/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2009-2017, 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.
/** Defines the boolean operation of gmx::SelectionTreeElement objects with type \ref SEL_BOOLEAN. */
typedef enum
{
- BOOL_NOT, /**< Not */
- BOOL_AND, /**< And */
- BOOL_OR, /**< Or */
- BOOL_XOR /**< Xor (not implemented). */
+ BOOL_NOT, /**< Not */
+ BOOL_AND, /**< And */
+ BOOL_OR, /**< Or */
+ BOOL_XOR /**< Xor (not implemented). */
} e_boolean_t;
/** Defines the arithmetic operation of gmx::SelectionTreeElement objects with type \ref SEL_ARITHMETIC. */
typedef enum
{
- ARITH_PLUS, /**< Addition (`+`) */
- ARITH_MINUS, /**< Subtraction (`-`) */
- ARITH_NEG, /**< Unary `-` */
- ARITH_MULT, /**< Multiplication (`*`) */
- ARITH_DIV, /**< Division (`/`) */
- ARITH_EXP /**< Power (`^`) */
+ ARITH_PLUS, /**< Addition (`+`) */
+ ARITH_MINUS, /**< Subtraction (`-`) */
+ ARITH_NEG, /**< Unary `-` */
+ ARITH_MULT, /**< Multiplication (`*`) */
+ ARITH_DIV, /**< Division (`/`) */
+ ARITH_EXP /**< Power (`^`) */
} e_arithmetic_t;
/** Returns a string representation of the type of a gmx::SelectionTreeElement. */
-extern const char *
-_gmx_selelem_type_str(const gmx::SelectionTreeElement &sel);
+extern const char* _gmx_selelem_type_str(const gmx::SelectionTreeElement& sel);
/** Returns a string representation of the boolean type of a \ref SEL_BOOLEAN gmx::SelectionTreeElement. */
-extern const char *
-_gmx_selelem_boolean_type_str(const gmx::SelectionTreeElement &sel);
+extern const char* _gmx_selelem_boolean_type_str(const gmx::SelectionTreeElement& sel);
/** Returns a string representation of the type of a \c gmx_ana_selvalue_t. */
-extern const char *
-_gmx_sel_value_type_str(const gmx_ana_selvalue_t *val);
+extern const char* _gmx_sel_value_type_str(const gmx_ana_selvalue_t* val);
//!\}
* If this flag is set, the flags covered by \ref SEL_VALFLAGMASK
* have been set properly for the element.
*/
-#define SEL_FLAGSSET 1
+#define SEL_FLAGSSET 1
/*! \brief
* The element evaluates to a single value.
*
* This flag is always set for \ref GROUP_VALUE elements.
*/
-#define SEL_SINGLEVAL 2
+#define SEL_SINGLEVAL 2
/*! \brief
* The element evaluates to one value for each input atom.
*/
-#define SEL_ATOMVAL 4
+#define SEL_ATOMVAL 4
/*! \brief
* The element evaluates to an arbitrary number of values.
*/
-#define SEL_VARNUMVAL 8
+#define SEL_VARNUMVAL 8
/*! \brief
* The element (or one of its children) is dynamic.
*/
-#define SEL_DYNAMIC 16
+#define SEL_DYNAMIC 16
/*! \brief
* The element may contain atom indices in an unsorted order.
*/
-#define SEL_UNSORTED 32
+#define SEL_UNSORTED 32
/*! \brief
* Mask that covers the flags that describe the number of values.
*/
* is changed and is used in places where this flag is not, so this would
* require a careful investigation of the selection code.
*/
-#define SEL_ALLOCVAL (1<<8)
+#define SEL_ALLOCVAL (1 << 8)
/*! \brief
* Data has been allocated for the group/position structure.
*
* This field has no effect if the value type is not \ref GROUP_VALUE or
* \ref POS_VALUE, but should not be set.
