protein.h

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

#ifndef BALL_KERNEL_PROTEIN_H
#define BALL_KERNEL_PROTEIN_H

#ifndef BALL_KERNEL_CHAINITERATOR_H
# include <BALL/KERNEL/chainIterator.h>
#endif

#ifndef BALL_KERNEL_MOLECULE_H
# include <BALL/KERNEL/molecule.h>
#endif

#define BALL_PROTEIN_DEFAULT_ID   ""

namespace BALL 
{
  class BALL_EXPORT Protein
    : public Molecule
  {
    public:

    BALL_CREATE_DEEP(Protein)

    
      
    
    enum Property
    {
      NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES
    };



    Protein();
  
    Protein(const Protein& protein, bool deep = true);
  
    Protein(const String& name, const String& id = BALL_PROTEIN_DEFAULT_ID);

    virtual ~Protein();
  
    virtual void clear();
  
    /* Clears the contents of the protein and removes it from all composite structures.
    */
    virtual void destroy();


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

    void persistentRead(PersistenceManager& pm);



    void set(const Protein& protein, bool deep = true);

    Protein& operator = (const Protein& protein);

    void get(Protein& protein, bool deep = true) const;
  
    void swap(Protein& protein);
  

    bool operator == (const Protein& protein) const;

    bool operator != (const Protein& protein) const;


    Chain* getChain(Position position);

    const Chain* getChain(Position position) const;

    SecondaryStructure* getSecondaryStructure(Position position);

    const SecondaryStructure* getSecondaryStructure(Position position) const;

    Residue* getResidue(Position position);

    const Residue* getResidue(Position position) const;

    Residue* getResidueByID(String residue_ID);

    const Residue* getResidueByID(String residue_ID) const;

    Residue* getNTerminal();

    const Residue* getNTerminal() const;

    Residue* getCTerminal();

    const Residue* getCTerminal() const;

    PDBAtom* getPDBAtom(Position position);

    const PDBAtom* getPDBAtom(Position position) const;

    void setID(const String& id);

    const String& getID() const;

    Size countChains() const;

    Size countSecondaryStructures() const;

    Size countResidues() const;

    Size countPDBAtoms() const;


    using Molecule::prepend;
    using Molecule::append;
    using Molecule::insert;
    using Molecule::insertBefore;
    using Molecule::insertAfter;
    using Molecule::remove;
    using Molecule::splice;
    using Molecule::spliceBefore;
    using Molecule::spliceAfter;


    virtual bool isValid() const;

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


    // --- EXTERNAL ITERATORS

    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Chain)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(SecondaryStructure)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Residue)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(PDBAtom)

    
    private:

    // --- ATTRIBUTES

    String id_;
  };
} // namespace BALL

#endif // BALL_KERNEL_PROTEIN_H