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| PDBAtom () |
| Default constructor. More...
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| PDBAtom (const PDBAtom &pdb_atom, bool deep=true) |
| Copy constructor. More...
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| PDBAtom (const String &name) |
| Constructor. More...
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| 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) |
| Detailed constructor. More...
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virtual | ~PDBAtom () |
| Destructor. More...
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virtual void | destroy () |
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bool | operator== (const PDBAtom &pdb_atom) const |
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bool | operator!= (const PDBAtom &pdb_atom) const |
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void | persistentWrite (PersistenceManager &pm, const char *name=0) const |
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void | persistentRead (PersistenceManager &pm) |
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void | set (const PDBAtom &pdb_atom, bool deep=true) |
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void | get (PDBAtom &pdb_atom, bool deep=true) const |
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PDBAtom & | operator= (const PDBAtom &pdb_atom) |
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void | swap (PDBAtom &pdb_atom) |
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virtual void | clear () |
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Protein * | getProtein () |
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const Protein * | getProtein () const |
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Chain * | getChain () |
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const Chain * | getChain () const |
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Residue * | getResidue () |
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const Residue * | getResidue () const |
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void | setBranchDesignator (char branch_designator) |
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char | getBranchDesignator () const |
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void | setRemotenessIndicator (char remoteness_indicator) |
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char | getRemotenessIndicator () const |
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void | setAlternateLocationIndicator (char alternate_location_indicator) |
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char | getAlternateLocationIndicator () const |
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void | setOccupancy (float occupancy) |
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float | getOccupancy () const |
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void | setTemperatureFactor (float temperature_factor) |
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float | getTemperatureFactor () const |
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virtual void | dump (std::ostream &s=std::cout, Size depth=0) const |
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| Atom () |
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| Atom (const Atom &atom, bool deep=true) |
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| 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) |
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virtual | ~Atom () |
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void | set (const Atom &atom, bool deep=true) |
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void | get (Atom &atom, bool deep=true) const |
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Atom & | operator= (const Atom &atom) |
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void | swap (Atom &atom) |
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bool | operator== (const Atom &atom) const |
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bool | operator!= (const Atom &atom) const |
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void | setElement (const Element &element) |
| Assign the atom's element. More...
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const Element & | getElement () const |
| Return the atom's element. More...
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void | setCharge (float charge) |
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float | getCharge () const |
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void | setFormalCharge (Index formal_charge) |
| Set the atom's formal charge. More...
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Index | getFormalCharge () const |
| Return the atom's formal charge. More...
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const Molecule * | getMolecule () const |
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Molecule * | getMolecule () |
| Return the molecule the atom is contained in (mutable) More...
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const Fragment * | getFragment () const |
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Fragment * | getFragment () |
| Return the fragment the atom is contained in (mutable) More...
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const Residue * | getResidue () const |
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Residue * | getResidue () |
| Return the residue the atom is contained in (mutable) More...
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const SecondaryStructure * | getSecondaryStructure () const |
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SecondaryStructure * | getSecondaryStructure () |
| Return the secondary structure the atom is contained in (mutable) More...
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const Chain * | getChain () const |
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Chain * | getChain () |
| Return the chain the atom is contained in (mutable) More...
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void | setName (const String &name) |
| Set the atom name. More...
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const String & | getName () const |
| Return the atom name. More...
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String | getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const |
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void | setPosition (const Vector3 &position) |
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Vector3 & | getPosition () |
| Return the atom coordinates (mutable) More...
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const Vector3 & | getPosition () const |
| Return the atom coordinates (const) More...
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void | setRadius (float radius) |
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float | getRadius () const |
| Return the atom radius. More...
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void | setType (Type atom_type) |
| Assign the numerical atom type. More...
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Type | getType () const |
| Return the (numerical) atom type. More...
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String | getTypeName () const |
| Return the atom type name. More...
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void | setTypeName (const String &name) |
| Assign the atom type name. More...
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void | setVelocity (const Vector3 &velocity) |
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Vector3 & | getVelocity () |
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const Vector3 & | getVelocity () const |
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void | setForce (const Vector3 &force) |
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const Vector3 & | getForce () const |
| Return the atom's force vector (const) More...
