BALL  1.5.0
BALL::Atom Member List

This is the complete list of members for BALL::Atom, 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
addInteraction(const Atom *atom, String interaction_type, double energy)BALL::Atom
addInteraction(String interaction_type, double energy)BALL::Atom
AncestorConstIterator typedefBALL::Composite
AncestorIterator typedefBALL::Composite
ANY_TYPE enum valueBALL::Atom
appendChild(Composite &composite)BALL::Composite
apply(UnaryProcessor< T > &processor)BALL::Composite
apply(ConstUnaryProcessor< T > &processor) constBALL::Composite
apply(UnaryProcessor< T > &processor)BALL::Composite
apply(ConstUnaryProcessor< T > &processor) constBALL::Composite
applyAncestor(UnaryProcessor< T > &processor)BALL::Composite
applyAncestor(ConstUnaryProcessor< T > &processor) constBALL::Composite
applyBonds(UnaryProcessor< Bond > &processor)BALL::Atom
applyChild(UnaryProcessor< T > &processor)BALL::Composite
applyChild(ConstUnaryProcessor< T > &processor) constBALL::Composite
applyDescendant(UnaryProcessor< T > &processor)BALL::Composite
applyDescendant(ConstUnaryProcessor< T > &processor) constBALL::Composite
applyDescendantPostorder(UnaryProcessor< T > &processor)BALL::Composite
applyDescendantPostorder(ConstUnaryProcessor< T > &processor) constBALL::Composite
applyDescendantPreorder(UnaryProcessor< T > &processor)BALL::Composite
applyDescendantPreorder(ConstUnaryProcessor< T > &processor) constBALL::Composite
applyLevel(UnaryProcessor< T > &processor, long level)BALL::Composite
applyLevel(ConstUnaryProcessor< T > &processor, long level) constBALL::Composite
applyPostorder(UnaryProcessor< T > &processor)BALL::Composite
applyPostorder(ConstUnaryProcessor< T > &processor) constBALL::Composite
applyPreorder(UnaryProcessor< T > &processor)BALL::Composite
applyPreorder(ConstUnaryProcessor< T > &processor) constBALL::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 typedefBALL::Atom
AtomPtrList typedefBALL::Atom
AutoDeletable()BALL::AutoDeletableprotected
AutoDeletable(const AutoDeletable &auto_deletable, bool deep=false)BALL::AutoDeletableprotected
beginAncestor()BALL::Compositeinline
beginAncestor() constBALL::Compositeinline
beginBond()BALL::Atominline
beginBond() constBALL::Atominline
beginChildComposite()BALL::Compositeinline
beginChildComposite() constBALL::Compositeinline
beginComposite()BALL::Compositeinline
beginComposite() constBALL::Compositeinline
beginNamedProperty()BALL::PropertyManager
Bond classBALL::Atomfriend
bond_BALL::Atomprotected
BondConstIterator typedefBALL::Atom
BondConstReverseIterator typedefBALL::Atom
BondIterator typedefBALL::Atom
BondIteratorPosition typedefBALL::Atom
BondIteratorTraits classBALL::Atomfriend
BondReverseIterator typedefBALL::Atom
BOTH enum valueBALL::Composite
charge_BALL::Atomprotected
ChildCompositeConstIterator typedefBALL::Composite
ChildCompositeConstReverseIterator typedefBALL::Composite
ChildCompositeIterator typedefBALL::Composite
ChildCompositeReverseIterator typedefBALL::Composite
clear()BALL::Atomvirtual
clearLastPtr()BALL::AutoDeletableinlinestatic
clearProperty(Property property)BALL::PropertyManager
clearProperty(const std::string &name)BALL::PropertyManager
clone(Composite &root) constBALL::Composite
cloneBond(Bond &bond, Atom &atom)BALL::Atom
compare(const Object &object) constBALL::Object
Composite()BALL::Composite
Composite(const Composite &composite, bool deep=true)BALL::Composite
CompositeConstIterator typedefBALL::Composite
CompositeConstReverseIterator typedefBALL::Composite
CompositeIterator typedefBALL::Composite
CompositeReverseIterator typedefBALL::Composite
containsSelection() constBALL::Composite
count(const KernelPredicateType &predicate) constBALL::Composite
countBonds() constBALL::Atom
countDescendants() constBALL::Composite
countNamedProperties() constBALL::PropertyManager
countProperties() constBALL::PropertyManager
createBond(Atom &atom)BALL::Atom
createBond(Bond &bond, Atom &atom)BALL::Atom
DEFAULT_PROCESSORBALL::Compositestatic
DEFAULT_UNARY_PREDICATEBALL::Compositestatic
deleteChildrenList_(std::list< Composite *> &composites)BALL::Composite
deselect()BALL::Compositevirtual
destroy()BALL::Atomvirtual
BALL::Composite::destroy(bool virtual_destroy)BALL::Composite
destroyBond(const Atom &atom)BALL::Atom
destroyBonds()BALL::Atom
disableStoreInteractions()BALL::Atom
dump(std::ostream &s=std::cout, Size depth=0) constBALL::Atomvirtual
BALL::PersistentObject::dump(::std::ostream &s=std::cout, Size depth=0) constBALL::Objectvirtual
