/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2009-2016, The GROMACS development team.
+ * Copyright (c) 2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_ana_selcollection_t
{
//! Position calculation collection used for selection position evaluation.
- gmx::PositionCalculationCollection pcc;
+ gmx::PositionCalculationCollection pcc;
//! Root of the selection element tree.
- gmx::SelectionTreeElementPointer root;
+ gmx::SelectionTreeElementPointer root;
/*! \brief
* Array of compiled selections.
*
* but note that gmx::Selection instances also hold pointers to the
* objects.
*/
- gmx::SelectionDataList sel;
+ gmx::SelectionDataList sel;
/** Number of variables defined. */
- int nvars;
+ int nvars;
/** Selection strings for variables. */
- char **varstrs;
+ char** varstrs;
/** Topology for the collection. */
- const gmx_mtop_t *top;
+ const gmx_mtop_t* top;
/** Index group that contains all the atoms. */
- gmx_ana_index_t gall;
+ gmx_ana_index_t gall;
/** Memory pool used for selection evaluation. */
- gmx_sel_mempool_t *mempool;
+ gmx_sel_mempool_t* mempool;
//! Parser symbol table.
// Never releases ownership.
- std::unique_ptr<gmx::SelectionParserSymbolTable> symtab;
+ std::unique_ptr<gmx::SelectionParserSymbolTable> symtab;
//! Root of help topic tree (NULL is no help yet requested).
- gmx::HelpTopicPointer rootHelp;
+ gmx::HelpTopicPointer rootHelp;
};
namespace gmx
*/
class SelectionCollection::Impl
{
- public:
- /*! \brief
- * Creates a new selection collection.
- *
- * \throws std::bad_alloc if out of memory.
- */
- Impl();
- ~Impl();
-
- /*! \brief
- * Clears the symbol table of the selection collection.
- *
- * Does not throw.
- */
- void clearSymbolTable();
- /*! \brief
- * Replace group references by group contents.
- *
- * \param[in] root Root of selection tree to process.
- * \param errors Object for reporting any error messages.
- * \throws std::bad_alloc if out of memory.
- *
- * Recursively searches the selection tree for unresolved external
- * references. If one is found, finds the referenced group in
- * \a grps_ and replaces the reference with a constant element that
- * contains the atoms from the referenced group. Any failures to
- * resolve references are reported to \p errors.
- */
- void resolveExternalGroups(const gmx::SelectionTreeElementPointer &root,
- ExceptionInitializer *errors);
-
- //! Whether forces have been requested for some selection.
- bool areForcesRequested() const;
- /*! \brief
- * Returns topology properties needed for a certain position type.
- */
- SelectionTopologyProperties
- requiredTopologyPropertiesForPositionType(const std::string &post,
- bool forces) const;
-
- //! Internal data, used for interfacing with old C code.
- gmx_ana_selcollection_t sc_;
- //! Default reference position type for selections.
- std::string rpost_;
- //! Default output position type for selections.
- std::string spost_;
- //! Atoms needed for evaluating the selections.
- gmx_ana_index_t requiredAtoms_;
- /*! \brief
- * Debugging level for the collection.
- *
- * Possible values:
- * - 0: no debugging
- * - 1: print selection trees after parsing and compilation
- * - 2: like 1, also print intermediate compilation trees
- * - 3: like 1, also print the tree after evaluation
- * - 4: combine 2 and 3
- */
- int debugLevel_;
- //! Whether setIndexGroups() has been called.
- bool bExternalGroupsSet_;
- //! External index groups (can be NULL).
- gmx_ana_indexgrps_t *grps_;
+public:
+ /*! \brief
+ * Creates a new selection collection.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ Impl();
+ ~Impl();
+
+ /*! \brief
+ * Clears the symbol table of the selection collection.
+ *
+ * Does not throw.
+ */
+ void clearSymbolTable();
+ /*! \brief
+ * Replace group references by group contents.
+ *
+ * \param[in] root Root of selection tree to process.
+ * \param errors Object for reporting any error messages.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Recursively searches the selection tree for unresolved external
+ * references. If one is found, finds the referenced group in
+ * \a grps_ and replaces the reference with a constant element that
+ * contains the atoms from the referenced group. Any failures to
+ * resolve references are reported to \p errors.
+ */
+ void resolveExternalGroups(const gmx::SelectionTreeElementPointer& root, ExceptionInitializer* errors);
+
+ //! Whether forces have been requested for some selection.
+ bool areForcesRequested() const;
+ /*! \brief
+ * Returns topology properties needed for a certain position type.
+ */
+ SelectionTopologyProperties requiredTopologyPropertiesForPositionType(const std::string& post,
+ bool forces) const;
+
+ //! Internal data, used for interfacing with old C code.
+ gmx_ana_selcollection_t sc_;
+ //! Default reference position type for selections.
+ std::string rpost_;
+ //! Default output position type for selections.
+ std::string spost_;
+ //! Atoms needed for evaluating the selections.
+ gmx_ana_index_t requiredAtoms_;
+ /*! \brief
+ * Debugging level for the collection.
+ *
+ * Possible values:
+ * - 0: no debugging
+ * - 1: print selection trees after parsing and compilation
+ * - 2: like 1, also print intermediate compilation trees
+ * - 3: like 1, also print the tree after evaluation
+ * - 4: combine 2 and 3
+ */
+ int debugLevel_;
+ //! Whether setIndexGroups() has been called.
+ bool bExternalGroupsSet_;
+ //! External index groups (can be NULL).
+ gmx_ana_indexgrps_t* grps_;
};
/*! \internal
*/
class SelectionEvaluator
{
- public:
- SelectionEvaluator();
-
- /*! \brief
- * Evaluates selections in a collection.
- */
- void evaluate(SelectionCollection *sc, t_trxframe *fr, t_pbc *pbc);
- /*! \brief
- * Evaluates the final state for dynamic selections.
- */
- void evaluateFinal(SelectionCollection *sc, int nframes);
+public:
+ SelectionEvaluator();
+
+ /*! \brief
+ * Evaluates selections in a collection.
+ */
+ void evaluate(SelectionCollection* sc, t_trxframe* fr, t_pbc* pbc);
+ /*! \brief
+ * Evaluates the final state for dynamic selections.
+ */
+ void evaluateFinal(SelectionCollection* sc, int nframes);
};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff