BALL
1.5.0
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#include <BALL/KERNEL/residue.h>
Public Member Functions | |
bool | operator== (const Residue &residue) const |
bool | operator!= (const Residue &residue) const |
Constructors and Destructors | |
Residue () | |
Default constructor. More... | |
Residue (const Residue &residue, bool deep=true) | |
Copy constructor. More... | |
Residue (const String &name, const String &id=BALL_RESIDUE_DEFAULT_ID, char insertion_code=BALL_RESIDUE_DEFAULT_INSERTION_CODE) | |
Detailled constructor. More... | |
virtual | ~Residue () |
Destructor. More... | |
virtual void | clear () |
Clears the contents of this instance. More... | |
virtual void | destroy () |
Clears the contents of this instance and removes it from all composite structures. More... | |
Persistence | |
void | persistentWrite (PersistenceManager &pm, const char *name=0) const |
void | persistentRead (PersistenceManager &pm) |
Assignment | |
void | set (const Residue &residue, bool deep=true) |
Residue & | operator= (const Residue &residue) |
void | get (Residue &residue, bool deep=true) const |
void | swap (Residue &residue) |
Accessors | |
String | getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const |
bool | hasTorsionPhi () const |
Angle | getTorsionPhi () const |
bool | hasTorsionPsi () const |
Angle | getTorsionPsi () const |
bool | hasTorsionOmega () const |
Angle | getTorsionOmega () const |
Protein * | getProtein () |
const Protein * | getProtein () const |
Chain * | getChain () |
const Chain * | getChain () const |
SecondaryStructure * | getSecondaryStructure () |
const SecondaryStructure * | getSecondaryStructure () const |
PDBAtom * | getPDBAtom (Position position) |
const PDBAtom * | getPDBAtom (Position position) const |
void | setID (const String &id) |
const String & | getID () const |
void | setInsertionCode (char insertion_code) |
void | unsetInsertionCode () |
char | getInsertionCode () const |
Size | countPDBAtoms () const |
void | prepend (PDBAtom &atom) |
void | append (PDBAtom &atom) |
void | insert (PDBAtom &atom) |
void | insertBefore (PDBAtom &atom, Composite &before) |
void | insertAfter (PDBAtom &atom, Composite &after) |
bool | remove (PDBAtom &atom) |
void | spliceBefore (Residue &residue) |
void | spliceAfter (Residue &residue) |
void | splice (Residue &residue) |
Predicates | |
bool | isAminoAcid () const |
bool | isTerminal () const |
bool | isNTerminal () const |
bool | isCTerminal () const |
Type predicates | |
virtual bool | isResidue () const |
Debugging and Diagnostics | |
virtual bool | isValid () const |
virtual void | dump (std::ostream &s=std::cout, Size depth=0) const |
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bool | operator== (const Fragment &fragment) const |
bool | operator!= (const Fragment &fragment) const |
Fragment () | |
Fragment (const Fragment &fragment, bool deep=true) | |
Fragment (const String &name) | |
virtual | ~Fragment () |
Fragment & | operator= (const Fragment &fragment) |
virtual bool | isFragment () const |
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AtomContainer () | |
AtomContainer (const AtomContainer &atom_container, bool deep=true) | |
AtomContainer (const String &name) | |
virtual | ~AtomContainer () |
void | set (const AtomContainer &atom_container, bool deep=true) |
AtomContainer & | operator= (const AtomContainer &atom_container) |
void | get (AtomContainer &atom_container, bool deep=true) const |
void | swap (AtomContainer &atom_container) |
bool | operator== (const AtomContainer &atom_container) const |
bool | operator!= (const AtomContainer &atom_container) const |
bool | isSubAtomContainerOf (const AtomContainer &atom_container) const |
bool | isSuperAtomContainerOf (const AtomContainer &atom_container) const |
void | setName (const String &name) |
const String & | getName () const |
AtomContainer * | getSuperAtomContainer () |
const AtomContainer * | getSuperAtomContainer () const |
AtomContainer * | getAtomContainer (Position position) |
const AtomContainer * | getAtomContainer (Position position) const |
Atom * | getAtom (Position position) |
const Atom * | getAtom (Position position) const |
Atom * | getAtom (const String &name) |
const Atom * | getAtom (const String &name) const |
Size | countAtomContainers () const |
Size | countAtoms () const |
Size | countBonds () const |
Size | countInterBonds () const |
Size | countIntraBonds () const |
void | prepend (Atom &atom) |
void | append (Atom &atom) |
void | insert (Atom &atom) |
void | insertBefore (Atom &atom, Composite &before) |
void | insertAfter (Atom &atom, Composite &after) |
bool | remove (Atom &atom) |
Size | removeHavingProperty (BALL::Property p) |
