mdtraj.hpp

/*
  This file is part of LOOS.
 
  LOOS (Lightweight Object-Oriented Structure library)
  Copyright (c) 2023, 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_MDTRAJ_HPP)
#define LOOS_MDTRAJ_HPP
 
#include <ios>
#include <fstream>
#include <sstream>
#include <iostream>
 
#include <stdexcept>
 
#include <loos_defs.hpp>
#include <AtomicGroup.hpp>
#include <H5Cpp.h>
#include <boost/json.hpp>
 
 
namespace loos {
 
 
  class MDTraj : public AtomicGroup {
  public:
    MDTraj() : _max_index(0) { }
    virtual ~MDTraj() {}
 
    explicit MDTraj(const std::string fname) : _max_index(0), _filename(fname) {
      read();
    }
 
    explicit MDTraj(std::istream &ifs) : _max_index(0), _filename("stream") {
      throw(LOOSError("Creating an MDTraj from a stream isn't implemented"));
    }
 
    static pAtomicGroup create(const std::string& fname) {
      return(pAtomicGroup(new MDTraj(fname)));
    }
 
    virtual MDTraj* clone(void) const;
 
    MDTraj copy(void) const;
 
    void read();  
 
 
  private:
 
    MDTraj(const AtomicGroup& grp) : AtomicGroup(grp) { }
 
    uint _max_index;
    std::string _filename;
 
    std::string getTopology(H5::H5File &file);
    void topologyToAtoms(const boost::json::value& topology);
    void topologyToBonds(const boost::json::value& topology);
 
  };
 
 
}
 
#endif