chain.h

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

#ifndef BALL_KERNEL_CHAIN_H
#define BALL_KERNEL_CHAIN_H

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

#ifndef BALL_KERNEL_SECONDARYSTRUCTUREITERATOR_H
# include <BALL/KERNEL/secondaryStructureIterator.h>
#endif


#define BALL_CHAIN_DEFAULT_NAME   ' '

namespace BALL
{
  class Protein;

  class BALL_EXPORT Chain
    : public AtomContainer
  {
    public:

    BALL_CREATE_DEEP(Chain)

    

    enum Property
    {
      NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES
    };



    Chain();

    Chain(const Chain& chain, bool deep = true);

    Chain(const String& name);

    virtual ~Chain();



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

    void persistentRead(PersistenceManager& pm);



    void set(const Chain& chain, bool deep = true);

    Chain& operator = (const Chain& chain);

    void get(Chain& chain, bool deep = true) const;

    void swap(Chain& chain);


    bool operator == (const Chain& chain) const;

    bool operator != (const Chain& chain) const;



    Protein* getProtein();

    const Protein* getProtein() const;

    SecondaryStructure* getSecondaryStructure(Position position);

    const SecondaryStructure* getSecondaryStructure(Position position) 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 countSecondaryStructures() const;

    Size countResidues() const;

    Size countPDBAtoms() const;

    void prepend(SecondaryStructure& secondary_structure);

    void append(SecondaryStructure& secondary_structure);

    void insert(SecondaryStructure& secondary_structure);

    void insertBefore(SecondaryStructure& secondary_structure, Composite& before);

    void insertAfter(SecondaryStructure& secondary_structure, Composite& after);

    bool remove(SecondaryStructure& secondary_structure);

    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(Chain& chain);

    void spliceAfter(Chain &chain);

    void splice(Chain &chain);


    virtual bool isChain() const { return true; }


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


    // --- EXTERNAL ITERATORS

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

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

  protected:

  private:
    AtomContainer* getAtomContainer(Position position);

    const AtomContainer* getAtomContainer(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(Chain, AtomContainer, atomContainers)
  };
} // namespace BALL

#endif // BALL_KERNEL_CHAIN_H