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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()
73 /********************************************************************
74 * SelectionOptionBehavior
77 class SelectionOptionBehavior::Impl
80 Impl(SelectionCollection *selections,
81 ITopologyProvider *topologyProvider)
82 : selections_(*selections), topologyProvider_(*topologyProvider),
83 manager_(selections), grps_(nullptr)
90 gmx_ana_indexgrps_free(grps_);
94 void promptSelections()
96 const bool isInteractive = StandardInputStream::instance().isInteractive();
98 manager_.parseRequestedFromStdin(isInteractive);
101 void initIndexGroups()
103 if (!selections_.requiresIndexGroups()
104 && !manager_.hasRequestedSelections())
106 if (!ndxfile_.empty())
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",
112 selections_.setIndexGroups(nullptr);
115 if (ndxfile_.empty())
117 gmx_mtop_t *top = topologyProvider_.getTopology(false);
118 gmx_ana_indexgrps_init(&grps_, top, nullptr);
122 gmx_ana_indexgrps_init(&grps_, nullptr, ndxfile_.c_str());
124 selections_.setIndexGroups(grps_);
126 void doneIndexGroups()
128 if (grps_ != nullptr)
130 selections_.setIndexGroups(nullptr);
131 gmx_ana_indexgrps_free(grps_);
136 void compileSelections()
138 const bool topRequired = selections_.requiredTopologyProperties().needsTopology;
139 gmx_mtop_t *top = topologyProvider_.getTopology(topRequired);
143 natoms = topologyProvider_.getAtomCount();
145 getMassesIfRequired(top);
146 selections_.setTopology(top, natoms);
147 selections_.compile();
148 // Situation may have changed after compilation.
149 getMassesIfRequired(top);
152 void getMassesIfRequired(gmx_mtop_t *top)
154 const bool massRequired = selections_.requiredTopologyProperties().needsMasses;
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 (int i = 0; i < top->nmoltype; ++i)
165 gmx_moltype_t &moltype = top->moltype[i];
166 if (!moltype.atoms.haveMass)
168 atomsSetMassesBasedOnNames(&moltype.atoms, TRUE);
169 if (!moltype.atoms.haveMass)
171 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."));
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(
186 SelectionCollection *selections,
187 ITopologyProvider *topologyProvider)
188 : impl_(new Impl(selections, topologyProvider))
192 SelectionOptionBehavior::~SelectionOptionBehavior()
197 SelectionOptionBehavior::initOptions(IOptionsContainer *options)
199 options->addOption(FileNameOption("n")
200 .filetype(eftIndex).inputFile()
201 .store(&impl_->ndxfile_)
202 .defaultBasename("index")
203 .description("Extra index groups"));
204 options->addOption(SelectionFileOption("sf"));
205 impl_->manager_.initOptions(options);
209 SelectionOptionBehavior::initBehavior(Options *options)
211 options->addManager(&impl_->manager_);
215 SelectionOptionBehavior::optionsFinished()
217 impl_->promptSelections();
218 impl_->compileSelections();