src/gromacs/selection.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
   5  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   6  * others, as listed in the AUTHORS file in the top-level source
   7  * directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \defgroup module_selection Parsing and Evaluation of Analysis Selections (selection)
  36  * \ingroup group_analysismodules
  37  * \brief
  38  * Provides functionality for initializing and evaluating selections.
  39  *
  40  * The core of the selection engine is accessed through
  41  * gmx::SelectionCollection, which manages a set of selections.
  42  * Documentation for that class explains the general selection mechanisms.
  43  *
  44  * For each selection that is parsed using a gmx::SelectionCollection, a
  45  * gmx::Selection handle is returned and can be used to access information
  46  * about that selection.  gmx::SelectionPosition is a helper class used to
  47  * access information about individual positions in a selection.  These classes
  48  * refer to internal state within the gmx::SelectionCollection, and their
  49  * contents update automatically when the gmx::SelectionCollection is compiled
  50  * or evaluated.
  51  *
  52  * This module also provides gmx::SelectionOption and gmx::SelectionOptionInfo
  53  * classes for declaring options that evaluate to selections (see \ref
  54  * module_options for general explanation of the options mechanism).  These
  55  * classes provide the main interface to obtain gmx::Selection objects in
  56  * trajectory analysis using gmx::TrajectoryAnalysisModule.
  57  * To use these classes outside the trajectory analysis framework,
  58  * a gmx::SelectionOptionManager needs to be created to serve as a bridge
  59  * between the selection option classes and the gmx::SelectionCollection
  60  * object.
  61  * \if libapi
  62  * gmx::SelectionFileOption can be used to implement generic file input for
  63  * selection options (done internally in the trajectory analysis framework).
  64  *
  65  * The selection module contains some lower-level functionality that is
  66  * currently internal to it (centerofmass.h, indexutil.h, poscalc.h,
  67  * position.h), but could possibly be useful also outside the module.
  68  * It should be considered whether they should be moved somewhere else.
  69  * \endif
  70  *
  71  * \if internal
  72  * Implementation details of different parts of the module are discussed on
  73  * separate pages:
  74  *   - \ref page_module_selection_custom
  75  *   - \ref page_module_selection_parser
  76  *   - \ref page_module_selection_compiler
  77  *   - \ref page_module_selection_insolidangle
  78  * \endif
  79  *
  80  * \author Teemu Murtola <teemu.murtola@gmail.com>
  81  */
  82 /*! \file
  83  * \brief
  84  * Public API convenience header for selection handling.
  85  *
  86  * \author Teemu Murtola <teemu.murtola@gmail.com>
  87  * \inpublicapi
  88  * \ingroup module_selection
  89  */
  90 #ifndef GMX_SELECTION_H
  91 #define GMX_SELECTION_H
  92
  93 #include "selection/selection.h"
  94 #include "selection/selectioncollection.h"
  95 #include "selection/selectionoption.h"
  96 #include "selection/selectionoptionmanager.h"
  97
  98 #endif