, including all inherited members.
| AncestorConstIterator typedef (defined in Composite) | Composite | |
| AncestorIterator typedef (defined in Composite) | Composite | |
| AncestorIteratorTraits (defined in Composite) | Composite | [friend] |
| append(Molecule &molecule) | System | |
| AtomContainer::append(Atom &atom) | AtomContainer | |
| AtomContainer::append(AtomContainer &atom_container) | AtomContainer | |
| 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() | AtomContainer | [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 | |
| countAtomContainers() const | AtomContainer | |
| countAtoms() const | System | |
| countBonds() const | AtomContainer | |
| countChains() const | System | |
| countDescendants() const | Composite | |
| countFragments() const | System | |
| countInterBonds() const | AtomContainer | |
| countIntraBonds() const | AtomContainer | |
| countMolecules() const | System | |
| countNamedProperties() const | PropertyManager | |
| countNucleicAcids() const | System | |
| countNucleotides() const | System | |
| countProperties() const | PropertyManager | |
| countProteins() const | System | |
| countResidues() const | System | |
| countSecondaryStructures() const | System | |
| DEFAULT_PROCESSOR (defined in Composite) | Composite | [static] |
| DEFAULT_UNARY_PREDICATE (defined in Composite) | Composite | [static] |
| deselect() | Composite | [virtual] |
| destroy() | AtomContainer | [virtual] |
| Composite::destroy(bool virtual_destroy) | Composite | |
| destroyBonds() | AtomContainer | |
| dump(std::ostream &s=std::cout, Size depth=0) const | AtomContainer | [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] |
| get(System &system, bool deep=true) const | System | |
| AtomContainer::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 | |
| getAtomContainer(Position position) | AtomContainer | |
| getAtomContainer(Position position) 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 | |
| getLastChild() | Composite | |
| getLastChild() const | Composite | |
| getLowestCommonAncestor(const Composite &composite) | Composite | |
| getLowestCommonAncestor(const Composite &composite) const | Composite | |
| getModificationTime() const | Composite | |
| getMolecule(Position position) | System | |
| getMolecule(Position position) const | System | |
| 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] |
| 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(Molecule &molecule) | System | |
| AtomContainer::insert(Atom &atom) | AtomContainer | |
| AtomContainer::insert(AtomContainer &atom_container) | AtomContainer | |
| insertAfter(Molecule &molecule, Composite &after) | System | |
| AtomContainer::insertAfter(Atom &atom, Composite &after) | AtomContainer | |
| AtomContainer::insertAfter(AtomContainer &atom_container, Composite &after) | AtomContainer | |
| Composite::insertAfter(Composite &composite) | Composite | |
| insertBefore(Molecule &molecule, Composite &before) | System | |
| AtomContainer::insertBefore(Atom &atom, Composite &before) | AtomContainer | |
| AtomContainer::insertBefore(AtomContainer &atom_container, Composite &before) | AtomContainer | |
| Composite::insertBefore(Composite &composite) | Composite | |
| insertParent(Composite &parent, Composite &first, Composite &last, bool destroy_parent=true) | Composite | [static] |
| 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 | |
| isSuperAtomContainerOf(const AtomContainer &atom_container) const | AtomContainer | |
| isValid() const | AtomContainer | [virtual] |
| KernelPredicateType typedef | Composite | |
| MODIFICATION enum value (defined in Composite) | Composite | |
| NUMBER_OF_PROPERTIES enum value (defined in AtomContainer) | AtomContainer | |
| 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 System &system) const | System | |
| 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 System &system) | System | |
| 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 System &system) const | System | |
| 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) | System | [virtual] |
| persistentWrite(PersistenceManager &pm, const char *name=0) const | System | [virtual] |
| prepend(Molecule &molecule) | System | |
| AtomContainer::prepend(Atom &atom) | AtomContainer | |
| AtomContainer::prepend(AtomContainer &atom_container) | AtomContainer | |
| prependChild(Composite &composite) | Composite | |
| Property enum name | AtomContainer | |
| 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(Molecule &molecule) | System | |
| AtomContainer::remove(Atom &atom) | AtomContainer | |
| AtomContainer::remove(AtomContainer &atom_container) | AtomContainer | |
| 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 System &system, bool deep=true) | System | |
| AtomContainer::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 | |
| 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(System &system) | System | |
| AtomContainer::splice(AtomContainer &atom_container) | AtomContainer | |
| Composite::splice(Composite &composite) | Composite | |
| spliceAfter(System &system) | System | |
| AtomContainer::spliceAfter(AtomContainer &atom_container) | AtomContainer | |
| Composite::spliceAfter(Composite &composite) | Composite | |
| spliceBefore(System &system) | System | |
| AtomContainer::spliceBefore(AtomContainer &atom_container) | AtomContainer | |
| Composite::spliceBefore(Composite &composite) | Composite | |
| stamp(StampType stamp=BOTH) | Composite | |
| StampType enum name | Composite | |
| swap(AtomContainer &atom_container) | AtomContainer | |
| Composite::swap(Composite &composite) | Composite | |
| Selectable::swap(Selectable &selectable) | Selectable | |
| PropertyManager::swap(PropertyManager &property_manager) | PropertyManager | |
| System() | System | |
| System(const System &system, bool deep=true) | System | |
| System(const String &name) | System | |
| toggleProperty(Property property) | PropertyManager | |
| write(PersistenceManager &pm) const | Selectable | |
| PropertyManager::write(PersistenceManager &pm) const | PropertyManager | |
| ~AtomContainer() | AtomContainer | [virtual] |
| ~AutoDeletable() | AutoDeletable | [virtual] |
| ~Composite() | Composite | [virtual] |
| ~Object() | Object | [virtual] |
| ~PersistentObject() | PersistentObject | [virtual] |
| ~PropertyManager() | PropertyManager | [virtual] |
| ~Selectable() | Selectable | [virtual] |
| ~System() | System | [virtual] |