/***************************************************************************
                          agresign_mod.cpp  -  description
                             -------------------
    begin                : Fri May  5 14:59:56 2006
    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 <molecules/molecules.h>
#include <misc/agretools.h>
namespace Almost {

  map<string, double> ref_ene;
  int init_ref_ene___(){
    //     ref_ene["ALA"] =  -95.1;
    //     ref_ene["ARG"] =  -127.38;
    //     ref_ene["ASN"] =  -115.34;
    //     ref_ene["ASP"] =  -123.13;
    //     ref_ene["CYS"] =  -98.02;
    //     ref_ene["GLN"] =  -112.63;
    //     ref_ene["GLU"] =  -114.91;
    //     ref_ene["GLY"] =  -93.27;
    //     ref_ene["HIS"] =  -109.73;
    //     ref_ene["ILE"] =  -91.97;
    //     ref_ene["LEU"] =  -94.05;
    //     ref_ene["LYS"] =  -114.92;
    //     ref_ene["MET"] =  -98.4;
    //     ref_ene["PHE"] =  -98.91;
    //     ref_ene["PRO"] =  -82.39;
    //     ref_ene["SER"] =  -102.18;
    //     ref_ene["THR"] =  -100.52;
    //     ref_ene["TRP"] =  -106.82;
    //     ref_ene["TYR"] =  -104.78;
    //     ref_ene["VAL"] =  -92.18;

    ref_ene["ALA"] = -95.806;
    ref_ene["ARG"] = -136.432;
    ref_ene["ASN"] = -112.758;
    ref_ene["ASP"] = -126.92;
    ref_ene["CYS"] = -98.722;
    ref_ene["GLN"] = -112.508;
    ref_ene["GLU"] = -125.408;
    ref_ene["GLY"] = -98.772;
    ref_ene["HIS"] = -112.908;
    ref_ene["ILE"] = -90.062;
    ref_ene["LEU"] = -92.16;
    ref_ene["LYS"] = -124.964;
    ref_ene["MET"] = -98.422;
    ref_ene["PHE"] = -97.662;
    ref_ene["PRO"] = -85.604;
    ref_ene["SER"] = -104.744;
    ref_ene["THR"] = -101.562;
    ref_ene["TRP"] = -109.206;
    ref_ene["TYR"] = -106.698;
    ref_ene["VAL"] = -91.022;

    return 1;
  }

  static int ref_ene_init = init_ref_ene___();
  double potter_energy(EnergyData<double> &e_from,
		       EnergyData<double> &e_to,
		       string from,
		       string to){
    double A=0.4;
    double B=1.5;
    double C=0.1;
    double D=1.2;

    double res = 
      A*(e_from["elec"]-e_to["elec"]) +
      B*(e_from["vdw"]-e_to["vdw"]) +
      C*(e_from["solv"]-e_to["solv"]) -
      D*(ref_ene[from]-ref_ene[to]);
    return -res;
  }


}
using namespace Almost;

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

ALMTOSTRING(Protein);
ALMTOSTRING(MDB);
ALMTOSTRING(DunbrackLib);

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

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

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

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

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

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

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

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

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

    Module mod = Module("aggresign","Aggregation propensity tools");
    Class<AggreSignRoule>(mod.self(),"roule")
      .def_method("add",&AggreSignRoule::add)
      //      .def_method("add",&AggreSignRoule::add)
      ;
    Class<AggreSignOpts>(mod.self(),"sign_options")
      .def_attribute("mini_steps",&AggreSignOpts::mini_steps,"Undocumented")
      .def_attribute("inhibt_lpatch",&AggreSignOpts::inhibt_lpatch,"Undocumented")
      .def_attribute("inhibt_fpatch",&AggreSignOpts::inhibt_fpatch,"Undocumented")
      .def_attribute("optimize_sc",&AggreSignOpts::optimize_sc,"Undocumented")
      ;

    Class<AggreCheckOpts>(mod.self(),"check_options")
      .def_attribute("mini_steps",&AggreCheckOpts::mini_steps,"Undocumented")
      .def_attribute("target_lpatch",&AggreCheckOpts::target_lpatch,"Undocumented")
      .def_attribute("target_fpatch",&AggreCheckOpts::target_fpatch,"Undocumented")
      .def_attribute("optimize_sc",&AggreCheckOpts::optimize_sc,"Undocumented")
      ;

    Class<AggreSign,ArgList6<const Protein &, const Protein &,
      const EnergyOptions<double> &,const MDB &, const DunbrackLib &, const AggreSignOpts &> >(mod.self(),
							   "aggresign")
      .def_method("guess",&AggreSign::guess)
      .def_method("search",&AggreSign::search)
      ;

    Class<AggreCheck,ArgList5<const Protein &,
      const EnergyOptions<double> &,const MDB &, const DunbrackLib &, const AggreCheckOpts &> >(mod.self(),
							   "aggrecheck")
      .def_method("search",&AggreCheck::search)
      ;

    Class<AutoTargetsOptions>(mod.self(),"autotargetsoptions")
      .def_attribute("para",&AutoTargetsOptions::para,"Undocumented")
      .def_attribute("anti",&AutoTargetsOptions::anti,"Undocumented")
      .def_attribute("mini",&AutoTargetsOptions::mini,"Undocumented")
      .def_attribute("dunbrack",&AutoTargetsOptions::dunbrack,"Undocumented")
      .def_attribute("steps",&AutoTargetsOptions::steps,"Undocumented")
      .def_attribute("project",&AutoTargetsOptions::project,"Undocumented")
      .def_attribute("dir",&AutoTargetsOptions::dir,"Undocumented")
      ;
    Class<AutoTargets,ArgList2<string,string> >(mod.self(),"autotargets")
      .def_method("run",&AutoTargets::run)
      .def_method("set_energy_options",&AutoTargets::set_energy_options)
      .def_method("energy_options",&AutoTargets::energy_options)

      ;

//     mod.def_function("default_roule","Default substitution roule",default_roule);

//     mod.def_function("roule","Substitution roule from file",roule);
  }
}