Atom.h

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#ifndef ATOM_H
#define ATOM_H

#include <string>
#include <iomanip>
#include <vcg/space/point3.h>

using namespace vcg;
using namespace std;

class Atom {
public:
  Atom(){};

 Atom(int _atomNumber, string _atomName, char _confID, string _residueName, char _chainID, int _residueNumber, Point3<float> _coord, float _charge, float _radius, string _segName):
  atomNumber(_atomNumber),
    atomName(_atomName),
    confID(_confID),
    residueName(_residueName),
    chainID(_chainID),
    residueNumber(_residueNumber),
    coord(_coord),
    charge(_charge),
    radius(_radius),
    segName(_segName)
    {
      
    }
  
  void print(){
    cout << "Atom number : " << atomNumber << endl;
    cout << "Atom name   : " << atomName << endl;
    cout << "Conform. nr : " << confID << endl;
    cout << "Residue name: " << residueName << endl;
    cout << "Chain nr    : " << chainID << endl;
    cout << "Residue nr  : " << residueNumber << endl;
    cout << "Coordinates : (" << coord.X() << ", " << coord.Y() << ", " << coord.Z() << ")" << endl;
    cout << "Charge      : " << charge << endl;
    cout << "Radius      : " << radius << endl;
    cout << "Segment name: " << segName << endl;
  }
  
  Point3<float> getCoord(){
    return coord;
  }
  
  float getRadius(){
    return radius;
  }
  
  int getResidueNumber(){
    return residueNumber;
  }
  
  string getResidueName(){
    return residueName;
  }
  
  void setResidueName(string _residueName){
    residueName = _residueName;
  }
  
  char getChainID(){
    return chainID;
  }
  
  string getAtomName(){
    return atomName;
  }
  
  void setCharge(float _charge){
    charge = _charge;
  }
  
  float getCharge(){
    return charge;
  }
  

  int getAtomNumber(){
    return atomNumber;
  }
  

  string pqrLine(){
    stringstream ss;
    ss << "ATOM" << setw(7) << atomNumber << setw(5) << atomName << setw(1)
       << confID << setw(3) << residueName << setw(2) << chainID << setw(4)
       << residueNumber << setw(12) << coord.X() << setw(8) << coord.Y()
       << setw(8) << coord.Z() << setw(6) << charge << setw(6)
       << radius << setw(7) << segName;
    return ss.str();
  }
  
 private:
  int atomNumber;
  string atomName;
  char confID;
  string residueName;
  char chainID;
  int residueNumber;
  Point3<float> coord;
  float charge;
  float radius;
  string segName;
};

#endif