atomContainer.h

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

#ifndef BALL_KERNEL_ATOMCONTAINER_H
#define BALL_KERNEL_ATOMCONTAINER_H

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

#ifndef BALL_KERNEL_ATOMCONTAINERITERATOR_H
# include <BALL/KERNEL/atomContainerIterator.h>
#endif

#define BALL_ATOMCONTAINER_DEFAULT_NAME   ""

namespace BALL
{
  class Molecule;

  class BALL_EXPORT AtomContainer
    : public Composite,
      public PropertyManager
  {
    public:

    BALL_CREATE_DEEP(AtomContainer)

    

    enum Property
    {
      NUMBER_OF_PROPERTIES = 0
    };



    AtomContainer();

    AtomContainer(const AtomContainer& atom_container, bool deep = true);

    AtomContainer(const String& name);

    virtual ~AtomContainer();

    virtual void clear();

    virtual void destroy();



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

    virtual void persistentRead(PersistenceManager& pm);



    void set(const AtomContainer& atom_container, bool deep = true);

    AtomContainer& operator = (const AtomContainer& atom_container);

    void get(AtomContainer& atom_container, bool deep = true) const;

    void swap(AtomContainer& atom_container);



    bool operator == (const AtomContainer& atom_container) const;

    bool operator != (const AtomContainer& atom_container) const;



    void setName(const String& name);

    const String& getName() const;

    AtomContainer* getSuperAtomContainer();

    const AtomContainer* getSuperAtomContainer() const;

    AtomContainer* getAtomContainer(Position position);

    const AtomContainer* getAtomContainer(Position position) const;

    Atom* getAtom(Position position);

    const Atom* getAtom(Position position) const;

    Atom* getAtom(const String& name);

    const Atom* getAtom(const String& name) const;

    Size countAtomContainers() const;

    Size countAtoms() const;

    Size countBonds() const;

    Size countInterBonds() const;

    Size countIntraBonds() 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);

    Size removeHavingProperty(BALL::Property p);
    Size removeNotHavingProperty(BALL::Property p);
    Size removeHavingProperty(const string& name);
    Size removeNotHavingProperty(const string& name);

    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);



    void destroyBonds();



    bool isSubAtomContainerOf(const AtomContainer& atom_container) const;

    bool isSuperAtomContainerOf(const AtomContainer& atom_container) const;



    virtual bool isValid() const;

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



    bool applyIntraBond(UnaryProcessor<Bond>& processor);

    bool applyInterBond(UnaryProcessor<Bond>& processor);


    // --- EXTERNAL ITERATORS

    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Atom)
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer)

    BALL_DECLARE_STD_ITERATOR_WRAPPER(AtomContainer, Atom, atoms)
    BALL_DECLARE_STD_ITERATOR_WRAPPER(AtomContainer, AtomContainer, atomContainers)

    private:

    /*_ The name of this container
    */
    String  name_;

  };

} // namespace BALL

#endif // BALL_KERNEL_ATOMCONTAINER_H