5#ifndef BALL_KERNEL_CHAIN_H
6#define BALL_KERNEL_CHAIN_H
8#ifndef BALL_KERNEL_RESIDUE_H
12#ifndef BALL_KERNEL_SECONDARYSTRUCTUREITERATOR_H
17#define BALL_CHAIN_DEFAULT_NAME ' '
45 NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES
90 void set(
const Chain& chain,
bool deep =
true);
118 bool operator == (
const Chain& chain)
const;
123 bool operator != (
const Chain& chain)
const;
326 virtual void dump(std::ostream& s = std::cout,
Size depth = 0)
const
352 void prepend(
Atom& atom);
354 void append(
Atom& atom);
356 void insert(
Atom& atom);
362 bool remove(
Atom& atom);
#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
#define BALL_CREATE_DEEP(name)
void insert(SecondaryStructure &secondary_structure)
bool remove(SecondaryStructure &secondary_structure)
void insertAfter(SecondaryStructure &secondary_structure, Composite &after)
void insertBefore(SecondaryStructure &secondary_structure, Composite &before)
void set(const Chain &chain, bool deep=true)
virtual bool isChain() const
Chain(const Chain &chain, bool deep=true)
Copy constructor.
void spliceAfter(Chain &chain)
Size countPDBAtoms() const
PDBAtom * getPDBAtom(Position position)
void splice(Chain &chain)
void persistentRead(PersistenceManager &pm)
void append(SecondaryStructure &secondary_structure)
void insertBefore(Residue &residue, Composite &before)
const Protein * getProtein() const
void append(Residue &residue)
bool remove(Residue &residue)
void insert(Residue &residue)
virtual void dump(std::ostream &s=std::cout, Size depth=0) const
SecondaryStructure * getSecondaryStructure(Position position)
Size countResidues() const
virtual ~Chain()
Destructor.
void prepend(Residue &residue)
void spliceBefore(Chain &chain)
void get(Chain &chain, bool deep=true) const
void persistentWrite(PersistenceManager &pm, const char *name=0) const
const SecondaryStructure * getSecondaryStructure(Position position) const
const PDBAtom * getPDBAtom(Position position) const
void insertAfter(Residue &residue, Composite &after)
void prepend(SecondaryStructure &secondary_structure)
const Residue * getResidue(Position position) const
const Residue * getCTerminal() const
Chain(const String &name)
Detailled constructor.
const Residue * getNTerminal() const
Chain()
Default constrcutor.
Size countSecondaryStructures() const
Residue * getResidue(Position position)