amber_traj.hpp

/*
  This file is part of LOOS.
 
  LOOS (Lightweight Object-Oriented Structure library)
  Copyright (c) 2008, Tod D. Romo, Alan Grossfield
  Department of Biochemistry and Biophysics
  School of Medicine & Dentistry, University of Rochester
 
  This package (LOOS) is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation under version 3 of the License.
 
  This package is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
 
  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/
 
#if !defined(LOOS_AMBER_TRAJ_HPP)
#define LOOS_AMBER_TRAJ_HPP
 
 
#include <string>
 
#include <loos_defs.hpp>
#include <Coord.hpp>
#include <Trajectory.hpp>
 
 
namespace loos {
 
 
  class AmberTraj : public Trajectory {
  public:
    explicit AmberTraj(const std::string& s, const int na) : Trajectory(s),
                                                             _natoms(na), frame_offset(0),
                                                             frame_size(0), periodic(false) { init(); }
 
    explicit AmberTraj(std::istream& is, const int na) : Trajectory(is), _natoms(na),
                                                     frame_offset(0), frame_size(0),
                                                     periodic(false) { init(); }
 
    std::string description() const { return("Amber trajectory"); }
    static pTraj create(const std::string& fname, const AtomicGroup& model) {
      return(pTraj(new AmberTraj(fname, model.size())));
    }
 
 
    virtual uint nframes(void) const { return(_nframes); }
    virtual uint natoms(void) const { return(_natoms); }
    virtual std::vector<GCoord> coords(void) const { return(frame); }
 
    virtual bool hasPeriodicBox(void) const { return(periodic); }
    virtual GCoord periodicBox(void) const { return(box); }
 
    virtual double velocityConversionFactor() const { return(20.455); }
 
    virtual float timestep(void) const { return(0.0); }  // Dummy routine...
 
    virtual bool parseFrame(void);
 
 
  private:
    void init(void);
    virtual void rewindImpl(void) { ifs->clear(); ifs->seekg(frame_offset); }
    virtual void seekNextFrameImpl(void) { }
    virtual void seekFrameImpl(const uint);
    virtual void updateGroupCoordsImpl(AtomicGroup&);
 
 
  private:
    uint _natoms, _nframes;
    unsigned long frame_offset, frame_size;
    bool periodic;
    GCoord box;
    std::vector<GCoord> frame;
 
  };
 
 
}
#endif