| AncestorConstIterator typedef (defined in
BALL::Composite) |
BALL::Composite |
|
| AncestorIterator typedef (defined in BALL::Composite) |
BALL::Composite |
|
| AncestorIteratorTraits (defined in BALL::Composite) |
BALL::Composite |
[friend] |
|
append(Residue &residue) |
BALL::SecondaryStructure |
|
|
appendChild(Composite &composite) |
BALL::Composite |
|
|
apply(UnaryProcessor< T > &processor) |
BALL::Composite |
|
|
applyAncestor(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyChild(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyDescendant(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyDescendantPostorder(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyDescendantPreorder(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyInterBond(UnaryProcessor< Bond >
&processor) |
BALL::AtomContainer |
|
|
applyIntraBond(UnaryProcessor< Bond >
&processor) |
BALL::AtomContainer |
|
|
applyLevel(UnaryProcessor< T > &processor,
long level) |
BALL::Composite |
|
|
applyPostorder(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyPreorder(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
AtomContainer() |
BALL::AtomContainer |
|
|
AtomContainer(const AtomContainer &atom_container,
bool deep=true) |
BALL::AtomContainer |
|
|
AtomContainer(const String &name) |
BALL::AtomContainer |
|
| AutoDeletable() (defined in BALL::AutoDeletable) |
BALL::AutoDeletable |
[protected] |
| AutoDeletable(const AutoDeletable
&auto_deletable, bool deep=false) (defined in BALL::AutoDeletable) |
BALL::AutoDeletable |
[protected] |
| beginAncestor() (defined in BALL::Composite) |
BALL::Composite |
|
| beginAncestor() const (defined in BALL::Composite) |
BALL::Composite |
|
| beginChildComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| beginChildComposite() const (defined in
BALL::Composite) |
BALL::Composite |
|
| beginComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| beginComposite() const (defined in BALL::Composite) |
BALL::Composite |
|
| BOTH enum value (defined in BALL::Composite) |
BALL::Composite |
|
| ChildCompositeConstIterator typedef (defined in
BALL::Composite) |
BALL::Composite |
|
| ChildCompositeConstReverseIterator typedef
(defined in BALL::Composite) |
BALL::Composite |
|
| ChildCompositeIterator typedef (defined in
BALL::Composite) |
BALL::Composite |
|
| ChildCompositeIteratorTraits (defined in
BALL::Composite) |
BALL::Composite |
[friend] |
| ChildCompositeReverseIterator typedef (defined
in BALL::Composite) |
BALL::Composite |
|
|
clear() |
BALL::SecondaryStructure |
[virtual] |
| clearLastPtr() (defined in BALL::AutoDeletable) |
BALL::AutoDeletable |
[static] |
|
clearProperty(Property property) |
BALL::PropertyManager |
|
|
clearProperty(const string &name) |
BALL::PropertyManager |
|
|
clone(Composite &root) const |
BALL::Composite |
|
| COIL enum value (defined in BALL::SecondaryStructure) |
BALL::SecondaryStructure |
|
|
compare(const Object &object) const |
BALL::Object |
|
|
Composite() |
BALL::Composite |
|
|
Composite(const Composite &composite, bool
deep=true) |
BALL::Composite |
|
| CompositeConstIterator typedef (defined in
BALL::Composite) |
BALL::Composite |
|
| CompositeConstReverseIterator typedef (defined
in BALL::Composite) |
BALL::Composite |
|
| CompositeIterator typedef (defined in BALL::Composite) |
BALL::Composite |
|
| CompositeIteratorTraits (defined in BALL::Composite) |
BALL::Composite |
[friend] |
| CompositeReverseIterator typedef (defined in
BALL::Composite) |
BALL::Composite |
|
|
containsSelection() const |
BALL::Composite |
|
|
count(const KernelPredicateType &predicate)
const |
BALL::Composite |
|
|
countAtomContainers() const |
BALL::AtomContainer |
|
|
countAtoms() const |
BALL::AtomContainer |
|
|
countBonds() const |
BALL::AtomContainer |
|
|
countDescendants() const |
BALL::Composite |
|
|
countInterBonds() const |