*/
-#define SEL_ALLOCDATA (1<<9)
+#define SEL_ALLOCDATA (1 << 9)
/*! \brief
* \p method->init_frame should be called for the frame.
*/
-#define SEL_INITFRAME (1<<10)
+#define SEL_INITFRAME (1 << 10)
/*! \brief
* Parameter has been evaluated for the current frame.
*
* It is not set for \ref SEL_ATOMVAL elements, because they may need to
* be evaluated multiple times.
*/
-#define SEL_EVALFRAME (1<<11)
+#define SEL_EVALFRAME (1 << 11)
/*! \brief
* \p method->init has been called.
*/
-#define SEL_METHODINIT (1<<12)
+#define SEL_METHODINIT (1 << 12)
/*! \brief
* \p method->outinit has been called.
*
* This flag is also used for \ref SEL_SUBEXPRREF elements.
*/
-#define SEL_OUTINIT (1<<13)
+#define SEL_OUTINIT (1 << 13)
//!\}
/*! \brief
* Function pointer for evaluating a gmx::SelectionTreeElement.
*/
-typedef void (*sel_evalfunc)(struct gmx_sel_evaluate_t *data,
- const SelectionTreeElementPointer &sel,
- gmx_ana_index_t *g);
+typedef void (*sel_evalfunc)(struct gmx_sel_evaluate_t* data,
+ const SelectionTreeElementPointer& sel,
+ gmx_ana_index_t* g);
//! \endcond
/*! \internal
//! Returns an empty location.
static SelectionLocation createEmpty()
{
- SelectionLocation empty = {0, 0};
+ SelectionLocation empty = { 0, 0 };
return empty;
}
//! Start index of the string where this element has been parsed from.
- int startIndex;
+ int startIndex;
//! End index of the string where this element has been parsed from.
- int endIndex;
+ int endIndex;
};
/*! \internal \brief
*/
class SelectionTreeElement
{
- public:
- /*! \brief
- * Allocates memory and performs common initialization.
+public:
+ /*! \brief
+ * Allocates memory and performs common initialization.
+ *
+ * \param[in] type Type of selection element to create.
+ * \param[in] location Location of the element.
+ *
+ * \a type is set to \p type,
+ * \a v::type is set to \ref GROUP_VALUE for boolean and comparison
+ * expressions and \ref NO_VALUE for others, and
+ * \ref SEL_ALLOCVAL is set for non-root elements (\ref SEL_ALLOCDATA
+ * is also set for \ref SEL_BOOLEAN elements).
+ * All the pointers are set to NULL.
+ */
+ SelectionTreeElement(e_selelem_t type, const SelectionLocation& location);
+ ~SelectionTreeElement();
+
+ //! Frees the memory allocated for the \a v union.
+ void freeValues();
+ //! Frees the memory allocated for the \a u union.
+ void freeExpressionData();
+ /* In compiler.cpp */
+ /*! \brief
+ * Frees the memory allocated for the selection compiler.
+ *
+ * This function only frees the data for the given selection, not its
+ * children. It is safe to call the function when compiler data has
+ * not been allocated or has already been freed; in such a case,
+ * nothing is done.
+ */
+ void freeCompilerData();
+
+ /*! \brief
+ * Reserves memory for value from a memory pool.
+ *
+ * \param[in] count Number of values to reserve memory for.
+ *
+ * Reserves memory for the values of this element from the \a mempool
+ * memory pool.
+ * If no memory pool is set, nothing is done.
+ */
+ void mempoolReserve(int count);
+ /*! \brief
+ * Releases memory pool used for value.
+ *
+ * Releases the memory allocated for the values of this element from the
+ * \a mempool memory pool.
+ * If no memory pool is set, nothing is done.
+ */
+ void mempoolRelease();
+
+ //! Returns the name of the element.
+ const std::string& name() const { return name_; }
+ //! Returns the location of the element.
