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Gromacs
2024.3
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Gromacs
2024.3
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#include <gromacs/selection/selection.h>
Internal data for a single selection.
This class is internal to the selection module, but resides in a public header because of efficiency reasons: it allows frequently used access methods in Selection to be inlined.
Methods in this class do not throw unless otherwise specified.
Public Member Functions | |
| SelectionData (SelectionTreeElement *elem, const char *selstr) | |
| Creates a new selection object. More... | |
| const char * | name () const |
| Returns the name for this selection. | |
| const char * | selectionText () const |
| Returns the string that was parsed to produce this selection. | |
| bool | isDynamic () const |
| Returns true if the size of the selection (posCount()) is dynamic. | |
| e_index_t | type () const |
| Returns the type of positions in the selection. | |
| bool | hasOnlyAtoms () const |
| Returns true if the selection only contains positions with a single atom each. | |
| bool | hasSortedAtomIndices () const |
Returns true if the atom indices in the selection are in ascending order. | |
| int | posCount () const |
| Number of positions in the selection. | |
| SelectionTreeElement & | rootElement () |
| Returns the root of the evaluation tree for this selection. | |
| bool | isCoveredFractionDynamic () const |
| Returns whether the covered fraction can change between frames. | |
| bool | hasFlag (SelectionFlag flag) const |
| Returns true if the given flag is set. | |
| void | setFlags (SelectionFlags flags) |
| Sets the flags for this selection. | |
| SelectionFlags | flags () const |
| Returns the current flags. | |
| bool | initCoveredFraction (e_coverfrac_t type) |
| Initializes information about covered fractions. More... | |
| void | refreshName () |
| Updates the name of the selection if missing. More... | |
| void | initializeMassesAndCharges (const gmx_mtop_t *top) |
| Computes total masses and charges for all selection positions. More... | |
| void | refreshMassesAndCharges (const gmx_mtop_t *top) |
| Updates masses and charges after dynamic selection has been evaluated. More... | |
| void | updateCoveredFractionForFrame () |
| Updates the covered fraction after a selection has been evaluated. More... | |
| void | computeAverageCoveredFraction (int nframes) |
| Computes average covered fraction after all frames have been evaluated. More... | |
| void | restoreOriginalPositions (const gmx_mtop_t *top) |
| Restores position information to state it was in after compilation. More... | |
Friends | |
| class | gmx::Selection |
| Needed to wrap access to information. | |
| class | gmx::SelectionPosition |
| Needed for proper access to position information. | |
| gmx::internal::SelectionData::SelectionData | ( | SelectionTreeElement * | elem, |
| const char * | selstr | ||
| ) |
Creates a new selection object.
| [in] | elem | Root of the evaluation tree for this selection. |
| [in] | selstr | String that was parsed to produce this selection. |
| std::bad_alloc | if out of memory. |
| void gmx::internal::SelectionData::computeAverageCoveredFraction | ( | int | nframes | ) |
Computes average covered fraction after all frames have been evaluated.
| [in] | nframes | Number of frames that have been evaluated. |
nframes should be equal to the number of calls to updateCoveredFractionForFrame(). Called by SelectionEvaluator::evaluateFinal().
| bool gmx::internal::SelectionData::initCoveredFraction | ( | e_coverfrac_t | type | ) |
Initializes information about covered fractions.
| [in] | type | Type of covered fraction required. |
| void gmx::internal::SelectionData::initializeMassesAndCharges | ( | const gmx_mtop_t * | top | ) |
Computes total masses and charges for all selection positions.
| [in] | top | Topology information. |
| std::bad_alloc | if out of memory. |
For dynamic selections, the values need to be updated after each evaluation with refreshMassesAndCharges(). This is done by SelectionEvaluator.
This function is called by SelectionCompiler.
Strong exception safety guarantee.
| void gmx::internal::SelectionData::refreshMassesAndCharges | ( | const gmx_mtop_t * | top | ) |
Updates masses and charges after dynamic selection has been evaluated.
| [in] | top | Topology information. |
Called by SelectionEvaluator.
| void gmx::internal::SelectionData::refreshName | ( | ) |
Updates the name of the selection if missing.
| std::bad_alloc | if out of memory. |
If selections get their value from a group reference that cannot be resolved during parsing, the name is final only after group references have been resolved.
This function is called by SelectionCollection::setIndexGroups().
| void gmx::internal::SelectionData::restoreOriginalPositions | ( | const gmx_mtop_t * | top | ) |
Restores position information to state it was in after compilation.
| [in] | top | Topology information. |
Depends on SelectionCompiler storing the original atoms in the rootElement_ object. Called by SelectionEvaluator::evaluateFinal().
| void gmx::internal::SelectionData::updateCoveredFractionForFrame | ( | ) |
Updates the covered fraction after a selection has been evaluated.
Called by SelectionEvaluator.
1.8.5