BALL::Nucleotide Member List

This is the complete list of members for BALL::Nucleotide, including all inherited members.

AncestorConstIterator typedef (defined in BALL::Composite)	BALL::Composite
AncestorIterator typedef (defined in BALL::Composite)	BALL::Composite
AncestorIteratorTraits (defined in BALL::Composite)	BALL::Composite	[friend]
append(Atom &atom)	BALL::Nucleotide
appendChild(Composite &composite)	BALL::Composite
apply(UnaryProcessor< T > &processor)	BALL::Composite
applyAncestor(UnaryProcessor< T > &processor)	BALL::Composite
applyChild(UnaryProcessor< T > &processor)	BALL::Composite
applyDescendant(UnaryProcessor< T > &processor)	BALL::Composite
applyDescendantPostorder(UnaryProcessor< T > &processor)	BALL::Composite
applyDescendantPreorder(UnaryProcessor< T > &processor)	BALL::Composite
applyInterBond(UnaryProcessor< Bond > &processor)	BALL::AtomContainer
applyIntraBond(UnaryProcessor< Bond > &processor)	BALL::AtomContainer
applyLevel(UnaryProcessor< T > &processor, long level)	BALL::Composite
applyPostorder(UnaryProcessor< T > &processor)	BALL::Composite
applyPreorder(UnaryProcessor< T > &processor)	BALL::Composite
AtomContainer()	BALL::AtomContainer
AtomContainer(const AtomContainer &atom_container, bool deep=true)	BALL::AtomContainer
AtomContainer(const String &name)	BALL::AtomContainer
AutoDeletable() (defined in BALL::AutoDeletable)	BALL::AutoDeletable	[protected]
AutoDeletable(const AutoDeletable &auto_deletable, bool deep=false) (defined in BALL::AutoDeletable)	BALL::AutoDeletable	[protected]
beginAncestor() (defined in BALL::Composite)	BALL::Composite
beginAncestor() const (defined in BALL::Composite)	BALL::Composite
beginChildComposite() (defined in BALL::Composite)	BALL::Composite
beginChildComposite() const (defined in BALL::Composite)	BALL::Composite
beginComposite() (defined in BALL::Composite)	BALL::Composite
beginComposite() const (defined in BALL::Composite)	BALL::Composite
BOTH enum value (defined in BALL::Composite)	BALL::Composite
ChildCompositeConstIterator typedef (defined in BALL::Composite)	BALL::Composite
ChildCompositeConstReverseIterator typedef (defined in BALL::Composite)	BALL::Composite
ChildCompositeIterator typedef (defined in BALL::Composite)	BALL::Composite
ChildCompositeIteratorTraits (defined in BALL::Composite)	BALL::Composite	[friend]
ChildCompositeReverseIterator typedef (defined in BALL::Composite)	BALL::Composite
clear()	BALL::Nucleotide	[virtual]
clearLastPtr() (defined in BALL::AutoDeletable)	BALL::AutoDeletable	[static]
clearProperty(Property property)	BALL::PropertyManager
clearProperty(const string &name)	BALL::PropertyManager
clone(Composite &root) const	BALL::Composite
compare(const Object &object) const	BALL::Object
Composite()	BALL::Composite
Composite(const Composite &composite, bool deep=true)	BALL::Composite
CompositeConstIterator typedef (defined in BALL::Composite)	BALL::Composite
CompositeConstReverseIterator typedef (defined in BALL::Composite)	BALL::Composite
CompositeIterator typedef (defined in BALL::Composite)	BALL::Composite
CompositeIteratorTraits (defined in BALL::Composite)	BALL::Composite	[friend]
CompositeReverseIterator typedef (defined in BALL::Composite)	BALL::Composite
containsSelection() const	BALL::Composite
count(const KernelPredicateType &predicate) const	BALL::Composite
countAtoms() const	BALL::AtomContainer
