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5 #ifndef BALL_KERNEL_ATOMCONTAINER_H
6 #define BALL_KERNEL_ATOMCONTAINER_H
8 #ifndef BALL_KERNEL_ATOMITERATOR_H
12 #ifndef BALL_KERNEL_ATOMCONTAINERITERATOR_H
16 #define BALL_ATOMCONTAINER_DEFAULT_NAME ""
45 NUMBER_OF_PROPERTIES = 0
378 virtual void dump(std::ostream& s = std::cout,
Size depth = 0)
const;
411 #endif // BALL_KERNEL_ATOMCONTAINER_H
BALL_EXPORT AtomList atoms(const AtomContainer &fragment, const String &expression=String())
void spliceBefore(AtomContainer &atom_container)
Size countAtomContainers() const
BALL_EXPORT bool operator!=(const String &s1, const String &s2)
AtomContainer(const AtomContainer &atom_container, bool deep=true)
bool applyInterBond(UnaryProcessor< Bond > &processor)
Apply to all bonds connected to atoms outside this AtomContainer.
virtual void persistentWrite(PersistenceManager &pm, const char *name=0) const
bool isSubAtomContainerOf(const AtomContainer &atom_container) const
void setName(const String &name)
#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
void swap(AtomContainer &atom_container)
#define BALL_CREATE_DEEP(name)
void insertBefore(AtomContainer &atom_container, Composite &before)
const Atom * getAtom(const String &name) const
void insertAfter(Atom &atom, Composite &after)
const AtomContainer * getAtomContainer(Position position) const
Size countIntraBonds() const
AtomContainer(const String &name)
void prepend(AtomContainer &atom_container)
Size removeNotHavingProperty(BALL::Property p)
const String & getName() const
Size removeHavingProperty(BALL::Property p)
AtomContainer * getAtomContainer(Position position)
void insert(AtomContainer &atom_container)
virtual bool isValid() const
void get(AtomContainer &atom_container, bool deep=true) const
virtual void dump(std::ostream &s=std::cout, Size depth=0) const
void append(AtomContainer &atom_container)
bool applyIntraBond(UnaryProcessor< Bond > &processor)
Apply to all bonds connecting two atoms inside this AtomContainer.
void insertBefore(Atom &atom, Composite &before)
const Atom * getAtom(Position position) const
Atom * getAtom(Position position)
BALL_EXPORT AtomContainerList atomContainers(const AtomContainer &fragment, bool selected_only=false)
bool isSuperAtomContainerOf(const AtomContainer &atom_container) const
Size removeHavingProperty(const string &name)
BALL_EXPORT bool operator==(const String &s1, const String &s2)
AtomContainer * getSuperAtomContainer()
bool remove(AtomContainer &atom_container)
void insertAfter(AtomContainer &atom_container, Composite &after)
Property
The number of predefined properties for AtomContainer.
const AtomContainer * getSuperAtomContainer() const
Size removeNotHavingProperty(const string &name)
void set(const AtomContainer &atom_container, bool deep=true)
Size countInterBonds() const
void spliceAfter(AtomContainer &atom_container)
virtual void persistentRead(PersistenceManager &pm)
void splice(AtomContainer &atom_container)
Atom * getAtom(const String &name)