BALL::AtomContainer |
|
|
countIntraBonds() const |
BALL::AtomContainer |
|
|
countNamedProperties() const |
BALL::PropertyManager |
|
|
countPDBAtoms() const |
BALL::SecondaryStructure |
|
|
countProperties() const |
BALL::PropertyManager |
|
|
countResidues() const |
BALL::SecondaryStructure |
|
| DEFAULT_PROCESSOR (defined in BALL::Composite) |
BALL::Composite |
[static] |
| DEFAULT_UNARY_PREDICATE (defined in BALL::Composite) |
BALL::Composite |
[static] |
| deleteChildrenList_(std::list< Composite *
> &composites) (defined in BALL::Composite) |
BALL::Composite |
|
|
deselect() |
BALL::Composite |
[virtual] |
|
destroy() |
BALL::SecondaryStructure |
[virtual] |
|
BALL::Composite::destroy(bool virtual_destroy) |
BALL::Composite |
|
|
destroyBonds() |
BALL::AtomContainer |
|
|
dump(std::ostream &s=std::cout, Size depth=0)
const |
BALL::SecondaryStructure |
[virtual] |
| dump(::std::ostream &s=std::cout, Size
depth=0) const (defined in BALL::Object) |
BALL::Object |
[virtual] |
| dump(::std::ostream &s=std::cout, Size
depth=0) const (defined in BALL::Selectable) |
BALL::Selectable |
[virtual] |
| endAncestor() (defined in BALL::Composite) |
BALL::Composite |
|
| endAncestor() const (defined in BALL::Composite) |
BALL::Composite |
|
| endChildComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| endChildComposite() const (defined in BALL::Composite) |
BALL::Composite |
|
| endComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| endComposite() const (defined in BALL::Composite) |
BALL::Composite |
|
|
finalize() |
BALL::PersistentObject |
[virtual] |
|
get(SecondaryStructure &secondary_structure, bool
deep=true) const |
BALL::SecondaryStructure |
|
|
BALL::AtomContainer::get(AtomContainer
&atom_container, bool deep=true) const |
BALL::AtomContainer |
|
|
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 |
|
|
getAncestor(const T &) const |
BALL::Composite |
|
|
BALL::AtomContainer::getAtom(const String
&name) |
BALL::AtomContainer |
|
|
BALL::AtomContainer::getAtom(const String &name)
const |
BALL::AtomContainer |
|
|
getAtomContainer(Position position) |
BALL::AtomContainer |
|
|
getAtomContainer(Position position) const |
BALL::AtomContainer |
|
|
getBitVector() |
BALL::PropertyManager |
|
|
getBitVector() const |
BALL::PropertyManager |
|
|
getChain() |
BALL::SecondaryStructure |
|
|
getChain() const |
BALL::SecondaryStructure |
|
|
getChild(Index index) |
BALL::Composite |
|
|
getChild(Index index) const |
BALL::Composite |
|
|
getCTerminal() |
BALL::SecondaryStructure |
|
|
getCTerminal() const |
BALL::SecondaryStructure |
|
|
getDegree() const |
BALL::Composite |
|
|
getDepth() const |
BALL::Composite |
|
|
getFirstChild() |
BALL::Composite |
|
|
getFirstChild() const |
BALL::Composite |
|
|
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 |
|
|
getName() const |
BALL::AtomContainer |
|
|
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 |
|
|
getNextHandle() |
BALL::Object |
[static] |
|
getNTerminal() |
BALL::SecondaryStructure |
|
|
getNTerminal() const |
BALL::SecondaryStructure |
|
|
getParent() |
BALL::Composite |
|
|
getParent() const |
BALL::Composite |
|
|
getPathLength(const Composite &composite)
const |
BALL::Composite |
|
|
getPDBAtom(Position position) |
BALL::SecondaryStructure |
|
|
getPDBAtom(Position position) const |
BALL::SecondaryStructure |
|
|
getPrevious(const T &) |
BALL::Composite |
|
|
getPrevious(const T &dummy) const |
BALL::Composite |
|
|
getProperty(const string &name) const |
BALL::PropertyManager |
|
|
getProtein() |
BALL::SecondaryStructure |
|
|
getProtein() const |
BALL::SecondaryStructure |
|
|
getResidue(Position position) |
BALL::SecondaryStructure |
|
|
getResidue(Position position) const |
BALL::SecondaryStructure |
|
|
getRoot() |
BALL::Composite |
|
|
getRoot() const |
BALL::Composite |
|
|
getSelectionTime() const |