countBonds() const	BALL::AtomContainer
countDescendants() const	BALL::Composite
countInterBonds() const	BALL::AtomContainer
countIntraBonds() const	BALL::AtomContainer
countNamedProperties() const	BALL::PropertyManager
countProperties() const	BALL::PropertyManager
DEFAULT_PROCESSOR (defined in BALL::Composite)	BALL::Composite	[static]
DEFAULT_UNARY_PREDICATE (defined in BALL::Composite)	BALL::Composite	[static]
deleteChildrenList_(std::list< Composite * > &composites) (defined in BALL::Composite)	BALL::Composite
deselect()	BALL::Composite	[virtual]
destroy()	BALL::Nucleotide	[virtual]
BALL::Composite::destroy(bool virtual_destroy)	BALL::Composite
destroyBonds()	BALL::AtomContainer
dump(std::ostream &s=std::cout, Size depth=0) const	BALL::Nucleotide	[virtual]
dump(::std::ostream &s=std::cout, Size depth=0) const (defined in BALL::Object)	BALL::Object	[virtual]
dump(::std::ostream &s=std::cout, Size depth=0) const (defined in BALL::Selectable)	BALL::Selectable	[virtual]
endAncestor() (defined in BALL::Composite)	BALL::Composite
endAncestor() const (defined in BALL::Composite)	BALL::Composite
endChildComposite() (defined in BALL::Composite)	BALL::Composite
endChildComposite() const (defined in BALL::Composite)	BALL::Composite
endComposite() (defined in BALL::Composite)	BALL::Composite
endComposite() const (defined in BALL::Composite)	BALL::Composite
finalize()	BALL::PersistentObject	[virtual]
Fragment()	BALL::Fragment
Fragment(const Fragment &fragment, bool deep=true)	BALL::Fragment
Fragment(const String &name)	BALL::Fragment
get(Nucleotide &nucleotide, bool deep=true) const	BALL::Nucleotide
BALL::Fragment::get(AtomContainer &atom_container, bool deep=true) const	BALL::AtomContainer
BALL::Composite::get(Composite &composite, bool deep=true) const	BALL::Composite
BALL::Selectable::get(Selectable &selectable, bool deep=true) const	BALL::Selectable
BALL::PropertyManager::get(PropertyManager &property_manager) const	BALL::PropertyManager
getAncestor(const T &)	BALL::Composite
getAncestor(const T &) const	BALL::Composite
getAtom(Position position)	BALL::AtomContainer
getAtom(Position position) const	BALL::AtomContainer
getAtom(const String &name)	BALL::AtomContainer
getAtom(const String &name) const	BALL::AtomContainer
getBitVector()	BALL::PropertyManager
getBitVector() const	BALL::PropertyManager
getChild(Index index)	BALL::Composite
getChild(Index index) const	BALL::Composite
getDegree() const	BALL::Composite
getDepth() const	BALL::Composite
getFirstChild()	BALL::Composite
getFirstChild() const	BALL::Composite
getHandle() const	BALL::Object
getHeight() const	BALL::Composite
getID() const	BALL::Nucleotide
getInsertionCode() const	BALL::Nucleotide
getLastChild()	BALL::Composite
getLastChild() const	BALL::Composite
getLowestCommonAncestor(const Composite &composite)	BALL::Composite
getLowestCommonAncestor(const Composite &composite) const	BALL::Composite
getModificationTime() const	BALL::Composite
getName() const	BALL::AtomContainer
getNamedProperty(Position index) const	BALL::PropertyManager
getNamedProperty(Position index)	BALL::PropertyManager
getNewHandle()	BALL::Object	[static]
getNext(const T &)	BALL::Composite
getNext(const T &dummy) const	BALL::Composite
getNextHandle()	BALL::Object	[static]
getNucleicAcid()	BALL::Nucleotide
getNucleicAcid() const	BALL::Nucleotide
getParent()	BALL::Composite
getParent() const	BALL::Composite
getPathLength(const Composite &composite) const	BALL::Composite
getPrevious(const T &)	BALL::Composite
getPrevious(const T &dummy) const	BALL::Composite
getProperty(const string &name) const	BALL::PropertyManager
getRoot()	BALL::Composite
getRoot() const	BALL::Composite
getSelectionTime() const	BALL::Composite
getSibling(Index index)	BALL::Composite
getSibling(Index index) const	BALL::Composite
getSuperAtomContainer()	BALL::AtomContainer
getSuperAtomContainer() const	BALL::AtomContainer
hasAncestor(const T &dummy) const	BALL::Composite
hasChild() const	BALL::Composite
hasNextSibling() const	BALL::Composite
hasParent() const	BALL::Composite
hasPreviousSibling() const	BALL::Composite
hasProperty(Property property) const	BALL::PropertyManager
hasProperty(const string &name) const	BALL::PropertyManager
hasSibling() const	BALL::Composite
host(Visitor< Composite > &visitor)	BALL::Composite
insert(Atom &atom)	BALL::Nucleotide
insertAfter(Atom &atom, Composite &after)	BALL::Nucleotide
BALL::Composite::insertAfter(Composite &composite)	BALL::Composite
insertBefore(Atom &atom, Composite &before)	BALL::Nucleotide
BALL::Composite::insertBefore(Composite &composite)	BALL::Composite
insertParent(Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)	BALL::Composite	[static]
is3Prime() const	BALL::Nucleotide
is5Prime() const	BALL::Nucleotide
isAncestorOf(const Composite &composite) const	BALL::Composite
isAutoDeletable() const	BALL::AutoDeletable
isChildOf(const Composite &composite) const	BALL::Composite
isDescendantOf(const Composite &composite) const	BALL::Composite
isEmpty() const	BALL::Composite
isFirstChild() const	BALL::Composite
isFirstChildOf(const Composite &composite) const	BALL::Composite
isHomomorph(const Composite &composite) const	BALL::Composite
isInterior() const	BALL::Composite
isLastChild() const	BALL::Composite
isLastChildOf(const Composite &composite) const	BALL::Composite
isNextSiblingOf(const Composite &composite) const	BALL::Composite
isParentOf(const Composite &composite) const	BALL::Composite
isPreviousSiblingOf(const Composite &composite) const	BALL::Composite
isRelatedWith(const Composite &composite) const	BALL::Composite
isRoot() const	BALL::Composite
isRootOf(const Composite &composite) const	BALL::Composite
isSelected() const	BALL::Selectable
isSiblingOf(const Composite &composite) const	BALL::Composite
isSubAtomContainerOf(const AtomContainer &atom_container) const	BALL::AtomContainer
isTerminal() const	BALL::Nucleotide
isValid() const	BALL::Nucleotide	[virtual]
KernelPredicateType typedef	BALL::Composite
MODIFICATION enum value (defined in BALL::Composite)	BALL::Composite
Nucleotide()	BALL::Nucleotide
Nucleotide(const Nucleotide &nucleotide, bool deep=true)	BALL::Nucleotide
Nucleotide(const String &name, const String &id=BALL_NUCLEOTIDE_DEFAULT_ID, char insertion_code=BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE)	BALL::Nucleotide
NUMBER_OF_PROPERTIES enum value (defined in BALL::Nucleotide)	BALL::Nucleotide
Object()	BALL::Object
Object(const Object &object)	BALL::Object
operator BitVector &()	BALL::PropertyManager
operator delete(void *ptr)	BALL::AutoDeletable
operator delete(void *ptr, void *)	BALL::AutoDeletable
operator new(size_t size)	BALL::AutoDeletable
operator new(size_t size, void *ptr)	BALL::AutoDeletable
operator!=(const Nucleotide &nucleotide) const	BALL::Nucleotide
