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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \file
* \brief API for handling index files and index groups.
* Some of the checking functions can be useful outside the selection engine to
* check the validity of input groups.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \inlibraryapi
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_INDEXUTIL_H
#define GMX_SELECTION_INDEXUTIL_H
-#include "../legacyheaders/typedefs.h"
+#include <cstdio>
+
+#include <string>
+
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/topology/block.h"
+
+struct t_topology;
/** Stores a set of index groups. */
-typedef struct gmx_ana_indexgrps_t gmx_ana_indexgrps_t;
+struct gmx_ana_indexgrps_t;
/*! \brief
* Specifies the type of index partition or index mapping in several contexts.
/*! \brief
* Stores a single index group.
*/
-typedef struct gmx_ana_index_t
+struct gmx_ana_index_t
{
/** Number of atoms. */
int isize;
/** List of atoms. */
atom_id *index;
- /** Group name. */
- char *name;
/** Number of items allocated for \p index. */
int nalloc_index;
-} gmx_ana_index_t;
+};
/*! \brief
* Data structure for calculating index group mappings.
*/
-typedef struct gmx_ana_indexmap_t
+struct gmx_ana_indexmap_t
{
/** Type of the mapping. */
e_index_t type;
- /*! \brief
- * Current number of mapped values.
- *
- * This is the current number of values in the \p refid and \p mapid
- * arrays.
- * If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this
- * is always equal to \p b.nr, i.e., the number of blocks in the
- * original index group.
- */
- int nr;
/*! \brief
* Current reference IDs.
*
* Mapped block structure.
*
* A block structure that corresponds to the current index group.
+ * \c mapb.nra and \c mapb.a correspond to the last mapped index group.
*/
- t_block mapb;
+ t_blocka mapb;
/*! \brief
* Arbitrary ID numbers for the blocks.
* actually static.
*/
bool bStatic;
- /*! \brief
- * true if the current mapping is for the whole group (internal use only).
- *
- * This is used internally to optimize the evaluation such that
- * gmx_ana_indexmap_update() does not take any time if the group is
- * actually static.
- */
- bool bMapStatic;
-} gmx_ana_indexmap_t;
+};
/*! \name Functions for handling gmx_ana_indexgrps_t
*/
/*@{*/
-/** Allocate memory for index groups. */
-void
-gmx_ana_indexgrps_alloc(gmx_ana_indexgrps_t **g, int ngrps);
/** Reads index groups from a file or constructs them from topology. */
void
gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
/** Frees memory allocated for index groups. */
void
gmx_ana_indexgrps_free(gmx_ana_indexgrps_t *g);
-/** Create a deep copy of \c gmx_ana_indexgrps_t. */
-void
-gmx_ana_indexgrps_clone(gmx_ana_indexgrps_t **dest, gmx_ana_indexgrps_t *src);
/** Returns true if the index group structure is emtpy. */
bool
gmx_ana_indexgrps_is_empty(gmx_ana_indexgrps_t *g);
gmx_ana_indexgrps_get_grp(gmx_ana_indexgrps_t *g, int n);
/** Extracts a single index group. */
bool
-gmx_ana_indexgrps_extract(gmx_ana_index_t *dest, gmx_ana_indexgrps_t *src, int n);
+gmx_ana_indexgrps_extract(gmx_ana_index_t *dest, std::string *destName,
+ gmx_ana_indexgrps_t *src, int n);
/** Finds and extracts a single index group by name. */
bool
-gmx_ana_indexgrps_find(gmx_ana_index_t *dest, gmx_ana_indexgrps_t *src, char *name);
+gmx_ana_indexgrps_find(gmx_ana_index_t *dest, std::string *destName,
+ gmx_ana_indexgrps_t *src, const char *name);
/** Writes out a list of index groups. */
void
gmx_ana_index_clear(gmx_ana_index_t *g);
/** Constructs a \c gmx_ana_index_t from given values. */
void
-gmx_ana_index_set(gmx_ana_index_t *g, int isize, atom_id *index, char *name,
- int nalloc);
+gmx_ana_index_set(gmx_ana_index_t *g, int isize, atom_id *index, int nalloc);
/** Creates a simple index group from the first to the \p natoms'th atom. */
void
-gmx_ana_index_init_simple(gmx_ana_index_t *g, int natoms, char *name);
+gmx_ana_index_init_simple(gmx_ana_index_t *g, int natoms);
/** Frees memory allocated for an index group. */
void
gmx_ana_index_deinit(gmx_ana_index_t *g);
/** Writes out the contents of a index group. */
void
-gmx_ana_index_dump(FILE *fp, gmx_ana_index_t *g, int i, int maxn);
+gmx_ana_index_dump(FILE *fp, gmx_ana_index_t *g, int maxn);
-/** Checks whether all indices are between 0 and \p natoms. */
-void
-gmx_ana_index_check(gmx_ana_index_t *g, int natoms);
+/*! \brief
+ * Returns maximum atom index that appears in an index group.
+ *
+ * \param[in] g Index group to query.
+ * \returns Largest atom index that appears in \p g, or zero if \p g is empty.
+ */
+int
+gmx_ana_index_get_max_index(gmx_ana_index_t *g);
/** Checks whether an index group is sorted. */
bool
gmx_ana_index_check_sorted(gmx_ana_index_t *g);
+/*! \brief
+ * Checks whether an index group has atoms from a defined range.
+ *
+ * \param[in] g Index group to check.
+ * \param[in] natoms Largest atom number allowed.
+ * \returns true if all atoms in the index group are in the
+ * range 0 to \p natoms (i.e., no atoms over \p natoms are referenced).
+ */
+bool
+gmx_ana_index_check_range(gmx_ana_index_t *g, int natoms);
/*@}*/
/*! \name Functions for set operations on gmx_ana_index_t
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff