AncestorConstIterator typedef | BALL::Composite | |
AncestorIterator typedef | BALL::Composite | |
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 | |
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 | |
AutoDeletable() | BALL::AutoDeletable | protected |
AutoDeletable(const AutoDeletable &auto_deletable, bool deep=false) | BALL::AutoDeletable | protected |
beginAncestor() | BALL::Composite | inline |
beginAncestor() const | BALL::Composite | inline |
beginChildComposite() | BALL::Composite | inline |
beginChildComposite() const | BALL::Composite | inline |
beginComposite() | BALL::Composite | inline |
beginComposite() const | BALL::Composite | inline |
beginNamedProperty() | BALL::PropertyManager | |
Bond() | BALL::Bond | |
Bond(const Bond &bond, bool deep=true) | BALL::Bond | |
Bond(const String &name, Atom &first, Atom &second, Order order=BALL_BOND_DEFAULT_ORDER, Type type=BALL_BOND_DEFAULT_TYPE) | BALL::Bond | |
bond_order_ | BALL::Bond | protected |
bond_type_ | BALL::Bond | protected |
BondOrder enum name | BALL::Bond | |
BondType enum name | BALL::Bond | |
BOTH enum value | BALL::Composite | |
ChildCompositeConstIterator typedef | BALL::Composite | |
ChildCompositeConstReverseIterator typedef | BALL::Composite | |
ChildCompositeIterator typedef | BALL::Composite | |
ChildCompositeReverseIterator typedef | BALL::Composite | |
clear() | BALL::Bond | virtual |
clearLastPtr() | BALL::AutoDeletable | inlinestatic |
clearProperty(Property property) | BALL::PropertyManager | |
clearProperty(const std::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 | 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 | |
countDescendants() const | BALL::Composite | |
countNamedProperties() const | BALL::PropertyManager | |
countProperties() const | BALL::PropertyManager | |
createBond(Bond &bond, Atom &first, Atom &second) | BALL::Bond | static |
DEFAULT_PROCESSOR | BALL::Composite | static |
DEFAULT_UNARY_PREDICATE | BALL::Composite | static |
deleteChildrenList_(std::list< Composite * > &composites) | BALL::Composite | |
deselect() | BALL::Composite | virtual |
destroy() | BALL::Bond | virtual |
BALL::Composite::destroy(bool virtual_destroy) | BALL::Composite | |
dump(std::ostream &s=std::cout, Size depth=0) const | BALL::Bond | 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 |
endAncestor() | BALL::Composite | inline |
endAncestor() const | BALL::Composite | inline |
endChildComposite() | BALL::Composite | inline |
endChildComposite() const | BALL::Composite | inline |
endComposite() | BALL::Composite | inline |
endComposite() const | BALL::Composite | inline |
endNamedProperty() | BALL::PropertyManager | |
finalize() | BALL::Bond | virtual |
first_ | BALL::Bond | protected |
BALL::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 | |
getAncestor(const T &) | BALL::Composite | |
getAncestor(const T &) const | BALL::Composite | |
getBitVector() | BALL::PropertyManager | |
getBitVector() const | BALL::PropertyManager | |
getBoundAtom(const Atom &atom) const | BALL::Bond | |
getBoundAtom(const Atom &atom) | BALL::Bond | |
getChild(Index index) | BALL::Composite | |
getChild(Index index) const | BALL::Composite | |
getDegree() const | BALL::Composite | |
getDepth() const | BALL::Composite | |
getFirstAtom() const | BALL::Bond | |
getFirstAtom() | BALL::Bond | |
getFirstChild() | BALL::Composite | |
getFirstChild() const | BALL::Composite | |
getHandle() const | BALL::Object | |
getHeight() const | BALL::Composite | |
getLastChild() | BALL::Composite | |
getLastChild() const | BALL::Composite | |
getLength() const | BALL::Bond | |
getLowestCommonAncestor(const Composite &composite) | BALL::Composite | |
getLowestCommonAncestor(const Composite &composite) const | BALL::Composite | |
getModificationTime() const | BALL::Composite | |
getName() const | BALL::Bond | |
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 |
getOrder() const | BALL::Bond | |
getParent() | BALL::Composite | |
getParent() const | BALL::Composite | |
getPartner(const Atom &atom) const | BALL::Bond | |
getPathLength(const Composite &composite) const | BALL::Composite | |
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 | |
getRoot() | BALL::Composite | |
getRoot() const | BALL::Composite | |
getSecondAtom() const | BALL::Bond | |
getSecondAtom() | BALL::Bond | |
getSelectionTime() const | BALL::Composite | |
getSibling(Index index) | BALL::Composite | |
getSibling(Index index) const | BALL::Composite | |
getType() const | BALL::Bond | |
getZEType() const | BALL::SmilesParser::SPBond | |
hasAncestor(const T &dummy) const | BALL::Composite | |
