PDBAtom Member List

This is the complete list of members for PDBAtom, including all inherited members.

ADD_CHAIN_RESIDUE_ID enum value (defined in Atom)	Atom
ADD_RESIDUE_ID enum value (defined in Atom)	Atom
ADD_VARIANT_EXTENSIONS enum value (defined in Atom)	Atom
ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID enum value (defined in Atom)	Atom
ADD_VARIANT_EXTENSIONS_AND_ID enum value (defined in Atom)	Atom
AncestorConstIterator typedef (defined in Composite)	Composite
AncestorIterator typedef (defined in Composite)	Composite
AncestorIteratorTraits (defined in Composite)	Composite	[friend]
ANY_TYPE enum value	Atom
appendChild(Composite &composite)	Composite
apply(UnaryProcessor< T > &processor)	Composite
applyAncestor(UnaryProcessor< T > &processor)	Composite
applyBonds(UnaryProcessor< Bond > &processor)	Atom
applyChild(UnaryProcessor< T > &processor)	Composite
applyDescendant(UnaryProcessor< T > &processor)	Composite
applyDescendantPostorder(UnaryProcessor< T > &processor)	Composite
applyDescendantPreorder(UnaryProcessor< T > &processor)	Composite
applyLevel(UnaryProcessor< T > &processor, long level)	Composite
applyPostorder(UnaryProcessor< T > &processor)	Composite
applyPreorder(UnaryProcessor< T > &processor)	Composite
Atom()	Atom
Atom(const Atom &atom, bool deep=true)	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)	Atom
AtomIndexList typedef (defined in Atom)	Atom
AtomPtrList typedef (defined in Atom)	Atom
attributes_changed_time_	Atom	[protected, static]
AutoDeletable() (defined in AutoDeletable)	AutoDeletable	[protected]
AutoDeletable(const AutoDeletable &auto_deletable, bool deep=false) (defined in AutoDeletable)	AutoDeletable	[protected]
beginAncestor() (defined in Composite)	Composite
beginAncestor() const (defined in Composite)	Composite
beginBond()	Atom
beginBond() const	Atom
beginChildComposite() (defined in Composite)	Composite
beginChildComposite() const (defined in Composite)	Composite
beginComposite() (defined in Composite)	Composite
beginComposite() const (defined in Composite)	Composite
Bond (defined in PDBAtom)	PDBAtom	[friend]
bond_ (defined in Atom)	Atom	[protected]
BondConstIterator typedef	Atom
BondConstReverseIterator typedef	Atom
BondIterator typedef	Atom
BondIteratorPosition typedef (defined in Atom)	Atom
BondIteratorTraits (defined in Atom)	Atom	[friend]
BondReverseIterator typedef	Atom
BOTH enum value (defined in Composite)	Composite
ChildCompositeConstIterator typedef (defined in Composite)	Composite
ChildCompositeConstReverseIterator typedef (defined in Composite)	Composite
ChildCompositeIterator typedef (defined in Composite)	Composite
ChildCompositeIteratorTraits (defined in Composite)	Composite	[friend]
ChildCompositeReverseIterator typedef (defined in Composite)	Composite
clear()	PDBAtom	[virtual]
clearLastPtr() (defined in AutoDeletable)	AutoDeletable	[static]
clearProperty(Property property)	PropertyManager
clearProperty(const string &name)	PropertyManager
clone(Composite &root) const	Composite
cloneBond(Bond &bond, Atom &atom)	Atom
compact(const AtomIndexList &indices)	Atom	[static]
compare(const Object &object) const	Object
Composite()	Composite
Composite(const Composite &composite, bool deep=true)	Composite
CompositeConstIterator typedef (defined in Composite)	Composite
CompositeConstReverseIterator typedef (defined in Composite)	Composite
CompositeIterator typedef (defined in Composite)	Composite
CompositeIteratorTraits (defined in Composite)	Composite	[friend]
CompositeReverseIterator typedef (defined in Composite)	Composite
containsSelection() const	Composite
count(const KernelPredicateType &predicate) const	Composite
countBonds() const	Atom
countDescendants() const	Composite
countNamedProperties() const	PropertyManager
countProperties() const	PropertyManager
createBond(Atom &atom)	Atom
createBond(Bond &bond, Atom &atom)	Atom
DEFAULT_PROCESSOR (defined in Composite)	Composite	[static]
DEFAULT_UNARY_PREDICATE (defined in Composite)	Composite	[static]
deselect()	Composite	[virtual]
destroy()	PDBAtom	[virtual]
Composite::destroy(bool virtual_destroy)	Composite
destroyBond(const Atom &atom)	Atom
