Residue Class Reference
[Molecular Datastructures]

Residue class. More...

#include <residue.h>

Inheritance diagram for Residue:

List of all members.

Public Types
Enums
enum	Property {   PROPERTY__NON_STANDARD = Fragment::NUMBER_OF_PROPERTIES + 1, PROPERTY__AMINO_ACID, PROPERTY__WATER, PROPERTY__HAS_SSBOND,   PROPERTY__C_TERMINAL, PROPERTY__N_TERMINAL, PROPERTY__CYCLIC, NUMBER_OF_PROPERTIES }
	The number of predefined properties for AtomContainer. More...
enum	FullNameType { NO_VARIANT_EXTENSIONS, ADD_VARIANT_EXTENSIONS, ADD_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_ID }
	Enum used to describe the kind of name constructed by getFullName . More...
Public Member Functions
bool	operator== (const Residue &residue) const throw ()
	Equality operator.
bool	operator!= (const Residue &residue) const throw ()
	Inequality operator.
Constructors and Destructors
	Residue () throw ()
	Default constructor.
	Residue (const Residue &residue, bool deep=true) throw ()
	Copy constructor.
	Residue (const String &name, const String &id=BALL_RESIDUE_DEFAULT_ID, char insertion_code=BALL_RESIDUE_DEFAULT_INSERTION_CODE) throw ()
	Detailled constructor.
virtual	~Residue () throw ()
	Destructor.
virtual void	clear () throw ()
	Clears the contents of this instance.
virtual void	destroy () throw ()
	Clears the contents of this instance and removes it from all composite structures.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Writes a Residue object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a Residue object from a persistent stream.
Assignment
void	set (const Residue &residue, bool deep=true) throw ()
	Assignment with cloning facility.
Residue &	operator= (const Residue &residue) throw ()
	Assignment operator.
void	get (Residue &residue, bool deep=true) const throw ()
	Assign a Residue object from another instance.
void	swap (Residue &residue) throw ()
	Swap the contents of two Residue objects.
Accessors
String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const throw ()
	Return the fully qualified name.
bool	hasTorsionPhi () const throw ()
	Check whether the torsion angle phi is defined.
Angle	getTorsionPhi () const throw ()
	Calculate the torsion angle phi.
bool	hasTorsionPsi () const throw ()
	Check whether the torsion angle psi is defined.
Angle	getTorsionPsi () const throw ()
	Calculate the torsion angle psi.
Protein *	getProtein () throw ()
	Get a pointer to the parent protein.
const Protein *	getProtein () const throw ()
	Get a constant pointer to the parent protein.
Chain *	getChain () throw ()
	Get a pointer to the parent chain.
const Chain *	getChain () const throw ()
	Get a pointer to the parent chain.
SecondaryStructure *	getSecondaryStructure () throw ()
	Get a pointer to the parent secondary structure.
const SecondaryStructure *	getSecondaryStructure () const throw ()
	Get a pointer to the parent secondary structure.
PDBAtom *	getPDBAtom (Position position) throw ()
	Get a pointer to a child PDBAtom at a given position.
const PDBAtom *	getPDBAtom (Position position) const throw ()
	Get a pointer to a child PDBAtom at a given position.
void	setID (const String &id) throw ()
	Set the ID.
const String &	getID () const throw ()
	Retrieve the ID.
void	setInsertionCode (char insertion_code) throw ()
	Set the insertion code.
char	getInsertionCode () const throw ()
	Get the insertion code.
Size	countPDBAtoms () const throw ()
	Count the child PDBAtoms.
void	prepend (PDBAtom &atom) throw ()
	Prepend a PDBAtom at position 0.
void	append (PDBAtom &atom) throw ()
	Append a PDBAtom at the last position.
void	insert (PDBAtom &atom) throw ()
	Insert a PDBAtom at the last position.
void	insertBefore (PDBAtom &atom, Composite &before) throw ()
	Insert a PDBAtom before a given Composite object.
void	insertAfter (PDBAtom &atom, Composite &after) throw ()
	Insert a PDBAtom after a given Composite object.
bool	remove (PDBAtom &atom) throw ()
	Remove a PDBAtom.
void	spliceBefore (Residue &residue) throw ()
	Cut all children of residue and prepend them before the children of this instance.
void	spliceAfter (Residue &residue) throw ()
	Cut all children of residue and append them after the children of this instance.
void	splice (Residue &residue) throw ()
	Move the children of residue into this instance.
Predicates
bool	isAminoAcid () const throw ()
	Test if this residue is an amino acid.
bool	isTerminal () const throw ()
	Test if this residue is terminal.
bool	isNTerminal () const throw ()
	Test if this residue is N-terminal.
bool	isCTerminal () const throw ()
	Test if this residue is C-terminal.
Debugging and Diagnostics
virtual bool	isValid () const throw ()
	Internal state and consistency self-validation.
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const throw ()
	Internal state dump.

