/***************************************************************************
                          anmr_mod.cpp  -  description
                             -------------------
    begin                : Fri Jun 15 17:25:01 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 <nmr/phaistos.h>
using namespace Almost;
struct FragH {
  enum { PLAIN, METHYL};
  vector<int> H;
  vector<string> name;
  int f_pos;
  string f_name;
  int kind;
  FragH(){
    kind = PLAIN;
  }
};

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

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


template<>
inline string to_string(const NMR::Atom &){
  return "<NMR::Atom>";
}

template<>
inline string to_string(const NMR::DB &){
  return "<NMR::DB>";
}

template<>
inline string to_string(const NMR::AlmNoesy &){
  return "<NMR::AlmNoesy>";
}

void extract_h(const Molecules & mols, vector<FragH> & frag_h){
  frag_h.clear();
  for(int i=0;i<mols.fragment_size();i++){
    FragH fh;
    vector<int> atm = mols.fragment_atoms(i);
    fh.f_name = mols.fragment_name(i,Molecules::BASE);
    string f_name_short = mols.fragment_name(i);
    fh.f_pos = i;
    {
      //Set kind
      

    }
    for(int aa=0;aa<atm.size();aa++){
      string atm_name = mols[atm[aa]].name();

      if(atm_name[0]=='H'){
	if(f_name_short=="ALA"&&atm_name[1]=='B') continue;
	if(f_name_short=="ILE"&&
	   ((atm_name[1]=='G'&&atm_name[2]=='2')||(atm_name[1]=='D'))
	   ) continue;
	if(f_name_short=="LEU"&&atm_name[1]=='D') continue;
	if(f_name_short=="LYS"&&atm_name[1]=='Z') continue;
	if(f_name_short=="MET"&&atm_name[1]=='E') continue;
	if(f_name_short=="THR"&&(atm_name[1]=='G'&&atm_name[1]=='2')) continue;
	if(f_name_short=="VAL"&&atm_name[1]=='G') continue;
	fh.H.push_back(atm[aa]);
	fh.name.push_back(atm_name);
      }
    }
    frag_h.push_back(fh);
  }
}


void mk_noesy(const Molecules & mols, const vector<FragH> & fh, string in_shx,
	      string out_noesy){

  map<string,double> shx;

  {
    ifstream in; in.open(in_shx.c_str());
    istream_iterator<string> iter(in),end;
    while(iter!=end){
      string s = *iter;++iter;
      double d = atof(iter->c_str()); ++iter;
      shx[s] = d;
    }
  }
  ofstream out; out.open(out_noesy.c_str());
  for(int i=0;i<fh.size();i++){
    cout<<"DEB i "<<i<<endl;;
    for(int j=0;j<fh.size();j++){
      cout<<"DEB j "<<i<<" "<<j<<endl;;
      for(int a1=0;a1<fh[i].H.size();a1++){
	int aa1 = fh[i].H[a1];
	string aa1_name = mols.atom_name(aa1,Molecules::BASE);
	double shx1 = shx[aa1_name];
	if(shx1==0) {
	  //	  cerr<<">> Missing shx for "<<aa1_name<<"\n";
	  continue;
	}
	for(int a2=0;a2<fh[j].H.size();a2++){
	  int aa2 = fh[j].H[a2];
	  string aa2_name = mols.atom_name(aa2,Molecules::BASE);
	  double shx2 = shx[aa2_name];
	  if(shx2==0) {
	    //	    cerr<<">> Missing shx for "<<aa2_name<<"\n";
	    continue;
	  }
	  if(aa1==aa2) continue;
	  double d = mols.distance(aa1,aa2);
	  if(d<6)
	    out<<shx1<<" "
	       <<shx2<<" "<<d<<" "
	       <<aa1_name<<" "
	       <<aa2_name<<"\n";
	  

	}
      }
    }
  }
}





extern "C" {
  void init_anmr(){
    //declarations here
    Module mod = Module("anmr","NMR Tools (incomplete)");

    Class<FragH>(mod.self(),"fragh")
      ;
    Class<vector<FragH> >(mod.self(),"fraghvect")
      .def_method("push_back",&vector<FragH>::push_back)
      .def_method("size",&vector<FragH>::size)
      .def_method("clear",&vector<FragH>::clear)
      //      .def_method("resize",&vector<int>::resize)
      ;


    Class<NMR::DB, ArgList1< string > >(mod.self(),"db");
    Class<NMR::AlmNoesy,ArgList4<string,string,string,vector<NMR::Atom> > >(mod.self(),"almnoesy")
      .def_method("bootstrap",&NMR::AlmNoesy::bootstrap)
      .def_method("set_dw",&NMR::AlmNoesy::set_dw)
      .def_method("validate",&NMR::AlmNoesy::validate)
      .def_method("validate_name",&NMR::AlmNoesy::validate_name)
      .def_method("validate_sym",&NMR::AlmNoesy::validate_sym)
      .def_method("validate_all",&NMR::AlmNoesy::validate_all)
      .def_method("validate_str",&NMR::AlmNoesy::validate_str)
      .def_method("validate_str2",&NMR::AlmNoesy::validate_str2)
      .def_method("mkmrg",&NMR::AlmNoesy::mkmrg)
      ;
    mod.def_function("extract_h","",extract_h);
    mod.def_function("mk_noesy","",mk_noesy);
    mod.def_function("mk_noesy3d","",NMR::mk_noesy3d);

    mod.def_function("mk_hlist","",NMR::mk_hlist);
  }
}