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5 #ifndef BALL_KERNEL_SECONDARYSTRUCTURE_H
6 #define BALL_KERNEL_SECONDARYSTRUCTURE_H
8 #ifndef BALL_KERNEL_RESIDUE_H
12 #ifndef BALL_KERNEL_RESIDUEITERATOR_H
16 #ifndef BALL_KERNEL_ATOMCONTAINER_H
311 virtual void dump(std::ostream& s = std::cout,
Size depth = 0)
const;
338 void prepend(
Atom& atom);
340 void append(
Atom& atom);
342 void insert(
Atom& atom);
348 bool remove(
Atom& atom);
374 #endif // BALL_KERNEL_SECONDARYSTRUCTURE_H
void spliceBefore(SecondaryStructure &secondary_structure)
Residue * getResidue(Position position)
virtual void destroy()
Clear the contents of the secondary structure and remove it from all composite structures.
void persistentWrite(PersistenceManager &pm, const char *name=0) const
SecondaryStructure(const String &name)
BALL_EXPORT bool operator!=(const String &s1, const String &s2)
void swap(SecondaryStructure &secondary_structure)
const Residue * getCTerminal() const
virtual ~SecondaryStructure()
Destructor.
const PDBAtom * getPDBAtom(Position position) const
Type getType() const
Return the type of secondary structure.
#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
#define BALL_CREATE_DEEP(name)
BALL_EXPORT ResidueList residues(const AtomContainer &fragment, bool selected_only=false)
SecondaryStructure()
Default constructor.
const Protein * getProtein() const
SecondaryStructure(const SecondaryStructure &secondary_structure, bool deep=true)
Copy constructor.
virtual void dump(std::ostream &s=std::cout, Size depth=0) const
void insertAfter(Residue &residue, Composite &after)
PDBAtom * getPDBAtom(Position position)
const Residue * getResidue(Position position) const
void spliceAfter(SecondaryStructure &secondary_structure)
void insertBefore(Residue &residue, Composite &before)
void set(const SecondaryStructure &secondary_structure, bool deep=true)
void prepend(Residue &residue)
BALL_EXPORT AtomContainerList atomContainers(const AtomContainer &fragment, bool selected_only=false)
void persistentRead(PersistenceManager &pm)
Type type_
The secondary structure type (helix, strand, coil, turn)
const Residue * getNTerminal() const
void insert(Residue &residue)
virtual bool isValid() const
Size countResidues() const
void get(SecondaryStructure &secondary_structure, bool deep=true) const
void append(Residue &residue)
void setType(Type type)
Set the type of secondary structure.
BALL_EXPORT bool operator==(const String &s1, const String &s2)
bool remove(Residue &residue)
const Chain * getChain() const
Size countPDBAtoms() const
virtual void clear()
Clear the contents of the secondary structure.
void splice(SecondaryStructure &secondary_structure)