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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;
77 * Internal data for a single selection.
79 * This class is internal to the selection module, but resides in a public
80 * header because of efficiency reasons: it allows frequently used access
81 * methods in \ref Selection to be inlined.
83 * Methods in this class do not throw unless otherwise specified.
85 * \ingroup module_selection
91 * Creates a new selection object.
93 * \param[in] elem Root of the evaluation tree for this selection.
94 * \param[in] selstr String that was parsed to produce this selection.
95 * \throws std::bad_alloc if out of memory.
97 SelectionData(SelectionTreeElement *elem, const char *selstr);
100 //! Returns the name for this selection.
101 const char *name() const { return name_.c_str(); }
102 //! Returns the string that was parsed to produce this selection.
103 const char *selectionText() const { return selectionText_.c_str(); }
104 //! Returns true if the size of the selection (posCount()) is dynamic.
105 bool isDynamic() const { return bDynamic_; }
106 //! Returns the type of positions in the selection.
107 e_index_t type() const { return rawPositions_.m.type; }
109 //! Number of positions in the selection.
110 int posCount() const { return rawPositions_.count(); }
111 //! Returns the root of the evaluation tree for this selection.
112 SelectionTreeElement &rootElement() { return rootElement_; }
114 //! Returns whether the covered fraction can change between frames.
115 bool isCoveredFractionDynamic() const { return bDynamicCoveredFraction_; }
117 //! Returns true if the given flag is set.
118 bool hasFlag(SelectionFlag flag) const { return flags_.test(flag); }
119 //! Sets the flags for this selection.
120 void setFlags(SelectionFlags flags) { flags_ = flags; }
122 //! \copydoc Selection::initCoveredFraction()
123 bool initCoveredFraction(e_coverfrac_t type);
126 * Updates the name of the selection if missing.
128 * \throws std::bad_alloc if out of memory.
130 * If selections get their value from a group reference that cannot be
131 * resolved during parsing, the name is final only after group
132 * references have been resolved.
134 * This function is called by SelectionCollection::setIndexGroups().
138 * Computes total masses and charges for all selection positions.
140 * \param[in] top Topology information.
141 * \throws std::bad_alloc if out of memory.
143 * For dynamic selections, the values need to be updated after each
144 * evaluation with refreshMassesAndCharges().
145 * This is done by SelectionEvaluator.
147 * This function is called by SelectionCompiler.
149 * Strong exception safety guarantee.
151 void initializeMassesAndCharges(const t_topology *top);
153 * Updates masses and charges after dynamic selection has been
156 * \param[in] top Topology information.
158 * Called by SelectionEvaluator.
160 void refreshMassesAndCharges(const t_topology *top);
162 * Updates the covered fraction after a selection has been evaluated.
164 * Called by SelectionEvaluator.
166 void updateCoveredFractionForFrame();
168 * Computes average covered fraction after all frames have been evaluated.
170 * \param[in] nframes Number of frames that have been evaluated.
172 * \p nframes should be equal to the number of calls to
173 * updateCoveredFractionForFrame().
174 * Called by SelectionEvaluator::evaluateFinal().
176 void computeAverageCoveredFraction(int nframes);
178 * Restores position information to state it was in after compilation.
180 * \param[in] top Topology information.
182 * Depends on SelectionCompiler storing the original atoms in the
183 * \a rootElement_ object.
184 * Called by SelectionEvaluator::evaluateFinal().
186 void restoreOriginalPositions(const t_topology *top);
189 //! Name of the selection.
191 //! The actual selection string.
192 std::string selectionText_;
193 //! Low-level representation of selected positions.
194 gmx_ana_pos_t rawPositions_;
195 //! Total masses for the current positions.
196 std::vector<real> posMass_;
197 //! Total charges for the current positions.
198 std::vector<real> posCharge_;
199 SelectionFlags flags_;
200 //! Root of the selection evaluation tree.
201 SelectionTreeElement &rootElement_;
202 //! Type of the covered fraction.
