dcdwriter.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_DCDWRITER_HPP)
#define LOOS_DCDWRITER_HPP
 
#include <ios>
#include <iostream>
#include <fstream>
#include <string>
#include <stdexcept>
#include <exception>
#include <vector>
 
//#include <sys/types.h>
//#include <sys/stat.h>
//#include <unistd.h>
 
#include <loos_defs.hpp>
 
#include <AtomicGroup.hpp>
#include <dcd.hpp>
#include <trajwriter.hpp>
 
namespace loos {
 
  class DCDWriter : public TrajectoryWriter {
 
    // Use a union to convert data to appropriate type...
    typedef union { unsigned int ui; int i; char c[4]; float f; } DataOverlay; 
 
  public:
 
    static pTrajectoryWriter create(const std::string& s, const bool append = false) {
      return(pTrajectoryWriter(new DCDWriter(s, append)));
    }
 
 
    explicit DCDWriter(const std::string& s, const bool append = false) :
      TrajectoryWriter(s, append),
      _natoms(0), _nsteps(0),
      _timestep(0.001), _current(0),
      _has_box(false),
      _header_written(false)
    {
      if (appending_)
    prepareToAppend();
      else
        _titles.push_back("AUTO GENERATED BY LOOS");
    }
 
    explicit DCDWriter(std::iostream& fs, const bool append = false) : 
      TrajectoryWriter(&fs, append),
      _natoms(0), _nsteps(0), _timestep(0.001), _current(0),
      _has_box(false), _header_written(false)
    {
      if (appending_)
    prepareToAppend();
      else
    _titles.push_back("AUTO GENERATED BY LOOS");
    }
 
    DCDWriter(const std::string& s, const std::vector<AtomicGroup>& grps, const bool append = false) :
      TrajectoryWriter(s, append),
      _natoms(grps[0].size()),
      _nsteps(grps.size()),
      _timestep(1e-3),
      _current(0),
      _has_box(grps[0].isPeriodic()),
      _header_written(false)
    {
      if (appending_)
    prepareToAppend();
      else
        _titles.push_back("AUTO GENERATED BY LOOS");
    
      writeHeader();
      writeFrames(grps);
    }
 
    DCDWriter(const std::string& s, const std::vector<AtomicGroup>& grps, const std::string& comment, const bool append = false) :
      TrajectoryWriter(s, append),
      _natoms(grps[0].size()),
      _nsteps(grps.size()),
      _timestep(1e-3),
      _current(0),
      _has_box(grps[0].isPeriodic()),
      _header_written(false)
    {
      if (appending_)
    prepareToAppend();
      else
        _titles.push_back(comment);
    
      writeHeader();
      writeFrames(grps);
    }
 
    DCDWriter(const std::string& s, const std::vector<AtomicGroup>& grps, const std::vector<std::string>& comments, const bool append = false) :
      TrajectoryWriter(s, append),
      _natoms(grps[0].size()),
      _nsteps(grps.size()),
      _timestep(1e-3),
      _current(0),
      _has_box(grps[0].isPeriodic()),
      _header_written(false)
    {
      _titles = comments;
 
      writeHeader();
      writeFrames(grps);
    }
 
    ~DCDWriter() {
    }
 
 
 
    void setHeader(const int na, const int ns, const greal ts, const bool bf) {
      if (_header_written)
        throw(std::logic_error("Cannot set header after having written it"));
 
      _natoms = na;
      _nsteps = ns;
      _timestep = ts;
      _has_box = bf;
    }
 
    void setTitles(const std::vector<std::string>& titles) {
      if (_header_written)
        throw(std::logic_error("Cannot set header after having written it"));
      _titles = titles;
    }
 
    void setTitle(const std::string& s) {
      if (_header_written)
        throw(std::logic_error("Cannot set header after having written it"));
      _titles.clear(); addTitle(s);
    }
 
    void addTitle(const std::string& s) {
      if (_header_written)
        throw(std::logic_error("Cannot set header after having written it"));
      _titles.push_back(s);
    }
 
    void setComments(const std::vector<std::string>& comments) { setTitles(comments); }
    bool hasComments() const { return(true); }
    
 
    void writeFrame(const AtomicGroup& grp);
 
 
    void writeFrames(const std::vector<AtomicGroup>& grps);
 
    void writeHeader(void);
 
    uint framesWritten(void) const { return(_current); }
 
  private:
    void writeF77Line(const char* const data, const unsigned int len); 
    std::string fixStringSize(const std::string& s, const unsigned int size);
    void writeBox(const GCoord& box);
 
    void prepareToAppend();
 
 
  private:
    uint _natoms, _nsteps;
    greal _timestep;
    uint _current;
    bool _has_box;
    bool _header_written;
    std::vector<std::string> _titles;
  };
 
}
 
 
#endif