, including all inherited members.
| ADD_CHAIN_RESIDUE_ID enum value | BALL::Atom | |
| ADD_RESIDUE_ID enum value | BALL::Atom | |
| ADD_VARIANT_EXTENSIONS enum value | BALL::Atom | |
| ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID enum value | BALL::Atom | |
| ADD_VARIANT_EXTENSIONS_AND_ID enum value | BALL::Atom | |
| AncestorConstIterator typedef | BALL::Composite | |
| AncestorIterator typedef | BALL::Composite | |
| AncestorIteratorTraits class | BALL::Composite | [friend] |
| ANY_TYPE enum value | BALL::Atom | |
| appendChild(Composite &composite) | BALL::Composite | |
| apply(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| applyAncestor(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| applyBonds(UnaryProcessor< Bond > &processor) | BALL::Atom | |
| applyChild(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| applyDescendant(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| applyDescendantPostorder(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| applyDescendantPreorder(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| applyLevel(UnaryProcessor< T > &processor, long level) | BALL::Composite | [inline] |
| applyPostorder(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| applyPreorder(UnaryProcessor< T > &processor) | BALL::Composite | [inline] |
| Atom() | BALL::Atom | |
| Atom(const Atom &atom, bool deep=true) | BALL::Atom | |
| Atom(Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE) | BALL::Atom | |
| AtomIndexList typedef | BALL::Atom | |
| AtomPtrList typedef | BALL::Atom | |
| attributes_changed_time_ | BALL::Atom | [protected, static] |
| AutoDeletable() | BALL::AutoDeletable | [protected] |
| AutoDeletable(const AutoDeletable &auto_deletable, bool deep=false) | BALL::AutoDeletable | [protected] |
| beginAncestor() | BALL::Composite | [inline] |
| beginAncestor() const | BALL::Composite | [inline] |
| beginBond() | BALL::Atom | [inline] |
| beginBond() const | BALL::Atom | [inline] |
| beginChildComposite() | BALL::Composite | [inline] |
| beginChildComposite() const | BALL::Composite | [inline] |
| beginComposite() | BALL::Composite | [inline] |
| beginComposite() const | BALL::Composite | [inline] |
| Bond class | BALL::Atom | [friend] |
| bond_ | BALL::Atom | [protected] |
| BondConstIterator typedef | BALL::Atom | |
| BondConstReverseIterator typedef | BALL::Atom | |
| BondIterator typedef | BALL::Atom | |
| BondIteratorPosition typedef | BALL::Atom | |
| BondIteratorTraits class | BALL::Atom | [friend] |
| BondReverseIterator typedef | BALL::Atom | |
| BOTH enum value | BALL::Composite | |
| ChildCompositeConstIterator typedef | BALL::Composite | |
| ChildCompositeConstReverseIterator typedef | BALL::Composite | |
| ChildCompositeIterator typedef | BALL::Composite | |
| ChildCompositeIteratorTraits class | BALL::Composite | [friend] |
| ChildCompositeReverseIterator typedef | BALL::Composite | |
| chirality_ | BALL::SmilesParser::SPAtom | [protected] |
| clear() | BALL::Atom | [virtual] |
| clearLastPtr() | BALL::AutoDeletable | [inline, static] |
| clearProperty(Property property) | BALL::PropertyManager | |
| clearProperty(const string &name) | BALL::PropertyManager | |
| clone(Composite &root) const | BALL::Composite | |
| cloneBond(Bond &bond, Atom &atom) | BALL::Atom | |
| compact(const AtomIndexList &indices) | BALL::Atom | [static] |
| compare(const Object &object) const | BALL::Object | |
| Composite() | BALL::Composite | |
| Composite(const Composite &composite, bool deep=true) | BALL::Composite | |
| CompositeConstIterator typedef | BALL::Composite | |
| CompositeConstReverseIterator typedef | BALL::Composite | |
| CompositeIterator typedef | BALL::Composite | |
| CompositeIteratorTraits class | BALL::Composite | [friend] |
| CompositeReverseIterator typedef | BALL::Composite | |
