BALL 1.5.0
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BALL::Chain Class Reference

#include <BALL/KERNEL/chain.h>

Inheritance diagram for BALL::Chain:
BALL::AtomContainer BALL::Composite BALL::PropertyManager BALL::PersistentObject BALL::Selectable BALL::Object BALL::AutoDeletable

Public Types

Enums
enum  Property { NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES }
 
- Public Types inherited from BALL::AtomContainer
enum  Property { NUMBER_OF_PROPERTIES = 0 }
 The number of predefined properties for AtomContainer. More...
 
- Public Types inherited from BALL::Composite
enum  StampType { MODIFICATION = 1 , SELECTION = 2 , BOTH = 3 }
 
typedef UnaryPredicate< CompositeKernelPredicateType
 
typedef ForwardIterator< Composite, Composite, Composite *, AncestorIteratorTraitsAncestorIterator
 
typedef ConstForwardIterator< Composite, Composite, Composite *, AncestorIteratorTraitsAncestorConstIterator
 
typedef BidirectionalIterator< Composite, Composite, Composite *, ChildCompositeIteratorTraitsChildCompositeIterator
 
typedef ConstBidirectionalIterator< Composite, Composite, Composite *, ChildCompositeIteratorTraitsChildCompositeConstIterator
 
typedef std::reverse_iterator< ChildCompositeIteratorChildCompositeReverseIterator
 
typedef std::reverse_iterator< ChildCompositeConstIteratorChildCompositeConstReverseIterator
 
typedef BidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraitsCompositeIterator
 
typedef ConstBidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraitsCompositeConstIterator
 
typedef std::reverse_iterator< CompositeIteratorCompositeReverseIterator
 
typedef std::reverse_iterator< CompositeConstIteratorCompositeConstReverseIterator
 

Public Member Functions

Constructors and Destructors
 Chain ()
 Default constrcutor.
 
 Chain (const Chain &chain, bool deep=true)
 Copy constructor.
 
 Chain (const String &name)
 Detailled constructor.
 
virtual ~Chain ()
 Destructor.
 
Persistence
void persistentWrite (PersistenceManager &pm, const char *name=0) const
 
void persistentRead (PersistenceManager &pm)
 
Assignment
void set (const Chain &chain, bool deep=true)
 
Chainoperator= (const Chain &chain)
 
void get (Chain &chain, bool deep=true) const
 
void swap (Chain &chain)
 
bool operator== (const Chain &chain) const
 
bool operator!= (const Chain &chain) const
 
Accessors
ProteingetProtein ()
 
const ProteingetProtein () const
 
SecondaryStructuregetSecondaryStructure (Position position)
 
const SecondaryStructuregetSecondaryStructure (Position position) const
 
ResiduegetResidue (Position position)
 
const ResiduegetResidue (Position position) const
 
ResiduegetNTerminal ()
 
const ResiduegetNTerminal () const
 
ResiduegetCTerminal ()
 
const ResiduegetCTerminal () const
 
PDBAtomgetPDBAtom (Position position)
 
const PDBAtomgetPDBAtom (Position position) const
 
Size countSecondaryStructures () const
 
Size countResidues () const
 
Size countPDBAtoms () const
 
void prepend (SecondaryStructure &secondary_structure)
 
void append (SecondaryStructure &secondary_structure)
 
void insert (SecondaryStructure &secondary_structure)
 
void insertBefore (SecondaryStructure &secondary_structure, Composite &before)
 
void insertAfter (SecondaryStructure &secondary_structure, Composite &after)
 
bool remove (SecondaryStructure &secondary_structure)
 
void prepend (Residue &residue)
 
void append (Residue &residue)
 
void insert (Residue &residue)
 
void insertBefore (Residue &residue, Composite &before)
 
void insertAfter (Residue &residue, Composite &after)
 
bool remove (Residue &residue)
 
void spliceBefore (Chain &chain)
 
void spliceAfter (Chain &chain)
 
void splice (Chain &chain)
 
