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Nucleotide Member List

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

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