text: //
  // Copyright (C) 2003-2016 Sereina Riniker, Paolo Tosco
  //
  //   @@ All Rights Reserved @@
  //  This file is part of the RDKit.
  //  The contents are covered by the terms of the BSD license
  //  which is included in the file license.txt, found at the root
  //  of the RDKit source tree.
  //
  
  #include <RDGeneral/export.h>
  #ifndef RD_TRAJECTORY_H
  #define RD_TRAJECTORY_H
  #include <vector>
  #include "Snapshot.h"
  
  namespace RDKit {
  
  class ROMol;
  
  class RDKIT_TRAJECTORY_EXPORT Trajectory {
    public:
      /*! \brief Constructor
          \param dimension represents the dimensionality of this Trajectory's coordinate tuples;
          this is normally 2 (2D coordinates) or 3 (3D coordinates)
          \param numPoints is the number of coordinate tuples associated to each Snapshot
          \param snapshotVect (optional, defaults to NULL) is a pointer to a SnapshotVect
                 used to initialize the Trajectory; if not NULL, the Trajectory takes ownership
                 of the SnapshotVect
       */
      Trajectory(unsigned int dimension, unsigned int numPoints, SnapshotVect *snapshotVect = NULL);
      /*! \brief Copy constructor
       */
      Trajectory(const Trajectory &other);
      /*! \return the dimensionality of this Trajectory's coordinate tuples
       */
      unsigned int dimension() const {
        return d_dimension;
      }
      /*! \return the number of coordinate tuples associated to each Snapshot
       */
      unsigned int numPoints() const {
        return d_numPoints;
      }
      /*! \return the number of Snapshots associated to this Trajectory
       */
      size_t size() const {
        return d_snapshotVect->size();
      }
      /*! \brief Appends a Snapshot to this Trajectory
          \param s is the Snapshot to be added; the Trajectory
                 takes ownership of the snapshot coordinates
          \return the zero-based index position of the added Snapshot
       */
      unsigned int addSnapshot(const Snapshot &s);
      /*! \param snapshotNum is the zero-based index of the retrieved Snapshot
          \return a const reference to the relevant Snapshot in the Trajectory
       */
      const Snapshot &getSnapshot(unsigned int snapshotNum) const;
      /*! \brief Inserts a Snapshot into this Trajectory
          \param snapshotNum is the zero-based index of the Trajectory's Snapshot
                 before which the Snapshot s will be inserted
          \param s is the Snapshot to be inserted; the Trajectory
                 takes ownership of the snapshot coordinates
          \return the zero-based index position of the inserted Snapshot
       */
      unsigned int insertSnapshot(unsigned int snapshotNum, Snapshot s);
      /*! \brief Removes a Snapshot from this Trajectory
          \param snapshotNum is the zero-based index of Snapshot to be removed
          \return the zero-based index position of the Snapshot after the
                  removed one; if the last Snapshot was removed, it returns the
                  size of the trajectory
       */
      unsigned int removeSnapshot(unsigned int snapshotNum);
      //! Clear all Snapshots from a Trajectory
      void clear() {
        d_snapshotVect->clear();
      };
      //! Add conformations from the Trajectory to a molecule
      /*!
        \param mol - ROMol to which Conformers with coordinates from the Trajectory will be added;
               the Trajectory must have numPoints() == mol.getNumAtoms()
        \param from - the first Snapshot that will be added as a Conformer; defaults to -1 (first available)
        \param to - the last Snapshot that will be added as a Conformer; defaults to -1 (all)
        \return the number of conformations added
      */
      unsigned int addConformersToMol(ROMol &mol, int from = -1, int to = -1);
    private:
      // dimensionality of this Trajectory's coordinates;
      // this is normally 2 (2D coordinates) or 3 (3D coordinates)
      const unsigned int d_dimension;
      // number of coordinate tuples associated to each Snapshot
      const unsigned int d_numPoints;
      // smart_ptr to vector holding the Snapshots for this Trajectory
      boost::shared_ptr<SnapshotVect> d_snapshotVect;
  };
  /*! \brief Reads coordinates from an AMBER trajectory file
             into the traj Trajectory object
      \return the number of Snapshot objects read in
   */
  RDKIT_TRAJECTORY_EXPORT unsigned int readAmberTrajectory(const std::string &fName, Trajectory &traj);
  /*! \brief Reads coordinates from a GROMOS trajectory file
             into the traj Trajectory object
      \return the number of Snapshot objects read in
   */
  RDKIT_TRAJECTORY_EXPORT unsigned int readGromosTrajectory(const std::string &fName, Trajectory &traj);
  
  }
  #endif
  