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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;
66 class SelectionPosition;
68 //! Container of selections used in public selection interfaces.
69 typedef std::vector<Selection> SelectionList;
75 * Internal data for a single selection.
77 * This class is internal to the selection module, but resides in a public
78 * header because of efficiency reasons: it allows frequently used access
79 * methods in \ref Selection to be inlined.
81 * Methods in this class do not throw unless otherwise specified.
83 * \ingroup module_selection
89 * Creates a new selection object.
91 * \param[in] elem Root of the evaluation tree for this selection.
92 * \param[in] selstr String that was parsed to produce this selection.
93 * \throws std::bad_alloc if out of memory.
95 SelectionData(SelectionTreeElement *elem, const char *selstr);
98 //! Returns the string that was parsed to produce this selection.
99 const char *selectionText() const { return selectionText_.c_str(); }
100 //! Returns true if the size of the selection (posCount()) is dynamic.
101 bool isDynamic() const { return bDynamic_; }
102 //! Returns the type of positions in the selection.
103 e_index_t type() const { return rawPositions_.m.type; }
105 //! Number of positions in the selection.
106 int posCount() const { return rawPositions_.nr; }
107 //! Returns the root of the evaluation tree for this selection.
108 SelectionTreeElement &rootElement() { return rootElement_; }
110 //! Returns whether the covered fraction can change between frames.
111 bool isCoveredFractionDynamic() const { return bDynamicCoveredFraction_; }
113 //! Returns true if the given flag is set.
114 bool hasFlag(SelectionFlag flag) const { return flags_.test(flag); }
115 //! Sets the flags for this selection.
116 void setFlags(SelectionFlags flags) { flags_ = flags; }
118 //! \copydoc Selection::initCoveredFraction()
119 bool initCoveredFraction(e_coverfrac_t type);
122 * Computes total masses and charges for all selection positions.
124 * \param[in] top Topology information.
125 * \throws std::bad_alloc if out of memory.
127 * For dynamic selections, the values need to be updated after each
128 * evaluation with refreshMassesAndCharges().
129 * This is done by SelectionEvaluator.
131 * This function is called by SelectionCompiler.
133 * Strong exception safety guarantee.
135 void initializeMassesAndCharges(const t_topology *top);
137 * Updates masses and charges after dynamic selection has been
140 * \param[in] top Topology information.
142 * Called by SelectionEvaluator.
144 void refreshMassesAndCharges(const t_topology *top);
146 * Updates the covered fraction after a selection has been evaluated.
148 * Called by SelectionEvaluator.
150 void updateCoveredFractionForFrame();
152 * Computes average covered fraction after all frames have been evaluated.
154 * \param[in] nframes Number of frames that have been evaluated.
156 * \p nframes should be equal to the number of calls to
157 * updateCoveredFractionForFrame().
158 * Called by SelectionEvaluator::evaluateFinal().
160 void computeAverageCoveredFraction(int nframes);
162 * Restores position information to state it was in after compilation.
164 * \param[in] top Topology information.
166 * Depends on SelectionCompiler storing the original atoms in the
167 * \a rootElement_ object.
168 * Called by SelectionEvaluator::evaluateFinal().
170 void restoreOriginalPositions(const t_topology *top);
173 //! Name of the selection.
175 //! The actual selection string.
176 std::string selectionText_;
177 //! Low-level representation of selected positions.
178 gmx_ana_pos_t rawPositions_;
179 //! Total masses for the current positions.
180 std::vector<real> posMass_;
181 //! Total charges for the current positions.
182 std::vector<real> posCharge_;
183 SelectionFlags flags_;
184 //! Root of the selection evaluation tree.
185 SelectionTreeElement &rootElement_;
186 //! Type of the covered fraction.
187 e_coverfrac_t coveredFractionType_;
188 //! Covered fraction of the selection for the current frame.
189 real coveredFraction_;
190 //! The average covered fraction (over the trajectory).
191 real averageCoveredFraction_;
192 //! true if the value can change as a function of time.
194 //! true if the covered fraction depends on the frame.
195 bool bDynamicCoveredFraction_;
198 * Needed to wrap access to information.
200 friend class gmx::Selection;
202 * Needed for proper access to position information.
204 friend class gmx::SelectionPosition;
206 GMX_DISALLOW_COPY_AND_ASSIGN(SelectionData);
209 } // namespace internal
212 * Provides access to a single selection.
214 * This class provides a public interface for accessing selection information.
215 * General information about the selection can be accessed with methods name(),
216 * selectionText(), isDynamic(), and type(). The first three can be accessed
217 * any time after the selection has been parsed, and type() can be accessed
218 * after the selection has been compiled.
