/***************************************************************************
                          dynamip_mod.cpp  -  description
                             -------------------
    begin                : Thu Sep 16 04:19:17 2004
    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 <dynamip_common.h>
#include <dynamip/dynamip.h>

// extern vector<Almost::MIPConstraint * > mip_constraints;
// namespace Almost {
//   vector<MIPConstraint *> get_mipconst(){ return  mip_constraints;}
//   void clear_mipconst(){
//     for(int i=0;i<mip_constraints.size();i++) delete mip_constraints[i];
//     mip_constraints.clear();
//   }
// }

using namespace Almost;

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

ALMTOSTRING(MoveSet<double>);
ALMTOSTRING(ConstraintCollection);

// typedef DynaMIPData<DefGoForceField<double>, 
// 		    DynaMIPGoOptions<double>, 
// 		    ENERGY> GoData;

// typedef DynaMIPTraits<double,
// 		      CoorManager<double>,
// 		      CoorManagerOptions<double>,
// 		      DefGoForceField<double>,
// 		      DefGoOptions<double>,
// 		      MoveSet<double>,
// 		      Metropolis<double>,
// 		      GoData,
// 		      DynaMIPGoOptions<double> > GoTraits;

// template<>
// void ForceFieldFactory::create(DefGoForceField<double> ** force_field,
// 			       const Molecules & molecules,
// 			       const DynaMIPGoOptions<double> &options,
// 			       const MDB & mdb,
// 			       const string & ff_pr){
//   logMsg(ff_pr,
// 	 "Initializing "+ DefGoOptions<double>::ff_name()+" force field");
  
//   *force_field = 
//     new DefGoForceField<double>(molecules,
// 				options.ff_options(),
// 				mdb);
//   logMsg(ff_pr,"Done\n");
// }


// typedef DynaMIPData<DefIGoForceField<double>,
// 		    DynaMIPIGoOptions<double>, 
// 		    ENERGY> IGoData;

// typedef DynaMIPTraits<double,
// 		      CoorManager<double>,
// 		      CoorManagerOptions<double>,
// 		      DefIGoForceField<double>,
// 		      DefIGoOptions<double>,
// 		      MoveSet<double>,
// 		      Metropolis<double>,
// 		      IGoData,
// 		      DynaMIPIGoOptions<double> > IGoTraits;


// template<>
// void ForceFieldFactory::create(DefIGoForceField<double> ** force_field,
// 			       const Molecules & molecules,
// 			       const DynaMIPIGoOptions<double> &options,
// 			       const MDB & mdb,
// 			       const string & ff_pr){
//   logMsg(ff_pr,
// 	 "Initializing "+ DefIGoOptions<double>::ff_name()+" force field");
  
//   *force_field = 
//     new DefIGoForceField<double>(molecules,
// 				 options.ff_options(),
// 				 mdb);
//   logMsg(ff_pr,"Done\n");
// }


		   
// template<typename float_type>
// inline string to_string(const DynaMIPGoOptions<float_type> & opt){
//   stringstream s;
//   s<<opt;
//   return s.str();
// }

// template<typename float_type>
// inline string to_string(const DynaMIPIGoOptions<float_type> & opt){
//   stringstream s;
//   s<<opt;
//   return s.str();
// }


typedef DynaMIPImpl<double,DynaMIPOptions<double> > * 
(DynaMIP<double>::*mc_factory_19)(const XMolecules & molecules,
				  const DynaMIPOptions<double> & options,
				  const MDB & mdb);



#if (__GNUC__ >= 3)
template<>
#endif
map<int,mc_factory_19> DynaMIP<double>::factory
#if (__GNUC__ >= 3)
= map<int,mc_factory_19>();
#endif
;


// template<>
// inline string to_string(const DynaMIPImplementation<GoTraits,GoTraits::Options> &){
//   return "<DynaMIPGo>";
// }

// template<>
// inline string to_string(const DynaMIPImplementation<IGoTraits,IGoTraits::Options> &){
//   return "<DynaMIPIGo>";
// }

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

template<typename DynaType>
DynaType const_dynamip(MoveSet<double> & ms, ConstraintCollection & cc){
  return DynaType(ms,cc);
}