Size | removeNotHavingProperty (BALL::Property p) |
Size | removeHavingProperty (const string &name) |
Size | removeNotHavingProperty (const string &name) |
void | prepend (AtomContainer &atom_container) |
void | append (AtomContainer &atom_container) |
void | insert (AtomContainer &atom_container) |
void | insertBefore (AtomContainer &atom_container, Composite &before) |
void | insertAfter (AtomContainer &atom_container, Composite &after) |
void | spliceBefore (AtomContainer &atom_container) |
void | spliceAfter (AtomContainer &atom_container) |
void | splice (AtomContainer &atom_container) |
bool | remove (AtomContainer &atom_container) |
void | destroyBonds () |
bool | applyIntraBond (UnaryProcessor< Bond > &processor) |
Apply to all bonds connecting two atoms inside this AtomContainer. More... | |
bool | applyInterBond (UnaryProcessor< Bond > &processor) |
Apply to all bonds connected to atoms outside this AtomContainer. More... | |
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template<typename T > | |
bool | applyLevel (ConstUnaryProcessor< T > &processor, long level) const |
AncestorIterator | beginAncestor () |
AncestorIterator | endAncestor () |
AncestorConstIterator | beginAncestor () const |
AncestorConstIterator | endAncestor () const |
ChildCompositeIterator | beginChildComposite () |
ChildCompositeIterator | endChildComposite () |
ChildCompositeConstIterator | beginChildComposite () const |
ChildCompositeConstIterator | endChildComposite () const |
ChildCompositeReverseIterator | rbeginChildComposite () |
ChildCompositeReverseIterator | rendChildComposite () |
ChildCompositeConstReverseIterator | rbeginChildComposite () const |
ChildCompositeConstReverseIterator | rendChildComposite () const |
CompositeIterator | beginComposite () |
CompositeIterator | endComposite () |
CompositeConstIterator | beginComposite () const |
CompositeConstIterator | endComposite () const |
CompositeReverseIterator | rbeginComposite () |
CompositeReverseIterator | rendComposite () |
CompositeConstReverseIterator | rbeginComposite () const |
CompositeConstReverseIterator | rendComposite () const |
void | deleteChildrenList_ (std::list< Composite *> &composites) |
template<typename T > | |
BALL_INLINE bool | apply (UnaryProcessor< T > &processor) |
template<typename T > | |
BALL_INLINE bool | apply (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
BALL_INLINE T * | getAncestor (const T &) |
template<typename T > | |
BALL_INLINE const T * | getAncestor (const T &) const |
template<typename T > | |
BALL_INLINE T * | getPrevious (const T &) |
template<typename T > | |
BALL_INLINE const T * | getPrevious (const T &dummy) const |
template<typename T > | |
BALL_INLINE T * | getNext (const T &) |
template<typename T > | |
BALL_INLINE const T * | getNext (const T &dummy) const |
template<typename T > | |
BALL_INLINE bool | hasAncestor (const T &dummy) const |
Composite () | |
Composite (const Composite &composite, bool deep=true) | |
virtual | ~Composite () |
void | destroy (bool virtual_destroy) |
void * | clone (Composite &root) const |
bool | operator== (const Composite &composite) const |
bool | operator!= (const Composite &composite) const |
bool | isEmpty () const |
bool | isRoot () const |
bool | isRootOf (const Composite &composite) const |
bool | isInterior () const |
bool | hasChild () const |
bool | isChildOf (const Composite &composite) const |
bool | isFirstChild () const |
bool | isFirstChildOf (const Composite &composite) const |
bool | isLastChild () const |
bool | isLastChildOf (const Composite &composite) const |
bool | hasParent () const |
bool | isParentOf (const Composite &composite) const |
bool | hasSibling () const |
bool | isSiblingOf (const Composite &composite) const |
bool | hasPreviousSibling () const |
bool | isPreviousSiblingOf (const Composite &composite) const |
bool | hasNextSibling () const |
bool | isNextSiblingOf (const Composite &composite) const |
bool | isDescendantOf (const Composite &composite) const |
template<typename T > | |
bool | hasAncestor (const T &dummy) const |
bool | isAncestorOf (const Composite &composite) const |
bool | isRelatedWith (const Composite &composite) const |
bool | isHomomorph (const Composite &composite) const |
bool | containsSelection () const |
virtual bool | isAtom () const |
virtual bool | isMolecule () const |
virtual bool | isProtein () const |
virtual bool | isChain () const |
void | host (Visitor< Composite > &visitor) |
template<typename T > | |
