/***************************************************************************
                          pdbatomline.cpp  -  description
                             -------------------
    begin                : Mon Feb 11 14:56:04 2002
    copyright            : (C) 2002 by Cavalli Andrea
    email                : cavalli.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 <pdb/pdbatomline.h>
#include <cstdio>

using namespace Almost;

PDBAtomLine::~PDBAtomLine(){
}
PDBAtomLine::PDBAtomLine(string line, int k){
  //                       1 -  6 
  serial = atoi(string(line.begin()+6,line.begin()+11).c_str());  
  name = simplify(string(line.begin()+12,line.begin()+16));  //CHANGED Sep 22
  //CHARMM bug 
  //name = simplify(string(line.begin()+12,line.begin()+17));
  altLoc= toupper(line[16]);     
  resName = simplify(string(line.begin()+17,line.begin()+21));
  chainID = line[21];
  //  cout<<"DEBUG >"<<chainID<<"<"<<line[20]<<line[21]<<line[22]<<endl;
  resSeq = atoi(string(line.begin()+22,line.begin()+27).c_str());
  iCode=line[26];
//   if(resSeq==27)
//     cout<<"DEB "<<line[26]<<"\n";
  x = atof(string(line.begin()+30,line.begin()+38).c_str());
  y = atof(string(line.begin()+38,line.begin()+46).c_str());
  z = atof(string(line.begin()+46,line.begin()+54).c_str());
  occupancy = atof(string(line.begin()+54,line.begin()+60).c_str());
  tempFact = atof(string(line.begin()+60,line.begin()+66).c_str());
  segID = simplify(string(line.begin()+72,line.begin()+76));//CHANGED Sep 22   
  element = simplify(string(line.begin()+76,line.begin()+78));
  charge = atof(string(line.begin()+78,line.begin()+80).c_str());
//   cout << " " <<    serial; 	
//   cout << " " <<   name;	
//   cout << " " <<    altLoc;	
//   cout << " " <<    resName;
//   cout << " " <<    chainID;	
//   cout << " " <<    resSeq;	
//   cout << " " <<    iCode;	
//   cout << " " <<    x;	
//   cout << " " <<    y;	
//   cout << " " <<    z;	
//   cout << " " <<    occupancy;
//   cout << " " <<    tempFact;
//   cout << " " <<    segID;	
//   cout << " " <<    element;
//   cout << " " <<    charge<< endl;;
  kind = k;
  checkName();
}

string PDBAtomLine::segment(){
  if(segID!="") return segID;
  if(chainID!=' '){ 
    string tmp;
    tmp =chainID;
    return tmp;
  }
  return string("NONE");
}


void  PDBAtomLine::checkName(){
  //move digits to the end .......
  if(isdigit(name[0])){
    char c = name[0];
    name = string(name.begin()+1,name.end());
    name = name +c;
  }
  //roules ----

//   if((name=="CD1")&&(resName=="ILE")){
//     name = "CD";
//     cout <<"Name of ILE/CD1 changed to ILE/CD"<<endl;
//   }
}

string PDBAtomLine::toString(){
  char buff[256];
//   sprintf(buff,
// 	  "%-6s%5i %-4s%s%3s  %3i    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s\n",
// 	  "ATOM",
// 	  serial,
// 	  name.c_str(),
// 	  altLoc,
// 	  resName.c_str(),
// 	  chainID,
// 	  resSeq,
// 	  x,
// 	  y,
// 	  z,
// 	  segID.c_str(),
// 	  element.c_str()
// 	  );
//   sprintf(buff,"%-6s%5i\n"
// 	  "ATOM",
// 	  serial
// 	  );
  sprintf(buff,
	  "%-6s%5i %-4s%c%3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s\n",
	  "ATOM",
	  serial,
	  name.c_str(),
	  altLoc,
	  resName.c_str(),
	  resSeq,
	  x,
	  y,
	  z,
	  occupancy,
	  tempFact,
	  segID.c_str(),
	  element.c_str());
  string tmp = buff;
  return tmp;
}