//operators for GO

// template<typename float_type>
// DynaLogStream & operator<<(DynaLogStream &log, 
// 			   const DynaMIPData<DefGoForceField<float_type>, 
// 			   DynaMIPGoOptions<float_type>, 
// 			   ENERGY> &data){
//   char buff[256];
//   string prmpt=Almost::DynaMIPStatPr;
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10s | %-10s | %-10s | %-10s | %-10s\n","step","energy","rmsd","rgyr","const");
//   log.stream()<<buff;
//   log.stream()<<prmpt;
//   log.stream()<<"---------------------------------------------------------\n";
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10i   %-10.2f   %-10.2f   %-10.2f   %-10.2f\n\n",
// 	  data.step,
// 	  data.current_energy,
// 	  data.rmsd,
// 	  data.rgyr,
// 	  data.ff_data.const_energy
// 	  );
//   log.stream()<<buff;
//   prmpt=Almost::EnerStatPr; 
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10s | %-10s | %-10s | %-10s\n","step","native","non native","Q");
//   log.stream()<<buff;
//   log.stream()<<prmpt;
//   log.stream()<<"----------------------------------------------------\n";
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10i   %-10i   %-10i   %-10.2f\n\n",
// 	  data.step,
// 	  data.ff_data.n_native,data.ff_data.n_non_native,
// 	  (float_type)(data.ff_data.n_native)/(float_type)data.ff_data.n_cont_max);
//   log.stream()<<buff;
//   return log;
// }  

// template<typename float_type>
// DynaDataStream & operator<<(DynaDataStream &dat, 
// 			    const DynaMIPData<DefGoForceField<float_type>, 
// 			    DynaMIPGoOptions<float_type>, 
// 			    ENERGY> &data){
//   dat.stream()<<data.step<<" "<<data.current_energy<<" "
// 	      <<data.rmsd<<" "<<data.rgyr<<" "<<data.ff_data.const_energy
// 	      <<" "<<data.ff_data.n_native<<" "
// 	      <<data.ff_data.n_non_native<<" "
// 	      <<(float_type)(data.ff_data.n_native)/(float_type)data.ff_data.n_cont_max<<"\n";
//   return dat;
// }  





// //template<typename float_type>
// template<>
// DynaLogStream & operator<< <DefIGoForceField<double>,
// 			    DynaMIPIGoOptions<double>,
// 			    ENERGY> (DynaLogStream &log, 
// 				     const DynaMIPData<DefIGoForceField<double>, 
// 				     DynaMIPIGoOptions<double>, 
//  ENERGY> &data){
//   char buff[256];
//   string prmpt=Almost::DynaMIPStatPr;
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10s | %-10s | %-10s | %-10s | %-10s\n","step","energy","rmsd","rgyr","const");
//   log.stream()<<buff;
//   log.stream()<<prmpt;
//   log.stream()<<"---------------------------------------------------------\n";
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10i   %-10.2f   %-10.2f   %-10.2f   %-10.2f\n\n",
// 	  data.step,
// 	  data.current_energy,
// 	  data.rmsd,
// 	  data.rgyr,
// 	  data.ff_data.const_energy
// 	  );
//   log.stream()<<buff;
//   prmpt=Almost::EnerStatPr; 
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10s | %-10s | %-10s | %-10s\n","step","native","non native","Q");
//   log.stream()<<buff;
//   log.stream()<<prmpt;
//   log.stream()<<"----------------------------------------------------\n";
//   log.stream()<<prmpt;
//   sprintf(buff,"%-10i   %-10i   %-10i   %-10.2f\n\n",
// 	  data.step,
// 	  data.ff_data.n_native,data.ff_data.n_non_native,
// 	  (double)(data.ff_data.n_native)/(double)data.ff_data.n_cont_max);
//   log.stream()<<buff;
//   return log;
// }  

// //template<typename float_type>
// template<>
// DynaDataStream & operator<<(DynaDataStream &dat, 
// 			    const DynaMIPData<DefIGoForceField<double>, 
// 			    DynaMIPIGoOptions<double>, 
// 			    ENERGY> &data){
//   dat.stream()<<data.step<<" "<<data.current_energy<<" "
// 	      <<data.rmsd<<" "<<data.rgyr<<" "<<data.ff_data.const_energy
// 	      <<" "<<data.ff_data.n_native<<" "
// 	      <<data.ff_data.n_non_native<<" "
// 	      <<(double)(data.ff_data.n_native)/(double)data.ff_data.n_cont_max<<"\n";
//   return dat;
// }  

DynaMIPOptions<double> c19_defaults_mip(int FF){
  DynaMIPOptions<double> opts(DynaMIPOptions<double>::C19);
  if(FF==DynaMIPOptions<double>::EEF1){
    opts.elec = DynaMIPOptions<double>::RDIE;
    opts. elec_cutoff = DynaMIPOptions<double>::SWITCH;
    opts.vdw = DynaMIPOptions<double>::LJ;
    opts.vdw_cutoff = DynaMIPOptions<double>::SWITCH;
    opts.eps = 1.0;
    opts.solv = DynaMIPOptions<double>::EEF1;
    opts.cut_on = 7.0;
    opts.cut_off = 9.0;
    opts.cut_nb = 10.0;
  }
  else if(FF!=DynaMIPOptions<double>::SASA)
    opts.solv = DynaMIPOptions<double>::NONE;


  return opts;
}

DynaMIPOptions<double> c19_options_mip(){
  return DynaMIPOptions<double>(DynaMIPOptions<double>::C19);
}