+ const SelectionLocation& location() const { return location_; }
+
+ /*! \brief
+ * Sets the name of the element.
+ *
+ * \param[in] name Name to set (can be NULL).
+ * \throws std::bad_alloc if out of memory.
+ */
+ void setName(const char* name) { name_ = (name != nullptr ? name : ""); }
+ //! \copydoc setName(const char *)
+ void setName(const std::string& name) { name_ = name; }
+ /*! \brief
+ * Sets the name of a root element if it is missing.
+ *
+ * \param[in] selectionText Full selection text to use as a fallback.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * If index groups have not yet been set and the selection is a result
+ * of a group reference, the name may still be empty after this call.
+ *
+ * Strong exception safety guarantee.
+ */
+ void fillNameIfMissing(const char* selectionText);
+
+ /*! \brief
+ * Returns which topology properties the selection element subtree requires
+ * for evaluation.
+ *
+ * \returns List of topology properties required for evaluation.
+ */
+ SelectionTopologyProperties requiredTopologyProperties() const;
+ /*! \brief
+ * Checks that this element and its children do not contain unsupported
+ * elements with unsorted atoms.
+ *
+ * \param[in] bUnsortedAllowed Whether this element's parents allow it
+ * to have unsorted atoms.
+ * \param errors Object for reporting any error messages.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Errors are reported as nested exceptions in \p errors.
+ */
+ void checkUnsortedAtoms(bool bUnsortedAllowed, ExceptionInitializer* errors) const;
+ /*! \brief
+ * Checks whether the element or its children have unresolved index
+ * group references.
+ *
+ * Does not throw.
+ */
+ bool requiresIndexGroups() const;
+ /*! \brief
+ * Resolves an unresolved reference to an index group.
+ *
+ * \param[in] grps Index groups to use to resolve the reference.
+ * \param[in] natoms Maximum number of atoms the selections can evaluate to
+ * (zero if the topology/atom count is not set yet).
+ * \throws std::bad_alloc if out of memory.
+ * \throws InconsistentInputError if the reference cannot be
+ * resolved.
+ */
+ void resolveIndexGroupReference(gmx_ana_indexgrps_t* grps, int natoms);
+ /*! \brief
+ * Checks that an index group has valid atom indices.
+ *
+ * \param[in] natoms Maximum number of atoms the selections can evaluate to.
+ * \throws std::bad_alloc if out of memory.
+ * \throws InconsistentInputError if there are invalid atom indices.
+ */
+ void checkIndexGroup(int natoms);
+
+ //! Type of the element.
+ e_selelem_t type;
+ /*! \brief
+ * Value storage of the element.
+ *
+ * This field contains the evaluated value of the element, as well as
+ * the output value type.
+ */
+ gmx_ana_selvalue_t v;
+ /*! \brief
+ * Evaluation function for the element.
+ *
+ * Can be either NULL (if the expression is a constant and does not
+ * require evaluation) or point to one of the functions defined in
+ * evaluate.h.
+ */
+ sel_evalfunc evaluate;
+ /*! \brief
+ * Information flags about the element.
+ *
+ * Allowed flags are listed here:
+ * \ref selelem_flags "flags for gmx::SelectionTreeElement".
+ */
+ int flags;
+ //! Data required by the evaluation function.
+ union {
+ /*! \brief Index group data for several element types.
*
- * \param[in] type Type of selection element to create.
- * \param[in] location Location of the element.
- *
- * \a type is set to \p type,
- * \a v::type is set to \ref GROUP_VALUE for boolean and comparison
- * expressions and \ref NO_VALUE for others, and
- * \ref SEL_ALLOCVAL is set for non-root elements (\ref SEL_ALLOCDATA
- * is also set for \ref SEL_BOOLEAN elements).
- * All the pointers are set to NULL.
- */
- SelectionTreeElement(e_selelem_t type, const SelectionLocation &location);
- ~SelectionTreeElement();
-
- //! Frees the memory allocated for the \a v union.