BALL::Selectable::dump(::std::ostream &s=std::cout, Size depth=0) constBALL::Selectablevirtual
element_BALL::Atomprotected
enableStoreInteractions()BALL::Atom
endAncestor()BALL::Compositeinline
endAncestor() constBALL::Compositeinline
endBond()BALL::Atominline
endBond() constBALL::Atominline
endChildComposite()BALL::Compositeinline
endChildComposite() constBALL::Compositeinline
endComposite()BALL::Compositeinline
endComposite() constBALL::Compositeinline
endNamedProperty()BALL::PropertyManager
finalize()BALL::PersistentObjectinlinevirtual
force_BALL::Atomprotected
formal_charge_BALL::Atomprotected
free_list_BALL::Atomprotectedstatic
FullNameType enum nameBALL::Atom
get(Atom &atom, bool deep=true) constBALL::Atom
BALL::Composite::get(Composite &composite, bool deep=true) constBALL::Composite
BALL::Selectable::get(Selectable &selectable, bool deep=true) constBALL::Selectable
BALL::PropertyManager::get(PropertyManager &property_manager) constBALL::PropertyManager
getAncestor(const T &)BALL::Composite
getAncestor(const T &) constBALL::Composite
getAncestor(const T &)BALL::Composite
getAncestor(const T &) constBALL::Composite
getBitVector()BALL::PropertyManager
getBitVector() constBALL::PropertyManager
getBond(Position index)BALL::Atom
getBond(Position index) constBALL::Atom
getBond(const Atom &atom)BALL::Atom
getBond(const Atom &atom) constBALL::Atom
getChain() constBALL::Atom
getChain()BALL::Atom
getCharge() constBALL::Atom
getChild(Index index)BALL::Composite
getChild(Index index) constBALL::Composite
getDegree() constBALL::Composite
getDepth() constBALL::Composite
getDistance(const Atom &a) constBALL::Atom
getElement() constBALL::Atom
getFirstChild()BALL::Composite
getFirstChild() constBALL::Composite
getForce() constBALL::Atom
getForce()BALL::Atom
getFormalCharge() constBALL::Atom
getFragment() constBALL::Atom
getFragment()BALL::Atom
getFullName(FullNameType type=ADD_VARIANT_EXTENSIONS) constBALL::Atom
getHandle() constBALL::Object
getHeight() constBALL::Composite
getLastChild()BALL::Composite
getLastChild() constBALL::Composite
getLowestCommonAncestor(const Composite &composite)BALL::Composite
getLowestCommonAncestor(const Composite &composite) constBALL::Composite
getModificationTime() constBALL::Composite
getMolecule() constBALL::Atom
getMolecule()BALL::Atom
getName() constBALL::Atom
getNamedProperty(Position index) constBALL::PropertyManager
getNamedProperty(Position index)BALL::PropertyManager
getNewHandle()BALL::Objectstatic
getNext(const T &)BALL::Composite
getNext(const T &dummy) constBALL::Composite
getNext(const T &)BALL::Composite
getNext(const T &dummy) constBALL::Composite
getNextHandle()BALL::Objectstatic
getParent()BALL::Composite
getParent() constBALL::Composite
getPartnerAtom(Position i)BALL::Atom
getPartnerAtom(Position i) constBALL::Atom
getPathLength(const Composite &composite) constBALL::Composite
getPosition()BALL::Atom
getPosition() constBALL::Atom
getPrevious(const T &)BALL::Composite
getPrevious(const T &dummy) constBALL::Composite
getPrevious(const T &)BALL::Composite
getPrevious(const T &dummy) constBALL::Composite
getProperty(const std::string &name) constBALL::PropertyManager
getRadius() constBALL::Atom
getResidue() constBALL::Atom
getResidue()BALL::Atom
getRoot()BALL::Composite
getRoot() constBALL::Composite
getSecondaryStructure() constBALL::Atom
getSecondaryStructure()BALL::Atom
getSelectionTime() constBALL::Composite
getSibling(Index index)BALL::Composite
getSibling(Index index) constBALL::Composite
getType() constBALL::Atom
getTypeName() constBALL::Atom
getVelocity()BALL::Atom
getVelocity() constBALL::Atom
hasAncestor(const T &dummy) constBALL::Composite
hasAncestor(const T &dummy) constBALL::Composite
hasBond(const Bond &bond) constBALL::Atom
hasChild() constBALL::Composite
hasNextSibling() constBALL::Composite
hasParent() constBALL::Composite
hasPreviousSibling() constBALL::Composite
hasProperty(Property property) constBALL::PropertyManager
hasProperty(const std::string &name) constBALL::PropertyManager
hasSibling() constBALL::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::Compositestatic
interactionsBALL::Atom
isAncestorOf(const Composite &composite) constBALL::Composite
isAtom() constBALL::Atominlinevirtual
isAutoDeletable() constBALL::AutoDeletable
isBound() constBALL::Atom
isBoundTo(const Atom &atom) constBALL::Atom
isChain() constBALL::Compositeinlinevirtual
isChildOf(const Composite &composite) constBALL::Composite
isDescendantOf(const Composite &composite) constBALL::Composite