bool | applyAncestor (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyAncestor (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | applyChild (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyChild (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | applyDescendantPreorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | applyDescendantPostorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | applyDescendant (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyDescendant (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | applyPreorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyPreorder (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | applyPostorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyPostorder (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | apply (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | apply (ConstUnaryProcessor< T > &processor) const |
template<typename T > | |
bool | applyLevel (UnaryProcessor< T > &processor, long level) |
void | set (const Composite &composite, bool deep=true) |
Composite & | operator= (const Composite &composite) |
void | get (Composite &composite, bool deep=true) const |
Size | getDegree () const |
Size | count (const KernelPredicateType &predicate) const |
Size | countDescendants () const |
Size | getPathLength (const Composite &composite) const |
Size | getDepth () const |
Size | getHeight () const |
Composite & | getRoot () |
const Composite & | getRoot () const |
Composite * | getLowestCommonAncestor (const Composite &composite) |
const Composite * | getLowestCommonAncestor (const Composite &composite) const |
template<typename T > | |
T * | getAncestor (const T &) |
template<typename T > | |
const T * | getAncestor (const T &) const |
template<typename T > | |
T * | getPrevious (const T &) |
template<typename T > | |
const T * | getPrevious (const T &dummy) const |
template<typename T > | |
T * | getNext (const T &) |
template<typename T > | |
const T * | getNext (const T &dummy) const |
Composite * | getParent () |
const Composite * | getParent () const |
Composite * | getChild (Index index) |
const Composite * | getChild (Index index) const |
Composite * | getSibling (Index index) |
const Composite * | getSibling (Index index) const |
Composite * | getFirstChild () |
const Composite * | getFirstChild () const |
Composite * | getLastChild () |
const Composite * | getLastChild () const |
const PreciseTime & | getModificationTime () const |
const PreciseTime & | getSelectionTime () const |
void | stamp (StampType stamp=BOTH) |
void | prependChild (Composite &composite) |
void | appendChild (Composite &composite) |
void | insertBefore (Composite &composite) |
void | insertAfter (Composite &composite) |
void | spliceBefore (Composite &composite) |
void | spliceAfter (Composite &composite) |
void | splice (Composite &composite) |
bool | removeChild (Composite &child) |
Size | removeSelected () |
Size | removeUnselected () |
void | replace (Composite &composite) |
void | swap (Composite &composite) |
virtual void | select () |
virtual void | deselect () |
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PersistentObject () | |
virtual | ~PersistentObject () |
PersistenceManager & | operator>> (PersistenceManager &pm) const |
virtual void | finalize () |
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Object () | |
Default constructor. More... | |
Object (const Object &object) | |
Copy constructor. More... | |
virtual | ~Object () |
Destructor. More... | |
const Object & | operator= (const Object &) |
bool | operator== (const Object &object) const |
bool | operator!= (const Object &object) const |
bool | operator< (const Object &object) const |
bool | operator<= (const Object &object) const |
bool | operator>= (const Object &object) const |
bool | operator> (const Object &object) const |
int | compare (const Object &object) const |
virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
Handle | getHandle () const |
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virtual | ~AutoDeletable () |
void * | operator new (size_t size) |
void | operator delete (void *ptr) |
void * | operator new (size_t size, void *ptr) |
void | operator delete (void *ptr, void *) |
bool | isAutoDeletable () const |
void | setAutoDeletable (bool enable) |
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Selectable () | |
Selectable (const Selectable &selectable, bool deep=true) | |
virtual | ~Selectable () |
void | set (const Selectable &selectable, bool deep=true) |
const Selectable & | operator= (const Selectable &selectable) |
void | get (Selectable &selectable, bool deep=true) const |
void | swap (Selectable &selectable) |
virtual void | setSelected (bool selected) |
bool | isSelected () const |
bool | operator== (const Selectable &selectable) const |
bool | operator!= (const Selectable &selectable) const |
void | write (PersistenceManager &pm) const |
bool | read (PersistenceManager &pm) |
virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
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BALL_INLINE | PropertyManager () |
Default constructor. More... | |
BALL_INLINE | PropertyManager (const PropertyManager &property_manager) |
Copy constructor. More... | |
virtual | ~PropertyManager () |
Destructor. More... | |
void | set (const PropertyManager &property_manager) |
const PropertyManager & | operator= (const PropertyManager &property_manager) |
void | get (PropertyManager &property_manager) const |
void | swap (PropertyManager &property_manager) |
BitVector & | getBitVector () |
const BitVector & | getBitVector () const |
operator BitVector & () | |
void | setProperty (Property property) |
void | clearProperty (Property property) |
void | toggleProperty (Property property) |
Size | countProperties () const |
const NamedProperty & | getNamedProperty (Position index) const |
NamedProperty & | getNamedProperty (Position index) |
void | setProperty (const NamedProperty &property) |
void | setProperty (const std::string &name) |
void | setProperty (const std::string &name, bool value) |
void | setProperty (const std::string &name, int value) |
void | setProperty (const std::string &name, unsigned int value) |
void | setProperty (const std::string &name, float value) |
void | setProperty (const std::string &name, double value) |
void | setProperty (const std::string &name, const std::string &value) |
void | setProperty (const std::string &name, const PersistentObject &value) |
const NamedProperty & | getProperty (const std::string &name) const |
NamedPropertyIterator | beginNamedProperty () |
NamedPropertyIterator | endNamedProperty () |
void | clearProperty (const std::string &name) |
Size | countNamedProperties () const |
bool | hasProperty (Property property) const |
Query for an unnamed property. More... | |
bool | hasProperty (const std::string &name) const |
Query for a named property. More... | |
bool | operator== (const PropertyManager &pm) const |
bool | operator!= (const PropertyManager &pm) const |
Inequality operator. More... | |
void | write (PersistenceManager &pm) const |
Persistent stream writing. More... | |
bool | read (PersistenceManager &pm) |
Persistent stream reading. More... | |
bool | isValid () const |
void | dump (std::ostream &s=std::cout, Size depth=0) const |
Additional Inherited Members | |
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static bool | insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true) |
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static Handle | getNextHandle () |
static Handle | getNewHandle () |
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static void | clearLastPtr () |
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static UnaryProcessor< Composite > | DEFAULT_PROCESSOR |
static KernelPredicateType | DEFAULT_UNARY_PREDICATE |
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AutoDeletable () | |
AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false) | |
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bool | selected_ |
Residue class. This class is used to represent residues in proteins.
Enum used to describe the kind of name constructed by getFullName .
BALL::Residue::Residue | ( | ) |
Default constructor.
BALL::Residue::Residue | ( | const String & | name, |
const String & | id = BALL_RESIDUE_DEFAULT_ID , |
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char | insertion_code = BALL_RESIDUE_DEFAULT_INSERTION_CODE |
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) |
Detailled constructor.
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virtual |
Destructor.
void BALL::Residue::append | ( | PDBAtom & | atom | ) |
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virtual |
Clears the contents of this instance.
Reimplemented from BALL::AtomContainer.
Size BALL::Residue::countPDBAtoms | ( | ) | const |
Count the child PDBAtoms.
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virtual |
Clears the contents of this instance and removes it from all composite structures.
Reimplemented from BALL::AtomContainer.
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virtual |
Internal state dump. Dump the current internal state to the output ostream s with dumping depth depth .
s | output stream where to output the internal state |
depth | the dumping depth |
Reimplemented from BALL::Fragment.
Assign a Residue object from another instance.
Chain* BALL::Residue::getChain | ( | ) |
Get a pointer to the parent chain. The pointer is 0 if this instance does not have a parent chain.
const Chain* BALL::Residue::getChain | ( | ) | const |
Get a pointer to the parent chain. The pointer is 0 if this instance does not have a parent chain.