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 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 |
IS_AROMATIC enum value | BALL::Bond | |
isAncestorOf(const Composite &composite) const | BALL::Composite | |
isAromatic() const | BALL::Bond | |
isAtom() const | BALL::Composite | inlinevirtual |
isAutoDeletable() const | BALL::AutoDeletable | |
isBondOf(const Atom &atom) const | BALL::Bond | |
isBound() const | BALL::Bond | |
isChain() const | BALL::Composite | inlinevirtual |
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 | inlinevirtual |
isHomomorph(const Composite &composite) const | BALL::Composite | |
isInterBond() const | BALL::Bond | |
isInterBondOf(const AtomContainer &atom_container) const | BALL::Bond | |
isInterior() const | BALL::Composite | |
isIntraBond() const | BALL::Bond | |
isIntraBondOf(const AtomContainer &atom_container) const | BALL::Bond | |
isLastChild() const | BALL::Composite | |
isLastChildOf(const Composite &composite) const | BALL::Composite | |
isMolecule() const | BALL::Composite | inlinevirtual |
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 | inlinevirtual |
isRelatedWith(const Composite &composite) const | BALL::Composite | |
isResidue() const | BALL::Composite | inlinevirtual |
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::Bond | virtual |
KernelPredicateType typedef | BALL::Composite | |
MODIFICATION enum value | BALL::Composite | |
name_ | BALL::Bond | protected |
NUMBER_OF_BOND_ORDERS enum value | BALL::Bond | |
NUMBER_OF_BOND_TYPES enum value | BALL::Bond | |
NUMBER_OF_PROPERTIES enum value | BALL::Bond | |
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 Bond &bond) const | BALL::Bond | |
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 Bond &bond) | BALL::Bond | |
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 Bond &bond) const | BALL::Bond | |
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 | |
Order typedef | BALL::Bond | |
ORDER__ANY enum value | BALL::Bond | |
ORDER__AROMATIC enum value | BALL::Bond | |
ORDER__DOUBLE enum value | BALL::Bond | |
ORDER__QUADRUPLE enum value | BALL::Bond | |
ORDER__SINGLE enum value | BALL::Bond | |
ORDER__TRIPLE enum value | BALL::Bond | |
ORDER__UNKNOWN enum value | BALL::Bond | |
PersistentObject() | BALL::PersistentObject | inline |
persistentRead(PersistenceManager &pm) | BALL::Bond | virtual |
persistentWrite(PersistenceManager &pm, const char *name=0) const | BALL::Bond | virtual |
prependChild(Composite &composite) | BALL::Composite | |
Property enum name | BALL::Bond | |
PropertyManager() | BALL::PropertyManager | |
PropertyManager(const PropertyManager &property_manager) | BALL::PropertyManager | |
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 | |
rendChildComposite() | BALL::Composite | inline |
rendChildComposite() const | BALL::Composite | inline |
rendComposite() | BALL::Composite | inline |
rendComposite() const | BALL::Composite | inline |
replace(Composite &composite) | BALL::Composite | |
second_ | BALL::Bond | protected |
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 | |
BALL::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 | |
setFirstAtom(Atom *atom) | BALL::Bond | |
setName(const String &name) | BALL::Bond | |
setOrder(Order bond_order) | BALL::Bond | |
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 | |
setSecondAtom(Atom *atom) | BALL::Bond | |
setSelected(bool selected) | BALL::Selectable | inlinevirtual |
setType(Type bond_type) | BALL::Bond | |
setZEType(ZEIsomerType type) | BALL::SmilesParser::SPBond | |
SPBond(SPAtom *first, SPAtom *second, Index order=1) | BALL::SmilesParser::SPBond | |
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 | |
swap(Bond &bond) | BALL::Bond | |
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::Bond | |
TYPE__COVALENT enum value | BALL::Bond | |
TYPE__DISULPHIDE_BRIDGE enum value | BALL::Bond | |
TYPE__HYDROGEN enum value | BALL::Bond | |
TYPE__PEPTIDE enum value | BALL::Bond | |
TYPE__SALT_BRIDGE enum value | BALL::Bond | |
TYPE__UNKNOWN enum value | BALL::Bond | |
BALL::write(PersistenceManager &pm) const | BALL::Selectable | |
BALL::PropertyManager::write(PersistenceManager &pm) const | BALL::PropertyManager | |
ze_type_ | BALL::SmilesParser::SPBond | protected |
~AutoDeletable() | BALL::AutoDeletable | virtual |
~Bond() | BALL::Bond | virtual |
~Composite() | BALL::Composite | virtual |
~Object() | BALL::Object | virtual |
~PersistentObject() | BALL::PersistentObject | inlinevirtual |
~PropertyManager() | BALL::PropertyManager | virtual |
~Selectable() | BALL::Selectable | virtual |
~SPBond() | BALL::SmilesParser::SPBond | virtual |