5#ifndef BALL_KERNEL_NUCLEOTIDE_H
6#define BALL_KERNEL_NUCLEOTIDE_H
8#ifndef BALL_KERNEL_FRAGMENT_H
12#ifndef BALL_KERNEL_RESIDUE_H
16#ifndef BALL_KERNEL_NUCLEOTIDEITERATOR_H
21#define BALL_NUCLEOTIDE_DEFAULT_ID ""
22#define BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE ' '
282 virtual void dump(std::ostream& s = std::cout,
Size depth = 0)
const;
292 Size countAtomContainers()
const;
312 bool isSuperAtomContainerOf(
const AtomContainer& atom_container)
const;
321 char insertion_code_;
325 template <
class Nucleot
ideContainerType>
329 for ( res_it = nucleotide_container.beginNucleotide(); !res_it.
isEnd(); ++res_it)
337 template <
class Nucleot
ideContainerType>
#define BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE
#define BALL_NUCLEOTIDE_DEFAULT_ID
#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
#define BALL_CREATE_DEEP(name)
BALL_EXPORT AtomContainerList atomContainers(const AtomContainer &fragment, bool selected_only=false)
const Nucleotide * get5Prime(const NucleotideContainerType &nucleotide_container)
BALL_EXPORT bool operator==(const String &s1, const String &s2)
BALL_EXPORT bool operator!=(const String &s1, const String &s2)
const Nucleotide * get3Prime(const NucleotideContainerType &nucleotide_container)
BALL_INLINE bool isEnd() const
Check whether the iterator points to the position after the last item of the container.
BALL_INLINE bool isREnd() const
Test wheter the iterator points to the position before the first element.
Property
The number of predefined properties for AtomContainer.
void persistentWrite(PersistenceManager &pm, const char *name=0) const
virtual void clear()
Clears the nucleotides contents.
void persistentRead(PersistenceManager &pm)
virtual void dump(std::ostream &s=std::cout, Size depth=0) const
void set(const Nucleotide &nucleotide, bool deep=true)
virtual bool isValid() const
void setInsertionCode(char insertion_code)
NucleicAcid * getNucleicAcid()
const String & getID() const
void splice(Nucleotide &nucleotide)
void swap(Nucleotide &nucleotide)
virtual void destroy()
Clears the nucleotides contents and removes it from all composite structures.
void insertAfter(Atom &atom, Composite &after)
void get(Nucleotide &nucleotide, bool deep=true) const
void spliceAfter(Nucleotide &nucleotide)
void setID(const String &id)
Nucleotide()
Default constructor.
void insertBefore(Atom &atom, Composite &before)
Nucleotide(const Nucleotide &nucleotide, bool deep=true)
Copy constructor.
void spliceBefore(Nucleotide &nucleotide)
Nucleotide(const String &name, const String &id=BALL_NUCLEOTIDE_DEFAULT_ID, char insertion_code=BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE)
Detailled constructor.
virtual ~Nucleotide()
Destructor.
const NucleicAcid * getNucleicAcid() const
void unsetInsertionCode()
char getInsertionCode() const