203 e_coverfrac_t coveredFractionType_;
204 //! Covered fraction of the selection for the current frame.
205 real coveredFraction_;
206 //! The average covered fraction (over the trajectory).
207 real averageCoveredFraction_;
208 //! true if the value can change as a function of time.
210 //! true if the covered fraction depends on the frame.
211 bool bDynamicCoveredFraction_;
214 * Needed to wrap access to information.
216 friend class gmx::Selection;
218 * Needed for proper access to position information.
220 friend class gmx::SelectionPosition;
222 GMX_DISALLOW_COPY_AND_ASSIGN(SelectionData);
225 } // namespace internal
228 * Provides access to a single selection.
230 * This class provides a public interface for accessing selection information.
231 * General information about the selection can be accessed with methods name(),
232 * selectionText(), isDynamic(), and type(). The first three can be accessed
233 * any time after the selection has been parsed, and type() can be accessed
234 * after the selection has been compiled.
236 * There are a few methods that can be used to change the behavior of the
237 * selection. setEvaluateVelocities() and setEvaluateForces() can be called
238 * before the selection is compiled to request evaluation of velocities and/or
239 * forces in addition to coordinates.
241 * Each selection is made of a set of positions. Each position has associated
242 * coordinates, and possibly velocities and forces if they have been requested
243 * and are available. It also has a set of atoms associated with it; typically
244 * the coordinates are the center-of-mass or center-of-geometry coordinates for
245 * that set of atoms. To access the number of positions in the selection, use
246 * posCount(). To access individual positions, use position().
247 * See SelectionPosition for details of how to use individual positions.
248 * setOriginalId() can be used to adjust the return value of
249 * SelectionPosition::mappedId(); see that method for details.
251 * It is also possible to access the list of atoms that make up all the
252 * positions directly: atomCount() returns the total number of atoms in the
253 * selection and atomIndices() an array of their indices.
254 * Similarly, it is possible to access the coordinates and other properties
255 * of the positions as continuous arrays through coordinates(), velocities(),
256 * forces(), masses(), charges(), refIds(), and mappedIds().
258 * Both positions and atoms can be accessed after the selection has been
259 * compiled. For dynamic selections, the return values of these methods change
260 * after each evaluation to reflect the situation for the current frame.
261 * Before any frame has been evaluated, these methods return the maximal set
262 * to which the selection can evaluate.
264 * There are two possible modes for how positions for dynamic selections are
265 * handled. In the default mode, posCount() can change, and for each frame,
266 * only the positions that are selected in that frame can be accessed. In a
267 * masked mode, posCount() remains constant, i.e., the positions are always
268 * evaluated for the maximal set, and SelectionPosition::selected() is used to
269 * determine whether a position is selected for a frame. The masked mode can
270 * be requested with SelectionOption::dynamicMask().
272 * The class also provides methods for printing out information: printInfo()
273 * and printDebugInfo(). These are mainly for internal use by Gromacs.
275 * This class works like a pointer type: copying and assignment is lightweight,
276 * and all copies work interchangeably, accessing the same internal data.
278 * Methods in this class do not throw.
280 * \see SelectionPosition
283 * \ingroup module_selection
289 * Creates a selection wrapper that has no associated selection.
291 * Any attempt to call methods in the object before a selection is
292 * assigned results in undefined behavior.
293 * isValid() returns `false` for the selection until it is initialized.
295 Selection() : sel_(NULL) {}
297 * Creates a new selection object.
299 * \param sel Selection data to wrap.
301 * Only for internal use by the selection module.
303 explicit Selection(internal::SelectionData *sel) : sel_(sel) {}
305 //! Returns whether the selection object is initialized.
306 bool isValid() const { return sel_ != NULL; }
308 //! Returns the name of the selection.
309 const char *name() const { return data().name(); }
310 //! Returns the string that was parsed to produce this selection.
311 const char *selectionText() const { return data().selectionText(); }
312 //! Returns true if the size of the selection (posCount()) is dynamic.
