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BALL::AtomContainer Class Reference

#include <BALL/KERNEL/atomContainer.h>

Inheritance diagram for BALL::AtomContainer:
BALL::Composite BALL::PropertyManager BALL::PersistentObject BALL::Selectable BALL::Object BALL::AutoDeletable BALL::Chain BALL::Fragment BALL::Molecule BALL::SecondaryStructure BALL::System BALL::Nucleotide BALL::Residue BALL::NucleicAcid BALL::Protein

Public Types

Enums
enum  Property { NUMBER_OF_PROPERTIES = 0 }
 The number of predefined properties for AtomContainer. More...
- Public Types inherited from BALL::Composite
typedef ForwardIterator
< Composite, Composite,
Composite
*, AncestorIteratorTraits
AncestorIterator
typedef ConstForwardIterator
< Composite, Composite,
Composite
*, AncestorIteratorTraits
AncestorConstIterator
typedef BidirectionalIterator
< Composite, Composite,
Composite
*, ChildCompositeIteratorTraits
ChildCompositeIterator
typedef
ConstBidirectionalIterator
< Composite, Composite,
Composite
*, ChildCompositeIteratorTraits
ChildCompositeConstIterator
typedef std::reverse_iterator
< ChildCompositeIterator
ChildCompositeReverseIterator
typedef std::reverse_iterator
< ChildCompositeConstIterator
ChildCompositeConstReverseIterator
typedef BidirectionalIterator
< Composite, Composite,
Composite
*, CompositeIteratorTraits
CompositeIterator
typedef
ConstBidirectionalIterator
< Composite, Composite,
Composite
*, CompositeIteratorTraits
CompositeConstIterator
typedef std::reverse_iterator
< CompositeIterator
CompositeReverseIterator
typedef std::reverse_iterator
< CompositeConstIterator
CompositeConstReverseIterator
enum  StampType { MODIFICATION = 1, SELECTION = 2, BOTH = 3 }
typedef UnaryPredicate< CompositeKernelPredicateType