220 * There are a few methods that can be used to change the behavior of the
221 * selection. setEvaluateVelocities() and setEvaluateForces() can be called
222 * before the selection is compiled to request evaluation of velocities and/or
223 * forces in addition to coordinates.
225 * Each selection is made of a set of positions. Each position has associated
226 * coordinates, and possibly velocities and forces if they have been requested
227 * and are available. It also has a set of atoms associated with it; typically
228 * the coordinates are the center-of-mass or center-of-geometry coordinates for
229 * that set of atoms. To access the number of positions in the selection, use
230 * posCount(). To access individual positions, use position().
231 * See SelectionPosition for details of how to use individual positions.
232 * setOriginalId() can be used to adjust the return value of
233 * SelectionPosition::mappedId(); see that method for details.
235 * It is also possible to access the list of atoms that make up all the
236 * positions directly: atomCount() returns the total number of atoms in the
237 * selection and atomIndices() an array of their indices.
238 * Similarly, it is possible to access the coordinates and other properties
239 * of the positions as continuous arrays through coordinates(), velocities(),
240 * forces(), masses(), charges(), refIds(), and mappedIds().
242 * Both positions and atoms can be accessed after the selection has been
243 * compiled. For dynamic selections, the return values of these methods change
244 * after each evaluation to reflect the situation for the current frame.
245 * Before any frame has been evaluated, these methods return the maximal set
246 * to which the selection can evaluate.
248 * There are two possible modes for how positions for dynamic selections are
249 * handled. In the default mode, posCount() can change, and for each frame,
250 * only the positions that are selected in that frame can be accessed. In a
251 * masked mode, posCount() remains constant, i.e., the positions are always
252 * evaluated for the maximal set, and SelectionPosition::selected() is used to
253 * determine whether a position is selected for a frame. The masked mode can
254 * be requested with SelectionOption::dynamicMask().
256 * The class also provides methods for printing out information: printInfo()
257 * and printDebugInfo(). These are mainly for internal use by Gromacs.
259 * This class works like a pointer type: copying and assignment is lightweight,
260 * and all copies work interchangeably, accessing the same internal data.
262 * Methods in this class do not throw.
264 * \see SelectionPosition
267 * \ingroup module_selection
273 * Creates a selection wrapper that has no associated selection.
275 * Any attempt to call methods in the object before a selection is
276 * assigned results in undefined behavior.
278 Selection() : sel_(NULL) {}
280 * Creates a new selection object.
282 * \param sel Selection data to wrap.
284 * Only for internal use by the selection module.
286 explicit Selection(internal::SelectionData *sel) : sel_(sel) {}
288 //! Returns the name of the selection.
289 const char *name() const { return data().name_.c_str(); }
290 //! Returns the string that was parsed to produce this selection.
291 const char *selectionText() const { return data().selectionText(); }
292 //! Returns true if the size of the selection (posCount()) is dynamic.
293 bool isDynamic() const { return data().isDynamic(); }
294 //! Returns the type of positions in the selection.
295 e_index_t type() const { return data().type(); }
297 //! Total number of atoms in the selection.
298 int atomCount() const
300 return data().rawPositions_.g != NULL ? data().rawPositions_.g->isize : 0;
302 //! Returns atom indices of all atoms in the selection.
303 ConstArrayRef<int> atomIndices() const
305 if (data().rawPositions_.g == NULL)
307 return ConstArrayRef<int>();
309 return ConstArrayRef<int>(data().rawPositions_.g->index,
310 data().rawPositions_.g->isize);
312 //! Number of positions in the selection.
313 int posCount() const { return data().posCount(); }
314 //! Access a single position.
315 SelectionPosition position(int i) const;
316 //! Returns coordinates for this selection as a continuous array.
317 ConstArrayRef<rvec> coordinates() const
319 return ConstArrayRef<rvec>(data().rawPositions_.x, posCount());
321 //! Returns whether velocities are available for this selection.
322 bool hasVelocities() const { return data().rawPositions_.v != NULL; }
324 * Returns velocities for this selection as a continuous array.
326 * Must not be called if hasVelocities() returns false.
328 ConstArrayRef<rvec> velocities() const
330 GMX_ASSERT(hasVelocities(), "Velocities accessed, but unavailable");
331 return ConstArrayRef<rvec>(data().rawPositions_.v, posCount());
333 //! Returns whether forces are available for this selection.
334 bool hasForces() const { return sel_->rawPositions_.f != NULL; }
336 * Returns forces for this selection as a continuous array.
338 * Must not be called if hasForces() returns false.
340 ConstArrayRef<rvec> forces() const
342 GMX_ASSERT(hasForces(), "Forces accessed, but unavailable");
343 return ConstArrayRef<rvec>(data().rawPositions_.f, posCount());
345 //! Returns masses for this selection as a continuous array.
