Public Member Functions |
| SPAtom (const String &symbol, bool in_brackets) |
virtual | ~SPAtom () |
Size | getDefaultValence () const |
Size | countRealValences () const |
Size | getIsotope () const |
void | setIsotope (Size isotope) |
Index | getFormalCharge () const |
| Return the atom's formal charge.
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void | setFormalCharge (Index charge) |
| Set the atom's formal charge.
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const ChiralDef & | getChirality () const |
void | setChirality (const ChiralDef &chirality) |
bool | isAromatic () const |
void | setAromatic (bool is_aromatic) |
bool | isInBrackets () const |
void | setInBrackets (bool in_brackets) |
| Atom () |
| Atom (const Atom &atom, bool deep=true) |
| 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) |
virtual | ~Atom () |
virtual void | clear () |
virtual void | destroy () |
virtual void | persistentWrite (PersistenceManager &pm, const char *name=0) const |
virtual void | persistentRead (PersistenceManager &pm) |
void | set (const Atom &atom, bool deep=true) |
void | get (Atom &atom, bool deep=true) const |
Atom & | operator= (const Atom &atom) |
void | swap (Atom &atom) |
bool | operator== (const Atom &atom) const |
bool | operator!= (const Atom &atom) const |
void | setElement (const Element &element) |
| Assign the atom's element.
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const Element & | getElement () const |
| Return the atom's element.
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void | setCharge (float charge) |
float | getCharge () const |
const Molecule * | getMolecule () const |
Molecule * | getMolecule () |
| Return the molecule the atom is contained in (mutable)
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const Fragment * | getFragment () const |
Fragment * | getFragment () |
| Return the fragment the atom is contained in (mutable)
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const Residue * | getResidue () const |
Residue * | getResidue () |
| Return the residue the atom is contained in (mutable)
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const SecondaryStructure * | getSecondaryStructure () const |
SecondaryStructure * | getSecondaryStructure () |
| Return the secondary structure the atom is contained in (mutable)
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const Chain * | getChain () const |
Chain * | getChain () |
| Return the chain the atom is contained in (mutable)
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void | setName (const String &name) |
| Set the atom name.
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const String & | getName () const |
| Return the atom name.
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String | getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const |
void | setPosition (const Vector3 &position) |
Vector3 & | getPosition () |
| Return the atom coordinates (mutable)
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const Vector3 & | getPosition () const |
| Return the atom coordinates (const)
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void | setRadius (float radius) |
float | getRadius () const |
| Return the atom radius.
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void | setType (Type atom_type) |
| Assign the numerical atom type.
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Type | getType () const |
| Return the (numerical) atom type.
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String | getTypeName () const |
| Return the atom type name.
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void | setTypeName (const String &name) |
| Assign the atom type name.
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void | setVelocity (const Vector3 &velocity) |
Vector3 & | getVelocity () |
const Vector3 & | getVelocity () const |
void | setForce (const Vector3 &force) |
const Vector3 & | getForce () const |
| Return the atom's force vector (const)
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Vector3 & | getForce () |
| Return the atom's force vector (mutable)
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Size | countBonds () const |
| Return the number of bonds.
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Bond * | getBond (Position index) |
const Bond * | getBond (Position index) const |
Bond * | getBond (const Atom &atom) |
const Bond * | getBond (const Atom &atom) const |
Bond * | createBond (Atom &atom) |
Bond * | createBond (Bond &bond, Atom &atom) |
Bond * | cloneBond (Bond &bond, Atom &atom) |
bool | destroyBond (const Atom &atom) |
void | destroyBonds () |
Atom * | getPartnerAtom (Position i) |
const Atom * | getPartnerAtom (Position i) const |
float | getDistance (const Atom &a) const |
bool | hasBond (const Bond &bond) const |
bool | isBoundTo (const Atom &atom) const |
bool | isBound () const |
bool | isGeminal (const Atom &atom) const |
bool | isVicinal (const Atom &atom) const |
virtual bool | isValid () const |
virtual void | dump (std::ostream &s=std::cout, Size depth=0) const |
bool | applyBonds (UnaryProcessor< Bond > &processor) |
BondIterator | beginBond () |
| Return a bond iterator pointing to the first bond of the atom.
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BondIterator | endBond () |
| Return a past-the-end bond iterator.
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BondConstIterator | beginBond () const |
| Return a constant bond iterator pointing to the first bond.
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BondConstIterator | endBond () const |
| Return a constant past-the-end bond iterator.
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BondReverseIterator | rbeginBond () |
| Return a reverse bond iterator pointing to the last bond.
