectionPosition::mappedId()
481 void setOriginalId(int i, int id) { data().rawPositions_.m.orgid[i] = id; }
484 * Prints out one-line description of the selection.
486 * \param[in] fp Where to print the information.
488 * The output contains the name of the selection, the number of atoms
489 * and the number of positions, and indication of whether the selection
492 void printInfo(FILE *fp) const;
494 * Prints out extended information about the selection for debugging.
496 * \param[in] fp Where to print the information.
497 * \param[in] nmaxind Maximum number of values to print in lists
500 void printDebugInfo(FILE *fp, int nmaxind) const;
503 internal::SelectionData &data()
505 GMX_ASSERT(sel_ != NULL,
506 "Attempted to access uninitialized selection");
509 const internal::SelectionData &data() const
511 GMX_ASSERT(sel_ != NULL,
512 "Attempted to access uninitialized selection");
517 * Pointer to internal data for the selection.
519 * The memory for this object is managed by a SelectionCollection
520 * object, and the \ref Selection class simply provides a public
521 * interface for accessing the data.
523 internal::SelectionData *sel_;
526 * Needed to access the data to adjust flags.
528 friend class SelectionOptionStorage;
532 * Provides access to information about a single selected position.
534 * Each position has associated coordinates, and possibly velocities and forces
535 * if they have been requested and are available. It also has a set of atoms
536 * associated with it; typically the coordinates are the center-of-mass or
537 * center-of-geometry coordinates for that set of atoms. It is possible that
538 * there are not atoms associated if the selection has been provided as a fixed
541 * After the selection has been compiled, but not yet evaluated, the contents
542 * of the coordinate, velocity and force vectors are undefined.
544 * Default copy constructor and assignment operators are used, and work as
545 * intended: the copy references the same position and works identically.
547 * Methods in this class do not throw.
552 * \ingroup module_selection
554 class SelectionPosition
558 * Constructs a wrapper object for given selection position.
560 * \param[in] sel Selection from which the position is wrapped.
561 * \param[in] index Zero-based index of the position to wrap.
563 * Asserts if \p index is out of range.
565 * Only for internal use of the library. To obtain a SelectionPosition
566 * object in other code, use Selection::position().
568 SelectionPosition(const internal::SelectionData &sel, int index)
569 : sel_(&sel), i_(index)
571 GMX_ASSERT(index >= 0 && index < sel.posCount(),
572 "Invalid selection position index");
576 * Returns type of this position.
578 * Currently always returns the same as Selection::type().
580 e_index_t type() const { return sel_->type(); }
581 //! Returns coordinates for this position.
582 const rvec &x() const
584 return sel_->rawPositions_.x[i_];
587 * Returns velocity for this position.
589 * Must not be called if Selection::hasVelocities() returns false.
591 const rvec &v() const
593 GMX_ASSERT(sel_->rawPositions_.v != NULL,
594 "Velocities accessed, but unavailable");
595 return sel_->rawPositions_.v[i_];
598 * Returns force for this position.
600 * Must not be called if Selection::hasForces() returns false.
602 const rvec &f() const
604 GMX_ASSERT(sel_->rawPositions_.f != NULL,
605 "Velocities accessed, but unavailable");
606 return sel_->rawPositions_.f[i_];
609 * Returns total mass for this position.
611 * Returns the total mass of atoms that make up this position.
612 * If there are no atoms associated or masses are not available,
617 return sel_->posMass_[i_];
620 * Returns total charge for this position.
622 * Returns the sum of charges of atoms that make up this position.
623 * If there are no atoms associated or charges are not available,
628 return sel_->posCharge_[i_];
630 //! Returns the number of atoms that make up this position.
631 int atomCount() const
633 return sel_->rawPositions_.m.mapb.index[i_ + 1]
634 - sel_->rawPositions_.m.mapb.index[i_];
636 //! Return atom indices that make up this position.
637 ConstArrayRef<int> atomIndices() const
639 if (sel_->rawPositions_.g == NULL)
641 return ConstArrayRef<int>();
643 int first = sel_->rawPositions_.m.mapb.index[i_];
644 return ConstArrayRef<int>(&sel_->rawPositions_.g->index[first],
648 * Returns whether this position is selected in the current frame.
650 * The return value is equivalent to \c refid() == -1. Returns always
651 * true if SelectionOption::dynamicMask() has not been set.
655 bool selected() const
660 * Returns reference ID for this position.
662 * For dynamic selections, this provides means to associate positions
663 * across frames. After compilation, these IDs are consequently
664 * numbered starting from zero. For each frame, the ID then reflects
665 * the location of the position in the original array of positions.
666 * If SelectionOption::dynamicMask() has been set for the parent
667 * selection, the IDs for positions not present in the current
668 * selection are set to -1, otherwise they are removed completely.
671 * If a dynamic selection consists of at most three positions, after
672 * compilation refId() will return 0, 1, 2 for them, respectively.
673 * If for a particular frame, only the first and the third are present,
674 * refId() will return 0, 2.
675 * If SelectionOption::dynamicMask() has been set, all three positions
676 * can be accessed also for that frame and refId() will return 0, -1,
681 return sel_->rawPositions_.m.refid[i_];
684 * Returns mapped ID for this position.
686 * Returns ID of the position that corresponds to that set with
687 * Selection::setOriginalId().
689 * If for an array \c id, \c setOriginalId(i, id[i]) has been called
690 * for each \c i, then it always holds that
691 * \c mappedId()==id[refId()].
693 * Selection::setOriginalId() has not been called, the default values
694 * are dependent on type():
695 * - ::INDEX_ATOM: atom indices
696 * - ::INDEX_RES: residue numbers
697 * - ::INDEX_MOL: molecule numbers
699 * All the default values are zero-based
703 return sel_->rawPositions_.m.mapid[i_];
707 * Allows passing a selection position directly to neighborhood searching.
709 * When initialized this way, AnalysisNeighborhoodPair objects return
710 * the index that can be used to access this position using
711 * Selection::position().
713 * Works exactly like if AnalysisNeighborhoodPositions had a
714 * constructor taking a SelectionPosition object as a parameter.
715 * See AnalysisNeighborhoodPositions for rationale and additional
718 operator AnalysisNeighborhoodPositions() const;
721 const internal::SelectionData *sel_;
726 inline SelectionPosition
727 Selection::position(int i) const
729 return SelectionPosition(data(), i);