| ADD_CHAIN_RESIDUE_ID enum value (defined in
BALL::Atom) |
BALL::Atom |
|
| ADD_RESIDUE_ID enum value (defined in BALL::Atom) |
BALL::Atom |
|
| ADD_VARIANT_EXTENSIONS enum value (defined in
BALL::Atom) |
BALL::Atom |
|
| ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID enum
value (defined in BALL::Atom) |
BALL::Atom |
|
| ADD_VARIANT_EXTENSIONS_AND_ID enum value
(defined in BALL::Atom) |
BALL::Atom |
|
| AncestorConstIterator typedef (defined in
BALL::Composite) |
BALL::Composite |
|
| AncestorIterator typedef (defined in BALL::Composite) |
BALL::Composite |
|
| AncestorIteratorTraits (defined in BALL::Composite) |
BALL::Composite |
[friend] |
|
ANY_TYPE enum value |
BALL::Atom |
|
|
appendChild(Composite &composite) |
BALL::Composite |
|
|
apply(UnaryProcessor< T > &processor) |
BALL::Composite |
|
|
applyAncestor(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
| applyBonds(UnaryProcessor<
Bond > &processor) |
BALL::Atom |
|
|
applyChild(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyDescendant(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyDescendantPostorder(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyDescendantPreorder(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyLevel(UnaryProcessor< T > &processor,
long level) |
BALL::Composite |
|
|
applyPostorder(UnaryProcessor< T >
&processor) |
BALL::Composite |
|
|
applyPreorder(UnaryProcessor< T >
&processor) |
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 (defined in BALL::Atom) |
BALL::Atom |
|
| AtomPtrList typedef (defined in BALL::Atom) |
BALL::Atom |
|
| attributes_changed_time_ |
BALL::Atom |
[protected, static] |
| 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 |
|
| beginBond() |
BALL::Atom |
|
| beginBond()
const |
BALL::Atom |
|
| 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 |
|
| Bond (defined in BALL::Atom) |
BALL::Atom |
[friend] |
| bond_ (defined in BALL::Atom) |
BALL::Atom |
[protected] |
| BondConstIterator
typedef |
BALL::Atom |
|
| BondConstReverseIterator
typedef |
BALL::Atom |
|
| BondIterator
typedef |
BALL::Atom |
|
| BondIteratorPosition typedef (defined in
BALL::Atom) |
BALL::Atom |
|
| BondIteratorTraits (defined in BALL::Atom) |
BALL::Atom |
[friend] |
| BondReverseIterator
typedef |
BALL::Atom |
|
| 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::Atom |
[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 |
|
| 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 (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 |
|
| 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 (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::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] |
| 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] |
| element_ (defined in BALL::Atom) |
BALL::Atom |
[protected] |
| endAncestor() (defined in BALL::Composite) |
BALL::Composite |
|
| endAncestor() const (defined in BALL::Composite) |
BALL::Composite |
|
| endBond() |
BALL::Atom |
|
| endBond()
const |
BALL::Atom |
|
| 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] |
| free_list_ (defined in BALL::Atom) |
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 |
|
|
getAncestor(const T &) const |
BALL::Composite |
|
| getAttributePtr() (defined in BALL::Atom) |
BALL::Atom |
|
| getAttributePtr() const (defined in BALL::Atom) |
BALL::Atom |
|
| getAttributes() |
BALL::Atom |
[static] |
| getAttributesModificationTime() |
BALL::Atom |
[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 |
|
|
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 |
|
| getIndex()
const |
BALL::Atom |
|
|
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 |
|
|
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 |
|
|
getPrevious(const T &dummy) const |
BALL::Composite |
|
|
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 |
|
| 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 |
|
| index_ (defined in BALL::Atom) |
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] |
|
isAncestorOf(const Composite &composite) const |
BALL::Composite |
|
|
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 |
|
|
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 |
|
| 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 (defined in BALL::Composite) |
BALL::Composite |
|
| name_ (defined in BALL::Atom) |
BALL::Atom |
[protected] |
| NO_VARIANT_EXTENSIONS enum value (defined in
BALL::Atom) |
BALL::Atom |
|
| number_of_bonds_ (defined in BALL::Atom) |
BALL::Atom |
[protected] |
| NUMBER_OF_PROPERTIES enum value (defined in
BALL::Atom) |
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 |
|
| 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_ (defined in BALL::Atom) |
BALL::Atom |
[protected] |
| rbeginBond() |
BALL::Atom |
|
| rbeginBond()
const |
BALL::Atom |
|
| 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 |
|
|
removeChild(Composite &child) |
BALL::Composite |
|
|
removeSelected() |
BALL::Composite |
|
|
removeUnselected() |
BALL::Composite |
|
| rendBond() |
BALL::Atom |
|
| rendBond()
const |
BALL::Atom |
|
| 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 |
|
|
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
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 |
|
|
setAutoDeletable(bool enable) |
BALL::AutoDeletable |
|
| 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 |
|
| 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 |
[virtual] |
| 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 |
|
| static_attributes_ (defined in BALL::Atom) |
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_ (defined in BALL::Atom) |
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 |
[virtual] |
|
~PropertyManager() |
BALL::PropertyManager |
[virtual] |
|
~Selectable() |
BALL::Selectable |
[virtual] |
