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         }
 109
 110         /*! \brief
 111          * Change coordinate frame information for output.
 112          *
 113          * Changes the frame t_atoms struct according to user choice and
 114          * availability.
 115          *
 116          * \param[in] input Coordinate frame to be modified later.
 117          */
 118         void processFrame(int /*framenumber*/, t_trxframe *input) override;
 119
 120         void checkAbilityDependencies(unsigned long abilities) const override;
 121
 122     private:
 123         //! Local function to check that we have a proper t_atoms struct available.
 124         bool haveStructureFileAtoms() const
 125         {
 126             return haveStructureFileAtoms_;
 127         }
 128         /*! \brief
 129          *  Checking if t_trxframe has the atom information saved within.
 130          *
 131          *  \param[in] input t_trxframe before we start modifying it.
 132          */
 133         bool haveFrameAtoms(const t_trxframe &input) const;
 134         //! Test if the atoms data is available for writing.
 135         bool haveAtoms(const t_trxframe &input) const
 136         {
 137             return haveStructureFileAtoms() || haveFrameAtoms(input);
 138         }
 139         //! Return pointer to t_atoms.
 140         t_atoms *atoms()
 141         {
 142             GMX_RELEASE_ASSERT(haveStructureFileAtoms(), "No atoms information available");
 143             return atoms_.get();
 144         }
 145         //! Flag provided for setting atoms in coordinate frame from user.
 146         ChangeAtomsType   atomFlag_;
 147         //! Flag set if input atoms have been valid from the beginning.
 148         bool              haveStructureFileAtoms_;
 149         /*! \brief
 150          *  Atoms information if available.
 151          *
 152          *  Note, the module takes ownership of the information and
 153          *  will clean it up on exit.
 154          */
 155         AtomsDataPtr        atoms_;
 156         //! Requirements obtained from user input.
 157         CoordinateFileFlags moduleRequirements_;
 158 };
 159
 160 //! Smart pointer to manage the object.
 161 using SetAtomsPointer = std::unique_ptr<SetAtoms>;
 162
 163 } // namespace gmx
 164
 165 #endif