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Detailed Description

Residue class.

This class is used to represent residues in proteins.

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Member Enumeration Documentation

enum Residue::FullNameType

Enum used to describe the kind of name constructed by getFullName . Enumeration values: NO_VARIANT_EXTENSIONS  This returns the unmodified residue name only. ADD_VARIANT_EXTENSIONS  Add the residue variant extensions (e.g. '-C' for C-terminal residues).

enum Residue::Property

The number of predefined properties for AtomContainer. Enumeration values: PROPERTY__CYCLIC  Property for cyclic peptides. This property is set by the build bonds processor, if an atom of the first and an atom of the last residue in a chain share a bond. Reimplemented from Fragment.

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Member Function Documentation

void Residue::append (  PDBAtom &  atom  )  throw ()

Append a PDBAtom at the last position. Parameters: atom  the PDBAtom to append

Size Residue::countPDBAtoms (   )  const throw ()

Count the child PDBAtoms. Returns: Size the number of PDBAtoms

virtual void Residue::dump (  std::ostream &  s = std::cout, Size  depth = 0 )  const throw () [virtual]

Internal state dump. Dump the current internal state to the output ostream s with dumping depth depth . Parameters: s  output stream where to output the internal state depth  the dumping depth Reimplemented from Fragment.

void Residue::get (  Residue &  residue, bool  deep = true )  const throw ()

Assign a Residue object from another instance.

const Chain* Residue::getChain (   )  const throw ()

Get a pointer to the parent chain. The pointer is 0 if this instance does not have a parent chain. Returns: Chain* - constant pointer to the parent chain

Chain* Residue::getChain (   )  throw ()

Get a pointer to the parent chain. The pointer is 0 if this instance does not have a parent chain. Returns: Chain* - mutable pointer to the parent chain

String Residue::getFullName (  FullNameType  type = ADD_VARIANT_EXTENSIONS  )  const throw ()

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) Parameters: type  if type is set to NO_VARIANT_EXTENSIONS, the variant extension (-XX) is omitted. Returns: String the full fragment name

const String& Residue::getID (   )  const throw ()

Retrieve the ID. Returns: String the ID

char Residue::getInsertionCode (   )  const throw ()

Get the insertion code. Returns: char the insertion code

const PDBAtom* Residue::getPDBAtom (  Position  position  )  const throw ()

Get a pointer to a child PDBAtom at a given position. The pointer is 0 if this instance does not have a PDBAtom at this position. Parameters: position  the position of the child PDBAtom Returns: PDBAtom* - constant pointer to the child

PDBAtom* Residue::getPDBAtom (  Position  position  )  throw ()

Get a pointer to a child PDBAtom at a given position. The pointer is 0 if this instance does not have a PDBAtom at this position. Parameters: position  the position of the child PDBAtom Returns: PDBAtom* - mutable pointer to the child

const Protein* Residue::getProtein (   )  const throw ()

Get a constant pointer to the parent protein. The pointer is 0 if this instance does not have a parent protein. Returns: Protein* - constant pointer to the parent protein

Protein* Residue::getProtein (   )  throw ()

Get a pointer to the parent protein. The pointer is 0 if this instance does not have a parent protein. Returns: Protein* - mutable pointer to the parent protein

const SecondaryStructure* Residue::getSecondaryStructure (   )  const throw ()

