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/*
*
* This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, The GROMACS development team,
* check out http://www.gromacs.org for more information.
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* For more info, check our website at http://www.gromacs.org
*/
/*! \file
* \brief API for handling selection (the \c gmx_ana_selection_t structure and related functions).
*
* There should be no need to use the data structures or call the
* functions in this file directly unless using the selection routines outside
* the main trajectory analysis API.
*/
#ifndef SELECTION_H
#define SELECTION_H
#include "position.h"
#include "indexutil.h"
#ifdef __cplusplus
extern "C"
{
#endif
/** Information for a collection of selections. */
typedef struct gmx_ana_selcollection_t gmx_ana_selcollection_t;
struct gmx_ana_poscalc_coll_t;
/** Defines the type of covered fraction. */
typedef enum
{
CFRAC_NONE, /**< No covered fraction (everything covered). */
CFRAC_SOLIDANGLE /**< Fraction of a solid (3D) angle covered. */
} e_coverfrac_t;
/*! \brief
* Describes a single selection.
*/
typedef struct gmx_ana_selection_t
{
/** Name of the selection. */
char *name;
/** The actual selection string. */
char *selstr;
/** Selected positions. */
gmx_ana_pos_t p;
/** Masses associated with the positions. */
real *m;
/** Charges associated with the positions. */
real *q;
/** Pointer to the index group that holds the selected atoms. */
struct gmx_ana_index_t *g;
/** TRUE if the value can change as a function of time. */
gmx_bool bDynamic;
/** Type of the covered fraction. */
e_coverfrac_t cfractype;
/** TRUE if the covered fraction depends on the frame. */
gmx_bool bCFracDyn;
/** Covered fraction of the selection for the current frame. */
real cfrac;
/** The average covered fraction (over the trajectory). */
real avecfrac;
/*! \brief
* Pointer to the root of the selection element tree (internal use only).
*
* \internal
* This field is NULL if the selection has been loaded directly from an
* index file.
*/
struct t_selelem *selelem;
/** Original masses of all possible positions (internal use only). */
real *orgm;
/** Original charges of all possible positions (internal use only). */
real *orgq;
} gmx_ana_selection_t;
/** Frees the memory allocated for a selection. */
void
gmx_ana_selection_free(gmx_ana_selection_t *sel);
/** Returns the name of a selection. */
char *
gmx_ana_selection_name(gmx_ana_selection_t *sel);
/** Prints out the selection information. */
void
gmx_ana_selection_print_info(gmx_ana_selection_t *sel);
/** Initializes the information for covered fraction. */
gmx_bool
gmx_ana_selection_init_coverfrac(gmx_ana_selection_t *sel, e_coverfrac_t type);
/** Creates a new empty selection collection. */
int
gmx_ana_selcollection_create(gmx_ana_selcollection_t **sc,
struct gmx_ana_poscalc_coll_t *pcc);
/** Frees the memory allocated for a selection collection. */
void
gmx_ana_selcollection_free(gmx_ana_selcollection_t *sc);
/** Sets the default reference position handling for a selection collection. */
void
gmx_ana_selcollection_set_refpostype(gmx_ana_selcollection_t *sc, const char *type);
/** Sets the default output position handling for a selection collection. */
void
gmx_ana_selcollection_set_outpostype(gmx_ana_selcollection_t *sc,
const char *type, gmx_bool bMaskOnly);
/** Request evaluation of velocities for selections. */
void
gmx_ana_selcollection_set_veloutput(gmx_ana_selcollection_t *sc,
gmx_bool bVelOut);
/** Request evaluation of forces for selections. */
void
gmx_ana_selcollection_set_forceoutput(gmx_ana_selcollection_t *sc,
gmx_bool bForceOut);
/** Sets the topology for a selection collection. */
int
gmx_ana_selcollection_set_topology(gmx_ana_selcollection_t *sc, t_topology *top,
int natoms);
/** Returns the number of selections specified by a selection collection. */
int
gmx_ana_selcollection_get_count(gmx_ana_selcollection_t *sc);
/** Returns a selection by index. */
gmx_ana_selection_t *
gmx_ana_selcollection_get_selection(gmx_ana_selcollection_t *sc, int i);
/** Returns TRUE if the collection requires topology information for evaluation. */
gmx_bool
gmx_ana_selcollection_requires_top(gmx_ana_selcollection_t *sc);
/** Prints a human-readable version of the internal selection element tree. */
void
gmx_ana_selcollection_print_tree(FILE *fp, gmx_ana_selcollection_t *sc, gmx_bool bValues);
/** Prints the selection strings into an XVGR file as comments. */
void
xvgr_selcollection(FILE *fp, gmx_ana_selcollection_t *sc,
const output_env_t oenv);
/* In parsetree.c */
/** Parses selection(s) from standard input. */
int
gmx_ana_selcollection_parse_stdin(gmx_ana_selcollection_t *sc, int nr,
gmx_ana_indexgrps_t *grps,
gmx_bool bInteractive);
/** Parses selection(s) from a file. */
int
gmx_ana_selcollection_parse_file(gmx_ana_selcollection_t *sc, const char *fnm,
gmx_ana_indexgrps_t *grps);
/** Parses selection(s) from a string. */
int
gmx_ana_selcollection_parse_str(gmx_ana_selcollection_t *sc, const char *str,
gmx_ana_indexgrps_t *grps);
/* In compiler.c */
/** Set debugging flag for selection compilation. */
void
gmx_ana_selcollection_set_compile_debug(gmx_ana_selcollection_t *sc, gmx_bool bDebug);
/** Prepares the selections for evaluation and performs some optimizations. */
int
gmx_ana_selcollection_compile(gmx_ana_selcollection_t *sc);
/* In evaluate.c */
/** Evaluates the selection. */
int
gmx_ana_selcollection_evaluate(gmx_ana_selcollection_t *sc,
t_trxframe *fr, t_pbc *pbc);
/** Evaluates the largest possible index groups from dynamic selections. */
int
gmx_ana_selcollection_evaluate_fin(gmx_ana_selcollection_t *sc, int nframes);
#ifdef __cplusplus
}
#endif
#endif
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