- void freeValues();
- //! Frees the memory allocated for the \a u union.
- void freeExpressionData();
- /* In compiler.cpp */
- /*! \brief
- * Frees the memory allocated for the selection compiler.
- *
- * This function only frees the data for the given selection, not its
- * children. It is safe to call the function when compiler data has
- * not been allocated or has already been freed; in such a case,
- * nothing is done.
- */
- void freeCompilerData();
-
- /*! \brief
- * Reserves memory for value from a memory pool.
- *
- * \param[in] count Number of values to reserve memory for.
- *
- * Reserves memory for the values of this element from the \a mempool
- * memory pool.
- * If no memory pool is set, nothing is done.
- */
- void mempoolReserve(int count);
- /*! \brief
- * Releases memory pool used for value.
- *
- * Releases the memory allocated for the values of this element from the
- * \a mempool memory pool.
- * If no memory pool is set, nothing is done.
- */
- void mempoolRelease();
-
- //! Returns the name of the element.
- const std::string &name() const { return name_; }
- //! Returns the location of the element.
- const SelectionLocation &location() const { return location_; }
-
- /*! \brief
- * Sets the name of the element.
- *
- * \param[in] name Name to set (can be NULL).
- * \throws std::bad_alloc if out of memory.
- */
- void setName(const char *name) { name_ = (name != nullptr ? name : ""); }
- //! \copydoc setName(const char *)
- void setName(const std::string &name) { name_ = name; }
- /*! \brief
- * Sets the name of a root element if it is missing.
- *
- * \param[in] selectionText Full selection text to use as a fallback.
- * \throws std::bad_alloc if out of memory.
- *
- * If index groups have not yet been set and the selection is a result
- * of a group reference, the name may still be empty after this call.
- *
- * Strong exception safety guarantee.
- */
- void fillNameIfMissing(const char *selectionText);
-
- /*! \brief
- * Returns which topology properties the selection element subtree requires
- * for evaluation.
- *
- * \returns List of topology properties required for evaluation.
- */
- SelectionTopologyProperties requiredTopologyProperties() const;
- /*! \brief
- * Checks that this element and its children do not contain unsupported
- * elements with unsorted atoms.
- *
- * \param[in] bUnsortedAllowed Whether this element's parents allow it
- * to have unsorted atoms.
- * \param errors Object for reporting any error messages.
- * \throws std::bad_alloc if out of memory.
- *
- * Errors are reported as nested exceptions in \p errors.
- */
- void checkUnsortedAtoms(bool bUnsortedAllowed,
- ExceptionInitializer *errors) const;
- /*! \brief
- * Checks whether the element or its children have unresolved index
- * group references.
- *
- * Does not throw.
- */
- bool requiresIndexGroups() const;
- /*! \brief
- * Resolves an unresolved reference to an index group.
- *
- * \param[in] grps Index groups to use to resolve the reference.
- * \param[in] natoms Maximum number of atoms the selections can evaluate to
- * (zero if the topology/atom count is not set yet).
- * \throws std::bad_alloc if out of memory.
- * \throws InconsistentInputError if the reference cannot be
- * resolved.
- */
- void resolveIndexGroupReference(gmx_ana_indexgrps_t *grps, int natoms);
- /*! \brief
- * Checks that an index group has valid atom indices.
- *
- * \param[in] natoms Maximum number of atoms the selections can evaluate to.
- * \throws std::bad_alloc if out of memory.
- * \throws InconsistentInputError if there are invalid atom indices.
- */
- void checkIndexGroup(int natoms);
-
- //! Type of the element.
- e_selelem_t type;
- /*! \brief
- * Value storage of the element.
- *
- * This field contains the evaluated value of the element, as well as
- * the output value type.
- */
- gmx_ana_selvalue_t v;
- /*! \brief
- * Evaluation function for the element.