BALL::Fragment::operator!=(const Fragment &fragment) const	BALL::Fragment
BALL::AtomContainer::operator!=(const AtomContainer &atom_container) const	BALL::AtomContainer
BALL::Composite::operator!=(const Composite &composite) const	BALL::Composite
BALL::PersistentObject::operator!=(const Object &object) const	BALL::Object
BALL::Selectable::operator!=(const Selectable &selectable) const	BALL::Selectable
BALL::PropertyManager::operator!=(const PropertyManager &pm) const	BALL::PropertyManager
operator<(const Object &object) const	BALL::Object
operator<=(const Object &object) const	BALL::Object
operator=(const Nucleotide &nucleotide)	BALL::Nucleotide
BALL::Fragment::operator=(const Fragment &fragment)	BALL::Fragment
BALL::AtomContainer::operator=(const AtomContainer &atom_container)	BALL::AtomContainer
BALL::Composite::operator=(const Composite &composite)	BALL::Composite
BALL::PersistentObject::operator=(const Object &)	BALL::Object
BALL::Selectable::operator=(const Selectable &selectable)	BALL::Selectable
BALL::PropertyManager::operator=(const PropertyManager &property_manager)	BALL::PropertyManager
operator==(const Nucleotide &nucleotide) const	BALL::Nucleotide
BALL::Fragment::operator==(const Fragment &fragment) const	BALL::Fragment
BALL::AtomContainer::operator==(const AtomContainer &atom_container) const	BALL::AtomContainer
BALL::Composite::operator==(const Composite &composite) const	BALL::Composite
BALL::PersistentObject::operator==(const Object &object) const	BALL::Object
BALL::Selectable::operator==(const Selectable &selectable) const	BALL::Selectable
BALL::PropertyManager::operator==(const PropertyManager &pm) const	BALL::PropertyManager
operator>(const Object &object) const	BALL::Object
operator>=(const Object &object) const	BALL::Object
operator>>(PersistenceManager &pm) const	BALL::PersistentObject
PersistentObject()	BALL::PersistentObject
persistentRead(PersistenceManager &pm)	BALL::Nucleotide	[virtual]
persistentWrite(PersistenceManager &pm, const char *name=0) const	BALL::Nucleotide	[virtual]
prepend(Atom &atom)	BALL::Nucleotide
prependChild(Composite &composite)	BALL::Composite
Property enum name	BALL::Nucleotide
PROPERTY__3_PRIME enum value (defined in BALL::Nucleotide)	BALL::Nucleotide
PROPERTY__5_PRIME enum value (defined in BALL::Nucleotide)	BALL::Nucleotide
PROPERTY__NUCLEOTIDE enum value (defined in BALL::Nucleotide)	BALL::Nucleotide
PropertyManager()	BALL::PropertyManager
PropertyManager(const PropertyManager &property_manager)	BALL::PropertyManager
rbeginChildComposite() (defined in BALL::Composite)	BALL::Composite
rbeginChildComposite() const (defined in BALL::Composite)	BALL::Composite
rbeginComposite() (defined in BALL::Composite)	BALL::Composite
rbeginComposite() const (defined in BALL::Composite)	BALL::Composite
BALL::read(PersistenceManager &pm)	BALL::Selectable
BALL::PropertyManager::read(PersistenceManager &pm)	BALL::PropertyManager
remove(Atom &atom)	BALL::Nucleotide
removeChild(Composite &child)	BALL::Composite
removeHavingProperty(BALL::Property p) (defined in BALL::AtomContainer)	BALL::AtomContainer
removeHavingProperty(const string &name) (defined in BALL::AtomContainer)	BALL::AtomContainer
removeNotHavingProperty(BALL::Property p) (defined in BALL::AtomContainer)	BALL::AtomContainer
removeNotHavingProperty(const string &name) (defined in BALL::AtomContainer)	BALL::AtomContainer