isEmpty() constBALL::Composite
isFirstChild() constBALL::Composite
isFirstChildOf(const Composite &composite) constBALL::Composite
isFragment() constBALL::Compositeinlinevirtual
isGeminal(const Atom &atom) constBALL::Atom
isHomomorph(const Composite &composite) constBALL::Composite
isInterior() constBALL::Composite
isLastChild() constBALL::Composite
isLastChildOf(const Composite &composite) constBALL::Composite
isMolecule() constBALL::Compositeinlinevirtual
isNextSiblingOf(const Composite &composite) constBALL::Composite
isParentOf(const Composite &composite) constBALL::Composite
isPreviousSiblingOf(const Composite &composite) constBALL::Composite
isProtein() constBALL::Compositeinlinevirtual
isRelatedWith(const Composite &composite) constBALL::Composite
isResidue() constBALL::Compositeinlinevirtual
isRoot() constBALL::Composite
isRootOf(const Composite &composite) constBALL::Composite
isSelected() constBALL::Selectable
isSiblingOf(const Composite &composite) constBALL::Composite
isValid() constBALL::Atomvirtual
isVicinal(const Atom &atom) constBALL::Atom
KernelPredicateType typedefBALL::Composite
MAX_NUMBER_OF_BONDS enum valueBALL::Atom
MODIFICATION enum valueBALL::Composite
name_BALL::Atomprotected
NO_VARIANT_EXTENSIONS enum valueBALL::Atom
number_of_bonds_BALL::Atomprotected
NUMBER_OF_PROPERTIES enum valueBALL::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) constBALL::Atom
BALL::Composite::operator!=(const Composite &composite) constBALL::Composite
BALL::PersistentObject::operator!=(const Object &object) constBALL::Object
BALL::Selectable::operator!=(const Selectable &selectable) constBALL::Selectable
BALL::PropertyManager::operator!=(const PropertyManager &pm) constBALL::PropertyManager
operator<(const Object &object) constBALL::Object
operator<=(const Object &object) constBALL::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) constBALL::Atom
BALL::Composite::operator==(const Composite &composite) constBALL::Composite
BALL::PersistentObject::operator==(const Object &object) constBALL::Object
BALL::Selectable::operator==(const Selectable &selectable) constBALL::Selectable
BALL::PropertyManager::operator==(const PropertyManager &pm) constBALL::PropertyManager
operator>(const Object &object) constBALL::Object
operator>=(const Object &object) constBALL::Object
operator>>(PersistenceManager &pm) constBALL::PersistentObject
PersistentObject()BALL::PersistentObjectinline
persistentRead(PersistenceManager &pm)BALL::Atomvirtual
persistentWrite(PersistenceManager &pm, const char *name=0) constBALL::Atomvirtual
position_BALL::Atomprotected
prependChild(Composite &composite)BALL::Composite
Property enum nameBALL::Atom
PropertyManager()BALL::PropertyManager
PropertyManager(const PropertyManager &property_manager)BALL::PropertyManager
radius_BALL::Atomprotected
rbeginBond()BALL::Atominline
rbeginBond() constBALL::Atominline
rbeginChildComposite()BALL::Compositeinline
rbeginChildComposite() constBALL::Compositeinline
rbeginComposite()BALL::Compositeinline
rbeginComposite() constBALL::Compositeinline
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::Atominline
rendBond() constBALL::Atominline
rendChildComposite()BALL::Compositeinline
rendChildComposite() constBALL::Compositeinline
rendComposite()BALL::Compositeinline
rendComposite() constBALL::Compositeinline
replace(Composite &composite)BALL::Composite
select()BALL::Compositevirtual
Selectable()BALL::Selectable
Selectable(const Selectable &selectable, bool deep=true)BALL::Selectable
selected_BALL::Selectableprotected
SELECTION enum valueBALL::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 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
setRadius(float radius)BALL::Atom
setSelected(bool selected)BALL::Selectableinlinevirtual
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
store_interactions_disabled_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
toggleProperty(Property property)BALL::PropertyManager
Type typedefBALL::Atom
type_BALL::Atomprotected
type_name_BALL::Atomprotected
UNKNOWN_TYPE enum valueBALL::Atom
velocity_BALL::Atomprotected
BALL::write(PersistenceManager &pm) constBALL::Selectable
BALL::PropertyManager::write(PersistenceManager &pm) constBALL::PropertyManager
~Atom()BALL::Atomvirtual
~AutoDeletable()BALL::AutoDeletablevirtual
~Composite()BALL::Compositevirtual
~Object()BALL::Objectvirtual
~PersistentObject()BALL::PersistentObjectinlinevirtual
~PropertyManager()BALL::PropertyManagervirtual
~Selectable()BALL::Selectablevirtual