gro.hpp

/*
  This file is part of LOOS.
 
  LOOS (Lightweight Object-Oriented Structure library)
  Copyright (c) 2009, 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_GRO_HPP)
#define LOOS_GRO_HPP
 
#include <iostream>
#include <string>
#include <sstream>
#include <fstream>
#include <stdexcept>
 
#include <loos_defs.hpp>
#include <AtomicGroup.hpp>
 
namespace loos
{
 
  class Gromacs : public AtomicGroup
  {
  public:
    Gromacs() {}
 
    explicit Gromacs(const std::string &fname) : _filename(fname), _max_index(0), _has_velocities(false)
    {
      std::ifstream ifs(fname.c_str());
      if (!ifs)
        throw(FileOpenError(fname));
      read(ifs);
    }
 
    explicit Gromacs(std::istream &ifs) : _filename("stream"), _max_index(0), _has_velocities(false) { read(ifs); }
 
    static pAtomicGroup create(const std::string &fname)
    {
      return (pAtomicGroup(new Gromacs(fname)));
    }
 
    bool hasVelocities() const { return (_has_velocities); }
 
    std::string asString() const;
    friend std::ostream &operator<<(std::ostream &, const Gromacs &);
 
    std::string title(void) const { return (title_); }
 
    static Gromacs fromAtomicGroup(const AtomicGroup &);
 
  private:
    std::string _filename;
    std::string title_;
    uint _max_index;
    bool _has_velocities;
 
  private:
    void read(std::istream &ifs);
 
    // Convert an Atom to a string representation in PDB format...
    std::string atomAsString(const pAtom p) const;
 
    Gromacs(const AtomicGroup &grp) : AtomicGroup(grp) {}
  };
 
}
 
#endif