tinker_arc.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_TINKER_ARC_HPP)
#define LOOS_TINKER_ARC_HPP
 
 
#include <iostream>
#include <string>
#include <stdexcept>
 
#include <loos_defs.hpp>
#include <Trajectory.hpp>
 
#include <tinkerxyz.hpp>
 
 
namespace loos {
 
 
  class TinkerArc : public Trajectory {
  public:
    explicit TinkerArc(const std::string& s) : Trajectory(s), _natoms(0), _nframes(0),
                                               current_index(0), at_end(false) { init(); }
  
    explicit TinkerArc(std::istream& is) : Trajectory(is), _natoms(0),
                       _nframes(0), current_index(0), at_end(false) { init(); }
 
    std::string description() const { return("Tinker Archive"); }
 
    static pTraj create(const std::string& fname, const AtomicGroup& model) {
      return(pTraj(new TinkerArc(fname)));
    }
 
    virtual uint nframes(void) const { return(_nframes); }
    virtual uint natoms(void) const { return(_natoms); }
    virtual std::vector<GCoord> coords(void) const;
 
    virtual bool hasPeriodicBox(void) const { return(frame.isPeriodic()); }
    virtual GCoord periodicBox(void) const { return(frame.periodicBox()); }
 
    virtual float timestep(void) const { return(0.001); }
 
 
    TinkerXYZ currentFrame(void) const { return(frame); }
 
    virtual bool parseFrame(void);
 
 
  private:
    void init(void);
    virtual void rewindImpl(void) { ifs->clear(); ifs->seekg(0); current_index = 0; at_end = false; }
    virtual void seekNextFrameImpl(void);
    virtual void seekFrameImpl(const uint);
    virtual void updateGroupCoordsImpl(AtomicGroup& g);
 
 
  private:
    uint _natoms, _nframes;
    uint current_index;
    bool at_end;
    TinkerXYZ frame;
    std::vector<long> indices;
  };
 
 
}
 
 
#endif