src/gromacs/coordinateio/outputadapters/setatoms.h

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  35 /*! \file
  36  * \brief
  37  * Declares gmx::SetAtoms.
  38  *
  39  * \author Paul Bauer <paul.bauer.q@gmail.com>
  40  * \inpublicapi
  41  * \ingroup module_coordinateio
  42  */
  43 #ifndef GMX_COORDINATEIO_SETATOMS_H
  44 #define GMX_COORDINATEIO_SETATOMS_H
  45
  46 #include <algorithm>
  47
  48 #include "gromacs/coordinateio/ioutputadapter.h"
  49 #include "gromacs/topology/atoms.h"
  50 #include "gromacs/utility/gmxassert.h"
  51
  52 namespace gmx
  53 {
  54
  55 /*!\brief
  56  * SetAtoms class controls availability of atoms data.
  57  *
  58  * This modules allows the user to specify if a coordinate frame
  59  * should contain the t_atoms data structure or not, and sets it in the
  60  * new coordinate frame from either the current topology or from
  61  * the data in the coordinate frame. The data is later used to identify
  62  * if certain output file types are legal or not.
  63  *
  64  * \inpublicapi
  65  * \ingroup module_coordinateio
  66  *
  67  */
  68 class SetAtoms : public IOutputAdapter
  69 {
  70 public:
  71     /*! \brief
  72      * Construct SetAtoms object with choice for boolean value
  73      * for availability of the t_atoms struct.
  74      *
  75      * Can be used to initialize SetAtoms from outside of trajectoryanalysis
  76      * framework.
  77      */
  78     explicit SetAtoms(ChangeAtomsType atomFlag, AtomsDataPtr inputAtoms) :
  79         atomFlag_(atomFlag),
  80         haveStructureFileAtoms_(false),
  81         atoms_(std::move(inputAtoms))
  82     {
  83         if (atoms_ != nullptr)
  84         {
  85             haveStructureFileAtoms_ = true;
  86         }
  87         if (atomFlag_ == ChangeAtomsType::Never)
  88         {
  89             moduleRequirements_ = CoordinateFileFlags::Base;
  90         }
  91         else
  92         {
  93             moduleRequirements_ = CoordinateFileFlags::RequireAtomInformation;
  94         }
  95     }
  96     /*! \brief
  97      *  Move constructor for SetAtoms.
  98      */
  99     SetAtoms(SetAtoms&& old) noexcept :
 100         atomFlag_(old.atomFlag_),
 101         haveStructureFileAtoms_(old.haveStructureFileAtoms_),
 102         atoms_(std::move(old.atoms_))
 103     {
 104     }
 105
 106     ~SetAtoms() override {}
 107
 108     /*! \brief
 109      * Change coordinate frame information for output.
 110      *
 111      * Changes the frame t_atoms struct according to user choice and
 112      * availability.
 113      *
 114      * \param[in] input Coordinate frame to be modified later.
 115      */
 116     void processFrame(int /*framenumber*/, t_trxframe* input) override;
 117
 118     void checkAbilityDependencies(unsigned long abilities) const override;
 119
 120 private:
 121     //! Local function to check that we have a proper t_atoms struct available.
 122     bool haveStructureFileAtoms() const { return haveStructureFileAtoms_; }
 123     /*! \brief
 124      *  Checking if t_trxframe has the atom information saved within.
 125      *
 126      *  \param[in] input t_trxframe before we start modifying it.
 127      */
 128     static bool haveFrameAtoms(const t_trxframe& input);
 129     //! Test if the atoms data is available for writing.
 130     bool haveAtoms(const t_trxframe& input) const
 131     {
 132         return haveStructureFileAtoms() || haveFrameAtoms(input);
 133     }
 134     //! Return pointer to t_atoms.
 135     t_atoms* atoms()
 136     {
 137         GMX_RELEASE_ASSERT(haveStructureFileAtoms(), "No atoms information available");
 138         return atoms_.get();
 139     }
 140     //! Flag provided for setting atoms in coordinate frame from user.
 141     ChangeAtomsType atomFlag_;
 142     //! Flag set if input atoms have been valid from the beginning.
 143     bool haveStructureFileAtoms_;
 144     /*! \brief
 145      *  Atoms information if available.
 146      *
 147      *  Note, the module takes ownership of the information and
 148      *  will clean it up on exit.
 149      */
 150     AtomsDataPtr atoms_;
 151     //! Requirements obtained from user input.
 152     CoordinateFileFlags moduleRequirements_;
 153 };
 154
 155 //! Smart pointer to manage the object.
 156 using SetAtomsPointer = std::unique_ptr<SetAtoms>;
 157
 158 } // namespace gmx
 159
 160 #endif