Public Member Functions

Constructors and Destructors
 AtomContainer ()
 AtomContainer (const AtomContainer &atom_container, bool deep=true)
 AtomContainer (const String &name)
virtual ~AtomContainer ()
virtual void clear ()
virtual void destroy ()
Persistence
virtual void persistentWrite (PersistenceManager &pm, const char *name=0) const
virtual void persistentRead (PersistenceManager &pm)
Assignment
void set (const AtomContainer &atom_container, bool deep=true)
AtomContaineroperator= (const AtomContainer &atom_container)
void get (AtomContainer &atom_container, bool deep=true) const
void swap (AtomContainer &atom_container)
Predicates
bool operator== (const AtomContainer &atom_container) const
bool operator!= (const AtomContainer &atom_container) const
bool isSubAtomContainerOf (const AtomContainer &atom_container) const
bool isSuperAtomContainerOf (const AtomContainer &atom_container) const
Accessors
void setName (const String &name)
const StringgetName () const
AtomContainergetSuperAtomContainer ()
const AtomContainergetSuperAtomContainer () const
AtomContainergetAtomContainer (Position position)
const AtomContainergetAtomContainer (Position position) const
AtomgetAtom (Position position)
const AtomgetAtom (Position position) const
AtomgetAtom (const String &name)
const AtomgetAtom (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)
Miscellaneous
void destroyBonds ()
virtual bool isValid () const
virtual void dump (std::ostream &s=std::cout, Size depth=0) const
Internal Iteration
bool applyIntraBond (UnaryProcessor< Bond > &processor)
 Apply to all bonds connecting two atoms inside this AtomContainer.
bool applyInterBond (UnaryProcessor< Bond > &processor)
 Apply to all bonds connected to atoms outside this AtomContainer.
- Public Member Functions inherited from BALL::Composite
AncestorIterator beginAncestor ()
AncestorIterator endAncestor ()
AncestorConstIterator beginAncestor () const
AncestorConstIterator endAncestor () const
ChildCompositeIterator beginChildComposite ()
ChildCompositeIterator endChildComposite ()
ChildCompositeConstIterator beginChildComposite () const
ChildCompositeConstIterator endChildComposite () const
ChildCompositeReverseIterator rbeginChildComposite ()
ChildCompositeReverseIterator rendChildComposite ()
ChildCompositeConstReverseIterator rbeginChildComposite () const
ChildCompositeConstReverseIterator rendChildComposite () const
CompositeIterator beginComposite ()
CompositeIterator endComposite ()
CompositeConstIterator beginComposite () const
CompositeConstIterator endComposite () const
CompositeReverseIterator rbeginComposite ()
CompositeReverseIterator rendComposite ()
CompositeConstReverseIterator rbeginComposite () const
CompositeConstReverseIterator rendComposite () const
void deleteChildrenList_ (std::list< Composite * > &composites)
 Composite ()
 Composite (const Composite &composite, bool deep=true)
virtual ~Composite ()
void destroy (bool virtual_destroy)
void * clone (Composite &root) const
bool operator== (const Composite &composite) const
bool operator!= (const Composite &composite) const
bool isEmpty () const
bool isRoot () const
bool isRootOf (const Composite &composite) const
bool isInterior () const
bool hasChild () const
bool isChildOf (const Composite &composite) const
bool isFirstChild () const
bool isFirstChildOf (const Composite &composite) const
bool isLastChild () const
bool isLastChildOf (const Composite &composite) const
bool hasParent () const
bool isParentOf (const Composite &composite) const
bool hasSibling () const
bool isSiblingOf (const Composite &composite) const
bool hasPreviousSibling () const
bool isPreviousSiblingOf (const Composite &composite) const
bool hasNextSibling () const
bool isNextSiblingOf (const Composite &composite) const
bool isDescendantOf (const Composite &composite) const
template<typename T >
bool hasAncestor (const T &dummy) const
bool isAncestorOf (const Composite &composite) const
bool isRelatedWith (const Composite &composite) const
bool isHomomorph (const Composite &composite) const
bool containsSelection () const
void host (Visitor< Composite > &visitor)
template<typename T >
bool applyAncestor (UnaryProcessor< T > &processor)
template<typename T >
bool applyChild (UnaryProcessor< T > &processor)
template<typename T >
bool applyDescendantPreorder (UnaryProcessor< T > &processor)
template<typename T >
bool applyDescendantPostorder (UnaryProcessor< T > &processor)
template<typename T >
bool applyDescendant (UnaryProcessor< T > &processor)
template<typename T >
bool applyPreorder (UnaryProcessor< T > &processor)
template<typename T >
bool applyPostorder (UnaryProcessor< T > &processor)
template<typename T >
bool apply (UnaryProcessor< T > &processor)
template<typename T >
bool applyLevel (UnaryProcessor< T > &processor, long level)
void set (const Composite &composite, bool deep=true)
Compositeoperator= (const Composite &composite)
void get (Composite &composite, bool deep=true) const
Size getDegree () const
Size count (const KernelPredicateType &predicate) const
Size countDescendants () const
Size getPathLength (const Composite &composite) const
Size getDepth () const