removeSelected()	BALL::Composite
removeUnselected()	BALL::Composite
rendChildComposite() (defined in BALL::Composite)	BALL::Composite
rendChildComposite() const (defined in BALL::Composite)	BALL::Composite
rendComposite() (defined in BALL::Composite)	BALL::Composite
rendComposite() const (defined in BALL::Composite)	BALL::Composite
replace(Composite &composite)	BALL::Composite
select()	BALL::Composite	[virtual]
Selectable()	BALL::Selectable
Selectable(const Selectable &selectable, bool deep=true)	BALL::Selectable
selected_ (defined in BALL::Selectable)	BALL::Selectable	[protected]
SELECTION enum value (defined in BALL::Composite)	BALL::Composite
set(const Nucleotide &nucleotide, bool deep=true)	BALL::Nucleotide
BALL::Fragment::set(const AtomContainer &atom_container, bool deep=true)	BALL::AtomContainer
BALL::Composite::set(const Composite &composite, bool deep=true)	BALL::Composite
BALL::Selectable::set(const Selectable &selectable, bool deep=true)	BALL::Selectable
BALL::PropertyManager::set(const PropertyManager &property_manager)	BALL::PropertyManager
setAutoDeletable(bool enable)	BALL::AutoDeletable
setID(const String &id)	BALL::Nucleotide
setInsertionCode(char insertion_code)	BALL::Nucleotide
setName(const String &name)	BALL::AtomContainer
setProperty(Property property)	BALL::PropertyManager
setProperty(const NamedProperty &property)	BALL::PropertyManager
setProperty(const string &name)	BALL::PropertyManager
setProperty(const string &name, bool value)	BALL::PropertyManager
setProperty(const string &name, int value)	BALL::PropertyManager
setProperty(const string &name, unsigned int value)	BALL::PropertyManager
setProperty(const string &name, float value)	BALL::PropertyManager
setProperty(const string &name, double value)	BALL::PropertyManager
setProperty(const string &name, const string &value)	BALL::PropertyManager
setProperty(const string &name, const PersistentObject &value)	BALL::PropertyManager
setSelected(bool selected)	BALL::Selectable	[virtual]
splice(Nucleotide &nucleotide)	BALL::Nucleotide
BALL::Composite::splice(Composite &composite)	BALL::Composite
spliceAfter(Nucleotide &nucleotide)	BALL::Nucleotide
BALL::Composite::spliceAfter(Composite &composite)	BALL::Composite
spliceBefore(Nucleotide &nucleotide)	BALL::Nucleotide
BALL::Composite::spliceBefore(Composite &composite)	BALL::Composite
stamp(StampType stamp=BOTH)	BALL::Composite
StampType enum name	BALL::Composite
swap(Nucleotide &nucleotide)	BALL::Nucleotide
BALL::Fragment::swap(AtomContainer &atom_container)	BALL::AtomContainer
BALL::Composite::swap(Composite &composite)	BALL::Composite
BALL::Selectable::swap(Selectable &selectable)	BALL::Selectable
BALL::PropertyManager::swap(PropertyManager &property_manager)	BALL::PropertyManager
toggleProperty(Property property)	BALL::PropertyManager
BALL::write(PersistenceManager &pm) const	BALL::Selectable
BALL::PropertyManager::write(PersistenceManager &pm) const	BALL::PropertyManager
~AtomContainer()	BALL::AtomContainer	[virtual]
~AutoDeletable()	BALL::AutoDeletable	[virtual]
~Composite()	BALL::Composite	[virtual]
~Fragment()	BALL::Fragment	[virtual]
~Nucleotide()	BALL::Nucleotide	[virtual]
~Object()	BALL::Object	[virtual]
~PersistentObject()	BALL::PersistentObject	[virtual]
~PropertyManager()	BALL::PropertyManager	[virtual]
~Selectable()	BALL::Selectable	[virtual]