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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 ' '
84 virtual void destroy();
111 void set(
const Nucleotide& nucleotide,
bool deep =
true);
126 void get(
Nucleotide& nucleotide,
bool deep =
true)
const;
164 void setID(
const String&
id);
169 const String& getID()
const;
180 void setInsertionCode(
char insertion_code);
187 void unsetInsertionCode();
192 char getInsertionCode()
const;
197 void prepend(
Atom& atom);
202 void append(
Atom& atom);
207 void insert(
Atom& atom);
224 bool remove(
Atom& atom);
251 bool isTerminal()
const;
257 bool is3Prime()
const;
263 bool is5Prime()
const;
274 virtual bool isValid()
const;
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>
350 #endif // BALL_KERNEL_NUCLEOTIDE_H
const Nucleotide * get5Prime(const NucleotideContainerType &nucleotide_container)
#define BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE
BALL_EXPORT bool operator!=(const String &s1, const String &s2)
Property
The number of predefined properties for AtomContainer.
#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
#define BALL_CREATE_DEEP(name)
#define BALL_NUCLEOTIDE_DEFAULT_ID
BALL_INLINE bool isREnd() const
Test wheter the iterator points to the position before the first element.
BALL_EXPORT AtomContainerList atomContainers(const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT bool operator==(const String &s1, const String &s2)
BALL_INLINE bool isEnd() const
Check whether the iterator points to the position after the last item of the container.
const Nucleotide * get3Prime(const NucleotideContainerType &nucleotide_container)