src/gromacs/selection/selectioncollection-impl.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2009,2010,2011,2012,2013, 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 /*! \internal \file
  36  * \brief
  37  * Declares private implementation class for gmx::SelectionCollection.
  38  *
  39  * This header also defines ::gmx_ana_selcollection_t, which is used in the old
  40  * C code for handling selection collections.
  41  *
  42  * \author Teemu Murtola <teemu.murtola@gmail.com>
  43  * \ingroup module_selection
  44  */
  45 #ifndef GMX_SELECTION_SELECTIONCOLLECTION_IMPL_H
  46 #define GMX_SELECTION_SELECTIONCOLLECTION_IMPL_H
  47
  48 #include <string>
  49 #include <vector>
  50
  51 #include <boost/scoped_ptr.hpp>
  52
  53 #include "../legacyheaders/typedefs.h"
  54
  55 #include "../onlinehelp/helptopicinterface.h"
  56 #include "../utility/uniqueptr.h"
  57 #include "indexutil.h"
  58 #include "poscalc.h"
  59 #include "selection.h" // For gmx::SelectionList
  60 #include "selectioncollection.h"
  61 #include "selelem.h"
  62
  63 namespace gmx
  64 {
  65
  66 //! Smart pointer for managing an internal selection data object.
  67 typedef gmx_unique_ptr<internal::SelectionData>::type SelectionDataPointer;
  68 //! Container for storing a list of selections internally.
  69 typedef std::vector<SelectionDataPointer> SelectionDataList;
  70
  71 class SelectionParserSymbolTable;
  72
  73 } // namespace gmx
  74
  75 /*! \internal \brief
  76  * Information for a collection of selections.
  77  *
  78  * \ingroup module_selection
  79  */
  80 struct gmx_ana_selcollection_t
  81 {
  82     //! Position calculation collection used for selection position evaluation.
  83     gmx::PositionCalculationCollection  pcc;
  84     //! Root of the selection element tree.
  85     gmx::SelectionTreeElementPointer    root;
  86     /*! \brief
  87      * Array of compiled selections.
  88      *
  89      * Has the responsibility of managing the memory for the contained objects,
  90      * but note that gmx::Selection instances also hold pointers to the
  91      * objects.
  92      */
  93     gmx::SelectionDataList         sel;
  94     /** Number of variables defined. */
  95     int                            nvars;
  96     /** Selection strings for variables. */
  97     char                         **varstrs;
  98
  99     /** Topology for the collection. */
 100     t_topology                                        *top;
 101     /** Index group that contains all the atoms. */
 102     struct gmx_ana_index_t                             gall;
 103     /** Memory pool used for selection evaluation. */
 104     struct gmx_sel_mempool_t                          *mempool;
 105     //! Parser symbol table.
 106     boost::scoped_ptr<gmx::SelectionParserSymbolTable> symtab;
 107     //! Root of help topic tree (NULL is no help yet requested).
 108     gmx::HelpTopicPointer                              rootHelp;
 109 };
 110
 111 namespace gmx
 112 {
 113
 114 class ExceptionInitializer;
 115
 116 /*! \internal \brief
 117  * Private implemention class for SelectionCollection.
 118  *
 119  * \ingroup module_selection
 120  */
 121 class SelectionCollection::Impl
 122 {
 123     public:
 124         /*! \brief
 125          * Creates a new selection collection.
 126          *
 127          * \throws  std::bad_alloc if out of memory.
 128          */
 129         Impl();
 130         ~Impl();
 131
 132         /*! \brief
 133          * Clears the symbol table of the selection collection.
 134          *
 135          * Does not throw.
 136          */
 137         void clearSymbolTable();
 138         /*! \brief
 139          * Replace group references by group contents.
 140          *
 141          * \param[in]    root    Root of selection tree to process.
 142          * \param        errors  Object for reporting any error messages.
 143          * \throws std::bad_alloc if out of memory.
 144          *
 145          * Recursively searches the selection tree for unresolved external
 146          * references.  If one is found, finds the referenced group in
 147          * \a grps_ and replaces the reference with a constant element that
 148          * contains the atoms from the referenced group.  Any failures to
 149          * resolve references are reported to \p errors.
 150          */
 151         void resolveExternalGroups(const gmx::SelectionTreeElementPointer &root,
 152                                    ExceptionInitializer                   *errors);
 153
 154         //! Internal data, used for interfacing with old C code.
 155         gmx_ana_selcollection_t sc_;
 156         //! Default reference position type for selections.
 157         std::string             rpost_;
 158         //! Default output position type for selections.
 159         std::string             spost_;
 160         /*! \brief
 161          * Debugging level for the collection.
 162          *
 163          * Possible values:
 164          *  - 0: no debugging
 165          *  - 1: print selection trees after parsing and compilation
 166          *  - 2: like 1, also print intermediate compilation trees
 167          *  - 3: like 1, also print the tree after evaluation
 168          *  - 4: combine 2 and 3
 169          */
 170         int                     debugLevel_;
 171         //! Whether setIndexGroups() has been called.
 172         bool                    bExternalGroupsSet_;
 173         //! External index groups (can be NULL).
 174         gmx_ana_indexgrps_t    *grps_;
 175 };
 176
 177 /*! \internal \brief
 178  * Implements selection evaluation.
 179  *
 180  * This class is used to implement SelectionCollection::evaluate() and
 181  * SelectionCollection::evaluateFinal().
 182  *
 183  * \ingroup module_selection
 184  */
 185 class SelectionEvaluator
 186 {
 187     public:
 188         SelectionEvaluator();
 189
 190         /*! \brief
 191          * Evaluates selections in a collection.
 192          */
 193         void evaluate(SelectionCollection *sc, t_trxframe *fr, t_pbc *pbc);
 194         /*! \brief
 195          * Evaluates the final state for dynamic selections.
 196          */
 197         void evaluateFinal(SelectionCollection *sc, int nframes);
 198 };
 199
 200 } // namespace gmx
 201
 202 #endif