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Vector3 & | getForce () |
| Return the atom's force vector (mutable) More...
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Size | countBonds () const |
| Return the number of bonds. More...
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Bond * | getBond (Position index) |
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const Bond * | getBond (Position index) const |
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Bond * | getBond (const Atom &atom) |
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const Bond * | getBond (const Atom &atom) const |
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bool | hasBond (const Bond &bond) const |
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bool | isBoundTo (const Atom &atom) const |
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bool | isBound () const |
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bool | isGeminal (const Atom &atom) const |
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bool | isVicinal (const Atom &atom) const |
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virtual bool | isAtom () const |
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virtual bool | isValid () const |
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bool | applyBonds (UnaryProcessor< Bond > &processor) |
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Bond * | createBond (Atom &atom) |
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Bond * | createBond (Bond &bond, Atom &atom) |
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Bond * | cloneBond (Bond &bond, Atom &atom) |
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bool | destroyBond (const Atom &atom) |
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void | destroyBonds () |
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Atom * | getPartnerAtom (Position i) |
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const Atom * | getPartnerAtom (Position i) const |
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float | getDistance (const Atom &a) const |
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void | addInteraction (const Atom *atom, String interaction_type, double energy) |
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void | addInteraction (String interaction_type, double energy) |
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void | disableStoreInteractions () |
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void | enableStoreInteractions () |
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BondIterator | beginBond () |
| Return a bond iterator pointing to the first bond of the atom. More...
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BondIterator | endBond () |
| Return a past-the-end bond iterator. More...
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BondConstIterator | beginBond () const |
| Return a constant bond iterator pointing to the first bond. More...
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BondConstIterator | endBond () const |
| Return a constant past-the-end bond iterator. More...
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BondReverseIterator | rbeginBond () |
| Return a reverse bond iterator pointing to the last bond. More...
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BondReverseIterator | rendBond () |
| Return a past-the-end bond iterator for reverse traversal. More...
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BondConstReverseIterator | rbeginBond () const |
| Return a constant reverse bond iterator pointing to the first atom. More...
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BondConstReverseIterator | rendBond () const |
| Return a constant past-the-end bond iterator for reverse traversal. More...
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template<typename T > |
bool | applyLevel (ConstUnaryProcessor< T > &processor, long level) const |
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AncestorIterator | beginAncestor () |
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AncestorIterator | endAncestor () |
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AncestorConstIterator | beginAncestor () const |
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AncestorConstIterator | endAncestor () const |
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ChildCompositeIterator | beginChildComposite () |
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ChildCompositeIterator | endChildComposite () |
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ChildCompositeConstIterator | beginChildComposite () const |
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ChildCompositeConstIterator | endChildComposite () const |
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ChildCompositeReverseIterator | rbeginChildComposite () |
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ChildCompositeReverseIterator | rendChildComposite () |
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ChildCompositeConstReverseIterator | rbeginChildComposite () const |
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ChildCompositeConstReverseIterator | rendChildComposite () const |
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CompositeIterator | beginComposite () |
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CompositeIterator | endComposite () |
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CompositeConstIterator | beginComposite () const |
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CompositeConstIterator | endComposite () const |
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CompositeReverseIterator | rbeginComposite () |
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CompositeReverseIterator | rendComposite () |
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CompositeConstReverseIterator | rbeginComposite () const |
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CompositeConstReverseIterator | rendComposite () const |
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void | deleteChildrenList_ (std::list< Composite * > &composites) |
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template<typename T > |
BALL_INLINE bool | apply (UnaryProcessor< T > &processor) |
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template<typename T > |
BALL_INLINE bool | apply (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
BALL_INLINE T * | getAncestor (const T &) |
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template<typename T > |
BALL_INLINE const T * | getAncestor (const T &) const |
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template<typename T > |
BALL_INLINE T * | getPrevious (const T &) |
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template<typename T > |
BALL_INLINE const T * | getPrevious (const T &dummy) const |
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template<typename T > |
BALL_INLINE T * | getNext (const T &) |
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template<typename T > |
BALL_INLINE const T * | getNext (const T &dummy) const |
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template<typename T > |
BALL_INLINE bool | hasAncestor (const T &dummy) const |
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| Composite () |
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| Composite (const Composite &composite, bool deep=true) |
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virtual | ~Composite () |
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void | destroy (bool virtual_destroy) |
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void * | clone (Composite &root) const |
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bool | operator== (const Composite &composite) const |
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bool | operator!= (const Composite &composite) const |
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bool | isEmpty () const |
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bool | isRoot () const |
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bool | isRootOf (const Composite &composite) const |
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bool | isInterior () const |
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bool | hasChild () const |
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bool | isChildOf (const Composite &composite) const |
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bool | isFirstChild () const |