346 ConstArrayRef<real> masses() const
348 // posMass_ may have more entries than posCount() in the case of
349 // dynamic selections that don't have a topology
350 // (and thus the masses and charges are fixed).
351 GMX_ASSERT(data().posMass_.size() >= static_cast<size_t>(posCount()),
352 "Internal inconsistency");
353 return ConstArrayRef<real>(data().posMass_.begin(),
354 data().posMass_.begin() + posCount());
356 //! Returns charges for this selection as a continuous array.
357 ConstArrayRef<real> charges() const
359 // posCharge_ may have more entries than posCount() in the case of
360 // dynamic selections that don't have a topology
361 // (and thus the masses and charges are fixed).
362 GMX_ASSERT(data().posCharge_.size() >= static_cast<size_t>(posCount()),
363 "Internal inconsistency");
364 return ConstArrayRef<real>(data().posCharge_.begin(),
365 data().posCharge_.begin() + posCount());
368 * Returns reference IDs for this selection as a continuous array.
370 * \see SelectionPosition::refId()
372 ConstArrayRef<int> refIds() const
374 return ConstArrayRef<int>(data().rawPositions_.m.refid, posCount());
377 * Returns mapped IDs for this selection as a continuous array.
379 * \see SelectionPosition::mappedId()
381 ConstArrayRef<int> mappedIds() const
383 return ConstArrayRef<int>(data().rawPositions_.m.mapid, posCount());
386 //! Deprecated method for direct access to position data.
387 const gmx_ana_pos_t *positions() const { return &data().rawPositions_; }
389 //! Returns whether the covered fraction can change between frames.
390 bool isCoveredFractionDynamic() const { return data().isCoveredFractionDynamic(); }
391 //! Returns the covered fraction for the current frame.
392 real coveredFraction() const { return data().coveredFraction_; }
395 * Initializes information about covered fractions.
397 * \param[in] type Type of covered fraction required.
398 * \returns true if the covered fraction can be calculated for the
401 bool initCoveredFraction(e_coverfrac_t type)
403 return data().initCoveredFraction(type);
406 * Sets whether this selection evaluates velocities for positions.
408 * \param[in] bEnabled If true, velocities are evaluated.
410 * If you request the evaluation, but then evaluate the selection for
411 * a frame that does not contain velocity information, results are
415 * Implement it such that in the above case, hasVelocities() will
416 * return false for such frames.
420 void setEvaluateVelocities(bool bEnabled)
422 data().flags_.set(efSelection_EvaluateVelocities, bEnabled);
425 * Sets whether this selection evaluates forces for positions.
427 * \param[in] bEnabled If true, forces are evaluated.
429 * If you request the evaluation, but then evaluate the selection for
430 * a frame that does not contain force information, results are
435 void setEvaluateForces(bool bEnabled)
437 data().flags_.set(efSelection_EvaluateForces, bEnabled);
441 * Sets the ID for the \p i'th position for use with
442 * SelectionPosition::mappedId().
444 * \param[in] i Zero-based index
445 * \param[in] id Identifier to set.
447 * This method is not part of SelectionPosition because that interface
448 * only provides access to const data by design.
450 * This method can only be called after compilation, before the
451 * selection has been evaluated for any frame.
453 * \see SelectionPosition::mappedId()
455 void setOriginalId(int i, int id) { data().rawPositions_.m.orgid[i] = id; }
458 * Prints out one-line description of the selection.
460 * \param[in] fp Where to print the information.
462 * The output contains the name of the selection, the number of atoms
463 * and the number of positions, and indication of whether the selection
466 void printInfo(FILE *fp) const;
468 * Prints out extended information about the selection for debugging.
470 * \param[in] fp Where to print the information.
471 * \param[in] nmaxind Maximum number of values to print in lists
474 void printDebugInfo(FILE *fp, int nmaxind) const;
477 internal::SelectionData &data()
479 GMX_ASSERT(sel_ != NULL,
480 "Attempted to access uninitialized selection");
483 const internal::SelectionData &data() const
485 GMX_ASSERT(sel_ != NULL,
486 "Attempted to access uninitialized selection");
491 * Pointer to internal data for the selection.
493 * The memory for this object is managed by a SelectionCollection
494 * object, and the \ref Selection class simply provides a public
495 * interface for accessing the data.
497 internal::SelectionData *sel_;
500 * Needed to access the data to adjust flags.
502 friend class SelectionOptionStorage;
506 * Provides access to information about a single selected position.
