PDBstructure.hpp

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#ifndef PROTEINDATABANKSTRUCTURE_HPP_
#define PROTEINDATABANKSTRUCTURE_HPP_

#include <stdlib.h>
#include <sstream>
#include <string>

// it has to be mentioned before Atom class, since that calls PDB
class PDB; 

class Atom
{
    Atom() {;};
    ~Atom();
    friend class PDB;
    friend class Residue;
    //friend class iterate;
    std::string Atom_Type; 
    int Atom_Number; 
public:
    //std::string Atom_Type;
    struct Coordinates
    {
        float X; 
        float Y; 
        float Z; 
    } Coord; // Store the (x,y,z) coordinates of the atoms

    // If given in pqr file, charge and radii will be assigned!
    float charge; 
    float radii; 
    //If not pqr, use the default parameters for vdW radii
    float VdW_Radius ();
    int Read_PDB_File();
};

class Residue
{
    Residue() {;};
    ~Residue();
    friend class PDB;
    //friend class iterate;
    
    std::string Residue_Type; 
    
public:
    int Number_of_Atoms; 
    Atom * Atoms; 
    int Read_PDB_File();
    Atom::Coordinates Center_of_Geometry();
};

class PDB
{
private:
    bool pqr; 
    //friend class iterate;
public:
    //PDB() {;};
    PDB();
    PDB(bool);
    ~PDB();

    int Number_of_Residues; 
    int Number_of_Atoms; 
    float max_vdw; 
    Residue * Residues; 
    Residue Dummy;
    
public:
    void Read_PDB_File(std::ifstream&);
    int Center_of_Geometry();
    Atom::Coordinates CoG; 
    int Get_Coordinates();  
};

/*class iterate
{
private:
    Atom * start;
    Atom * finish;
    void * iter;
    Atom begin();
    Atom end();
    iterate (PDB * THIS);
    Atom operator++ ();
};*/

#endif /* PROTEINDATABANKSTRUCTURE_HPP_ */