/***************************************************************************
                          tmd_mod.cpp  -  description
                             -------------------
    begin                : Tue Sep 18 13:46:28 2007
    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 <tmd/tmd.h>
#include <ffdoc.h>
#include <rundoc.h>
using namespace Almost;
using namespace TMD;

int MoleculesNode::id_counter = 0;

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

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

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

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

extern "C" {
  void init_tmd(){
    //declarations here
    Module mod = Module("tmd","Torsion Angle Molecular Dynamics");

    Class<TmdOptions,ArgList1<double> >(mod.self(),"tmd_options")
      .def_attribute("kind",&EnergyOptions< double >::kind,FFDoc::kind)
      .def_attribute("elec",&EnergyOptions<double>::elec,FFDoc::elec)
      .def_attribute("elec_cutoff",&EnergyOptions<double>::elec_cutoff,FFDoc::elec_cutoff)
      .def_attribute("vdw",&EnergyOptions<double>::vdw,FFDoc::vdw)
      .def_attribute("vdw_cutoff",&EnergyOptions<double>::vdw_cutoff,FFDoc::vdw_cutoff)
      .def_attribute("solv",&EnergyOptions<double>::solv,FFDoc::solv)
      .def_attribute("solv_ignore_h",&EnergyOptions<double>::solv_ignore_h,FFDoc::solv_ignore_h)
      .def_attribute("geometry",&EnergyOptions<double>::geometry,RunDoc::geometry)
      .def_attribute("Lx",&EnergyOptions<double>::Lx,RunDoc::Lx)
      .def_attribute("Ly",&EnergyOptions<double>::Ly,RunDoc::Ly)
      .def_attribute("Lz",&EnergyOptions<double>::Lz,RunDoc::Lz)
      .def_attribute("vect",&EnergyOptions<double>::vect,RunDoc::vect)
      .def_attribute("cut_on",&EnergyOptions<double>::cut_on,FFDoc::cut_on)
      .def_attribute("cut_off",&EnergyOptions<double>::cut_off,FFDoc::cut_off)
      .def_attribute("cut_nb",&EnergyOptions<double>::cut_nb,FFDoc::cut_nb)
      .def_attribute("alpha",&EnergyOptions<double>::alpha,FFDoc::alpha)
      .def_attribute("e_zero",&EnergyOptions<double>::e_zero,FFDoc::e_zero)
      .def_attribute("e_14",&EnergyOptions<double>::e_14,FFDoc::e_14)
      .def_attribute("eps",&EnergyOptions<double>::eps,FFDoc::eps)
      .def_attribute("r_water",&EnergyOptions<double>::r_water,FFDoc::r_water)
      .def_attribute("rgbmax",&EnergyOptions<double>::rgbmax,"Undocumented")
      .def_attribute("fsmax",&EnergyOptions<double>::fsmax,"Undocumented")
      .def_attribute("eps_water",&EnergyOptions<double>::eps_water,"Undocumented")
      .def_attribute("offset",&EnergyOptions<double>::offset,"Undocumented")
      .def_attribute("surftens",&EnergyOptions<double>::surftens,"Undocumented")
      .def_attribute("nsmooth",&EnergyOptions<double>::nsmooth,"Undocumented")
      .def_attribute("memb_width",&EnergyOptions<double>::memb_width,"Undocumented")
      .def_attribute("elec_strength",&EnergyOptions<double>::elec_strength,"Undocumented")
      .def_method("energy_options",&TmdOptions::energy_options)
      .def_attribute("trj",&TmdOptions::trj,"Undocumented")
      .def_attribute("rst",&TmdOptions::rst,"Undocumented")
      .def_attribute("log",&TmdOptions::log,"Undocumented")
      .def_attribute("dat",&TmdOptions::dat,"Undocumented")
      .def_attribute("steps",&TmdOptions::steps,"Undocumented")
      .def_attribute("nprint",&TmdOptions::nprint,"Undocumented")
      .def_attribute("nsave",&TmdOptions::nsave,"Undocumented")
      .def_attribute("nupdate",&TmdOptions::nupdate,"Undocumented")
      .def_attribute("temp",&TmdOptions::temp,"Undocumented")
      .def_attribute("time_step",&TmdOptions::time_step,"Undocumented")
      .def_attribute("tau",&TmdOptions::tau,"Undocumented")
      .def_attribute("seed",&TmdOptions::seed,"Undocumented")
      .def_attribute("ene_accuracy",&TmdOptions::ene_accuracy,"Undocumented")
      ;



    Class<MoleculesTree,ArgList1<const Protein &> >(mod.self(),"tree")
      .def_method("run",&MoleculesTree::run)
      .def_method("cont",&MoleculesTree::cont)
      .def_method("anneal",&MoleculesTree::anneal)
      .def_method("set_cc",&MoleculesTree::set_cc)
      .def_method("unset_cc",&MoleculesTree::unset_cc)
      .def_method("mini",&MoleculesTree::mini)
      .def_method("const_mini",&MoleculesTree::const_mini)
      .def_method("scan",&MoleculesTree::scan);
      ;
    ;

    mod
      .def_const("C19",(int)EnergyOptions<double>::C19)
      .def_const("C22",(int)EnergyOptions<double>::C22)
      .def_const("AMBER",(int)EnergyOptions<double>::AMBER)
      .def_const("NONE",(int)EnergyOptions<double>::NONE)
      .def_const("SASA",(int)EnergyOptions<double>::SASA)
      .def_const("EEF1",(int)EnergyOptions<double>::EEF1)
      .def_const("IMM1",(int)EnergyOptions<double>::IMM1)
      .def_const("GB",(int)EnergyOptions<double>::GB)
      .def_const("GB2",(int)EnergyOptions<double>::GB2)
      .def_const("OFF",(int)EnergyOptions<double>::OFF)
      .def_const("RDIE",(int)EnergyOptions<double>::RDIE)
      .def_const("CDIE",(int)EnergyOptions<double>::CDIE)
      .def_const("LJ",(int)EnergyOptions<double>::LJ)
      .def_const("SHIFT",(int)EnergyOptions<double>::SHIFT)
      .def_const("SWITCH",(int)EnergyOptions<double>::SWITCH)
      .def_const("TRUNC",(int)EnergyOptions<double>::TRUNC)
      .def_const("PLAIN",(int)EnergyOptions<double>::PLAIN)
      .def_const("CUBIC",(int)EnergyOptions<double>::CUBIC)
      .def_const("SSE",(int)EnergyOptions<double>::SSE)
      ;


  }
}