508 * Each position has associated coordinates, and possibly velocities and forces
509 * if they have been requested and are available. It also has a set of atoms
510 * associated with it; typically the coordinates are the center-of-mass or
511 * center-of-geometry coordinates for that set of atoms. It is possible that
512 * there are not atoms associated if the selection has been provided as a fixed
515 * After the selection has been compiled, but not yet evaluated, the contents
516 * of the coordinate, velocity and force vectors are undefined.
518 * Default copy constructor and assignment operators are used, and work as
519 * intended: the copy references the same position and works identically.
521 * Methods in this class do not throw.
526 * \ingroup module_selection
528 class SelectionPosition
532 * Constructs a wrapper object for given selection position.
534 * \param[in] sel Selection from which the position is wrapped.
535 * \param[in] index Zero-based index of the position to wrap.
537 * Asserts if \p index is out of range.
539 * Only for internal use of the library. To obtain a SelectionPosition
540 * object in other code, use Selection::position().
542 SelectionPosition(const internal::SelectionData &sel, int index)
543 : sel_(&sel), i_(index)
545 GMX_ASSERT(index >= 0 && index < sel.posCount(),
546 "Invalid selection position index");
550 * Returns type of this position.
552 * Currently always returns the same as Selection::type().
554 e_index_t type() const { return sel_->type(); }
555 //! Returns coordinates for this position.
556 const rvec &x() const
558 return sel_->rawPositions_.x[i_];
561 * Returns velocity for this position.
563 * Must not be called if Selection::hasVelocities() returns false.
565 const rvec &v() const
567 GMX_ASSERT(sel_->rawPositions_.v != NULL,
568 "Velocities accessed, but unavailable");
569 return sel_->rawPositions_.v[i_];
572 * Returns force for this position.
574 * Must not be called if Selection::hasForces() returns false.
576 const rvec &f() const
578 GMX_ASSERT(sel_->rawPositions_.f != NULL,
579 "Velocities accessed, but unavailable");
580 return sel_->rawPositions_.f[i_];
583 * Returns total mass for this position.
585 * Returns the total mass of atoms that make up this position.
586 * If there are no atoms associated or masses are not available,
591 return sel_->posMass_[i_];
594 * Returns total charge for this position.
596 * Returns the sum of charges of atoms that make up this position.
597 * If there are no atoms associated or charges are not available,
602 return sel_->posCharge_[i_];
604 //! Returns the number of atoms that make up this position.
605 int atomCount() const
607 return sel_->rawPositions_.m.mapb.index[i_ + 1]
608 - sel_->rawPositions_.m.mapb.index[i_];
610 //! Return atom indices that make up this position.
611 ConstArrayRef<int> atomIndices() const
613 if (sel_->rawPositions_.g == NULL)
615 return ConstArrayRef<int>();
617 int first = sel_->rawPositions_.m.mapb.index[i_];
618 return ConstArrayRef<int>(&sel_->rawPositions_.g->index[first],
622 * Returns whether this position is selected in the current frame.
624 * The return value is equivalent to \c refid() == -1. Returns always
625 * true if SelectionOption::dynamicMask() has not been set.
629 bool selected() const
634 * Returns reference ID for this position.
636 * For dynamic selections, this provides means to associate positions
637 * across frames. After compilation, these IDs are consequently
638 * numbered starting from zero. For each frame, the ID then reflects
639 * the location of the position in the original array of positions.
640 * If SelectionOption::dynamicMask() has been set for the parent
641 * selection, the IDs for positions not present in the current
642 * selection are set to -1, otherwise they are removed completely.
645 * If a dynamic selection consists of at most three positions, after
646 * compilation refId() will return 0, 1, 2 for them, respectively.
647 * If for a particular frame, only the first and the third are present,
648 * refId() will return 0, 2.
649 * If SelectionOption::dynamicMask() has been set, all three positions
650 * can be accessed also for that frame and refId() will return 0, -1,
655 return sel_->rawPositions_.m.refid[i_];
658 * Returns mapped ID for this position.
660 * Returns ID of the position that corresponds to that set with
661 * Selection::setOriginalId().
663 * If for an array \c id, \c setOriginalId(i, id[i]) has been called
664 * for each \c i, then it always holds that
665 * \c mappedId()==id[refId()].
667 * Selection::setOriginalId() has not been called, the default values
668 * are dependent on type():
669 * - ::INDEX_ATOM: atom indices
670 * - ::INDEX_RES: residue numbers
671 * - ::INDEX_MOL: molecule numbers
673 * All the default values are zero-based
677 return sel_->rawPositions_.m.mapid[i_];
681 const internal::SelectionData *sel_;
686 inline SelectionPosition
687 Selection::position(int i) const
689 return SelectionPosition(data(), i);