pdbtraj.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_PDBTRAJ_HPP)
#define LOOS_PDBTRAJ_HPP
 
 
#include <iostream>
#include <fstream>
#include <string>
#include <sstream>
#include <stdexcept>
 
 
#include <loos_defs.hpp>
#include <AtomicGroup.hpp>
#include <Trajectory.hpp>
 
#include <pdb.hpp>
 
 
namespace loos {
 
 
 
  class PDBTraj : public Trajectory {
  public:
 
 
    explicit PDBTraj(const std::string& s, uint st, uint en, uint str=1) : Trajectory(), pattern(s), start(st), end(en),
                                                                           stride(str), _natoms(0), _nframes(0), current_index(0),
                                                                           at_end(false) { init(); readFrame(0); cached_first = true; }
 
    explicit PDBTraj(const char *p, uint st, uint en, uint str=1) : Trajectory(), pattern(std::string(p)),
                                                                    start(st), end(en), stride(str), _natoms(0),
                                                                    _nframes(0), current_index(0), at_end(false) { init(); readFrame(0); cached_first = true; }
 
 
    std::string description() const { return("Trajectory from set of PDB files"); }
 
    virtual uint nframes(void) const;
    virtual uint natoms(void) const;
    virtual std::vector<GCoord> coords(void) const;
 
    virtual void updateGroupCoords(AtomicGroup& g);
 
    virtual bool hasPeriodicBox(void) const;
    virtual GCoord periodicBox(void) const;
 
    virtual float timestep(void) const;
 
    std::string currentName(void) const;
 
    PDB currentFrame(void) const;
 
    virtual bool parseFrame(void);
 
  private:
    void init(void);
    virtual void rewindImpl(void);
    virtual void seekNextFrameImpl(void);
    virtual void seekFrameImpl(const uint);
 
 
 
  private:
    std::string pattern;
    uint start, end, stride;
    uint _natoms, _nframes;
    uint current_index;
    bool at_end;
    std::string current_name;
    PDB frame;
  };
 
 
}
 
#endif