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BALL::PDBAtom Member List

This is the complete list of members for BALL::PDBAtom, 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 |
addInteraction(const Atom *atom, String interaction_type, double energy) | BALL::Atom |
addInteraction(String interaction_type, double energy) | BALL::Atom |
AncestorConstIterator typedef | BALL::Composite |
AncestorIterator typedef | BALL::Composite |
ANY_TYPE enum value | BALL::Atom |
appendChild(Composite &composite) | BALL::Composite |
apply(UnaryProcessor< T > &processor) | BALL::Composite |
apply(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
apply(UnaryProcessor< T > &processor) | BALL::Composite |
apply(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
applyAncestor(UnaryProcessor< T > &processor) | BALL::Composite |
applyAncestor(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
applyBonds(UnaryProcessor< Bond > &processor) | BALL::Atom |
applyChild(UnaryProcessor< T > &processor) | BALL::Composite |
applyChild(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
applyDescendant(UnaryProcessor< T > &processor) | BALL::Composite |
applyDescendant(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
applyDescendantPostorder(UnaryProcessor< T > &processor) | BALL::Composite |
applyDescendantPostorder(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
applyDescendantPreorder(UnaryProcessor< T > &processor) | BALL::Composite |
applyDescendantPreorder(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
applyLevel(UnaryProcessor< T > &processor, long level) | BALL::Composite |
applyLevel(ConstUnaryProcessor< T > &processor, long level) const | BALL::Composite |
applyPostorder(UnaryProcessor< T > &processor) | BALL::Composite |
applyPostorder(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
applyPreorder(UnaryProcessor< T > &processor) | BALL::Composite |
applyPreorder(ConstUnaryProcessor< T > &processor) const | BALL::Composite |
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 |
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
beginNamedProperty() | BALL::PropertyManager |
Bond class | BALL::PDBAtom | friend
bond_ | BALL::Atom | protected
BondConstIterator typedef | BALL::Atom |
BondConstReverseIterator typedef | BALL::Atom |
BondIterator typedef | BALL::Atom |
BondIteratorPosition typedef | BALL::Atom |
BondReverseIterator typedef | BALL::Atom |
BOTH enum value | BALL::Composite |
charge_ | BALL::Atom | protected
ChildCompositeConstIterator typedef | BALL::Composite |
ChildCompositeConstReverseIterator typedef | BALL::Composite |
ChildCompositeIterator typedef | BALL::Composite |
ChildCompositeReverseIterator typedef | BALL::Composite |
clear() | BALL::PDBAtom | virtual
clearLastPtr() | BALL::AutoDeletable | inline static
clearProperty(Property property) | BALL::PropertyManager |
clearProperty(const std::string &name) | BALL::PropertyManager |
clone(Composite &root) const | BALL::Composite |
cloneBond(Bond &bond, Atom &atom) | BALL::Atom |
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 |
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 |
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::PDBAtom | virtual
BALL::Composite::destroy(bool virtual_destroy) | BALL::Composite |
destroyBond(const Atom &atom) | BALL::Atom |
destroyBonds() | BALL::Atom |
disableStoreInteractions() | BALL::Atom |
dump(std::ostream &s=std::cout, Size depth=0) const | BALL::PDBAtom | 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
enableStoreInteractions() | BALL::Atom |
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
endNamedProperty() | BALL::PropertyManager |
finalize() | BALL::PersistentObject | inline virtual
force_ | BALL::Atom | protected
formal_charge_ | BALL::Atom | protected
free_list_ | BALL::Atom | protected static
FullNameType enum name | BALL::Atom |
get(PDBAtom &pdb_atom, bool deep=true) const | BALL::PDBAtom |
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 |
getAlternateLocationIndicator() const | BALL::PDBAtom |
getAncestor(const T &) | BALL::Composite |
getAncestor(const T &) const | BALL::Composite |
getAncestor(const T &) | BALL::Composite |
getAncestor(const T &) const | BALL::Composite |
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 |
getBranchDesignator() const | BALL::PDBAtom |
getChain() | BALL::PDBAtom |
getChain() const | BALL::PDBAtom |
getCharge() const | BALL::Atom |
getChild(Index index) | BALL::Composite |
getChild(Index index) const | BALL::Composite |
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::Atom |
getFragment() const | BALL::Atom |
getFragment() | BALL::Atom |
getFullName(FullNameType type=ADD_VARIANT_EXTENSIONS) const | BALL::Atom |
getHandle() const | BALL::Object |
getHeight() const | BALL::Composite |
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 |
getNext(const T &dummy) const | BALL::Composite |
getNext(const T &) | BALL::Composite |
getNext(const T &dummy) const | BALL::Composite |
getNextHandle() | BALL::Object | static
getOccupancy() const | BALL::PDBAtom |
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 |
getPrevious(const T &dummy) const | BALL::Composite |
getPrevious(const T &) | BALL::Composite |
getPrevious(const T &dummy) const | BALL::Composite |
getProperty(const std::string &name) const | BALL::PropertyManager |
getProtein() | BALL::PDBAtom |
getProtein() const | BALL::PDBAtom |
getRadius() const | BALL::Atom |
getRemotenessIndicator() const | BALL::PDBAtom |
getResidue() | BALL::PDBAtom |
getResidue() const | BALL::PDBAtom |
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 |
getTemperatureFactor() const | BALL::PDBAtom |
getType() const | BALL::Atom |
getTypeName() const | BALL::Atom |
getVelocity() | BALL::Atom |
getVelocity() const | BALL::Atom |
hasAncestor(const T &dummy) const | BALL::Composite |
hasAncestor(const T &dummy) const | BALL::Composite |
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 std::string &name) const | BALL::PropertyManager |
hasSibling() const | BALL::Composite |
host(Visitor< Composite > &visitor) | BALL::Composite |
insertAfter(Composite &composite) | BALL::Composite |
insertBefore(Composite &composite) | BALL::Composite |
insertParent(Composite &parent, Composite &first, Composite &last, bool destroy_parent=true) | BALL::Composite | static
interactions | BALL::Atom |
isAncestorOf(const Composite &composite) const | BALL::Composite |
isAtom() const | BALL::Atom | inline virtual
isAutoDeletable() const | BALL::AutoDeletable |
isBound() const | BALL::Atom |
isBoundTo(const Atom &atom) const | BALL::Atom |
isChain() const | BALL::Composite | inline virtual
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 |
isFragment() const | BALL::Composite | inline virtual
isGeminal(const Atom &atom) const | BALL::Atom |
isHomomorph(const Composite &composite) const | BALL::Composite |
isInterior() const | BALL::Composite |
isLastChild() const | BALL::Composite |
isLastChildOf(const Composite &composite) const | BALL::Composite |
isMolecule() const | BALL::Composite | inline virtual
isNextSiblingOf(const Composite &composite) const | BALL::Composite |
isParentOf(const Composite &composite) const | BALL::Composite |
isPreviousSiblingOf(const Composite &composite) const | BALL::Composite |
isProtein() const | BALL::Composite | inline virtual
isRelatedWith(const Composite &composite) const | BALL::Composite |
isResidue() const | BALL::Composite | inline virtual
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::PDBAtom |
NUMBER_OF_REMOTENESS_INDICATORS enum value | BALL::PDBAtom |
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 PDBAtom &pdb_atom) const | BALL::PDBAtom |
BALL::Atom::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 PDBAtom &pdb_atom) | BALL::PDBAtom |
BALL::Atom::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 PDBAtom &pdb_atom) const | BALL::PDBAtom |
BALL::Atom::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 |
PDBAtom() | BALL::PDBAtom |
PDBAtom(const PDBAtom &pdb_atom, bool deep=true) | BALL::PDBAtom |
PDBAtom(const String &name) | BALL::PDBAtom |