| containsSelection() const | BALL::Composite | |
| count(const KernelPredicateType &predicate) const | BALL::Composite | |
| countBonds() const | BALL::Atom | |
| countDescendants() const | BALL::Composite | |
| countNamedProperties() const | BALL::PropertyManager | |
| countProperties() const | BALL::PropertyManager | |
| countRealValences() const | BALL::SmilesParser::SPAtom | |
| createBond(Atom &atom) | BALL::Atom | |
| createBond(Bond &bond, Atom &atom) | BALL::Atom | |
| DEFAULT_PROCESSOR | BALL::Composite | [static] |
| DEFAULT_UNARY_PREDICATE | BALL::Composite | [static] |
| deleteChildrenList_(std::list< Composite * > &composites) | BALL::Composite | |
| deselect() | BALL::Composite | [virtual] |
| destroy() | BALL::Atom | [virtual] |
| BALL::Composite::destroy(bool virtual_destroy) | BALL::Composite | |
| destroyBond(const Atom &atom) | BALL::Atom | |
| destroyBonds() | BALL::Atom | |
| dump(std::ostream &s=std::cout, Size depth=0) const | BALL::Atom | [virtual] |
| BALL::PersistentObject::dump(::std::ostream &s=std::cout, Size depth=0) const | BALL::Object | [virtual] |
| BALL::Selectable::dump(::std::ostream &s=std::cout, Size depth=0) const | BALL::Selectable | [virtual] |
| element_ | BALL::Atom | [protected] |
| endAncestor() | BALL::Composite | [inline] |
| endAncestor() const | BALL::Composite | [inline] |
| endBond() | BALL::Atom | [inline] |
| endBond() const | BALL::Atom | [inline] |
| endChildComposite() | BALL::Composite | [inline] |
| endChildComposite() const | BALL::Composite | [inline] |
| endComposite() | BALL::Composite | [inline] |
| endComposite() const | BALL::Composite | [inline] |
| finalize() | BALL::PersistentObject | [inline, virtual] |
| formal_charge_ | BALL::SmilesParser::SPAtom | [protected] |
| free_list_ | BALL::Atom | [protected, static] |
| FullNameType enum name | BALL::Atom | |
| get(Atom &atom, bool deep=true) const | BALL::Atom | |
| 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 | [inline] |
| getAncestor(const T &) const | BALL::Composite | [inline] |
| getAttributePtr() | BALL::Atom | |
| getAttributePtr() const | BALL::Atom | |
| getAttributes() | BALL::Atom | [static] |
| getAttributesModificationTime() | BALL::Atom | [inline, static] |
| getBitVector() | BALL::PropertyManager | |
| getBitVector() const | BALL::PropertyManager | |
| getBond(Position index) | BALL::Atom | |
| getBond(Position index) const | BALL::Atom | |
| getBond(const Atom &atom) | BALL::Atom | |
| getBond(const Atom &atom) const | BALL::Atom | |
| getChain() const | BALL::Atom | |
| getChain() | BALL::Atom | |
| getCharge() const | BALL::Atom | |
| getChild(Index index) | BALL::Composite | |
| getChild(Index index) const | BALL::Composite | |
| getChirality() const | BALL::SmilesParser::SPAtom | [inline] |
| getDefaultValence() const | BALL::SmilesParser::SPAtom | |
| getDegree() const | BALL::Composite | |
| getDepth() const | BALL::Composite | |
| getDistance(const Atom &a) const | BALL::Atom | |
| getElement() const | BALL::Atom | |
| getFirstChild() | BALL::Composite | |
| getFirstChild() const | BALL::Composite | |
| getForce() const | BALL::Atom | |
| getForce() | BALL::Atom | |
| getFormalCharge() const | BALL::SmilesParser::SPAtom | [inline] |
| getFragment() const | BALL::Atom | |
| getFragment() | BALL::Atom | |
| getFullName(FullNameType type=ADD_VARIANT_EXTENSIONS) const | BALL::Atom | |
| getHandle() const | BALL::Object | |
| getHeight() const | BALL::Composite | |
| getIndex() const | BALL::Atom | |
| getIsotope() const | BALL::SmilesParser::SPAtom | [inline] |
| getLastChild() | BALL::Composite | |
| getLastChild() const | BALL::Composite | |
| getLowestCommonAncestor(const Composite &composite) | BALL::Composite | |
| getLowestCommonAncestor(const Composite &composite) const | BALL::Composite | |
| getModificationTime() const | BALL::Composite | |
