KERNEL/system.h

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

#ifndef BALL_KERNEL_SYSTEM_H
#define BALL_KERNEL_SYSTEM_H

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

#ifndef BALL_KERNEL_MOLECULEITERATOR_H
# include <BALL/KERNEL/moleculeIterator.h>
#endif

#ifndef BALL_KERNEL_PROTEINITERATOR_H
# include <BALL/KERNEL/proteinIterator.h>
#endif

#ifndef BALL_KERNEL_NUCLEICACIDITERATOR_H
# include <BALL/KERNEL/nucleicAcidIterator.h>
#endif

#ifndef BALL_KERNEL_NUCLEOTIDEIDITERATOR_H
# include <BALL/KERNEL/nucleotideIterator.h>
#endif

#define BALL_SYSTEM_DEFAULT_NAME   ""

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

    BALL_CREATE_DEEP(System)

    

    System();
  
    System(const System& system, bool deep = true);
  
    System(const String& name);

    virtual ~System();



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

    void persistentRead(PersistenceManager& pm);



    void set(const System& system, bool deep = true);

    System& operator = (const System& system);

    void get(System& system, bool deep = true) const;
  

    bool operator == (const System& system) const;

    bool operator != (const System& system) const;


    Molecule* getMolecule(Position position);

    const Molecule* getMolecule(Position position) const;

    Protein* getProtein(Position position);

    const Protein* getProtein(Position position) const;

    Size countMolecules() const;

    Size countFragments() const;

    Size countAtoms() const;

    Size countProteins() const;

    Size countChains() const;

    Size countSecondaryStructures() const;

    Size countResidues() const;

    Size countNucleicAcids() const;

    Size countNucleotides() const;

    void prepend(Molecule& molecule);

    void append(Molecule& molecule);

    void insert(Molecule& molecule);

    void insertBefore(Molecule& molecule, Composite& before);

    void insertAfter(Molecule& molecule, Composite& after);

    bool remove(Molecule& molecule);

    void spliceBefore(System& system);

    void spliceAfter(System& system);

    void splice(System& system);

    
    // --- EXTERNAL ITERATORS ---

    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Atom)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Fragment)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Molecule)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Protein)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Residue)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Chain)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(SecondaryStructure)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Nucleotide)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(NucleicAcid)

  };
} // namespace BALL

#endif // BALL_KERNEL_SYSTEM_H