destroyBonds()	Atom
dump(std::ostream &s=std::cout, Size depth=0) const	PDBAtom	[virtual]
dump(::std::ostream &s=std::cout, Size depth=0) const (defined in Object)	Object	[virtual]
dump(::std::ostream &s=std::cout, Size depth=0) const (defined in Selectable)	Selectable	[virtual]
element_ (defined in Atom)	Atom	[protected]
endAncestor() (defined in Composite)	Composite
endAncestor() const (defined in Composite)	Composite
endBond()	Atom
endBond() const	Atom
endChildComposite() (defined in Composite)	Composite
endChildComposite() const (defined in Composite)	Composite
endComposite() (defined in Composite)	Composite
endComposite() const (defined in Composite)	Composite
finalize()	PersistentObject	[virtual]
free_list_ (defined in Atom)	Atom	[protected, static]
FullNameType enum name	Atom
get(PDBAtom &pdb_atom, bool deep=true) const	PDBAtom
Atom::get(Atom &atom, bool deep=true) const	Atom
Composite::get(Composite &composite, bool deep=true) const	Composite
Selectable::get(Selectable &selectable, bool deep=true) const	Selectable
PropertyManager::get(PropertyManager &property_manager) const	PropertyManager
getAlternateLocationIndicator() const	PDBAtom
getAncestor(const T &)	Composite
getAncestor(const T &) const	Composite
getAttributePtr() (defined in Atom)	Atom
getAttributePtr() const (defined in Atom)	Atom
getAttributes()	Atom	[static]
getAttributesModificationTime()	Atom	[static]
getBitVector()	PropertyManager
getBitVector() const	PropertyManager
getBond(Position index)	Atom
getBond(Position index) const	Atom
getBond(const Atom &atom)	Atom
getBond(const Atom &atom) const	Atom
getBranchDesignator() const	PDBAtom
getChain()	PDBAtom
getChain() const	PDBAtom
getCharge() const	Atom
getChild(Index index)	Composite
getChild(Index index) const	Composite
getDegree() const	Composite
getDepth() const	Composite
getElement() const	Atom
getFirstChild()	Composite
getFirstChild() const	Composite
getForce() const	Atom
getForce()	Atom
getFormalCharge() const	Atom
getFragment() const	Atom
getFragment()	Atom
getFullName(FullNameType type=ADD_VARIANT_EXTENSIONS) const	Atom
getHandle() const	Object
getHeight() const	Composite
getIndex() const	Atom
getLastChild()	Composite
getLastChild() const	Composite
getLowestCommonAncestor(const Composite &composite)	Composite
getLowestCommonAncestor(const Composite &composite) const	Composite
getModificationTime() const	Composite
getMolecule() const	Atom
getMolecule()	Atom
getName() const	Atom
getNamedProperty(Position index) const	PropertyManager
getNamedProperty(Position index)	PropertyManager
getNewHandle()	Object	[static]
getNext(const T &)	Composite
getNext(const T &dummy) const	Composite
getNextHandle()	Object	[static]
getOccupancy() const	PDBAtom
getParent()	Composite
getParent() const	Composite
getPathLength(const Composite &composite) const	Composite
getPosition()	Atom
getPosition() const	Atom
getPrevious(const T &)	Composite
getPrevious(const T &dummy) const	Composite
getProperty(const string &name) const	PropertyManager
getProtein()	PDBAtom
getProtein() const	PDBAtom
getRadius() const	Atom
getRemotenessIndicator() const	PDBAtom
getResidue()	PDBAtom
getResidue() const	PDBAtom
getRoot()	Composite
getRoot() const	Composite
getSecondaryStructure() const	Atom
getSecondaryStructure()	Atom
getSelectionTime() const	Composite
getSibling(Index index)	Composite
getSibling(Index index) const	Composite
getTemperatureFactor() const	PDBAtom
getType() const	Atom
getTypeName() const	Atom
getVelocity() const	Atom
hasAncestor(const T &dummy) const	Composite
hasBond(const Bond &bond) const	Atom
hasChild() const	Composite
hasNextSibling() const	Composite
hasParent() const	Composite
hasPreviousSibling() const	Composite
hasProperty(Property property) const	PropertyManager
hasProperty(const string &name) const	PropertyManager
hasSibling() const	Composite
host(Visitor< Composite > &visitor)	Composite
index_ (defined in Atom)	Atom	[protected]
insertAfter(Composite &composite)	Composite
insertBefore(Composite &composite)	Composite
insertParent(Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)	Composite	[static]
isAncestorOf(const Composite &composite) const	Composite