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BondReverseIterator | rendBond () |
| Return a past-the-end bond iterator for reverse traversal.
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BondConstReverseIterator | rbeginBond () const |
| Return a constant reverse bond iterator pointing to the first atom.
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BondConstReverseIterator | rendBond () const |
| Return a constant past-the-end bond iterator for reverse traversal.
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AncestorIterator | beginAncestor () |
AncestorIterator | endAncestor () |
AncestorConstIterator | beginAncestor () const |
AncestorConstIterator | endAncestor () const |
ChildCompositeIterator | beginChildComposite () |
ChildCompositeIterator | endChildComposite () |
ChildCompositeConstIterator | beginChildComposite () const |
ChildCompositeConstIterator | endChildComposite () const |
ChildCompositeReverseIterator | rbeginChildComposite () |
ChildCompositeReverseIterator | rendChildComposite () |
ChildCompositeConstReverseIterator | rbeginChildComposite () const |
ChildCompositeConstReverseIterator | rendChildComposite () const |
CompositeIterator | beginComposite () |
CompositeIterator | endComposite () |
CompositeConstIterator | beginComposite () const |
CompositeConstIterator | endComposite () const |
CompositeReverseIterator | rbeginComposite () |
CompositeReverseIterator | rendComposite () |
CompositeConstReverseIterator | rbeginComposite () const |
CompositeConstReverseIterator | rendComposite () const |
void | deleteChildrenList_ (std::list< Composite * > &composites) |
| Composite () |
| Composite (const Composite &composite, bool deep=true) |
virtual | ~Composite () |
void | destroy (bool virtual_destroy) |
void * | clone (Composite &root) const |
bool | operator== (const Composite &composite) const |
bool | operator!= (const Composite &composite) const |
bool | isEmpty () const |
bool | isRoot () const |
bool | isRootOf (const Composite &composite) const |
bool | isInterior () const |
bool | hasChild () const |
bool | isChildOf (const Composite &composite) const |
bool | isFirstChild () const |
bool | isFirstChildOf (const Composite &composite) const |
bool | isLastChild () const |
bool | isLastChildOf (const Composite &composite) const |
bool | hasParent () const |
bool | isParentOf (const Composite &composite) const |
bool | hasSibling () const |
bool | isSiblingOf (const Composite &composite) const |
bool | hasPreviousSibling () const |
bool | isPreviousSiblingOf (const Composite &composite) const |
bool | hasNextSibling () const |
bool | isNextSiblingOf (const Composite &composite) const |
bool | isDescendantOf (const Composite &composite) const |
template<typename T > |
bool | hasAncestor (const T &dummy) const |
bool | isAncestorOf (const Composite &composite) const |
bool | isRelatedWith (const Composite &composite) const |
bool | isHomomorph (const Composite &composite) const |
bool | containsSelection () const |
void | host (Visitor< Composite > &visitor) |
template<typename T > |
bool | applyAncestor (UnaryProcessor< T > &processor) |
template<typename T > |
bool | applyChild (UnaryProcessor< T > &processor) |
template<typename T > |
bool | applyDescendantPreorder (UnaryProcessor< T > &processor) |
template<typename T > |
bool | applyDescendantPostorder (UnaryProcessor< T > &processor) |
template<typename T > |
bool | applyDescendant (UnaryProcessor< T > &processor) |
template<typename T > |
bool | applyPreorder (UnaryProcessor< T > &processor) |
template<typename T > |
bool | applyPostorder (UnaryProcessor< T > &processor) |
template<typename T > |
bool | apply (UnaryProcessor< T > &processor) |
template<typename T > |
bool | applyLevel (UnaryProcessor< T > &processor, long level) |
void | set (const Composite &composite, bool deep=true) |
Composite & | operator= (const Composite &composite) |
void | get (Composite &composite, bool deep=true) const |
Size | getDegree () const |
Size | count (const KernelPredicateType &predicate) const |
Size | countDescendants () const |
Size | getPathLength (const Composite &composite) const |
Size | getDepth () const |
Size | getHeight () const |
Composite & | getRoot () |
const Composite & | getRoot () const |
Composite * | getLowestCommonAncestor (const Composite &composite) |
const Composite * | getLowestCommonAncestor (const Composite &composite) const |
template<typename T > |
T * | getAncestor (const T &) |
template<typename T > |
const T * | getAncestor (const T &) const |
template<typename T > |
T * | getPrevious (const T &) |
template<typename T > |
const T * | getPrevious (const T &dummy) const |
template<typename T > |
T * | getNext (const T &) |
template<typename T > |
const T * | getNext (const T &dummy) const |
Composite * | getParent () |
const Composite * | getParent () const |
Composite * | getChild (Index index) |
const Composite * | getChild (Index index) const |
Composite * | getSibling (Index index) |
const Composite * | getSibling (Index index) const |
Composite * | getFirstChild () |
const Composite * | getFirstChild () const |
Composite * | getLastChild () |
const Composite * | getLastChild () const |
const PreciseTime & | getModificationTime () const |
const PreciseTime & | getSelectionTime () const |
void | stamp (StampType stamp=BOTH) |
void | prependChild (Composite &composite) |
void | appendChild (Composite &composite) |
void | insertBefore (Composite &composite) |
void | insertAfter (Composite &composite) |
void | spliceBefore (Composite &composite) |
void | spliceAfter (Composite &composite) |
void | splice (Composite &composite) |
bool | removeChild (Composite &child) |
Size | removeSelected () |
Size | removeUnselected () |
void | replace (Composite &composite) |
void | swap (Composite &composite) |
virtual void | select () |
virtual void | deselect () |
| PersistentObject () |
virtual | ~PersistentObject () |
PersistenceManager & | operator>> (PersistenceManager &pm) const |
virtual void | finalize () |
| Object () |
| Default constructor.
