/***************************************************************************
                          md_mod.cpp  -  description
                             -------------------
    begin                : Mon Dec 29 03:17:34 2003
    copyright            : (C) 2002 by Cavalli Andrea
    email                : cavalli@bioc.unizh.ch
**************************************************************************/
/***************************************************************************
 *                                                                         *
 *   This program 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; either version 2 of the License, or     *
 *   (at your option) any later version.                                   *
 *                                                                         *
 ***************************************************************************/

#include <zeta/module.h>
#include <zeta/class.h>
#include <zeta/zextclass.h>
#include <zeta/zobj.hpp>

#include <md_common.h>

using namespace Almost;
#define ALMTOSTRING(s) \
template<> \
inline string to_string(const s & ){ \
  return "<" #s ">"; \
}


ALMTOSTRING(ConstraintCollection);

typedef MDImpl<double,MDOptions<double> > * 
(MD<double>::*md_factory)(const Molecules & molecules,
			  const MDOptions<double> & options,
			  const MDB & mdb);


#if (__GNUC__ >= 3)
template<>
#endif
map<MDSelector<double>,MD<double>::md_factory > MD<double>::factory
#if (__GNUC__ >= 3)
=  map<MDSelector<double>,MD<double>::md_factory >();
#endif

;




template<>
inline string to_string(const MD<double> &){
  return "<MD>";
}


template<>
inline string to_string(const Molecules & molecules){
  return "<Molecules>";
}

template<>
inline string to_string(const MDB & mdb){
  return "<MDB>";
}

namespace Almost {
  void run_md_help(ConstraintCollection & cc,
		   const Molecules & mol,
		   const MDOptions<double> & opts,
		   const MDB & mdb){
    
    MD<double> md(cc);
    md.run(mol,opts,mdb);
  }  
}

extern "C" {
  void init_md(){
    //declarations here

    Module mod = Module("md","Molecular dynamics");

    REGISTER_MDC19_OPTIONS(double);    
    REGISTER_CONST(double);

    Class<MD<double> >(mod.self(),"md")
      .def_method("run",&MD<double>::run)
      .def_method("cont",&MD<double>::cont)
      .def_method("run_from_mol",&MD<double>::run_from_mol)
      .def_method("restart",&MD<double>::restart)
      .def_method("rst2molecules",&MD<double>::rst2molecules)
      ;


    mod.def_function("const_md","Run a constrained MD simulation",
		     const_md<MD<double> >);


    mod
//       .def_function("c19_options","Return options with right defaults",c19_md_options<double>)
      .def_function("c22_defaults","Return options with right defaults",c22_md_options<double>)
      .def_function("amber_defaults","Return options with right defaults",amber_md_options<double>)
      .def_function("c19_defaults","Return options with right defaults",c19_defaults<double>);


  }
}