Size getHeight () const
CompositegetRoot ()
const CompositegetRoot () const
CompositegetLowestCommonAncestor (const Composite &composite)
const CompositegetLowestCommonAncestor (const Composite &composite) const
template<typename T >
T * getAncestor (const T &)
template<typename T >
const T * getAncestor (const T &) const
template<typename T >
T * getPrevious (const T &)
template<typename T >
const T * getPrevious (const T &dummy) const
template<typename T >
T * getNext (const T &)
template<typename T >
const T * getNext (const T &dummy) const
CompositegetParent ()
const CompositegetParent () const
CompositegetChild (Index index)
const CompositegetChild (Index index) const
CompositegetSibling (Index index)
const CompositegetSibling (Index index) const
CompositegetFirstChild ()
const CompositegetFirstChild () const
CompositegetLastChild ()
const CompositegetLastChild () const
const PreciseTimegetModificationTime () const
const PreciseTimegetSelectionTime () const
void stamp (StampType stamp=BOTH)
void prependChild (Composite &composite)
void appendChild (Composite &composite)
void insertBefore (Composite &composite)
void insertAfter (Composite &composite)
void spliceBefore (Composite &composite)
void spliceAfter (Composite &composite)
void splice (Composite &composite)
bool removeChild (Composite &child)
Size removeSelected ()
Size removeUnselected ()
void replace (Composite &composite)
void swap (Composite &composite)
virtual void select ()
virtual void deselect ()
- Public Member Functions inherited from BALL::PersistentObject
 PersistentObject ()
virtual ~PersistentObject ()
PersistenceManageroperator>> (PersistenceManager &pm) const
virtual void finalize ()
- Public Member Functions inherited from BALL::Object
 Object ()
 Default constructor.
 Object (const Object &object)
 Copy constructor.
virtual ~Object ()
 Destructor.
const Objectoperator= (const Object &)
bool operator== (const Object &object) const
bool operator!= (const Object &object) const
bool operator< (const Object &object) const
bool operator<= (const Object &object) const
bool operator>= (const Object &object) const
bool operator> (const Object &object) const
int compare (const Object &object) const
virtual void dump (::std::ostream &s=std::cout, Size depth=0) const
Handle getHandle () const
- Public Member Functions inherited from BALL::AutoDeletable
virtual ~AutoDeletable ()
void * operator new (size_t size)
void operator delete (void *ptr)
void * operator new (size_t size, void *ptr)
void operator delete (void *ptr, void *)
bool isAutoDeletable () const
void setAutoDeletable (bool enable)
- Public Member Functions inherited from BALL::Selectable
 Selectable ()
 Selectable (const Selectable &selectable, bool deep=true)
virtual ~Selectable ()
void set (const Selectable &selectable, bool deep=true)
const Selectableoperator= (const Selectable &selectable)
void get (Selectable &selectable, bool deep=true) const
void swap (Selectable &selectable)
virtual void setSelected (bool selected)
bool isSelected () const
bool operator== (const Selectable &selectable) const
bool operator!= (const Selectable &selectable) const
void write (PersistenceManager &pm) const
bool read (PersistenceManager &pm)
virtual void dump (::std::ostream &s=std::cout, Size depth=0) const
- Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE PropertyManager ()
 Default constructor.
BALL_INLINE PropertyManager (const PropertyManager &property_manager)
 Copy constructor.
virtual ~PropertyManager ()
 Destructor.
void set (const PropertyManager &property_manager)
const PropertyManageroperator= (const PropertyManager &property_manager)
void get (PropertyManager &property_manager) const
void swap (PropertyManager &property_manager)
BitVectorgetBitVector ()
const BitVectorgetBitVector () const
 operator BitVector & ()
void setProperty (Property property)
void clearProperty (Property property)
void toggleProperty (Property property)
Size countProperties () const
const NamedPropertygetNamedProperty (Position index) const
NamedPropertygetNamedProperty (Position index)
void setProperty (const NamedProperty &property)
void setProperty (const string &name)
void setProperty (const string &name, bool value)
void setProperty (const string &name, int value)
void setProperty (const string &name, unsigned int value)
void setProperty (const string &name, float value)
void setProperty (const string &name, double value)
void setProperty (const string &name, const string &value)
void setProperty (const string &name, const PersistentObject &value)
const NamedPropertygetProperty (const string &name) const
NamedPropertyIterator beginNamedProperty ()
NamedPropertyIterator endNamedProperty ()
void clearProperty (const string &name)
Size countNamedProperties () const
bool hasProperty (Property property) const
 Query for an unnamed property.
bool hasProperty (const string &name) const
 Query for a named property.
bool operator== (const PropertyManager &pm) const
bool operator!= (const PropertyManager &pm) const
 Inequality operator.
void write (PersistenceManager &pm) const
 Persistent stream writing.
bool read (PersistenceManager &pm)
 Persistent stream reading.

