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