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37 * Implements gmx::SelectionOptionBehavior.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
44 #include "selectionoptionbehavior.h"
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"
65 /********************************************************************
69 ITopologyProvider::~ITopologyProvider() {}
71 /********************************************************************
72 * SelectionOptionBehavior
75 class SelectionOptionBehavior::Impl
78 Impl(SelectionCollection* selections, ITopologyProvider* topologyProvider) :
79 selections_(*selections),
80 topologyProvider_(*topologyProvider),
89 gmx_ana_indexgrps_free(grps_);
93 void promptSelections()
95 const bool isInteractive = StandardInputStream::isInteractive();
97 manager_.parseRequestedFromStdin(isInteractive);
100 void initIndexGroups()
102 if (!selections_.requiresIndexGroups() && !manager_.hasRequestedSelections())
104 if (!ndxfile_.empty())
107 "NOTE: You provided an index file\n"
108 " %s\n(with -n), but it was not used by any selection.\n",
111 selections_.setIndexGroups(nullptr);
114 if (ndxfile_.empty())
116 gmx_mtop_t* top = topologyProvider_.getTopology(false);
117 gmx_ana_indexgrps_init(&grps_, top, nullptr);
121 gmx_ana_indexgrps_init(&grps_, nullptr, ndxfile_.c_str());
123 selections_.setIndexGroups(grps_);
125 void doneIndexGroups()
127 if (grps_ != nullptr)
129 selections_.setIndexGroups(nullptr);
130 gmx_ana_indexgrps_free(grps_);
135 void compileSelections()
137 const bool topRequired = selections_.requiredTopologyProperties().needsTopology;
138 gmx_mtop_t* top = topologyProvider_.getTopology(topRequired);
142 natoms = topologyProvider_.getAtomCount();
144 getMassesIfRequired(top);
145 selections_.setTopology(top, natoms);
146 selections_.compile();
147 // Situation may have changed after compilation.
148 getMassesIfRequired(top);
151 void getMassesIfRequired(gmx_mtop_t* top) const
153 const bool massRequired = selections_.requiredTopologyProperties().needsMasses;
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)
163 if (!moltype.atoms.haveMass)
165 atomsSetMassesBasedOnNames(&moltype.atoms, TRUE);
166 if (!moltype.atoms.haveMass)
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."));
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_;
185 SelectionOptionBehavior::SelectionOptionBehavior(SelectionCollection* selections,
186 ITopologyProvider* topologyProvider) :
187 impl_(new Impl(selections, topologyProvider))
191 SelectionOptionBehavior::~SelectionOptionBehavior() {}
193 void SelectionOptionBehavior::initOptions(IOptionsContainer* options)
195 options->addOption(FileNameOption("n")
196 .filetype(OptionFileType::Index)
198 .store(&impl_->ndxfile_)
199 .defaultBasename("index")
200 .description("Extra index groups"));
201 options->addOption(SelectionFileOption("sf"));
202 impl_->manager_.initOptions(options);
205 void SelectionOptionBehavior::initBehavior(Options* options)
207 options->addManager(&impl_->manager_);
210 void SelectionOptionBehavior::optionsFinished()
212 impl_->promptSelections();
213 impl_->compileSelections();