Private Attributes

String name_

Additional Inherited Members

- Static Public Member Functions inherited from BALL::Composite
static bool insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)
- Static Public Member Functions inherited from BALL::Object
static Handle getNextHandle ()
static Handle getNewHandle ()
- Static Public Member Functions inherited from BALL::AutoDeletable
static void clearLastPtr ()
- Static Public Attributes inherited from BALL::Composite
static UnaryProcessor< CompositeDEFAULT_PROCESSOR
static KernelPredicateType DEFAULT_UNARY_PREDICATE
- Protected Member Functions inherited from BALL::AutoDeletable
 AutoDeletable ()
 AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)
- Protected Attributes inherited from BALL::Selectable
bool selected_

Detailed Description

Atom Container Base Class. The AtomContainer class is the base class of all kernel classes containing atoms.

Definition at line 30 of file atomContainer.h.

Member Enumeration Documentation

The number of predefined properties for AtomContainer.

Enumerator:
NUMBER_OF_PROPERTIES 

Definition at line 43 of file atomContainer.h.

Constructor & Destructor Documentation

BALL::AtomContainer::AtomContainer ( )

Default constructor

BALL::AtomContainer::AtomContainer ( const AtomContainer atom_container,
bool  deep = true 
)

Copy constructor

Parameters
atom_containerthe AtomContainer to construct from
deepa flag indicating cloning
BALL::AtomContainer::AtomContainer ( const String name)

Detailed Constructor

Parameters
namethe name of the AtomContainer
virtual BALL::AtomContainer::~AtomContainer ( )
virtual

Destructor

Member Function Documentation

void BALL::AtomContainer::append ( Atom atom)

Append an atom to the last position.

Parameters
atomthe atom to append

Reimplemented in BALL::Nucleotide, and BALL::Molecule.

void BALL::AtomContainer::append ( AtomContainer atom_container)

Append an AtomContainer at the last position.

Parameters
atom_containerthe AtomContainer to prepend

Reimplemented in BALL::Molecule.

bool BALL::AtomContainer::applyInterBond ( UnaryProcessor< Bond > &  processor)

Apply to all bonds connected to atoms outside this AtomContainer.

bool BALL::AtomContainer::applyIntraBond ( UnaryProcessor< Bond > &  processor)

Apply to all bonds connecting two atoms inside this AtomContainer.

virtual void BALL::AtomContainer::clear ( )
virtual

Clear the contents of this instance of AtomContainer. This methods clears the base fragment's name, destroys all its children (as in Composite::clear ), but does not remove it from its parent composite structures.

Reimplemented from BALL::Composite.

Reimplemented in BALL::Residue, BALL::Nucleotide, BALL::SecondaryStructure, BALL::NucleicAcid, and BALL::Protein.

Size BALL::AtomContainer::countAtomContainers ( ) const

Count the child AtomContainers.

Returns
Size the number of AtomContainers
Size BALL::AtomContainer::countAtoms ( ) const

Count the child atoms.

Returns
Size the number of atoms

Reimplemented in BALL::System.

Size BALL::AtomContainer::countBonds ( ) const

Count the child bonds.

Returns
Size the number of bonds
Size BALL::AtomContainer::countInterBonds ( ) const

Count all bonds which connect atoms in this instance with atoms outside.

Returns
Size the number of inter bonds
Size BALL::AtomContainer::countIntraBonds ( ) const

Count all bonds which connect 2 atoms in this instance.

Returns
Size the number of intra bonds
virtual void BALL::AtomContainer::destroy ( )
virtual

Clear the contents of this instance of AtomContainer and removes it from parent composite structures. This methods clears the base fragment's name, destroys all its children (as in Composite::destroy ), and removes it from its parent composite structures.

Reimplemented from BALL::Composite.

Reimplemented in BALL::Residue, BALL::Nucleotide, BALL::SecondaryStructure, BALL::NucleicAcid, and BALL::Protein.

void BALL::AtomContainer::destroyBonds ( )

Destroy all bonds in this instance.

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

Internal state dump. Dump the current internal state of this instance to the output ostream s with dumping depth depth .

Parameters
s- output stream where to output the internal state of this instance
depth- the dumping depth

Reimplemented from BALL::Composite.

Reimplemented in BALL::Residue, BALL::Chain, BALL::SecondaryStructure, BALL::Protein, BALL::Nucleotide, BALL::Molecule, BALL::NucleicAcid, and BALL::Fragment.

void BALL::AtomContainer::get ( AtomContainer atom_container,
bool  deep = true 
) const

Copy to another instance of AtomContainer. The assignment is either deep or shallow (default is deep).

Parameters
atom_containerthe AtomContainer to be assigned to
See Also
Composite::get
Atom* BALL::AtomContainer::getAtom ( Position  position)

Get a pointer to a child atom at a given position. The pointer is 0 if this instance does not have an atom at the given position.