313 bool isDynamic() const { return data().isDynamic(); }
314 //! Returns the type of positions in the selection.
315 e_index_t type() const { return data().type(); }
317 //! Total number of atoms in the selection.
318 int atomCount() const
320 return data().rawPositions_.m.mapb.nra;
322 //! Returns atom indices of all atoms in the selection.
323 ConstArrayRef<int> atomIndices() const
325 return ConstArrayRef<int>(sel_->rawPositions_.m.mapb.a,
326 sel_->rawPositions_.m.mapb.nra);
328 //! Number of positions in the selection.
329 int posCount() const { return data().posCount(); }
330 //! Access a single position.
331 SelectionPosition position(int i) const;
332 //! Returns coordinates for this selection as a continuous array.
333 ConstArrayRef<rvec> coordinates() const
335 return ConstArrayRef<rvec>(data().rawPositions_.x, posCount());
337 //! Returns whether velocities are available for this selection.
338 bool hasVelocities() const { return data().rawPositions_.v != NULL; }
340 * Returns velocities for this selection as a continuous array.
342 * Must not be called if hasVelocities() returns false.
344 ConstArrayRef<rvec> velocities() const
346 GMX_ASSERT(hasVelocities(), "Velocities accessed, but unavailable");
347 return ConstArrayRef<rvec>(data().rawPositions_.v, posCount());
349 //! Returns whether forces are available for this selection.
350 bool hasForces() const { return sel_->rawPositions_.f != NULL; }
352 * Returns forces for this selection as a continuous array.
354 * Must not be called if hasForces() returns false.
356 ConstArrayRef<rvec> forces() const
358 GMX_ASSERT(hasForces(), "Forces accessed, but unavailable");
359 return ConstArrayRef<rvec>(data().rawPositions_.f, posCount());
361 //! Returns masses for this selection as a continuous array.
362 ConstArrayRef<real> masses() const
364 // posMass_ may have more entries than posCount() in the case of
365 // dynamic selections that don't have a topology
366 // (and thus the masses and charges are fixed).
367 GMX_ASSERT(data().posMass_.size() >= static_cast<size_t>(posCount()),
368 "Internal inconsistency");
369 return ConstArrayRef<real>(data().posMass_.begin(),
370 data().posMass_.begin() + posCount());
372 //! Returns charges for this selection as a continuous array.
373 ConstArrayRef<real> charges() const
375 // posCharge_ may have more entries than posCount() in the case of
376 // dynamic selections that don't have a topology
377 // (and thus the masses and charges are fixed).
378 GMX_ASSERT(data().posCharge_.size() >= static_cast<size_t>(posCount()),
379 "Internal inconsistency");
380 return ConstArrayRef<real>(data().posCharge_.begin(),
381 data().posCharge_.begin() + posCount());
384 * Returns reference IDs for this selection as a continuous array.
386 * \see SelectionPosition::refId()
388 ConstArrayRef<int> refIds() const
390 return ConstArrayRef<int>(data().rawPositions_.m.refid, posCount());
393 * Returns mapped IDs for this selection as a continuous array.
395 * \see SelectionPosition::mappedId()
397 ConstArrayRef<int> mappedIds() const
399 return ConstArrayRef<int>(data().rawPositions_.m.mapid, posCount());
402 //! Returns whether the covered fraction can change between frames.
403 bool isCoveredFractionDynamic() const { return data().isCoveredFractionDynamic(); }
404 //! Returns the covered fraction for the current frame.
405 real coveredFraction() const { return data().coveredFraction_; }
408 * Allows passing a selection directly to neighborhood searching.
410 * When initialized this way, AnalysisNeighborhoodPair objects return
411 * indices that can be used to index the selection positions with
414 * Works exactly like if AnalysisNeighborhoodPositions had a
415 * constructor taking a Selection object as a parameter.
416 * See AnalysisNeighborhoodPositions for rationale and additional
419 operator AnalysisNeighborhoodPositions() const;
422 * Initializes information about covered fractions.