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bool | isFirstChildOf (const Composite &composite) const |
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bool | isLastChild () const |
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bool | isLastChildOf (const Composite &composite) const |
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bool | hasParent () const |
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bool | isParentOf (const Composite &composite) const |
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bool | hasSibling () const |
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bool | isSiblingOf (const Composite &composite) const |
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bool | hasPreviousSibling () const |
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bool | isPreviousSiblingOf (const Composite &composite) const |
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bool | hasNextSibling () const |
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bool | isNextSiblingOf (const Composite &composite) const |
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bool | isDescendantOf (const Composite &composite) const |
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template<typename T > |
bool | hasAncestor (const T &dummy) const |
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bool | isAncestorOf (const Composite &composite) const |
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bool | isRelatedWith (const Composite &composite) const |
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bool | isHomomorph (const Composite &composite) const |
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bool | containsSelection () const |
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virtual bool | isMolecule () const |
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virtual bool | isProtein () const |
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virtual bool | isFragment () const |
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virtual bool | isResidue () const |
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virtual bool | isChain () const |
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void | host (Visitor< Composite > &visitor) |
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template<typename T > |
bool | applyAncestor (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | applyAncestor (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | applyChild (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | applyChild (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | applyDescendantPreorder (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | applyDescendantPostorder (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | applyDescendant (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | applyDescendant (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | applyPreorder (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | applyPreorder (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | applyPostorder (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | applyPostorder (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | apply (UnaryProcessor< T > &processor) |
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template<typename T > |
bool | apply (ConstUnaryProcessor< T > &processor) const |
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template<typename T > |
bool | applyLevel (UnaryProcessor< T > &processor, long level) |
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void | set (const Composite &composite, bool deep=true) |
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Composite & | operator= (const Composite &composite) |
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void | get (Composite &composite, bool deep=true) const |
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Size | getDegree () const |
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Size | count (const KernelPredicateType &predicate) const |
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Size | countDescendants () const |
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Size | getPathLength (const Composite &composite) const |
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Size | getDepth () const |
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Size | getHeight () const |
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Composite & | getRoot () |
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const Composite & | getRoot () const |
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Composite * | getLowestCommonAncestor (const Composite &composite) |
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const Composite * | getLowestCommonAncestor (const Composite &composite) const |
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template<typename T > |
T * | getAncestor (const T &) |
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template<typename T > |
const T * | getAncestor (const T &) const |
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template<typename T > |
T * | getPrevious (const T &) |
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template<typename T > |
const T * | getPrevious (const T &dummy) const |
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template<typename T > |
T * | getNext (const T &) |
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template<typename T > |
const T * | getNext (const T &dummy) const |
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Composite * | getParent () |
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const Composite * | getParent () const |
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Composite * | getChild (Index index) |
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const Composite * | getChild (Index index) const |
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Composite * | getSibling (Index index) |
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const Composite * | getSibling (Index index) const |
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Composite * | getFirstChild () |
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const Composite * | getFirstChild () const |
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Composite * | getLastChild () |
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const Composite * | getLastChild () const |
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const PreciseTime & | getModificationTime () const |
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const PreciseTime & | getSelectionTime () const |
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void | stamp (StampType stamp=BOTH) |
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void | prependChild (Composite &composite) |
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void | appendChild (Composite &composite) |
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void | insertBefore (Composite &composite) |
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void | insertAfter (Composite &composite) |
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void | spliceBefore (Composite &composite) |
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void | spliceAfter (Composite &composite) |
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void | splice (Composite &composite) |
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bool | removeChild (Composite &child) |
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Size | removeSelected () |
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Size | removeUnselected () |
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void | replace (Composite &composite) |
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void | swap (Composite &composite) |
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virtual void | select () |
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virtual void | deselect () |
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| PersistentObject () |
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virtual | ~PersistentObject () |
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PersistenceManager & | operator>> (PersistenceManager &pm) const |
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virtual void | finalize () |
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| Object () |
| Default constructor. More...