Parameters
positionthe position of the child atom
Returns
Atom* - mutable pointer to the child
const Atom* BALL::AtomContainer::getAtom ( Position  position) const

Get a pointer to a child atom at a given position. The pointer is 0 if this instance does not have an atom at the given position.

Parameters
positionthe position of the child atom
Returns
Atom* - constant pointer to the child
Atom* BALL::AtomContainer::getAtom ( const String name)

Get a pointer to a child atom with the name name . The pointer is 0 if this instance does not have an atom with this name.

Parameters
namethe name of the child atom
Returns
Atom* - mutable pointer to the child
const Atom* BALL::AtomContainer::getAtom ( const String name) const

Get a pointer to a child atom with the name name . The pointer is 0 if this instance AtomContainer does not have an atom with this name.

Parameters
namethe name of the child atom
Returns
Atom* - constant pointer to the child
AtomContainer* BALL::AtomContainer::getAtomContainer ( Position  position)

Get a pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters
positionof the child AtomContainer
Returns
AtomContainer* - mutable pointer to the child
const AtomContainer* BALL::AtomContainer::getAtomContainer ( Position  position) const

Get a constant pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters
positionof the child AtomContainer
Returns
AtomContainer* - constant pointer to the child
const String& BALL::AtomContainer::getName ( ) const

Return the name.

Returns
String& - constant reference to the name of this instance
AtomContainer* BALL::AtomContainer::getSuperAtomContainer ( )

Get a mutable pointer to the parent AtomContainer. The pointer is 0 if this instance does not have a parent AtomContainer.

Returns
AtomContainer* - mutable pointer to the parent AtomContainer

Reimplemented in BALL::Molecule.

const AtomContainer* BALL::AtomContainer::getSuperAtomContainer ( ) const

Get a constant pointer to the parent AtomContainer. The pointer is 0 if this instance does not have a parent AtomContainer.

Returns
AtomContainer* - constant pointer to the parent AtomContainer

Reimplemented in BALL::Molecule.

void BALL::AtomContainer::insert ( Atom atom)

Insert an atom to the last position.

Parameters
atomthe atom to insert

Reimplemented in BALL::Nucleotide, and BALL::Molecule.

void BALL::AtomContainer::insert ( AtomContainer atom_container)

Insert an AtomContainer at the last position.

Parameters
atom_containerthe AtomContainer to insert

Reimplemented in BALL::Molecule.

void BALL::AtomContainer::insertAfter ( Atom atom,
Composite after 
)

Insert an atom after a given Composite object.

Parameters
atomthe atom to insert
afterthe Composite object to insert after

Reimplemented in BALL::Nucleotide, and BALL::Molecule.

void BALL::AtomContainer::insertAfter ( AtomContainer atom_container,
Composite after 
)

Insert an AtomContainer after a given Composite object.

Parameters
atom_containerthe AtomContainer to insert
afterthe Composite object to insert after

Reimplemented in BALL::Molecule.

void BALL::AtomContainer::insertBefore ( Atom atom,
Composite before 
)

Insert an atom before a given Composite object.

Parameters
atomthe atom to insert
beforethe Composite object to insert before

Reimplemented in BALL::Nucleotide, and BALL::Molecule.

void BALL::AtomContainer::insertBefore ( AtomContainer atom_container,
Composite before 
)

Insert an AtomContainer before a given Composite object.

Parameters
atom_containerthe AtomContainer to insert
beforethe Composite object to insert before

Reimplemented in BALL::Molecule.

bool BALL::AtomContainer::isSubAtomContainerOf ( const AtomContainer atom_container) const

Test if an AtomContainer is a child.

Parameters
atom_containerthe AtomContainer to test

Reimplemented in BALL::Molecule.

bool BALL::AtomContainer::isSuperAtomContainerOf ( const AtomContainer atom_container) const

Test if an AtomContainer is the parent.

Parameters
atom_containerthe AtomContainer to test
virtual bool BALL::AtomContainer::isValid ( ) const
virtual

Debugging and Diagnostics Internal state and consistency self-validation. If the internal state of this instance is correct (self-validated) and consistent true is returned, false otherwise.