- *
- * Can be either NULL (if the expression is a constant and does not
- * require evaluation) or point to one of the functions defined in
- * evaluate.h.
- */
- sel_evalfunc evaluate;
- /*! \brief
- * Information flags about the element.
- *
- * Allowed flags are listed here:
- * \ref selelem_flags "flags for gmx::SelectionTreeElement".
+ * - \ref SEL_CONST : if the value type is \ref GROUP_VALUE,
+ * this field holds the unprocessed group value.
+ * - \ref SEL_ROOT : holds the group value for which the
+ * selection subtree should be evaluated.
+ * - \ref SEL_SUBEXPR : holds the group for which the subexpression
+ * has been evaluated.
*/
- int flags;
- //! Data required by the evaluation function.
- union {
- /*! \brief Index group data for several element types.
- *
- * - \ref SEL_CONST : if the value type is \ref GROUP_VALUE,
- * this field holds the unprocessed group value.
- * - \ref SEL_ROOT : holds the group value for which the
- * selection subtree should be evaluated.
- * - \ref SEL_SUBEXPR : holds the group for which the subexpression
- * has been evaluated.
- */
- gmx_ana_index_t cgrp;
- //! Data for \ref SEL_EXPRESSION and \ref SEL_MODIFIER elements.
- struct {
- //! Pointer the method used in this expression.
- struct gmx_ana_selmethod_t *method;
- //! Pointer to the data allocated by the method's \p init_data (see sel_datafunc()).
- void *mdata;
- //! Pointer to the position data passed to the method.
- struct gmx_ana_pos_t *pos;
- //! Pointer to the evaluation data for \p pos.
- struct gmx_ana_poscalc_t *pc;
- } expr;
- //! Operation type for \ref SEL_BOOLEAN elements.
- e_boolean_t boolt;
- //! Operation type for \ref SEL_ARITHMETIC elements.
- struct {
- //! Operation type.
- e_arithmetic_t type;
- //! String representation.
- char *opstr;
- } arith;
- //! Associated selection parameter for \ref SEL_SUBEXPRREF elements.
- struct gmx_ana_selparam_t *param;
- //! The string/number used to reference the group.
- struct {
- //! Name of the referenced external group.
- char *name;
- //! If \a name is NULL, the index number of the referenced group.
- int id;
- } gref;
- } u;
- //! Memory pool to use for values, or NULL if standard memory handling.
- struct gmx_sel_mempool_t *mempool;
- //! Internal data for the selection compiler.
- t_compiler_data *cdata;
-
- /*! \brief The first child element.
- *
- * Other children can be accessed through the \p next field of \p child.
- */
- SelectionTreeElementPointer child;
- //! The next sibling element.
- SelectionTreeElementPointer next;
-
- private:
- /*! \brief
- * Name of the element.
- *
- * This field is only used for diagnostic purposes.
- */
- std::string name_;
- /*! \brief
- * Location of the element in the selection text.
- *
- * This field is only used for diagnostic purposes (including error
- * messages).
- */
- SelectionLocation location_;
-
- GMX_DISALLOW_COPY_AND_ASSIGN(SelectionTreeElement);
+ gmx_ana_index_t cgrp;
+ //! Data for \ref SEL_EXPRESSION and \ref SEL_MODIFIER elements.
+ struct
+ {
+ //! Pointer the method used in this expression.
+ struct gmx_ana_selmethod_t* method;
+ //! Pointer to the data allocated by the method's \p init_data (see sel_datafunc()).
+ void* mdata;
+ //! Pointer to the position data passed to the method.
+ struct gmx_ana_pos_t* pos;
+ //! Pointer to the evaluation data for \p pos.
+ struct gmx_ana_poscalc_t* pc;
+ } expr;
+ //! Operation type for \ref SEL_BOOLEAN elements.
+ e_boolean_t boolt;
+ //! Operation type for \ref SEL_ARITHMETIC elements.