BALL::Composite |
|
|
getSibling(Index index) |
BALL::Composite |
|
|
getSibling(Index index) const |
BALL::Composite |
|
|
getSuperAtomContainer() |
BALL::AtomContainer |
|
|
getSuperAtomContainer() const |
BALL::AtomContainer |
|
|
getType() const |
BALL::SecondaryStructure |
|
|
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 string &name) const |
BALL::PropertyManager |
|
|
hasSibling() const |
BALL::Composite |
|
| HELIX enum value (defined in BALL::SecondaryStructure) |
BALL::SecondaryStructure |
|
|
host(Visitor< Composite > &visitor) |
BALL::Composite |
|
|
insert(Residue &residue) |
BALL::SecondaryStructure |
|
|
insertAfter(Residue &residue, Composite
&after) |
BALL::SecondaryStructure |
|
|
BALL::Composite::insertAfter(Composite
&composite) |
BALL::Composite |
|
|
insertBefore(Residue &residue, Composite
&before) |
BALL::SecondaryStructure |
|
|
BALL::Composite::insertBefore(Composite
&composite) |
BALL::Composite |
|
|
insertParent(Composite &parent, Composite
&first, Composite &last, bool
destroy_parent=true) |
BALL::Composite |
[static] |
|
isAncestorOf(const Composite &composite) const |
BALL::Composite |
|
|
isAutoDeletable() const |
BALL::AutoDeletable |
|
|
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 |
|
|
isHomomorph(const Composite &composite) const |
BALL::Composite |
|
|
isInterior() const |
BALL::Composite |
|
|
isLastChild() const |
BALL::Composite |
|
|
isLastChildOf(const Composite &composite)
const |
BALL::Composite |
|
|
isNextSiblingOf(const Composite &composite)
const |
BALL::Composite |
|
|
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 |
|
|
isSubAtomContainerOf(const AtomContainer
&atom_container) const |
BALL::AtomContainer |
|
|
isSuperAtomContainerOf(const AtomContainer
&atom_container) const |
BALL::AtomContainer |
|
|
isValid() const |
BALL::SecondaryStructure |
[virtual] |
|
KernelPredicateType typedef |
BALL::Composite |
|
| MODIFICATION enum value (defined in BALL::Composite) |
BALL::Composite |
|
| NUMBER_OF_PROPERTIES enum value (defined in
BALL::AtomContainer) |
BALL::AtomContainer |
|
| NUMBER_OF_TYPES enum value (defined in BALL::SecondaryStructure) |
BALL::SecondaryStructure |
|
|
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 SecondaryStructure
&secondary_structure) const |
BALL::SecondaryStructure |
|
|
BALL::AtomContainer::operator!=(const AtomContainer
&atom_container) const |
BALL::AtomContainer |
|
|
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 SecondaryStructure
&secondary_structure) |
BALL::SecondaryStructure |
|
|
BALL::AtomContainer::operator=(const AtomContainer
&atom_container) |
BALL::AtomContainer |
|
|
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 SecondaryStructure
&secondary_structure) const |
BALL::SecondaryStructure |
|
|
BALL::AtomContainer::operator==(const AtomContainer
&atom_container) const |
BALL::AtomContainer |
|
|
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 |
|
|
persistentRead(PersistenceManager &pm) |
BALL::SecondaryStructure |
[virtual] |
|
persistentWrite(PersistenceManager &pm, const char
*name=0) const |
BALL::SecondaryStructure |
[virtual] |
|
prepend(Residue &residue) |
BALL::SecondaryStructure |
|
|
prependChild(Composite &composite) |
BALL::Composite |
|
|
Property enum name |
BALL::AtomContainer |
|
|
PropertyManager() |
BALL::PropertyManager |
|
|
PropertyManager(const PropertyManager
&property_manager) |
BALL::PropertyManager |
|
| rbeginChildComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| rbeginChildComposite() const (defined in
BALL::Composite) |
BALL::Composite |
|
| rbeginComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| rbeginComposite() const (defined in BALL::Composite) |
BALL::Composite |
|
|
BALL::read(PersistenceManager &pm) |
BALL::Selectable |
|
|
BALL::PropertyManager::read(PersistenceManager
&pm) |
BALL::PropertyManager |