isAutoDeletable() const	AutoDeletable
isBound() const	Atom
isBoundTo(const Atom &atom) const	Atom
isChildOf(const Composite &composite) const	Composite
isDescendantOf(const Composite &composite) const	Composite
isEmpty() const	Composite
isFirstChild() const	Composite
isFirstChildOf(const Composite &composite) const	Composite
isGeminal(const Atom &atom) const	Atom
isHomomorph(const Composite &composite) const	Composite
isInterior() const	Composite
isLastChild() const	Composite
isLastChildOf(const Composite &composite) const	Composite
isNextSiblingOf(const Composite &composite) const	Composite
isParentOf(const Composite &composite) const	Composite
isPreviousSiblingOf(const Composite &composite) const	Composite
isRelatedWith(const Composite &composite) const	Composite
isRoot() const	Composite
isRootOf(const Composite &composite) const	Composite
isSelected() const	Selectable
isSiblingOf(const Composite &composite) const	Composite
isValid() const	Atom	[virtual]
isVicinal(const Atom &atom) const	Atom
KernelPredicateType typedef	Composite
MAX_NUMBER_OF_BONDS enum value	Atom
MODIFICATION enum value (defined in Composite)	Composite
name_ (defined in Atom)	Atom	[protected]
NO_VARIANT_EXTENSIONS enum value (defined in Atom)	Atom
number_of_bonds_ (defined in Atom)	Atom	[protected]
NUMBER_OF_PROPERTIES enum value (defined in PDBAtom)	PDBAtom
NUMBER_OF_REMOTENESS_INDICATORS enum value (defined in PDBAtom)	PDBAtom
Object()	Object
Object(const Object &object)	Object
operator BitVector &()	PropertyManager
operator delete(void *ptr)	AutoDeletable
operator delete(void *ptr, void *)	AutoDeletable
operator new(size_t size)	AutoDeletable
operator new(size_t size, void *ptr)	AutoDeletable
operator!=(const PDBAtom &pdb_atom) const	PDBAtom
Atom::operator!=(const Atom &atom) const	Atom
Composite::operator!=(const Composite &composite) const	Composite
PersistentObject::operator!=(const Object &object) const	Object
Selectable::operator!=(const Selectable &selectable) const	Selectable
PropertyManager::operator!=(const PropertyManager &pm) const	PropertyManager
operator<(const Object &object) const	Object
operator<=(const Object &object) const	Object
operator=(const PDBAtom &pdb_atom)	PDBAtom
Atom::operator=(const Atom &atom)	Atom
Composite::operator=(const Composite &composite)	Composite
PersistentObject::operator=(const Object &)	Object
Selectable::operator=(const Selectable &selectable)	Selectable
PropertyManager::operator=(const PropertyManager &property_manager)	PropertyManager
operator==(const PDBAtom &pdb_atom) const	PDBAtom
Atom::operator==(const Atom &atom) const	Atom
Composite::operator==(const Composite &composite) const	Composite
PersistentObject::operator==(const Object &object) const	Object
Selectable::operator==(const Selectable &selectable) const	Selectable
PropertyManager::operator==(const PropertyManager &pm) const	PropertyManager
operator>(const Object &object) const	Object
operator>=(const Object &object) const	Object
operator>>(PersistenceManager &pm) const	PersistentObject
PDBAtom()	PDBAtom
PDBAtom(const PDBAtom &pdb_atom, bool deep=true)	PDBAtom
PDBAtom(const String &name)	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)	PDBAtom
PersistentObject()	PersistentObject
persistentRead(PersistenceManager &pm)	PDBAtom	[virtual]
persistentWrite(PersistenceManager &pm, const char *name=0) const	PDBAtom	[virtual]
prependChild(Composite &composite)	Composite
Property enum name	PDBAtom
PropertyManager()	PropertyManager
PropertyManager(const PropertyManager &property_manager)	PropertyManager
radius_ (defined in Atom)	Atom	[protected]
rbeginBond()	Atom
rbeginBond() const	Atom
rbeginChildComposite() (defined in Composite)	Composite
rbeginChildComposite() const (defined in Composite)	Composite
rbeginComposite() (defined in Composite)	Composite
rbeginComposite() const (defined in Composite)	Composite
read(PersistenceManager &pm)	Selectable
PropertyManager::read(PersistenceManager &pm)	PropertyManager
