secondaryStructure.h

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

#ifndef BALL_KERNEL_SECONDARYSTRUCTURE_H
#define BALL_KERNEL_SECONDARYSTRUCTURE_H

#ifndef BALL_KERNEL_RESIDUE_H
# include <BALL/KERNEL/residue.h>
#endif

#ifndef BALL_KERNEL_RESIDUEITERATOR_H
# include <BALL/KERNEL/residueIterator.h>
#endif

#ifndef BALL_KERNEL_ATOMCONTAINER_H
# include <BALL/KERNEL/atomContainer.h>
#endif

namespace BALL 
{
  class BALL_EXPORT SecondaryStructure
    : public AtomContainer
  {
    public:

    BALL_CREATE_DEEP(SecondaryStructure)

    

    enum Type
    {
      HELIX,
      COIL,
      STRAND,
      TURN,
      UNKNOWN,
      NUMBER_OF_TYPES
    };




    SecondaryStructure();
  
    SecondaryStructure(const SecondaryStructure& secondary_structure, bool deep = true);
  
    SecondaryStructure(const String& name);

    virtual ~SecondaryStructure();

    virtual void clear();
  
    virtual void destroy();

    bool operator == (const SecondaryStructure& secondary_structure) const;

    bool operator != (const SecondaryStructure& secondary_structure) const;


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

    void persistentRead(PersistenceManager& pm);


    void set(const SecondaryStructure& secondary_structure, bool deep = true);

    SecondaryStructure& operator = (const SecondaryStructure& secondary_structure);

    void get(SecondaryStructure& secondary_structure, bool deep = true) const;

    void swap(SecondaryStructure& secondary_structure);


    Type getType() const { return type_; }

    void setType(Type type) { type_ = type; }
      
    Protein* getProtein();

    const Protein* getProtein() const;

    Chain* getChain();

    const Chain* getChain() const;

    Residue* getResidue(Position position);
  
    const Residue* getResidue(Position position) const;

    Residue* getNTerminal();
  
    const Residue* getNTerminal() const;

    Residue* getCTerminal();
  
    const Residue* getCTerminal() const;

    PDBAtom* getPDBAtom(Position position);
  
    const PDBAtom* getPDBAtom(Position position) const;
  
    Size countResidues() const;

    Size countPDBAtoms() const;

    void prepend(Residue& residue);

    void append(Residue& residue);

    void insert(Residue& residue);

    void insertBefore(Residue& residue, Composite& before);

    void insertAfter(Residue& residue, Composite& after);

    bool remove(Residue& residue);

    void spliceBefore(SecondaryStructure& secondary_structure);

    void spliceAfter(SecondaryStructure& secondary_structure);

    void splice(SecondaryStructure& secondary_structure);

  
    virtual bool isValid() const;

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

      
    // --- EXTERNAL ITERATORS

    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Residue)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(PDBAtom)

    BALL_DECLARE_STD_ITERATOR_WRAPPER(SecondaryStructure, Residue, residues)
    BALL_DECLARE_STD_ITERATOR_WRAPPER(SecondaryStructure, PDBAtom, pdbAtoms)

    protected:
    
    Type type_;

    private:

    Fragment* getFragment(Position position);
  
    const Fragment* getFragment(Position position) const;
  
    Atom* getAtom(Position position);
  
    const Atom* getAtom(Position position) const;

    void prepend(Atom& atom);

    void append(Atom& atom);

    void insert(Atom& atom);

    void insertBefore(Atom& atom, Composite& before);

    void insertAfter(Atom& atom, Composite& after);

    bool remove(Atom& atom);

    void prepend(AtomContainer& atom_container);

    void append(AtomContainer& atom_container);

    void insert(AtomContainer& atom_container);
      
    void insertBefore(AtomContainer& atom_container, Composite& before);

    void insertAfter(AtomContainer& atom_container, Composite& after);

    void spliceBefore(AtomContainer& atom_container);

    void spliceAfter(AtomContainer& atom_container);

    void splice(AtomContainer& atom_container);

    bool remove(AtomContainer& atom_container);

    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer)
    BALL_DECLARE_STD_ITERATOR_WRAPPER(SecondaryStructure, AtomContainer, atomContainers)
  };

} // namespace BALL

#endif // BALL_KERNEL_SECONDARYSTRUCTURE_H