DynaMIPOptions<double> c22_options_mip(){
  return DynaMIPOptions<double>(DynaMIPOptions<double>::C22);
}

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

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

    Module mod = Module("dynamip","Replica Monte Carlo simulations");

    //     Class<DynaMIPGoOptions<double> >(mod.self(),"go_options")
    //       .def_attribute("e_native",&DynaMIPGoOptions<double>::e_native)
    //       .def_attribute("e_non_native",&DynaMIPGoOptions<double>::e_non_native)
    //       .def_attribute("alpha",&DynaMIPGoOptions<double>::alpha)
    //       .def_attribute("lambda",&DynaMIPGoOptions<double>::lambda)
    //       .def_attribute("ignore_mode",&DynaMIPGoOptions<double>::ignore_mode)
    //       .def_attribute("native_map",&DynaMIPGoOptions<double>::native_map)
    //       .def_attribute("const_file",&DynaMIPGoOptions<double>::const_file)
    //       .def_attribute("move_set",&DynaMIPGoOptions<double>::move_set)
    //       .def_attribute("trj",&DynaMIPGoOptions<double>::trj)
    //       .def_attribute("rst",&DynaMIPGoOptions<double>::rst)
    //       .def_attribute("log",&DynaMIPGoOptions<double>::log)
    //       .def_attribute("dat",&DynaMIPGoOptions<double>::dat)
    //       .def_attribute("steps",&DynaMIPGoOptions<double>::steps)
    //       .def_attribute("nprint",&DynaMIPGoOptions<double>::nprint)
    //       .def_attribute("nsave",&DynaMIPGoOptions<double>::nsave)
    //       .def_attribute("temp",&DynaMIPGoOptions<double>::temp)
    //       .def_attribute("seed",&DynaMIPGoOptions<double>::seed)
    //       .def_attribute("selection",&DynaMIPGoOptions<double>::selection)
    //       .def_attribute("save_fitted",&DynaMIPGoOptions<double>::save_fitted)
    //       .def_attribute("nreplica",&DynaMIPGoOptions<double>::nreplica)
    //       ;


    //     Class<DynaMIPIGoOptions<double> >(mod.self(),"vdw_go_options")
    //       .def_attribute("nn_factor",&DynaMIPIGoOptions<double>::nn_factor)
    //       .def_attribute("alpha",&DynaMIPIGoOptions<double>::alpha)
    //       .def_attribute("lambda",&DynaMIPIGoOptions<double>::lambda)
    //       .def_attribute("ignore_mode",&DynaMIPIGoOptions<double>::ignore_mode)
    //       .def_attribute("native_map",&DynaMIPIGoOptions<double>::native_map)
    //       .def_attribute("const_file",&DynaMIPIGoOptions<double>::const_file)
    //       .def_attribute("move_set",&DynaMIPIGoOptions<double>::move_set)
    //       .def_attribute("trj",&DynaMIPIGoOptions<double>::trj)
    //       .def_attribute("rst",&DynaMIPIGoOptions<double>::rst)
    //       .def_attribute("log",&DynaMIPIGoOptions<double>::log)
    //       .def_attribute("dat",&DynaMIPIGoOptions<double>::dat)
    //       .def_attribute("steps",&DynaMIPIGoOptions<double>::steps)
    //       .def_attribute("nprint",&DynaMIPIGoOptions<double>::nprint)
    //       .def_attribute("nsave",&DynaMIPIGoOptions<double>::nsave)
    //       .def_attribute("temp",&DynaMIPIGoOptions<double>::temp)
    //       .def_attribute("seed",&DynaMIPIGoOptions<double>::seed)
    //       .def_attribute("selection",&DynaMIPIGoOptions<double>::selection)
    //       .def_attribute("save_fitted",&DynaMIPIGoOptions<double>::save_fitted)
    //       .def_attribute("nreplica",&DynaMIPIGoOptions<double>::nreplica)
    //       ;



    //     Class<DynaMIPImplementation<GoTraits,
    //       GoTraits::Options> >(mod.self(),"dyna_go")
    //       .def_method("run",
    // 		  &DynaMIPImplementation<GoTraits,GoTraits::Options>::run)
    //       .def_method("run_from_mol",
    // 		  &DynaMIPImplementation<GoTraits,GoTraits::Options>::run_from_mol)
    //       .def_method("cont",&DynaMIPImplementation<GoTraits,GoTraits::Options>::cont)
    //       .def_method("restart",
    // 		  &DynaMIPImplementation<GoTraits,GoTraits::Options>::restart)
    //       ;


