/***************************************************************************
                          gas_mod.cpp  -  description
                             -------------------
    begin                : Thu Mar 29 09:19:24 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 <module.h>
#include <class.h>
#include <zextclass.h>
#include <zobj.hpp>

using namespace Almost;
void mkcamdb(vector<string> seq, string f){
  for(int i=0;i<seq.size();i++){
    string t;
    for(int j=0;j<seq[i].size();j++)
      if(seq[i][j]!='_') t += seq[i][j];
    seq[i] = t;

  }
  ofstream out;
  out.open(f.c_str());
  if(!out) throw "Unable to open file.";

  //Def fragments
  for(int i=0;i<seq.size();i++){
    out<<"template_fragment "<<seq[i]<<" = { \n";
    out<<"   template_attr attr = { "<<seq[i]<<", 0.00000, SOLVENT };\n";
    out<<"   tatom_list atom = { \n";
    out<<"     { "<<seq[i]<<", "<<seq[i]<<", 0.00}\n";
    out<<"   };\n";
    out<<"   tbond_list bond = { \n";
    out<<"   };\n";
    out<<"   tgroup_list grp = {\n";
    out<<"   {\n";
    out<<"    "<<seq[i]<<"\n";
    out<<"   }\n";
    out<<"   };\n";
    out<<"   def_patch patch =  { NONE, NONE};\n";
    out<<"};\n";
  }

  //Atom types
  out<<"atom_type_list charmm_atom = {\n";
  for(int i=0;i<seq.size();i++){
    out<<"{ "<<seq[i]<<", 10.00, CA, yes}";
      if(i!=seq.size()-1) out<<",\n";
      else out<<"\n";
  }
  out<<"};\n";

  //NBType
  out<<"nbond_type_list charmm_nbond = {\n";
  for(int i=0;i<seq.size();i++){
    out<<"{ "<<seq[i]<<", -1.00, 2.0, -1.00, 2.0}";
      if(i!=seq.size()-1) out<<",\n";
      else out<<"\n";
  }
  out<<"};\n";

  //NBFix ...
  out<<"nbfix_list fix = {\n";
  for(int i=0;i<seq.size()-1;i++){
    out<<"{ "<<seq[i]<<", "<<seq[i+1]<<", -10.00, 3.8, -10.00, 3.8}";
    if(i!=seq.size()-2) out<<",\n";
    else out<<"\n";    
  }
  out<<"};";
}

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

    Module mod = Module("gas");
    mod
      .def_function("mkcamdb",
		    "Make CA-mdb",
		    mkcamdb);
  }
}