Type predicates
virtual bool isChain () const
 
- Public Member Functions inherited from BALL::AtomContainer
 AtomContainer ()
 
 AtomContainer (const AtomContainer &atom_container, bool deep=true)
 
 AtomContainer (const String &name)
 
virtual ~AtomContainer ()
 
virtual void clear ()
 
virtual void destroy ()
 
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)
 
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
 
virtual bool isValid () const
 
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)
 
void destroyBonds ()
 
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
template<typename T >
BALL_INLINE bool apply (UnaryProcessor< T > &processor)
 
template<typename T >
BALL_INLINE bool apply (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
BALL_INLINE T * getAncestor (const T &)
 
template<typename T >
BALL_INLINE const T * getAncestor (const T &) const
 
template<typename T >
BALL_INLINE T * getPrevious (const T &)
 
template<typename T >
BALL_INLINE const T * getPrevious (const T &dummy) const
 
template<typename T >
BALL_INLINE T * getNext (const T &)
 
template<typename T >
BALL_INLINE const T * getNext (const T &dummy) const
 
template<typename T >
BALL_INLINE bool hasAncestor (const T &dummy) const
 
 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
 
virtual bool isAtom () const
 
virtual bool isMolecule () const
 
virtual bool isProtein () const
 
virtual bool isFragment () const
 
virtual bool isResidue () const
 
void host (Visitor< Composite > &visitor)
 
template<typename T >
bool applyAncestor (UnaryProcessor< T > &processor)
 
template<typename T >
bool applyAncestor (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool applyChild (UnaryProcessor< T > &processor)
 
template<typename T >
bool applyChild (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool applyDescendantPreorder (UnaryProcessor< T > &processor)
 
template<typename T >
bool applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool applyDescendantPostorder (UnaryProcessor< T > &processor)
 
template<typename T >
bool applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool applyDescendant (UnaryProcessor< T > &processor)
 
template<typename T >
bool applyDescendant (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool applyPreorder (UnaryProcessor< T > &processor)
 
template<typename T >
bool applyPreorder (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool applyPostorder (UnaryProcessor< T > &processor)
 
template<typename T >
bool applyPostorder (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool apply (UnaryProcessor< T > &processor)
 
template<typename T >
bool apply (ConstUnaryProcessor< T > &processor) const
 
template<typename T >
bool applyLevel (UnaryProcessor< T > &processor, long level)
 
template<typename T >
bool applyLevel (ConstUnaryProcessor< T > &processor, long level) const
 
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)
 
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 std::string &name)
 
void setProperty (const std::string &name, bool value)
 
void setProperty (const std::string &name, int value)
 
void setProperty (const std::string &name, unsigned int value)
 
void setProperty (const std::string &name, float value)
 
void setProperty (const std::string &name, double value)
 
void setProperty (const std::string &name, const std::string &value)
 
void setProperty (const std::string &name, const PersistentObject &value)
 
const NamedPropertygetProperty (const std::string &name) const
 
NamedPropertyIterator beginNamedProperty ()
 
NamedPropertyIterator endNamedProperty ()
 
void clearProperty (const std::string &name)
 
Size countNamedProperties () const
 
bool hasProperty (Property property) const
 Query for an unnamed property.
 
bool hasProperty (const std::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.
 
bool isValid () const
 
void dump (std::ostream &s=std::cout, Size depth=0) const
 

Debugging and Diagnostics

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

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

Protein chain class. This class represents a polypeptide chain within a Protein . Chains can contain SecondaryStructure s or Residue s.

Definition at line 30 of file chain.h.

Member Enumeration Documentation

◆ Property

Enumerator
NUMBER_OF_PROPERTIES 

Definition at line 43 of file chain.h.

Constructor & Destructor Documentation

◆ Chain() [1/3]

BALL::Chain::Chain ( )

Default constrcutor.

◆ Chain() [2/3]

BALL::Chain::Chain ( const Chain & chain,
bool deep = true )

Copy constructor.

◆ Chain() [3/3]

BALL::Chain::Chain ( const String & name)

Detailled constructor.