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| Object (const Object &object) |
| Copy constructor. More...
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virtual | ~Object () |
| Destructor. More...
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const Object & | operator= (const Object &) |
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bool | operator== (const Object &object) const |
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bool | operator!= (const Object &object) const |
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bool | operator< (const Object &object) const |
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bool | operator<= (const Object &object) const |
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bool | operator>= (const Object &object) const |
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bool | operator> (const Object &object) const |
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int | compare (const Object &object) const |
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virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
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Handle | getHandle () const |
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virtual | ~AutoDeletable () |
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void * | operator new (size_t size) |
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void | operator delete (void *ptr) |
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void * | operator new (size_t size, void *ptr) |
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void | operator delete (void *ptr, void *) |
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bool | isAutoDeletable () const |
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void | setAutoDeletable (bool enable) |
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| Selectable () |
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| Selectable (const Selectable &selectable, bool deep=true) |
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virtual | ~Selectable () |
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void | set (const Selectable &selectable, bool deep=true) |
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const Selectable & | operator= (const Selectable &selectable) |
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void | get (Selectable &selectable, bool deep=true) const |
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void | swap (Selectable &selectable) |
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virtual void | setSelected (bool selected) |
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bool | isSelected () const |
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bool | operator== (const Selectable &selectable) const |
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bool | operator!= (const Selectable &selectable) const |
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void | write (PersistenceManager &pm) const |
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bool | read (PersistenceManager &pm) |
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virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
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BALL_INLINE | PropertyManager () |
| Default constructor. More...
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BALL_INLINE | PropertyManager (const PropertyManager &property_manager) |
| Copy constructor. More...
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virtual | ~PropertyManager () |
| Destructor. More...
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void | set (const PropertyManager &property_manager) |
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const PropertyManager & | operator= (const PropertyManager &property_manager) |
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void | get (PropertyManager &property_manager) const |
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void | swap (PropertyManager &property_manager) |
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BitVector & | getBitVector () |
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const BitVector & | getBitVector () const |
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| operator BitVector & () |
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void | setProperty (Property property) |
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void | clearProperty (Property property) |
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void | toggleProperty (Property property) |
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Size | countProperties () const |
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const NamedProperty & | getNamedProperty (Position index) const |
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NamedProperty & | getNamedProperty (Position index) |
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void | setProperty (const NamedProperty &property) |
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void | setProperty (const std::string &name) |
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void | setProperty (const std::string &name, bool value) |
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void | setProperty (const std::string &name, int value) |
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void | setProperty (const std::string &name, unsigned int value) |
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void | setProperty (const std::string &name, float value) |
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void | setProperty (const std::string &name, double value) |
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void | setProperty (const std::string &name, const std::string &value) |
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void | setProperty (const std::string &name, const PersistentObject &value) |
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const NamedProperty & | getProperty (const std::string &name) const |
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NamedPropertyIterator | beginNamedProperty () |
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NamedPropertyIterator | endNamedProperty () |
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void | clearProperty (const std::string &name) |
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Size | countNamedProperties () const |
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bool | hasProperty (Property property) const |
| Query for an unnamed property. More...
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bool | hasProperty (const std::string &name) const |
| Query for a named property. More...
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bool | operator== (const PropertyManager &pm) const |
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bool | operator!= (const PropertyManager &pm) const |
| Inequality operator. More...
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void | write (PersistenceManager &pm) const |
| Persistent stream writing. More...
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bool | read (PersistenceManager &pm) |
| Persistent stream reading. More...
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bool | isValid () const |
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void | dump (std::ostream &s=std::cout, Size depth=0) const |
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Atom class with additional attributes. This class represents atoms read from PDB files. It contains additional attributes to hold the crystallographic properties of atoms from a PDB file (e.g., temperature factor, occupancy). For details on the PDB format and the detailed meaning of those fields, please refer to the PDB documentation at http://www.rcsb.org
- See also
- PDBFile
Definition at line 38 of file PDBAtom.h.