BALL::PDBAtom Member List

This is the complete list of members for BALL::PDBAtom, including all inherited members.
ADD_CHAIN_RESIDUE_ID enum valueBALL::Atom
ADD_RESIDUE_ID enum valueBALL::Atom
ADD_VARIANT_EXTENSIONS enum valueBALL::Atom
ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID enum valueBALL::Atom
ADD_VARIANT_EXTENSIONS_AND_ID enum valueBALL::Atom
alternate_location_indicator_BALL::PDBAtom [private]
AncestorConstIterator typedefBALL::Composite
AncestorIterator typedefBALL::Composite
AncestorIteratorTraits classBALL::Composite [friend]
ANY_TYPE enum valueBALL::Atom
appendChild(Composite &composite)BALL::Composite
apply(UnaryProcessor< T > &processor)BALL::Composite [inline]
applyAncestor(UnaryProcessor< T > &processor)BALL::Composite [inline]
applyBonds(UnaryProcessor< Bond > &processor)BALL::Atom
applyChild(UnaryProcessor< T > &processor)BALL::Composite [inline]
applyDescendant(UnaryProcessor< T > &processor)BALL::Composite [inline]
applyDescendantPostorder(UnaryProcessor< T > &processor)BALL::Composite [inline]
applyDescendantPreorder(UnaryProcessor< T > &processor)BALL::Composite [inline]
applyLevel(UnaryProcessor< T > &processor, long level)BALL::Composite [inline]
applyPostorder(UnaryProcessor< T > &processor)BALL::Composite [inline]
applyPreorder(UnaryProcessor< T > &processor)BALL::Composite [inline]
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 typedefBALL::Atom
AtomPtrList typedefBALL::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 classBALL::PDBAtom [friend]
bond_BALL::Atom [protected]
BondConstIterator typedefBALL::Atom
BondConstReverseIterator typedefBALL::Atom
BondIterator typedefBALL::Atom
BondIteratorPosition typedefBALL::Atom
BondIteratorTraits classBALL::Atom [friend]
BondReverseIterator typedefBALL::Atom
BOTH enum valueBALL::Composite
branch_designator_BALL::PDBAtom [private]
charge_BALL::Atom [protected]
ChildCompositeConstIterator typedefBALL::Composite
ChildCompositeConstReverseIterator typedefBALL::Composite
ChildCompositeIterator typedefBALL::Composite
ChildCompositeIteratorTraits classBALL::Composite [friend]
ChildCompositeReverseIterator typedefBALL::Composite
clear()BALL::PDBAtom [virtual]
clear_()BALL::PDBAtom [private]
clearLastPtr()BALL::AutoDeletable [inline, 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
compare(const Object &object) const BALL::Object
Composite()BALL::Composite
Composite(const Composite &composite, bool deep=true)BALL::Composite
CompositeConstIterator typedefBALL::Composite
CompositeConstReverseIterator typedefBALL::Composite
CompositeIterator typedefBALL::Composite
CompositeIteratorTraits classBALL::Composite [friend]
CompositeReverseIterator typedefBALL::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_PROCESSORBALL::Composite [static]
DEFAULT_UNARY_PREDICATEBALL::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
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]
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 nameBALL::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 [inline]
getAncestor(const T &) const BALL::Composite [inline]
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 [inline]
getNext(const T &dummy) const BALL::Composite [inline]
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 [inline]
getPrevious(const T &dummy) const BALL::Composite [inline]
getProperty(const 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 [inline]
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
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 typedefBALL::Composite
MAX_NUMBER_OF_BONDS enum valueBALL::Atom
MODIFICATION enum valueBALL::Composite
name_BALL::Atom [protected]
NO_VARIANT_EXTENSIONS enum valueBALL::Atom
number_of_bonds_BALL::Atom [protected]
NUMBER_OF_PROPERTIES enum valueBALL::PDBAtom
NUMBER_OF_REMOTENESS_INDICATORS enum valueBALL::PDBAtom
Object()BALL::Object
Object(const Object &object)BALL::Object
occupancy_BALL::PDBAtom [private]
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 nameBALL::PDBAtom
PROPERTY__HETATM enum valueBALL::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_BALL::PDBAtom [private]
REMOTENESS_INDICATOR__ALPHA enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__alpha enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__BETA enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__beta enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__delta enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__DELTA enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__epsilon enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__EPSILON enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__eta enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__ETA enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__gamma enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__GAMMA enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__UNKNOWN enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__zeta enum valueBALL::PDBAtom
REMOTENESS_INDICATOR__ZETA enum valueBALL::PDBAtom
RemotenessIndicator enum nameBALL::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 valueBALL::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 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
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 nameBALL::Composite
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
temperature_factor_BALL::PDBAtom [private]
toggleProperty(Property property)BALL::PropertyManager
Type typedefBALL::Atom
type_BALL::Atom [protected]
type_name_BALL::Atom [protected]
UNKNOWN_TYPE enum valueBALL::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]
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