◆ ~Chain()

virtual BALL::Chain::~Chain ( )
virtual

Destructor.

Member Function Documentation

◆ append() [1/2]

void BALL::Chain::append ( Residue & residue)

Append a Residue after the last position.

Parameters
residuethe Residue to append

◆ append() [2/2]

void BALL::Chain::append ( SecondaryStructure & secondary_structure)

Append a SecondaryStructure after the last position.

Parameters
secondary_structurethe SecondaryStructure to append

◆ countPDBAtoms()

Size BALL::Chain::countPDBAtoms ( ) const

Count the PDBAtoms

Returns
Size the number of PDBAtoms

◆ countResidues()

Size BALL::Chain::countResidues ( ) const

Count the Residues

Returns
Size the number of residues

◆ countSecondaryStructures()

Size BALL::Chain::countSecondaryStructures ( ) const

Count the SecondaryStructures

Returns
Size the number of secondary structures

◆ dump()

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

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

Parameters
s- output stream where to output the internal state.
depth- the dumping depth

Reimplemented from BALL::AtomContainer.

◆ get()

void BALL::Chain::get ( Chain & chain,
bool deep = true ) const

Copying with cloning facility. The assignment is either deep or shallow (default).

Parameters
chainthe chain to be assigned to
See also
chain::set

◆ getCTerminal() [1/2]

Residue * BALL::Chain::getCTerminal ( )

Get a pointer to the C-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns
Residue* - mutable pointer to the C-terminal Residue

◆ getCTerminal() [2/2]

const Residue * BALL::Chain::getCTerminal ( ) const

Get a constant pointer to the C-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns
Residue* - constant pointer to the C-terminal Residue

◆ getNTerminal() [1/2]

Residue * BALL::Chain::getNTerminal ( )

Get a pointer to the N-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns
Residue* - mutable pointer to the N-terminal Residue

◆ getNTerminal() [2/2]

const Residue * BALL::Chain::getNTerminal ( ) const

Get a constant pointer to the N-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns
Residue* - constant pointer to the N-terminal Residue

◆ getPDBAtom() [1/2]

PDBAtom * BALL::Chain::getPDBAtom ( Position position)

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

Parameters
positionthe position of the child PDBAtom
Returns
PDBAtom* - mutable pointer to the child PDBAtom at position

◆ getPDBAtom() [2/2]

const PDBAtom * BALL::Chain::getPDBAtom ( Position position) const

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

Parameters
positionthe position of the child PDBAtom
Returns
PDBAtom* - constant pointer to the child PDBAtom at position

◆ getProtein() [1/2]

Protein * BALL::Chain::getProtein ( )

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

Returns
Protein* - mutable pointer to the parent protein

◆ getProtein() [2/2]

const Protein * BALL::Chain::getProtein ( ) const

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

Returns
Protein* - constant pointer to the parent protein

◆ getResidue() [1/2]

Residue * BALL::Chain::getResidue ( Position position)

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

Parameters
positionthe position of the child Residue
Returns
Residue* - mutable pointer to the child Residue at position

◆ getResidue() [2/2]

const Residue * BALL::Chain::getResidue ( Position position) const

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

Parameters
positionthe position of the child Residue
Returns
Residue* - constant pointer to the child Residue at position

◆ getSecondaryStructure() [1/2]

SecondaryStructure * BALL::Chain::getSecondaryStructure ( Position position)

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

Parameters
positionthe position of the child SecondaryStructure
Returns
SecondaryStructure* - mutable pointer to the child SecondaryStructure at position

◆ getSecondaryStructure() [2/2]

const SecondaryStructure * BALL::Chain::getSecondaryStructure ( Position position) const

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

Parameters
positionthe position of the child SecondaryStructure
Returns
SecondaryStructure* - constant pointer to the child SecondaryStructure at position

◆ insert() [1/2]

void BALL::Chain::insert ( Residue & residue)

Insert a Residue after the last position.