+ struct
+ {
+ //! Operation type.
+ e_arithmetic_t type;
+ //! String representation.
+ char* opstr;
+ } arith;
+ //! Associated selection parameter for \ref SEL_SUBEXPRREF elements.
+ struct gmx_ana_selparam_t* param;
+ //! The string/number used to reference the group.
+ struct
+ {
+ //! Name of the referenced external group.
+ char* name;
+ //! If \a name is NULL, the index number of the referenced group.
+ int id;
+ } gref;
+ } u;
+ //! Memory pool to use for values, or NULL if standard memory handling.
+ struct gmx_sel_mempool_t* mempool;
+ //! Internal data for the selection compiler.
+ t_compiler_data* cdata;
+
+ /*! \brief The first child element.
+ *
+ * Other children can be accessed through the \p next field of \p child.
+ */
+ SelectionTreeElementPointer child;
+ //! The next sibling element.
+ SelectionTreeElementPointer next;
+
+private:
+ /*! \brief
+ * Name of the element.
+ *
+ * This field is only used for diagnostic purposes.
+ */
+ std::string name_;
+ /*! \brief
+ * Location of the element in the selection text.
+ *
+ * This field is only used for diagnostic purposes (including error
+ * messages).
+ */
+ SelectionLocation location_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(SelectionTreeElement);
};
} // namespace gmx
/* In evaluate.c */
/** Writes out a human-readable name for an evaluation function. */
-void
-_gmx_sel_print_evalfunc_name(FILE *fp, gmx::sel_evalfunc evalfunc);
+void _gmx_sel_print_evalfunc_name(FILE* fp, gmx::sel_evalfunc evalfunc);
/** Sets the value type of a gmx::SelectionTreeElement. */
-void
-_gmx_selelem_set_vtype(const gmx::SelectionTreeElementPointer &sel,
- e_selvalue_t vtype);
+void _gmx_selelem_set_vtype(const gmx::SelectionTreeElementPointer& sel, e_selvalue_t vtype);
/*! \brief
* Frees the memory allocated for a selection method parameter.
*
* \param[in] param Parameter to free.
*/
-void
-_gmx_selelem_free_param(struct gmx_ana_selparam_t *param);
+void _gmx_selelem_free_param(struct gmx_ana_selparam_t* param);
/*! \brief
* Frees the memory allocated for a selection method.
*
* \param[in] method Method to free.
* \param[in] mdata Method data to free.
*/
-void
-_gmx_selelem_free_method(struct gmx_ana_selmethod_t *method, void *mdata);
+void _gmx_selelem_free_method(struct gmx_ana_selmethod_t* method, void* mdata);
/** Prints a human-readable version of a selection element subtree. */
-void
-_gmx_selelem_print_tree(FILE *fp, const gmx::SelectionTreeElement &sel,
- bool bValues, int level);
+void _gmx_selelem_print_tree(FILE* fp, const gmx::SelectionTreeElement& sel, bool bValues, int level);
/* In compiler.c */
/** Prints a human-readable version of the internal compiler data structure. */
-void
-_gmx_selelem_print_compiler_info(FILE *fp, const gmx::SelectionTreeElement &sel,
- int level);
+void _gmx_selelem_print_compiler_info(FILE* fp, const gmx::SelectionTreeElement& sel, int level);
/* In sm_insolidangle.c */
/** Returns true if the covered fraction of the selection can be calculated. */
-bool
-_gmx_selelem_can_estimate_cover(const gmx::SelectionTreeElement &sel);
+bool _gmx_selelem_can_estimate_cover(const gmx::SelectionTreeElement& sel);
/** Returns the covered fraction of the selection for the current frame. */
-real
-_gmx_selelem_estimate_coverfrac(const gmx::SelectionTreeElement &sel);
+real _gmx_selelem_estimate_coverfrac(const gmx::SelectionTreeElement& sel);
//!\}
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