PDBAtom(Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Atom::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, char branch_designator=BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, char remoteness_indicator=BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, char alternate_location_indicator=BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, float occupancy=BALL_PDBATOM_DEFAULT_OCCUPANCY, float temperature_factor=BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR)

BALL::PDBAtom

PersistentObject() | BALL::PersistentObject | inline
persistentRead(PersistenceManager &pm) | BALL::PDBAtom | virtual
persistentWrite(PersistenceManager &pm, const char *name=0) const | BALL::PDBAtom | virtual
position_ | BALL::Atom | protected
prependChild(Composite &composite) | BALL::Composite |
Property enum name | BALL::PDBAtom |
PROPERTY__HETATM enum value | BALL::PDBAtom |
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 |
REMOTENESS_INDICATOR__ALPHA enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__alpha enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__BETA enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__beta enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__DELTA enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__delta enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__EPSILON enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__epsilon enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__ETA enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__eta enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__GAMMA enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__gamma enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__UNKNOWN enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__ZETA enum value | BALL::PDBAtom |
REMOTENESS_INDICATOR__zeta enum value | BALL::PDBAtom |
RemotenessIndicator enum name | BALL::PDBAtom |
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 PDBAtom &pdb_atom, bool deep=true) | BALL::PDBAtom |
BALL::Atom::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 |
setAlternateLocationIndicator(char alternate_location_indicator) | BALL::PDBAtom |
setAutoDeletable(bool enable) | BALL::AutoDeletable |
setBranchDesignator(char branch_designator) | BALL::PDBAtom |
setCharge(float charge) | BALL::Atom |
setElement(const Element &element) | BALL::Atom |
setForce(const Vector3 &force) | BALL::Atom |
setFormalCharge(Index formal_charge) | BALL::Atom |
setName(const String &name) | BALL::Atom |
setOccupancy(float occupancy) | BALL::PDBAtom |
setPosition(const Vector3 &position) | BALL::Atom |
setProperty(Property property) | BALL::PropertyManager |
setProperty(const NamedProperty &property) | BALL::PropertyManager |
setProperty(const std::string &name) | BALL::PropertyManager |
setProperty(const std::string &name, bool value) | BALL::PropertyManager |
setProperty(const std::string &name, int value) | BALL::PropertyManager |
setProperty(const std::string &name, unsigned int value) | BALL::PropertyManager |
setProperty(const std::string &name, float value) | BALL::PropertyManager |
setProperty(const std::string &name, double value) | BALL::PropertyManager |
setProperty(const std::string &name, const std::string &value) | BALL::PropertyManager |
setProperty(const std::string &name, const PersistentObject &value) | BALL::PropertyManager |
setRadius(float radius) | BALL::Atom |
setRemotenessIndicator(char remoteness_indicator) | BALL::PDBAtom |
setSelected(bool selected) | BALL::Selectable | inline virtual
setTemperatureFactor(float temperature_factor) | BALL::PDBAtom |
setType(Type atom_type) | BALL::Atom |
setTypeName(const String &name) | BALL::Atom |
setVelocity(const Vector3 &velocity) | BALL::Atom |
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 |
store_interactions_disabled_ | BALL::Atom |
swap(PDBAtom &pdb_atom) | BALL::PDBAtom |
BALL::Atom::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_ | BALL::Atom | protected
type_name_ | BALL::Atom | protected
UNKNOWN_TYPE enum value | BALL::Atom |
velocity_ | BALL::Atom | protected
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
~PDBAtom() | BALL::PDBAtom | virtual
~PersistentObject() | BALL::PersistentObject | inline virtual
~PropertyManager() | BALL::PropertyManager | virtual
~Selectable() | BALL::Selectable | virtual