PDBAtom.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_KERNEL_PDBATOM_H
#define BALL_KERNEL_PDBATOM_H

#ifndef BALL_KERNEL_ATOM_H
# include <BALL/KERNEL/atom.h>
#endif


#define BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR              ' '
#define BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR           ' '
#define BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR   ' '
#define BALL_PDBATOM_DEFAULT_OCCUPANCY                      1.0
#define BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR             0.0


namespace BALL 
{
  class Chain;
  class Protein;
  class Residue;

  class BALL_EXPORT PDBAtom
    : public Atom
  {
    public:
    
    friend class Bond;

    BALL_CREATE_DEEP(PDBAtom)

    

    enum RemotenessIndicator
    {
      REMOTENESS_INDICATOR__UNKNOWN = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR,
      REMOTENESS_INDICATOR__ALPHA   = 'A',
      REMOTENESS_INDICATOR__alpha   = 'a',
      REMOTENESS_INDICATOR__BETA    = 'B',
      REMOTENESS_INDICATOR__beta    = 'b',
      REMOTENESS_INDICATOR__GAMMA   = 'G',
      REMOTENESS_INDICATOR__gamma   = 'g',
      REMOTENESS_INDICATOR__DELTA   = 'D',
      REMOTENESS_INDICATOR__delta   = 'd',
      REMOTENESS_INDICATOR__EPSILON = 'E',
      REMOTENESS_INDICATOR__epsilon = 'e',
      REMOTENESS_INDICATOR__ZETA    = 'Z',
      REMOTENESS_INDICATOR__zeta    = 'z',
      REMOTENESS_INDICATOR__ETA     = 'H',
      REMOTENESS_INDICATOR__eta     = 'h',

      NUMBER_OF_REMOTENESS_INDICATORS
    };

    enum Property
    {
      PROPERTY__HETATM = Atom::NUMBER_OF_PROPERTIES + 1,

      NUMBER_OF_PROPERTIES
    };


    PDBAtom();

    PDBAtom(const PDBAtom& pdb_atom, bool deep = true);
  
    PDBAtom(const String& name);

    PDBAtom
      (Element& element,
       const String& name,
       const String& type_name = BALL_ATOM_DEFAULT_TYPE_NAME,
       Atom::Type atom_type = BALL_ATOM_DEFAULT_TYPE,
       const Vector3& position = Vector3(BALL_ATOM_DEFAULT_POSITION),
       const Vector3& velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY),
       const Vector3& force = Vector3(BALL_ATOM_DEFAULT_FORCE),
       float charge = BALL_ATOM_DEFAULT_CHARGE,
       float radius = BALL_ATOM_DEFAULT_RADIUS,
       char branch_designator =BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR,
       char remoteness_indicator =BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR,
       char alternate_location_indicator = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR,
       float occupancy = BALL_PDBATOM_DEFAULT_OCCUPANCY,
       float temperature_factor = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR);

    virtual ~PDBAtom();
  
    virtual void destroy();



    bool operator == (const PDBAtom& pdb_atom) const;

    bool operator != (const PDBAtom& pdb_atom) const;



    void persistentWrite(PersistenceManager& pm, const char* name = 0) const;

    void persistentRead(PersistenceManager& pm);



    void set(const PDBAtom& pdb_atom, bool deep = true);

    void get(PDBAtom& pdb_atom, bool deep = true) const;

    PDBAtom& operator = (const PDBAtom& pdb_atom);

    void swap(PDBAtom& pdb_atom);

    virtual void clear();
    


    Protein* getProtein();

    const Protein* getProtein() const;

    Chain* getChain();

    const Chain* getChain() const;

    Residue* getResidue();

    const Residue* getResidue() const;

    void setBranchDesignator(char branch_designator);

    char getBranchDesignator() const;

    void setRemotenessIndicator(char remoteness_indicator);

    char getRemotenessIndicator() const;

    void setAlternateLocationIndicator(char alternate_location_indicator);

    char getAlternateLocationIndicator() const;

    void setOccupancy(float occupancy);

    float getOccupancy() const;

    void setTemperatureFactor(float temperature_factor);

    float getTemperatureFactor() const;



    virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;


    private:

    void clear_();

    /*_ The PDB branch designator
    */
    char  branch_designator_;

    /*_ The PDB remoteness indicator
    */
    char  remoteness_indicator_;

    /*_ The PDB alternate location indicator
    */
    char  alternate_location_indicator_;

    /*_ The PDB occupancy
    */
    float occupancy_;

    /*_ The PDB temperature factor
    */
    float temperature_factor_;

  };
} // namespace BALL

#endif // BALL_KERNEL_PDBATOM_H

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