    //     Class<DynaMIPImplementation<IGoTraits,
    //       IGoTraits::Options> >(mod.self(),"dyna_vdw_go")
    //       .def_method("run",
    // 		  &DynaMIPImplementation<IGoTraits,IGoTraits::Options>::run)
    //       .def_method("run_from_mol",
    // 		  &DynaMIPImplementation<IGoTraits,IGoTraits::Options>::run_from_mol)
    //       .def_method("cont",&DynaMIPImplementation<IGoTraits,IGoTraits::Options>::cont)
    //       .def_method("restart",
    // 		  &DynaMIPImplementation<IGoTraits,IGoTraits::Options>::restart)
    //       ;


    Class<DynaMIPOptions<double> >(mod.self(),"options")
      .def_attribute("kind",&DynaMIPOptions<double>::kind,"Undocumented")
      .def_attribute("elec",&DynaMIPOptions<double>::elec,"Undocumented")
      .def_attribute("elec_cutoff",&DynaMIPOptions<double>::elec_cutoff,"Undocumented")
      .def_attribute("vdw",&DynaMIPOptions<double>::vdw,"Undocumented")
      .def_attribute("vdw_cutoff",&DynaMIPOptions<double>::vdw_cutoff,"Undocumented")
      .def_attribute("solv",&DynaMIPOptions<double>::solv,"Undocumented")
      .def_attribute("solv_ignore_h",&DynaMIPOptions<double>::solv_ignore_h,"Undocumented")
      .def_attribute("cut_on",&DynaMIPOptions<double>::cut_on,"Undocumented")
      .def_attribute("cut_off",&DynaMIPOptions<double>::cut_off,"Undocumented")
      .def_attribute("e_zero",&DynaMIPOptions<double>::e_zero,"Undocumented")
      .def_attribute("e_14",&DynaMIPOptions<double>::e_14,"Undocumented")
      .def_attribute("eps",&DynaMIPOptions<double>::eps,"Undocumented")
      .def_attribute("r_water",&DynaMIPOptions<double>::r_water,"Undocumented")
      .def_attribute("vect",&DynaMIPOptions<double>::vect,"Undocumented")
      .def_attribute("trj",&DynaMIPOptions<double>::trj,"Undocumented")
      .def_attribute("rst",&DynaMIPOptions<double>::rst,"Undocumented")
      .def_attribute("log",&DynaMIPOptions<double>::log,"Undocumented")
      .def_attribute("dat",&DynaMIPOptions<double>::dat,"Undocumented")
      .def_attribute("steps",&DynaMIPOptions<double>::steps,"Undocumented")
      .def_attribute("nprint",&DynaMIPOptions<double>::nprint,"Undocumented")
      .def_attribute("nsave",&DynaMIPOptions<double>::nsave,"Undocumented")
      .def_attribute("temp",&DynaMIPOptions<double>::temp,"Undocumented")
      .def_attribute("seed",&DynaMIPOptions<double>::seed,"Undocumented")
      .def_attribute("selection",&DynaMIPOptions<double>::selection,"Undocumented")
      .def_attribute("save_fitted",&DynaMIPOptions<double>::save_fitted,"Undocumented")
      .def_attribute("nreplica",&DynaMIPOptions<double>::nreplica,"Undocumented")
      ;
      

    Class<DynaMIP<double>,ArgList1<MoveSet<double> & >  >(mod.self(),"dynamip")
      .def_method("run",
		  &DynaMIP<double>::run)
      .def_method("run_from_mol",
		  &DynaMIP<double>::run_from_mol)
      .def_method("cont",&DynaMIP<double>::cont)
      .def_method("restart",
		  &DynaMIP<double>::restart)
      ;

    mod.def_function("const_dynamip","Run a constrained MC simulation",
		     const_dynamip<DynaMIP<double> >);

    mod
      .def_const("C19",(int)DynaMIPOptions<double>::C19)
      .def_const("C22",(int)DynaMIPOptions<double>::C22)
      .def_const("NONE",(int)DynaMIPOptions<double>::NONE)
      .def_const("SASA",(int)DynaMIPOptions<double>::SASA)
      .def_const("EEF1",(int)DynaMIPOptions<double>::EEF1)
      ;


    mod
      .def_function("c19_defaults","Return options with right defaults",c19_defaults_mip)
      .def_function("c19_options","Return options with right defaults",c19_options_mip)
      .def_function("c22_options","Return options with right defaults",c22_options_mip);

  }
}