molecule.h

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

#ifndef BALL_KERNEL_MOLECULE_H
#define BALL_KERNEL_MOLECULE_H

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

#ifndef BALL_KERNEL_FRAGMENT_H
# include <BALL/KERNEL/fragment.h>
#endif

#ifndef BALL_KERNEL_FRAGMENTITERATOR_H
# include <BALL/KERNEL/fragmentIterator.h>
#endif

namespace BALL 
{
  class System;

  class BALL_EXPORT Molecule
    : public AtomContainer
  {
    public:

    BALL_CREATE_DEEP(Molecule)

    

    enum Property
    {
      IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES,
      NUMBER_OF_PROPERTIES
    };



    Molecule();
  
    Molecule(const Molecule& molecule, bool deep = true);
  
    Molecule(const String& name);

    virtual ~Molecule();
    


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

    void persistentRead(PersistenceManager& pm);



    void set(const Molecule& molecule, bool deep = true);

    Molecule& operator = (const Molecule& molecule);

    void get(Molecule& molecule, bool deep = true) const;

    void swap(Molecule& molecule);
  


    System* getSystem();

    const System* getSystem() 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);



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


    bool operator == (const Molecule& molecule) const;

    bool operator != (const Molecule& molecule) const;


    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Fragment)


    protected:

    Molecule* getMolecule();

    const Molecule* getMolecule() const;

    AtomContainer* getSuperAtomContainer();

    const AtomContainer* getSuperAtomContainer() const;

    void prepend(Molecule& molecule);

    void append(Molecule& molecule);

    void insert(Molecule& molecule);

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

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

    bool remove(Molecule& molecule);

    bool isSubAtomContainerOf(const AtomContainer& atom_container) const;
  };
} // namespace BALL 

#endif // BALL_KERNEL_MOLECULE_H

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