Parameters
residuethe Residue to insert

◆ insert() [2/2]

void BALL::Chain::insert ( SecondaryStructure & secondary_structure)

Insert a SecondaryStructure after the last position.

Parameters
secondary_structurethe SecondaryStructure to insert

◆ insertAfter() [1/2]

void BALL::Chain::insertAfter ( Residue & residue,
Composite & after )

Insert a Residue after a given Composite object.

Parameters
residuethe Residue to insert
afterthe Composite object to insert after

◆ insertAfter() [2/2]

void BALL::Chain::insertAfter ( SecondaryStructure & secondary_structure,
Composite & after )

Insert a SecondaryStructure after a given Composite object.

Parameters
secondary_structurethe SecondaryStructure to insert
afterthe Composite object to insert after

◆ insertBefore() [1/2]

void BALL::Chain::insertBefore ( Residue & residue,
Composite & before )

Insert a Residue before a given Composite object.

Parameters
residuethe Residue to insert
beforethe Composite object to insert before

◆ insertBefore() [2/2]

void BALL::Chain::insertBefore ( SecondaryStructure & secondary_structure,
Composite & before )

Insert a SecondaryStructure before a given Composite object.

Parameters
secondary_structurethe SecondaryStructure to insert
beforethe Composite object to insert before

◆ isChain()

virtual bool BALL::Chain::isChain ( ) const
inlinevirtual

Test if the Composite is a Chain

Reimplemented from BALL::Composite.

Definition at line 313 of file chain.h.

◆ operator!=()

bool BALL::Chain::operator!= ( const Chain & chain) const

Inequality operator

See also
operator ==

◆ operator=()

Chain & BALL::Chain::operator= ( const Chain & chain)

Assignment operator. The assignment is deep.

Parameters
chainthe chain to be copied (cloned)
Returns
chain& - this instance.
See also
chain::set

◆ operator==()

bool BALL::Chain::operator== ( const Chain & chain) const

Equality operator. Two chains are equal if they have the same handle.

See also
Object::operator ==

◆ persistentRead()

void BALL::Chain::persistentRead ( PersistenceManager & pm)
virtual

Reads a Chain object from a persistent stream.

Parameters
pmthe persistence manager

Reimplemented from BALL::AtomContainer.

◆ persistentWrite()

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

Writes a Chain object to a persistent stream.

Parameters
pmthe persistence manager

Reimplemented from BALL::AtomContainer.

◆ prepend() [1/2]

void BALL::Chain::prepend ( Residue & residue)

Prepend a Residue at position 0.

Parameters
residuethe Residue to prepend

◆ prepend() [2/2]

void BALL::Chain::prepend ( SecondaryStructure & secondary_structure)

Prepend a SecondaryStructure at position 0.

Parameters
secondary_structurethe SecondaryStructure to prepend

◆ remove() [1/2]

bool BALL::Chain::remove ( Residue & residue)

Remove a Residue.

Parameters
residuethe Residue to remove

◆ remove() [2/2]

bool BALL::Chain::remove ( SecondaryStructure & secondary_structure)

Remove a SecondaryStructure

Parameters
secondary_structurethe SecondaryStructure to remove

◆ set()

void BALL::Chain::set ( const Chain & chain,
bool deep = true )

Assignment with cloning facility. The assignment is either deep or shallow (default).

Parameters
chainthe chain to be copied (cloned)
deepmake a deep (=true) or shallow (=false) copy

◆ splice()

void BALL::Chain::splice ( Chain & chain)

Move the children of chain into this chain. The children of chain are inserted using spliceBefore .

◆ spliceAfter()

void BALL::Chain::spliceAfter ( Chain & chain)

Cut all children of chain and append them after the children of this chain.

Parameters
chainthe chain to access

◆ spliceBefore()

void BALL::Chain::spliceBefore ( Chain & chain)

Cut all children of chain and prepend them before the children of this chain.

Parameters
chainthe chain to access

◆ swap()

void BALL::Chain::swap ( Chain & chain)

Swapping of chains.

Parameters
chainthe chain this instance is being swapped with