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5 #ifndef BALL_KERNEL_RESIDUE_H
6 #define BALL_KERNEL_RESIDUE_H
8 #ifndef BALL_KERNEL_FRAGMENT_H
12 #ifndef BALL_KERNEL_PDBATOMITERATOR_H
16 #ifndef BALL_KERNEL_RESIDUEITERATOR_H
21 #define BALL_RESIDUE_DEFAULT_ID ""
22 #define BALL_RESIDUE_DEFAULT_INSERTION_CODE ' '
28 class SecondaryStructure;
85 ADD_VARIANT_EXTENSIONS_AND_ID
388 virtual bool isResidue()
const {
return true; }
408 virtual void dump(std::ostream& s = std::cout,
Size depth = 0)
const;
424 Size countAtomContainers()
const;
444 bool isSuperAtomContainerOf(
const AtomContainer& atom_container)
const;
453 char insertion_code_;
456 template <
class Res
idueContainerType>
460 for (; res_it != residue_container.endResidue(); ++res_it)
462 if (res_it->isAminoAcid() ==
true)
471 template <
class Res
idueContainerType>
475 for (; res_it != residue_container.rendResidue(); ++res_it)
478 if (res_it->isAminoAcid() ==
true)
489 #endif // BALL_KERNEL_RESIDUE_H
void append(PDBAtom &atom)
#define BALL_RESIDUE_DEFAULT_INSERTION_CODE
SecondaryStructure * getSecondaryStructure()
virtual void clear()
Clears the contents of this instance.
void spliceBefore(Residue &residue)
void insert(PDBAtom &atom)
const Chain * getChain() const
void swap(Residue &residue)
BALL_EXPORT bool operator!=(const String &s1, const String &s2)
Angle getTorsionPhi() const
void get(Residue &residue, bool deep=true) const
void prepend(PDBAtom &atom)
#define BALL_RESIDUE_DEFAULT_ID
#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
void unsetInsertionCode()
char getInsertionCode() const
#define BALL_CREATE_DEEP(name)
void insertBefore(PDBAtom &atom, Composite &before)
@ NO_VARIANT_EXTENSIONS
This returns the unmodified residue name only.
void persistentRead(PersistenceManager &pm)
PDBAtom * getPDBAtom(Position position)
const Residue * getNTerminal(const ResidueContainerType &residue_container)
bool remove(PDBAtom &atom)
bool hasTorsionOmega() const
const PDBAtom * getPDBAtom(Position position) const
virtual void dump(std::ostream &s=std::cout, Size depth=0) const
Size countPDBAtoms() const
void insertAfter(PDBAtom &atom, Composite &after)
virtual ~Residue()
Destructor.
virtual void destroy()
Clears the contents of this instance and removes it from all composite structures.
void spliceAfter(Residue &residue)
Residue(const String &name, const String &id=BALL_RESIDUE_DEFAULT_ID, char insertion_code=BALL_RESIDUE_DEFAULT_INSERTION_CODE)
Detailled constructor.
bool hasTorsionPhi() const
Residue()
Default constructor.
bool hasTorsionPsi() const
BALL_EXPORT AtomContainerList atomContainers(const AtomContainer &fragment, bool selected_only=false)
void setID(const String &id)
Angle getTorsionOmega() const
const SecondaryStructure * getSecondaryStructure() const
BALL_EXPORT bool operator==(const String &s1, const String &s2)
const String & getID() const
Residue(const Residue &residue, bool deep=true)
Copy constructor.
virtual bool isValid() const
Property
The number of predefined properties for AtomContainer.
void splice(Residue &residue)
const Residue * getCTerminal(const ResidueContainerType &residue_container)
String getFullName(FullNameType type=ADD_VARIANT_EXTENSIONS) const
void setInsertionCode(char insertion_code)
@ ADD_VARIANT_EXTENSIONS
Add the residue variant extensions (e.g. '-C' for C-terminal residues)
std::reverse_iterator< ResidueConstIterator > ResidueConstReverseIterator
Angle getTorsionPsi() const
void persistentWrite(PersistenceManager &pm, const char *name=0) const
const Protein * getProtein() const
void set(const Residue &residue, bool deep=true)