REMOTENESS_INDICATOR__ALPHA enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__alpha enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__BETA enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__beta enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__DELTA enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__delta enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__EPSILON enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__epsilon enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__ETA enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__eta enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__gamma enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__GAMMA enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__UNKNOWN enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__ZETA enum value (defined in PDBAtom)	PDBAtom
REMOTENESS_INDICATOR__zeta enum value (defined in PDBAtom)	PDBAtom
RemotenessIndicator enum name	PDBAtom
removeChild(Composite &child)	Composite
removeSelected()	Composite
rendBond()	Atom
rendBond() const	Atom
rendChildComposite() (defined in Composite)	Composite
rendChildComposite() const (defined in Composite)	Composite
rendComposite() (defined in Composite)	Composite
rendComposite() const (defined in Composite)	Composite
replace(Composite &composite)	Composite
select()	Composite	[virtual]
Selectable()	Selectable
Selectable(const Selectable &selectable, bool deep=true)	Selectable
selected_ (defined in Selectable)	Selectable	[protected]
SELECTION enum value (defined in Composite)	Composite
set(const PDBAtom &pdb_atom, bool deep=true)	PDBAtom
Atom::set(const Atom &atom, bool deep=true)	Atom
Composite::set(const Composite &composite, bool deep=true)	Composite
Selectable::set(const Selectable &selectable, bool deep=true)	Selectable
PropertyManager::set(const PropertyManager &property_manager)	PropertyManager
setAlternateLocationIndicator(char alternate_location_indicator)	PDBAtom
setAutoDeletable(bool enable)	AutoDeletable
setBranchDesignator(char branch_designator)	PDBAtom
setCharge(float charge)	Atom
setElement(const Element &element)	Atom
setForce(const Vector3 &force)	Atom
setFormalCharge(Index formal_charge)	Atom
setName(const String &name)	Atom
setOccupancy(float occupancy)	PDBAtom
setPosition(const Vector3 &position)	Atom
setProperty(Property property)	PropertyManager
setProperty(const NamedProperty &property)	PropertyManager
setProperty(const string &name)	PropertyManager
setProperty(const string &name, bool value)	PropertyManager
setProperty(const string &name, int value)	PropertyManager
setProperty(const string &name, unsigned int value)	PropertyManager
setProperty(const string &name, float value)	PropertyManager
setProperty(const string &name, double value)	PropertyManager
setProperty(const string &name, const string &value)	PropertyManager
setProperty(const string &name, const PersistentObject &value)	PropertyManager
setRadius(float radius)	Atom
setRemotenessIndicator(char remoteness_indicator)	PDBAtom
setSelected(bool selected)	Selectable	[virtual]
setTemperatureFactor(float temperature_factor)	PDBAtom
setType(Type atom_type)	Atom
setTypeName(const String &name)	Atom
setVelocity(const Vector3 &velocity)	Atom
splice(Composite &composite)	Composite
spliceAfter(Composite &composite)	Composite
spliceBefore(Composite &composite)	Composite
stamp(StampType stamp=BOTH)	Composite
StampType enum name	Composite
static_attributes_ (defined in Atom)	Atom	[protected, static]
swap(PDBAtom &pdb_atom)	PDBAtom
Atom::swap(Atom &atom)	Atom
Composite::swap(Composite &composite)	Composite
Selectable::swap(Selectable &selectable)	Selectable
PropertyManager::swap(PropertyManager &property_manager)	PropertyManager
toggleProperty(Property property)	PropertyManager
Type typedef	Atom
type_name_ (defined in Atom)	Atom	[protected]
UNKNOWN_TYPE enum value	Atom
write(PersistenceManager &pm) const	Selectable
PropertyManager::write(PersistenceManager &pm) const	PropertyManager
~Atom()	Atom	[virtual]
~AutoDeletable()	AutoDeletable	[virtual]
~Composite()	Composite	[virtual]
~Object()	Object	[virtual]
~PDBAtom()	PDBAtom	[virtual]
~PersistentObject()	PersistentObject	[virtual]
~PropertyManager()	PropertyManager	[virtual]
~Selectable()	Selectable	[virtual]