Returns
bool

Reimplemented from BALL::Composite.

Reimplemented in BALL::Residue, BALL::SecondaryStructure, BALL::Protein, BALL::Nucleotide, and BALL::NucleicAcid.

bool BALL::AtomContainer::operator!= ( const AtomContainer atom_container) const

Inequality operator.

See Also
operator ==
AtomContainer& BALL::AtomContainer::operator= ( const AtomContainer atom_container)

Assignment operator. The assignment is deep.

Parameters
atom_containerthe AtomContainer to be copied (cloned)
Returns
AtomContainer& - this instance AtomContainer
See Also
AtomContainer::set
bool BALL::AtomContainer::operator== ( const AtomContainer atom_container) const

Equality operator. Two instances of AtomContainer are equal if they have the same handle.

virtual void BALL::AtomContainer::persistentRead ( PersistenceManager pm)
virtual

Read an AtomContainer object from a persistent stream.

Parameters
pmthe persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::Residue, BALL::SecondaryStructure, BALL::Nucleotide, BALL::NucleicAcid, BALL::Protein, BALL::Molecule, BALL::Chain, BALL::System, and BALL::Fragment.

virtual void BALL::AtomContainer::persistentWrite ( PersistenceManager pm,
const char *  name = 0 
) const
virtual

Write an AtomContainer object to a persistent stream.

Parameters
pmthe persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::Residue, BALL::SecondaryStructure, BALL::Nucleotide, BALL::NucleicAcid, BALL::Protein, BALL::Molecule, BALL::Chain, BALL::System, and BALL::Fragment.

void BALL::AtomContainer::prepend ( Atom atom)

Prepend an atom at position 0.

Parameters
atomthe atom to prepend

Reimplemented in BALL::Nucleotide, and BALL::Molecule.

void BALL::AtomContainer::prepend ( AtomContainer atom_container)

Prepend an AtomContainer at position 0.

Parameters
atom_containerthe AtomContainer to prepend

Reimplemented in BALL::Molecule.

bool BALL::AtomContainer::remove ( Atom atom)

Remove an atom

Parameters
atomthe atom to remove

Reimplemented in BALL::Nucleotide, and BALL::Molecule.

bool BALL::AtomContainer::remove ( AtomContainer atom_container)

Remove an AtomContainer

Parameters
atom_containerthe AtomContainer to remove
Returns
false if {atom_container} could not be removed

Reimplemented in BALL::Molecule.

Size BALL::AtomContainer::removeHavingProperty ( BALL::Property  p)
Size BALL::AtomContainer::removeHavingProperty ( const string &  name)
Size BALL::AtomContainer::removeNotHavingProperty ( BALL::Property  p)
Size BALL::AtomContainer::removeNotHavingProperty ( const string &  name)
void BALL::AtomContainer::set ( const AtomContainer atom_container,
bool  deep = true 
)

Assign the contents of an AtomContainer The assignment is either deep or shallow (default is deep).

Parameters
atom_containerthe atom_container to be copied (cloned)
deepmake a deep (=true) or shallow (=false) copy
See Also
Composite::set
void BALL::AtomContainer::setName ( const String name)

Set the name.

Parameters
namethe new name
void BALL::AtomContainer::splice ( AtomContainer atom_container)

Move the children of {atom_container} into this instance. The children of atom_container are inserted at its position if it is is a child of this. Otherwise the children are inserted using spliceBefore .

Reimplemented in BALL::Molecule.

void BALL::AtomContainer::spliceAfter ( AtomContainer atom_container)

Cut all children of atom_container and append them after the children of this instance.

Parameters
atom_containerthe AtomContainer to access

Reimplemented in BALL::Molecule.

void BALL::AtomContainer::spliceBefore ( AtomContainer atom_container)

Cut all children of atom_container and prepend them before the children of this instance.

Parameters
atom_containerthe AtomContainer to access

Reimplemented in BALL::Molecule.

void BALL::AtomContainer::swap ( AtomContainer atom_container)

Swap the contents of two AtomContainers.

Parameters
atom_containerthe AtomContainer this instance is being swapped with.

Member Data Documentation

String BALL::AtomContainer::name_
private

Definition at line 404 of file atomContainer.h.