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| Object (const Object &object) |
| Copy constructor.
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virtual | ~Object () |
| Destructor.
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const Object & | operator= (const Object &) |
bool | operator== (const Object &object) const |
bool | operator!= (const Object &object) const |
bool | operator< (const Object &object) const |
bool | operator<= (const Object &object) const |
bool | operator>= (const Object &object) const |
bool | operator> (const Object &object) const |
int | compare (const Object &object) const |
virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
Handle | getHandle () const |
virtual | ~AutoDeletable () |
void * | operator new (size_t size) |
void | operator delete (void *ptr) |
void * | operator new (size_t size, void *ptr) |
void | operator delete (void *ptr, void *) |
bool | isAutoDeletable () const |
void | setAutoDeletable (bool enable) |
| Selectable () |
| Selectable (const Selectable &selectable, bool deep=true) |
virtual | ~Selectable () |
void | set (const Selectable &selectable, bool deep=true) |
const Selectable & | operator= (const Selectable &selectable) |
void | get (Selectable &selectable, bool deep=true) const |
void | swap (Selectable &selectable) |
virtual void | setSelected (bool selected) |
bool | isSelected () const |
bool | operator== (const Selectable &selectable) const |
bool | operator!= (const Selectable &selectable) const |
void | write (PersistenceManager &pm) const |
bool | read (PersistenceManager &pm) |
virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
BALL_INLINE | PropertyManager () |
| Default constructor.
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BALL_INLINE | PropertyManager (const PropertyManager &property_manager) |
| Copy constructor.
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virtual | ~PropertyManager () |
| Destructor.
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void | set (const PropertyManager &property_manager) |
const PropertyManager & | operator= (const PropertyManager &property_manager) |
void | get (PropertyManager &property_manager) const |
void | swap (PropertyManager &property_manager) |
BitVector & | getBitVector () |
const BitVector & | getBitVector () const |
| operator BitVector & () |
void | setProperty (Property property) |
void | clearProperty (Property property) |
void | toggleProperty (Property property) |
Size | countProperties () const |
const NamedProperty & | getNamedProperty (Position index) const |
NamedProperty & | getNamedProperty (Position index) |
void | setProperty (const NamedProperty &property) |
void | setProperty (const string &name) |
void | setProperty (const string &name, bool value) |
void | setProperty (const string &name, int value) |
void | setProperty (const string &name, unsigned int value) |
void | setProperty (const string &name, float value) |
void | setProperty (const string &name, double value) |
void | setProperty (const string &name, const string &value) |
void | setProperty (const string &name, const PersistentObject &value) |
const NamedProperty & | getProperty (const string &name) const |
NamedPropertyIterator | beginNamedProperty () |
NamedPropertyIterator | endNamedProperty () |
void | clearProperty (const string &name) |
Size | countNamedProperties () const |
bool | hasProperty (Property property) const |
| Query for an unnamed property.
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bool | hasProperty (const string &name) const |
| Query for a named property.
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bool | operator== (const PropertyManager &pm) const |
bool | operator!= (const PropertyManager &pm) const |
| Inequality operator.
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void | write (PersistenceManager &pm) const |
| Persistent stream writing.
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bool | read (PersistenceManager &pm) |
| Persistent stream reading.
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