src/gromacs/selection/selectionoptionbehavior.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements gmx::SelectionOptionBehavior.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "selectionoptionbehavior.h"
  45
  46 #include <cstdio>
  47
  48 #include <string>
  49
  50 #include "gromacs/options/filenameoption.h"
  51 #include "gromacs/options/ioptionscontainer.h"
  52 #include "gromacs/options/options.h"
  53 #include "gromacs/selection/indexutil.h"
  54 #include "gromacs/selection/selectioncollection.h"
  55 #include "gromacs/selection/selectionfileoption.h"
  56 #include "gromacs/selection/selectionoptionmanager.h"
  57 #include "gromacs/topology/atoms.h"
  58 #include "gromacs/topology/topology.h"
  59 #include "gromacs/utility/exceptions.h"
  60 #include "gromacs/utility/filestream.h"
  61
  62 namespace gmx
  63 {
  64
  65 /********************************************************************
  66  * ITopologyProvider
  67  */
  68
  69 ITopologyProvider::~ITopologyProvider()
  70 {
  71 }
  72
  73 /********************************************************************
  74  * SelectionOptionBehavior
  75  */
  76
  77 class SelectionOptionBehavior::Impl
  78 {
  79     public:
  80         Impl(SelectionCollection *selections,
  81              ITopologyProvider   *topologyProvider)
  82             : selections_(*selections), topologyProvider_(*topologyProvider),
  83               manager_(selections), grps_(nullptr)
  84         {
  85         }
  86         ~Impl()
  87         {
  88             if (grps_ != nullptr)
  89             {
  90                 gmx_ana_indexgrps_free(grps_);
  91             }
  92         }
  93
  94         void promptSelections()
  95         {
  96             const bool isInteractive = StandardInputStream::instance().isInteractive();
  97             initIndexGroups();
  98             manager_.parseRequestedFromStdin(isInteractive);
  99             doneIndexGroups();
 100         }
 101         void initIndexGroups()
 102         {
 103             if (!selections_.requiresIndexGroups()
 104                 && !manager_.hasRequestedSelections())
 105             {
 106                 if (!ndxfile_.empty())
 107                 {
 108                     std::fprintf(stderr, "NOTE: You provided an index file\n"
 109                                  "  %s\n(with -n), but it was not used by any selection.\n",
 110                                  ndxfile_.c_str());
 111                 }
 112                 selections_.setIndexGroups(nullptr);
 113                 return;
 114             }
 115             if (ndxfile_.empty())
 116             {
 117                 gmx_mtop_t *top = topologyProvider_.getTopology(false);
 118                 gmx_ana_indexgrps_init(&grps_, top, nullptr);
 119             }
 120             else
 121             {
 122                 gmx_ana_indexgrps_init(&grps_, nullptr, ndxfile_.c_str());
 123             }
 124             selections_.setIndexGroups(grps_);
 125         }
 126         void doneIndexGroups()
 127         {
 128             if (grps_ != nullptr)
 129             {
 130                 selections_.setIndexGroups(nullptr);
 131                 gmx_ana_indexgrps_free(grps_);
 132                 grps_ = nullptr;
 133             }
 134         }
 135
 136         void compileSelections()
 137         {
 138             const bool  topRequired = selections_.requiredTopologyProperties().needsTopology;
 139             gmx_mtop_t *top         = topologyProvider_.getTopology(topRequired);
 140             int         natoms      = -1;
 141             if (top == nullptr)
 142             {
 143                 natoms = topologyProvider_.getAtomCount();
 144             }
 145             getMassesIfRequired(top);
 146             selections_.setTopology(top, natoms);
 147             selections_.compile();
 148             // Situation may have changed after compilation.
 149             getMassesIfRequired(top);
 150         }
 151
 152         void getMassesIfRequired(gmx_mtop_t *top)
 153         {
 154             const bool massRequired = selections_.requiredTopologyProperties().needsMasses;
 155             if (!massRequired)
 156             {
 157                 return;
 158             }
 159             // TODO: There can be some corner cases that still hit this assert
 160             // when the user has not provided the topology.
 161             GMX_RELEASE_ASSERT(top != nullptr,
 162                                "Masses are required, but no topology is loaded");
 163             for (gmx_moltype_t &moltype : top->moltype)
 164             {
 165                 if (!moltype.atoms.haveMass)
 166                 {
 167                     atomsSetMassesBasedOnNames(&moltype.atoms, TRUE);
 168                     if (!moltype.atoms.haveMass)
 169                     {
 170                         GMX_THROW(InconsistentInputError("Selections require mass information for evaluation, but it is not available in the input and could not be determined for all atoms based on atom names."));
 171                     }
 172                 }
 173             }
 174         }
 175
 176         SelectionCollection    &selections_;
 177         ITopologyProvider      &topologyProvider_;
 178         SelectionOptionManager  manager_;
 179         //! Name of the index file (empty if no index file provided).
 180         std::string             ndxfile_;
 181         gmx_ana_indexgrps_t    *grps_;
 182 };
 183
 184 SelectionOptionBehavior::SelectionOptionBehavior(
 185         SelectionCollection *selections,
 186         ITopologyProvider   *topologyProvider)
 187     : impl_(new Impl(selections, topologyProvider))
 188 {
 189 }
 190
 191 SelectionOptionBehavior::~SelectionOptionBehavior()
 192 {
 193 }
 194
 195 void
 196 SelectionOptionBehavior::initOptions(IOptionsContainer *options)
 197 {
 198     options->addOption(FileNameOption("n")
 199                            .filetype(eftIndex).inputFile()
 200                            .store(&impl_->ndxfile_)
 201                            .defaultBasename("index")
 202                            .description("Extra index groups"));
 203     options->addOption(SelectionFileOption("sf"));
 204     impl_->manager_.initOptions(options);
 205 }
 206
 207 void
 208 SelectionOptionBehavior::initBehavior(Options *options)
 209 {
 210     options->addManager(&impl_->manager_);
 211 }
 212
 213 void
 214 SelectionOptionBehavior::optionsFinished()
 215 {
 216     impl_->promptSelections();
 217     impl_->compileSelections();
 218 }
 219
 220 } // namespace gmx