String BALL::Residue::getFullName | ( | FullNameType | type = ADD_VARIANT_EXTENSIONS | ) | const |
Return the fully qualified name. Residue names are modified as follows:
-N
is added for N terminal residues-C
is added for C terminal residue[-]S
is added for CYS involved in a disulphide bridge-M
is added for individual amino acids (C and N terminal)type | if type is set to NO_VARIANT_EXTENSIONS , the variant extension (-XX ) is omitted. |
char BALL::Residue::getInsertionCode | ( | ) | const |
Get the insertion code.
Protein* BALL::Residue::getProtein | ( | ) |
Get a pointer to the parent protein. The pointer is 0 if this instance does not have a parent protein.
const Protein* BALL::Residue::getProtein | ( | ) | const |
Get a constant pointer to the parent protein. The pointer is 0 if this instance does not have a parent protein.
SecondaryStructure* BALL::Residue::getSecondaryStructure | ( | ) |
Get a pointer to the parent secondary structure. The pointer is 0 if this instance does not have a parent secondary structure.
const SecondaryStructure* BALL::Residue::getSecondaryStructure | ( | ) | const |
Get a pointer to the parent secondary structure. The pointer is 0 if this instance does not have a parent secondary structure.
Angle BALL::Residue::getTorsionOmega | ( | ) | const |
Calculate the torsion angle psi.
Angle BALL::Residue::getTorsionPhi | ( | ) | const |
Calculate the torsion angle phi.
Angle BALL::Residue::getTorsionPsi | ( | ) | const |
Calculate the torsion angle psi.
bool BALL::Residue::hasTorsionOmega | ( | ) | const |
Check whether the torsion angle omega is defined.
bool BALL::Residue::hasTorsionPhi | ( | ) | const |
Check whether the torsion angle phi is defined.
bool BALL::Residue::hasTorsionPsi | ( | ) | const |
Check whether the torsion angle psi is defined.
void BALL::Residue::insert | ( | PDBAtom & | atom | ) |
bool BALL::Residue::isAminoAcid | ( | ) | const |
Test if this residue is an amino acid. Returns true, if this instance has the property "PROPERTY__AMINO_ACID".
bool BALL::Residue::isCTerminal | ( | ) | const |
Test if this residue is C-terminal. Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the last amino acid residue in its parent chain.
bool BALL::Residue::isNTerminal | ( | ) | const |
Test if this residue is N-terminal. Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the first amino acid residue in its parent chain.
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Test if the Composite is a Residue
Reimplemented from BALL::Composite.
bool BALL::Residue::isTerminal | ( | ) | const |
Test if this residue is terminal. Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the first or last amino acid residue in its parent chain.
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virtual |
Internal state and consistency self-validation.
true
if the internal state is correct (self-validated) and consistent, false
otherwise Reimplemented from BALL::AtomContainer.
Inequality operator
Equality operator. Two residues are equal if they have the same handle.
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virtual |
Reads a Residue object from a persistent stream.
pm | the persistence manager |
Reimplemented from BALL::Fragment.
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virtual |
Writes a Residue object to a persistent stream.
pm | the persistence manager |
Reimplemented from BALL::Fragment.
void BALL::Residue::prepend | ( | PDBAtom & | atom | ) |
Assignment with cloning facility. The assignment is either deep or shallow (default).
residue | the Residue to be copied (cloned) |
deep | make a deep (=true ) or shallow (=false ) copy |
void BALL::Residue::setID | ( | const String & | id | ) |
Set the ID.
id | the new ID |
void BALL::Residue::setInsertionCode | ( | char | insertion_code | ) |
Set the insertion code.
An insertion code is a visible ASCII character as well as the space character ' '.
insertion_code | the new insertion code |
InvalidArgument | if an unsupported insertion code has been specified. |
void BALL::Residue::splice | ( | Residue & | residue | ) |
Move the children of residue
into this instance. The children are inserted using spliceBefore .
void BALL::Residue::spliceAfter | ( | Residue & | residue | ) |
Cut all children of residue
and append them after the children of this instance.
residue | the residue to access |
void BALL::Residue::spliceBefore | ( | Residue & | residue | ) |
Cut all children of residue
and prepend them before the children of this instance.
residue | the residue to access |
void BALL::Residue::unsetInsertionCode | ( | ) |
Unset the current insertion code.
This is equivalent to calling setInsertionCode(' ').