Get a pointer to the parent secondary structure. The pointer is 0 if this instance does not have a parent secondary structure. Returns: SecondaryStructure* - mutable pointer to the parent chain

SecondaryStructure* Residue::getSecondaryStructure (   )  throw ()

Get a pointer to the parent secondary structure. The pointer is 0 if this instance does not have a parent secondary structure. Returns: SecondaryStructure* - mutable pointer to the parent chain

Angle Residue::getTorsionPhi (   )  const throw ()

Calculate the torsion angle phi. Returns: Angle - the torsion angle phi

Angle Residue::getTorsionPsi (   )  const throw ()

Calculate the torsion angle psi. Returns: Angle - the torsion angle phi

bool Residue::hasTorsionPhi (   )  const throw ()

Check whether the torsion angle phi is defined. Returns: bool

bool Residue::hasTorsionPsi (   )  const throw ()

Check whether the torsion angle psi is defined. Returns: bool

void Residue::insert (  PDBAtom &  atom  )  throw ()

Insert a PDBAtom at the last position. Parameters: atom  the PDBAtom to append

void Residue::insertAfter (  PDBAtom &  atom, Composite &  after )  throw ()

Insert a PDBAtom after a given Composite object. Parameters: atom  the PDBAtom to insert after  the Composite object to insert after

void Residue::insertBefore (  PDBAtom &  atom, Composite &  before )  throw ()

Insert a PDBAtom before a given Composite object. Parameters: atom  the PDBAtom to insert before  the Composite object to insert before

bool Residue::isAminoAcid (   )  const throw ()

Test if this residue is an amino acid. Returns true, if this instance has the property "PROPERTY__AMINO_ACID". Returns: bool

bool Residue::isCTerminal (   )  const throw ()

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. Returns: bool

bool Residue::isNTerminal (   )  const throw ()

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. Returns: bool

bool Residue::isTerminal (   )  const throw ()

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. Returns: bool

virtual bool Residue::isValid (   )  const throw () [virtual]

Internal state and consistency self-validation. Returns: bool - true if the internal state is correct (self-validated) and consistent, false otherwise Reimplemented from AtomContainer.

bool Residue::operator!= (  const Residue &  residue  )  const throw ()

Inequality operator. See also: operator ==

bool Residue::operator== (  const Residue &  residue  )  const throw ()

Equality operator. Two residues are equal if they have the same handle. See also: Object::operator ==

void Residue::persistentRead (  PersistenceManager &  pm  )  throw (Exception::GeneralException) [virtual]

Reads a Residue object from a persistent stream. Parameters: pm  the persistence manager Reimplemented from Fragment.

void Residue::persistentWrite (  PersistenceManager &  pm, const char *  name = 0 )  const throw (Exception::GeneralException) [virtual]

Writes a Residue object to a persistent stream. Parameters: pm  the persistence manager Reimplemented from Fragment.

void Residue::prepend (  PDBAtom &  atom  )  throw ()

Prepend a PDBAtom at position 0. Parameters: atom  the PDBAtom to prepend

bool Residue::remove (  PDBAtom &  atom  )  throw ()

Remove a PDBAtom. Parameters: atom  the PDBAtom to remove

void Residue::set (  const Residue &  residue, bool  deep = true )  throw ()

Assignment with cloning facility. The assignment is either deep or shallow (default). Parameters: residue  the Residue to be copied (cloned) deep  make a deep (=true) or shallow (=false) copy

void Residue::setID (  const String &  id  )  throw ()

Set the ID. Parameters: id  the new ID

void Residue::setInsertionCode (  char  insertion_code  )  throw ()

Set the insertion code. Parameters: insertion_code  the new insertion code

void Residue::splice (  Residue &  residue  )  throw ()

Move the children of residue into this instance. The children are inserted using spliceBefore .

void Residue::spliceAfter (  Residue &  residue  )  throw ()

Cut all children of residue and append them after the children of this instance. Parameters: residue  the residue to access

void Residue::spliceBefore (  Residue &  residue  )  throw ()

Cut all children of residue and prepend them before the children of this instance. Parameters: residue  the residue to access

void Residue::swap (  Residue &  residue  )  throw ()

Swap the contents of two Residue objects.