| getMolecule() const | BALL::Atom | |
| getMolecule() | BALL::Atom | |
| getName() const | BALL::Atom | |
| getNamedProperty(Position index) const | BALL::PropertyManager | |
| getNamedProperty(Position index) | BALL::PropertyManager | |
| getNewHandle() | BALL::Object | [static] |
| getNext(const T &) | BALL::Composite | [inline] |
| getNext(const T &dummy) const | BALL::Composite | [inline] |
| getNextHandle() | BALL::Object | [static] |
| getParent() | BALL::Composite | |
| getParent() const | BALL::Composite | |
| getPartnerAtom(Position i) | BALL::Atom | |
| getPartnerAtom(Position i) const | BALL::Atom | |
| getPathLength(const Composite &composite) const | BALL::Composite | |
| getPosition() | BALL::Atom | |
| getPosition() const | BALL::Atom | |
| getPrevious(const T &) | BALL::Composite | [inline] |
| getPrevious(const T &dummy) const | BALL::Composite | [inline] |
| getProperty(const string &name) const | BALL::PropertyManager | |
| getRadius() const | BALL::Atom | |
| getResidue() const | BALL::Atom | |
| getResidue() | BALL::Atom | |
| getRoot() | BALL::Composite | |
| getRoot() const | BALL::Composite | |
| getSecondaryStructure() const | BALL::Atom | |
| getSecondaryStructure() | BALL::Atom | |
| getSelectionTime() const | BALL::Composite | |
| getSibling(Index index) | BALL::Composite | |
| getSibling(Index index) const | BALL::Composite | |
| getType() const | BALL::Atom | |
| getTypeName() const | BALL::Atom | |
| getVelocity() const | BALL::Atom | |
| hasAncestor(const T &dummy) const | BALL::Composite | [inline] |
| hasBond(const Bond &bond) const | BALL::Atom | |
| 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 | |
| in_brackets_ | BALL::SmilesParser::SPAtom | [protected] |
| index_ | BALL::Atom | [protected] |
| insertAfter(Composite &composite) | BALL::Composite | |
| insertBefore(Composite &composite) | BALL::Composite | |
| insertParent(Composite &parent, Composite &first, Composite &last, bool destroy_parent=true) | BALL::Composite | [static] |
| is_aromatic_ | BALL::SmilesParser::SPAtom | [protected] |
| isAncestorOf(const Composite &composite) const | BALL::Composite | |
| isAromatic() const | BALL::SmilesParser::SPAtom | [inline] |
| isAutoDeletable() const | BALL::AutoDeletable | |
| isBound() const | BALL::Atom | |
| isBoundTo(const Atom &atom) const | BALL::Atom | |
| 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 | |
| isGeminal(const Atom &atom) const | BALL::Atom | |
| isHomomorph(const Composite &composite) const | BALL::Composite | |
| isInBrackets() const | BALL::SmilesParser::SPAtom | [inline] |
| isInterior() const | BALL::Composite | |
| isLastChild() const | BALL::Composite | |
| isLastChildOf(const Composite &composite) const | BALL::Composite | |
| isNextSiblingOf(const Composite &composite) const | BALL::Composite | |
| isotope_ | BALL::SmilesParser::SPAtom | [protected] |
| 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 | |
| isValid() const | BALL::Atom | [virtual] |
| isVicinal(const Atom &atom) const | BALL::Atom | |
| KernelPredicateType typedef | BALL::Composite | |
| MAX_NUMBER_OF_BONDS enum value | BALL::Atom | |
| MODIFICATION enum value | BALL::Composite | |
| name_ | BALL::Atom | [protected] |
| NO_VARIANT_EXTENSIONS enum value | BALL::Atom | |
| number_of_bonds_ | BALL::Atom | [protected] |
| NUMBER_OF_PROPERTIES enum value | BALL::Atom | |
| 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 Atom &atom) const | BALL::Atom | |
| 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 Atom &atom) | BALL::Atom | |
| 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 Atom &atom) const | BALL::Atom | |
| 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 | [inline] |
| persistentRead(PersistenceManager &pm) | BALL::Atom | [virtual] |