424 * \param[in] type Type of covered fraction required.
425 * \returns true if the covered fraction can be calculated for the
428 bool initCoveredFraction(e_coverfrac_t type)
430 return data().initCoveredFraction(type);
433 * Sets whether this selection evaluates velocities for positions.
435 * \param[in] bEnabled If true, velocities are evaluated.
437 * If you request the evaluation, but then evaluate the selection for
438 * a frame that does not contain velocity information, results are
442 * Implement it such that in the above case, hasVelocities() will
443 * return false for such frames.
447 void setEvaluateVelocities(bool bEnabled)
449 data().flags_.set(efSelection_EvaluateVelocities, bEnabled);
452 * Sets whether this selection evaluates forces for positions.
454 * \param[in] bEnabled If true, forces are evaluated.
456 * If you request the evaluation, but then evaluate the selection for
457 * a frame that does not contain force information, results are
462 void setEvaluateForces(bool bEnabled)
464 data().flags_.set(efSelection_EvaluateForces, bEnabled);
468 * Sets the ID for the \p i'th position for use with
469 * SelectionPosition::mappedId().
471 * \param[in] i Zero-based index
472 * \param[in] id Identifier to set.
474 * This method is not part of SelectionPosition because that interface
475 * only provides access to const data by design.
477 * This method can only be called after compilation, before the
478 * selection has been evaluated for any frame.
480 * \see SelectionPosition::mappedId()
482 void setOriginalId(int i, int id) { data().rawPositions_.m.orgid[i] = id; }
485 * Prints out one-line description of the selection.
487 * \param[in] fp Where to print the information.
489 * The output contains the name of the selection, the number of atoms
490 * and the number of positions, and indication of whether the selection
493 void printInfo(FILE *fp) const;
495 * Prints out extended information about the selection for debugging.
497 * \param[in] fp Where to print the information.
498 * \param[in] nmaxind Maximum number of values to print in lists
501 void printDebugInfo(FILE *fp, int nmaxind) const;
504 internal::SelectionData &data()
506 GMX_ASSERT(sel_ != NULL,
507 "Attempted to access uninitialized selection");
510 const internal::SelectionData &data() const
512 GMX_ASSERT(sel_ != NULL,
513 "Attempted to access uninitialized selection");
518 * Pointer to internal data for the selection.
520 * The memory for this object is managed by a SelectionCollection
521 * object, and the \ref Selection class simply provides a public
522 * interface for accessing the data.
524 internal::SelectionData *sel_;
527 * Needed to access the data to adjust flags.
529 friend class SelectionOptionStorage;
533 * Provides access to information about a single selected position.
535 * Each position has associated coordinates, and possibly velocities and forces
536 * if they have been requested and are available. It also has a set of atoms
537 * associated with it; typically the coordinates are the center-of-mass or
538 * center-of-geometry coordinates for that set of atoms. It is possible that
539 * there are not atoms associated if the selection has been provided as a fixed
542 * After the selection has been compiled, but not yet evaluated, the contents
543 * of the coordinate, velocity and force vectors are undefined.
545 * Default copy constructor and assignment operators are used, and work as
546 * intended: the copy references the same position and works identically.
548 * Methods in this class do not throw.
553 * \ingroup module_selection
555 class SelectionPosition
559 * Constructs a wrapper object for given selection position.
561 * \param[in] sel Selection from which the position is wrapped.
562 * \param[in] index Zero-based index of the position to wrap.
564 * Asserts if \p index is out of range.
566 * Only for internal use of the library. To obtain a SelectionPosition
567 * object in other code, use Selection::position().
569 SelectionPosition(const internal::SelectionData &sel, int index)
570 : sel_(&sel), i_(index)
572 GMX_ASSERT(index >= 0 && index < sel.posCount(),
573 "Invalid selection position index");
577 * Returns type of this position.
579 * Currently always returns the same as Selection::type().
