src/gromacs/trajectoryanalysis/topologyinformation.h

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  35 /*! \file
  36  * \brief
  37  * Declares gmx::TopologyInformation.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \author Mark Abraham <mark.j.abraham@gmail.com>
  41  * \inlibraryapi
  42  * \ingroup module_trajectoryanalysis
  43  */
  44 #ifndef GMX_TRAJECTORYANALYSIS_TOPOLOGYINFORMATION_H
  45 #define GMX_TRAJECTORYANALYSIS_TOPOLOGYINFORMATION_H
  46
  47 #include <memory>
  48 #include <string>
  49 #include <vector>
  50
  51 #include "gromacs/math/vectypes.h"
  52 #include "gromacs/topology/atoms.h"
  53 #include "gromacs/topology/topology.h"
  54 #include "gromacs/utility/classhelpers.h"
  55
  56 //! Forward declaration
  57 typedef struct gmx_rmpbc *gmx_rmpbc_t;
  58
  59 namespace gmx
  60 {
  61
  62 template<typename T> class ArrayRef;
  63
  64 class TopologyInformation;
  65 class TrajectoryAnalysisRunnerCommon;
  66
  67 /*! \libinternal
  68  * \brief Topology information available to a trajectory analysis module.
  69  *
  70  * This class is used to provide topology information to trajectory
  71  * analysis modules and to manage memory for them. Having a single
  72  * wrapper object instead of passing each item separately makes
  73  * TrajectoryAnalysisModule interface simpler, and also reduces the
  74  * need to change existing code if additional information is added.
  75  *
  76  * It is intended that eventually most clients of this class will be
  77  * analysis tools ported to the new analysis framework, but we will
  78  * use this infrastructure also from the legacy analysis tools during
  79  * the transition period. That will make it easier to put those tools
  80  * under tests, and eventually port them.
  81  *
  82  * Methods in this class do not throw if not explicitly stated.
  83  *
  84  * The main data content is constant once loaded, but some content is
  85  * constructed only when required (e.g. atoms_ and
  86  * expandedTopology_). Their data members are mutable, so that the
  87  * lazy construction idiom works properly. Some clients wish to modify
  88  * the t_atoms, so there is an efficient mechanism for them to get a
  89  * copy they can modify without disturbing this class. (The
  90  * implementation releases the cached lazily constructed atoms_, but
  91  * from the point of view of the caller, that is a copy.) The getters
  92  * and copy functions are const for callers, which correctly expresses
  93  * that the topology information is not being changed, merely copied
  94  * and presented in a different form.
  95  *
  96  * \ingroup module_trajectoryanalysis
  97  */
  98 class TopologyInformation
  99 {
 100     public:
 101         //! Returns true if a topology file was loaded.
 102         bool hasTopology() const { return hasLoadedMtop_; }
 103         //! Returns true if a full topology file was loaded.
 104         bool hasFullTopology() const { return bTop_; }
 105         /*! \brief Builder function to fill the contents of
 106          * TopologyInformation in \c topInfo from \c filename.
 107          *
 108          * Different tools require, might need, would benefit from, or
 109          * do not need topology information. This functions implements
 110          * the two-phase construction that is currently needed to
 111          * support that.
 112          *
 113          * Any coordinate or run input file format will work, but the
 114          * kind of data available from the getter methods afterwards
 115          * will vary. For example, the mtop() available after reading
 116          * a plain structure file will have a single molecule block and
 117          * molecule type, regardless of contents.
 118          *
 119          * After reading, this object can return many kinds of primary
 120          * and derived data structures to its caller.
 121          *
 122          * \todo This should throw upon error but currently does
 123          * not. */
 124         void fillFromInputFile(const std::string &filename);
 125         /*! \brief Returns the loaded topology, or nullptr if not loaded. */
 126         gmx_mtop_t *mtop() const { return mtop_.get(); }
 127         //! Returns the loaded topology fully expanded, or nullptr if no topology is available.
 128         const gmx_localtop_t *expandedTopology() const;
 129         /*! \brief Returns a read-only handle to the fully expanded
 130          * atom data arrays, which might be valid but empty if no
 131          * topology is available. */
 132         const t_atoms *atoms() const;
 133         /*! \brief Copies the fully expanded atom data arrays, which
 134          * might be valid but empty if no topology is available. */
 135         AtomsDataPtr copyAtoms() const;
 136         //! Returns the ePBC field from the topology.
 137         int ePBC() const { return ePBC_; }
 138         /*! \brief
 139          * Gets the configuration positions from the topology file.
 140          *
 141          * If TrajectoryAnalysisSettings::efUseTopX has not been specified,
 142          * this method should not be called.
 143          *
 144          * \throws  APIError if topology position coordinates are not available
 145          */
 146         ArrayRef<const RVec> x() const;
 147         /*! \brief
 148          * Gets the configuration velocities from the topology file.
 149          *
 150          * If TrajectoryAnalysisSettings::efUseTopV has not been specified,
 151          * this method should not be called.
 152          *
 153          * \throws  APIError if topology velocity coordinates are not available
 154          */
 155         ArrayRef<const RVec> v() const;
 156         /*! \brief
 157          * Gets the configuration box from the topology file.
 158          *
 159          * \param[out] box   Box size from the topology file, must not be nullptr.
 160          */
 161         void getBox(matrix box) const;
 162         /*! \brief Returns a name for the topology.
 163          *
 164          * If a full topology was read from a a file, returns the name
 165          * it contained, otherwise the empty string. */
 166         const char *name() const;
 167
 168         TopologyInformation();
 169         ~TopologyInformation();
 170
 171     private:
 172         //! The topology structure, or nullptr if no topology loaded.
 173         std::unique_ptr<gmx_mtop_t> mtop_;
 174         //! Whether a topology has been loaded.
 175         bool hasLoadedMtop_;
 176         //! The fully expanded topology structure, nullptr if not yet constructed.
 177         mutable ExpandedTopologyPtr      expandedTopology_;
 178         //! The fully expanded atoms data structure, nullptr if not yet constructed.
 179         mutable AtomsDataPtr             atoms_;
 180         //! true if full tpx file was loaded, false otherwise.
 181         bool                             bTop_;
 182         //! Position coordinates from the topology (can be nullptr).
 183         std::vector<RVec>                xtop_;
 184         //! Velocity coordinates from the topology (can be nullptr).
 185         std::vector<RVec>                vtop_;
 186         //! The box loaded from the topology file.
 187         matrix                           boxtop_ {};
 188         //! The ePBC field loaded from the topology file.
 189         int                              ePBC_;
 190
 191         // TODO This type is probably movable if we need that.
 192         GMX_DISALLOW_COPY_AND_ASSIGN(TopologyInformation);
 193
 194         /*! \brief
 195          * Needed to initialize the data.
 196          */
 197         friend class TrajectoryAnalysisRunnerCommon;
 198 };
 199
 200 //! Convenience overload useful for implementing legacy tools.
 201 gmx_rmpbc_t gmx_rmpbc_init(const gmx::TopologyInformation &topInfo);
 202
 203 } // namespace gmx
 204
 205 #endif