| persistentWrite(PersistenceManager &pm, const char *name=0) const | BALL::Atom | [virtual] |
| prependChild(Composite &composite) | BALL::Composite | |
| Property enum name | BALL::Atom | |
| PropertyManager() | BALL::PropertyManager | |
| PropertyManager(const PropertyManager &property_manager) | BALL::PropertyManager | |
| radius_ | BALL::Atom | [protected] |
| rbeginBond() | BALL::Atom | [inline] |
| rbeginBond() const | BALL::Atom | [inline] |
| rbeginChildComposite() | BALL::Composite | [inline] |
| rbeginChildComposite() const | BALL::Composite | [inline] |
| rbeginComposite() | BALL::Composite | [inline] |
| rbeginComposite() const | BALL::Composite | [inline] |
| BALL::read(PersistenceManager &pm) | BALL::Selectable | |
| BALL::PropertyManager::read(PersistenceManager &pm) | BALL::PropertyManager | |
| removeChild(Composite &child) | BALL::Composite | |
| removeSelected() | BALL::Composite | |
| removeUnselected() | BALL::Composite | |
| rendBond() | BALL::Atom | [inline] |
| rendBond() const | BALL::Atom | [inline] |
| rendChildComposite() | BALL::Composite | [inline] |
| rendChildComposite() const | BALL::Composite | [inline] |
| rendComposite() | BALL::Composite | [inline] |
| rendComposite() const | BALL::Composite | [inline] |
| replace(Composite &composite) | BALL::Composite | |
| select() | BALL::Composite | [virtual] |
| Selectable() | BALL::Selectable | |
| Selectable(const Selectable &selectable, bool deep=true) | BALL::Selectable | |
| selected_ | BALL::Selectable | [protected] |
| SELECTION enum value | BALL::Composite | |
| set(const Atom &atom, bool deep=true) | BALL::Atom | |
| 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 | |
| setAromatic(bool is_aromatic) | BALL::SmilesParser::SPAtom | [inline] |
| setAutoDeletable(bool enable) | BALL::AutoDeletable | |
| setCharge(float charge) | BALL::Atom | |
| setChirality(const ChiralDef &chirality) | BALL::SmilesParser::SPAtom | [inline] |
| setElement(const Element &element) | BALL::Atom | |
| setForce(const Vector3 &force) | BALL::Atom | |
| setFormalCharge(Index charge) | BALL::SmilesParser::SPAtom | [inline] |
| setInBrackets(bool in_brackets) | BALL::SmilesParser::SPAtom | [inline] |
| setIsotope(Size isotope) | BALL::SmilesParser::SPAtom | [inline] |
| setName(const String &name) | BALL::Atom | |
| setPosition(const Vector3 &position) | BALL::Atom | |
| 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 | |
| setRadius(float radius) | BALL::Atom | |
| setSelected(bool selected) | BALL::Selectable | [inline, virtual] |
| setType(Type atom_type) | BALL::Atom | |
| setTypeName(const String &name) | BALL::Atom | |
| setVelocity(const Vector3 &velocity) | BALL::Atom | |
| SPAtom(const String &symbol, bool in_brackets) | BALL::SmilesParser::SPAtom | |
| splice(Composite &composite) | BALL::Composite | |
| spliceAfter(Composite &composite) | BALL::Composite | |
| spliceBefore(Composite &composite) | BALL::Composite | |
| stamp(StampType stamp=BOTH) | BALL::Composite | |
| StampType enum name | BALL::Composite | |
| static_attributes_ | BALL::Atom | [protected, static] |
| swap(Atom &atom) | BALL::Atom | |
| 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 | |
| Type typedef | BALL::Atom | |
| type_name_ | BALL::Atom | [protected] |
| UNKNOWN_TYPE enum value | BALL::Atom | |
| BALL::write(PersistenceManager &pm) const | BALL::Selectable | |
| BALL::PropertyManager::write(PersistenceManager &pm) const | BALL::PropertyManager | |
| ~Atom() | BALL::Atom | [virtual] |
| ~AutoDeletable() | BALL::AutoDeletable | [virtual] |
| ~Composite() | BALL::Composite | [virtual] |
| ~Object() | BALL::Object | [virtual] |
| ~PersistentObject() | BALL::PersistentObject | [inline, virtual] |
| ~PropertyManager() | BALL::PropertyManager | [virtual] |
| ~Selectable() | BALL::Selectable | [virtual] |
| ~SPAtom() | BALL::SmilesParser::SPAtom | [virtual] |