581 e_index_t type() const { return sel_->type(); }
582 //! Returns coordinates for this position.
583 const rvec &x() const
585 return sel_->rawPositions_.x[i_];
588 * Returns velocity for this position.
590 * Must not be called if Selection::hasVelocities() returns false.
592 const rvec &v() const
594 GMX_ASSERT(sel_->rawPositions_.v != NULL,
595 "Velocities accessed, but unavailable");
596 return sel_->rawPositions_.v[i_];
599 * Returns force for this position.
601 * Must not be called if Selection::hasForces() returns false.
603 const rvec &f() const
605 GMX_ASSERT(sel_->rawPositions_.f != NULL,
606 "Velocities accessed, but unavailable");
607 return sel_->rawPositions_.f[i_];
610 * Returns total mass for this position.
612 * Returns the total mass of atoms that make up this position.
613 * If there are no atoms associated or masses are not available,
618 return sel_->posMass_[i_];
621 * Returns total charge for this position.
623 * Returns the sum of charges of atoms that make up this position.
624 * If there are no atoms associated or charges are not available,
629 return sel_->posCharge_[i_];
631 //! Returns the number of atoms that make up this position.
632 int atomCount() const
634 return sel_->rawPositions_.m.mapb.index[i_ + 1]
635 - sel_->rawPositions_.m.mapb.index[i_];
637 //! Return atom indices that make up this position.
638 ConstArrayRef<int> atomIndices() const
640 const int *atoms = sel_->rawPositions_.m.mapb.a;
643 return ConstArrayRef<int>();
645 const int first = sel_->rawPositions_.m.mapb.index[i_];
646 return ConstArrayRef<int>(&atoms[first], atomCount());
649 * Returns whether this position is selected in the current frame.
651 * The return value is equivalent to \c refid() == -1. Returns always
652 * true if SelectionOption::dynamicMask() has not been set.
656 bool selected() const
661 * Returns reference ID for this position.
663 * For dynamic selections, this provides means to associate positions
664 * across frames. After compilation, these IDs are consequently
665 * numbered starting from zero. For each frame, the ID then reflects
666 * the location of the position in the original array of positions.
667 * If SelectionOption::dynamicMask() has been set for the parent
668 * selection, the IDs for positions not present in the current
669 * selection are set to -1, otherwise they are removed completely.
672 * If a dynamic selection consists of at most three positions, after
673 * compilation refId() will return 0, 1, 2 for them, respectively.
674 * If for a particular frame, only the first and the third are present,
675 * refId() will return 0, 2.
676 * If SelectionOption::dynamicMask() has been set, all three positions
677 * can be accessed also for that frame and refId() will return 0, -1,
682 return sel_->rawPositions_.m.refid[i_];
685 * Returns mapped ID for this position.
687 * Returns ID of the position that corresponds to that set with
688 * Selection::setOriginalId().
690 * If for an array \c id, \c setOriginalId(i, id[i]) has been called
691 * for each \c i, then it always holds that
692 * \c mappedId()==id[refId()].
694 * Selection::setOriginalId() has not been called, the default values
695 * are dependent on type():
696 * - ::INDEX_ATOM: atom indices
697 * - ::INDEX_RES: residue numbers
698 * - ::INDEX_MOL: molecule numbers
700 * All the default values are zero-based
704 return sel_->rawPositions_.m.mapid[i_];
708 * Allows passing a selection position directly to neighborhood searching.
710 * When initialized this way, AnalysisNeighborhoodPair objects return
711 * the index that can be used to access this position using
712 * Selection::position().
714 * Works exactly like if AnalysisNeighborhoodPositions had a
715 * constructor taking a SelectionPosition object as a parameter.
716 * See AnalysisNeighborhoodPositions for rationale and additional
719 operator AnalysisNeighborhoodPositions() const;
722 const internal::SelectionData *sel_;
727 inline SelectionPosition
728 Selection::position(int i) const
730 return SelectionPosition(data(), i);