|
|
remove(Residue &residue) |
BALL::SecondaryStructure |
|
|
removeChild(Composite &child) |
BALL::Composite |
|
| removeHavingProperty(BALL::Property p) (defined
in BALL::AtomContainer) |
BALL::AtomContainer |
|
| removeHavingProperty(const string &name)
(defined in BALL::AtomContainer) |
BALL::AtomContainer |
|
| removeNotHavingProperty(BALL::Property p)
(defined in BALL::AtomContainer) |
BALL::AtomContainer |
|
| removeNotHavingProperty(const string &name)
(defined in BALL::AtomContainer) |
BALL::AtomContainer |
|
|
removeSelected() |
BALL::Composite |
|
|
removeUnselected() |
BALL::Composite |
|
| rendChildComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| rendChildComposite() const (defined in BALL::Composite) |
BALL::Composite |
|
| rendComposite() (defined in BALL::Composite) |
BALL::Composite |
|
| rendComposite() const (defined in BALL::Composite) |
BALL::Composite |
|
|
replace(Composite &composite) |
BALL::Composite |
|
|
SecondaryStructure() |
BALL::SecondaryStructure |
|
|
SecondaryStructure(const SecondaryStructure
&secondary_structure, bool deep=true) |
BALL::SecondaryStructure |
|
| SecondaryStructure(const String &name)
(defined in BALL::SecondaryStructure) |
BALL::SecondaryStructure |
|
|
select() |
BALL::Composite |
[virtual] |
|
Selectable() |
BALL::Selectable |
|
|
Selectable(const Selectable &selectable, bool
deep=true) |
BALL::Selectable |
|
| selected_ (defined in BALL::Selectable) |
BALL::Selectable |
[protected] |
| SELECTION enum value (defined in BALL::Composite) |
BALL::Composite |
|
|
set(const SecondaryStructure &secondary_structure,
bool deep=true) |
BALL::SecondaryStructure |
|
|
BALL::AtomContainer::set(const AtomContainer
&atom_container, bool deep=true) |
BALL::AtomContainer |
|
|
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 |
|
|
setAutoDeletable(bool enable) |
BALL::AutoDeletable |
|
|
setName(const String &name) |
BALL::AtomContainer |
|
|
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 |
|
|
setSelected(bool selected) |
BALL::Selectable |
[virtual] |
|
setType(Type type) |
BALL::SecondaryStructure |
|
|
splice(SecondaryStructure
&secondary_structure) |
BALL::SecondaryStructure |
|
|
BALL::Composite::splice(Composite &composite) |
BALL::Composite |
|
|
spliceAfter(SecondaryStructure
&secondary_structure) |
BALL::SecondaryStructure |
|
|
BALL::Composite::spliceAfter(Composite
&composite) |
BALL::Composite |
|
|
spliceBefore(SecondaryStructure
&secondary_structure) |
BALL::SecondaryStructure |
|
|
BALL::Composite::spliceBefore(Composite
&composite) |
BALL::Composite |
|
|
stamp(StampType stamp=BOTH) |
BALL::Composite |
|
|
StampType enum name |
BALL::Composite |
|
| STRAND enum value (defined in BALL::SecondaryStructure) |
BALL::SecondaryStructure |
|
|
swap(SecondaryStructure &secondary_structure) |
BALL::SecondaryStructure |
|
|
BALL::AtomContainer::swap(AtomContainer
&atom_container) |
BALL::AtomContainer |
|
|
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 |
|
| TURN enum value (defined in BALL::SecondaryStructure) |
BALL::SecondaryStructure |
|
|
Type enum name |
BALL::SecondaryStructure |
|
|
type_ |
BALL::SecondaryStructure |
[protected] |
| UNKNOWN enum value (defined in BALL::SecondaryStructure) |
BALL::SecondaryStructure |
|
|
BALL::write(PersistenceManager &pm) const |
BALL::Selectable |
|
|
BALL::PropertyManager::write(PersistenceManager
&pm) const |
BALL::PropertyManager |
|
|
~AtomContainer() |
BALL::AtomContainer |
[virtual] |
|
~AutoDeletable() |
BALL::AutoDeletable |
[virtual] |
|
~Composite() |
BALL::Composite |
[virtual] |
|
~Object() |
BALL::Object |
[virtual] |
|
~PersistentObject() |
BALL::PersistentObject |
[virtual] |
|
~PropertyManager() |
BALL::PropertyManager |
[virtual] |
|
~SecondaryStructure() |
BALL::SecondaryStructure |
[virtual] |
|
~Selectable() |
BALL::Selectable |
[virtual] |
