Representation of a residue. More...

#include <OpenMS/CHEMISTRY/Residue.h>

Public Types
Enums

enum	ResidueType { Full = 0, Internal, NTerminal, CTerminal, AIon, BIon, CIonMinusOne, CIon, CIonPlusOne, CIonPlusTwo, XIon, YIon, ZIonMinusOne, ZIon, ZIonPlusOne, ZIonPlusTwo, SizeOfResidueType }
Public Member Functions
Constructors

	Residue ()
	default contructor
	Residue (const Residue &residue)
	copy constructor
	Residue (const String &name, const String &three_letter_code, const String &one_letter_code, const EmpiricalFormula &formula)
	detailed constructor
virtual	~Residue ()
	destructor
Assignment

Residue &	operator= (const Residue &residue)
	assignment operator


void	setName (const String &name)
	sets the name of the residue
const String &	getName () const
	returns the name of the residue
void	setShortName (const String &short_name)
	sets the short name of the residue, this name is used in the PeptideSequence for output
const String &	getShortName () const
	returns the short name of the residue
void	setSynonyms (const std::set< String > &synonyms)
	sets the synonyms
void	addSynonym (const String &synonym)
	adds a synonym
const std::set< String > &	getSynonyms () const
	returns the sysnonyms
void	setThreeLetterCode (const String &three_letter_code)
	sets the name of the residue as three letter code
const String &	getThreeLetterCode () const
	returns the name of the residue as three letter code
void	setOneLetterCode (const String &one_letter_code)
	sets the name as one letter code
const String &	getOneLetterCode () const
	returns the name as one letter code
void	addLossFormula (const EmpiricalFormula &)
	adds a neutral loss formula
void	setLossFormulas (const std::vector< EmpiricalFormula > &)
	sets the neutral loss formulas
void	addNTermLossFormula (const EmpiricalFormula &)
	adds N-terminal losses
void	setNTermLossFormulas (const std::vector< EmpiricalFormula > &)
	sets the N-terminal losses
const std::vector < EmpiricalFormula > &	getLossFormulas () const
	returns the neutral loss formulas
const std::vector < EmpiricalFormula > &	getNTermLossFormulas () const
	returns N-terminal loss formulas
void	setLossNames (const std::vector< String > &name)
	set the neutral loss molecule name
void	setNTermLossNames (const std::vector< String > &name)
	sets the N-terminal loss names
void	addLossName (const String &name)
	add neutral loss molecule name
void	addNTermLossName (const String &name)
	adds a N-terminal loss name
const std::vector< String > &	getLossNames () const
	gets neutral loss name (if there is one, else returns an empty string)
const std::vector< String > &	getNTermLossNames () const
	returns the N-terminal loss names
void	setFormula (const EmpiricalFormula &formula)
	set empirical formula of the residue (must be full, with N and C-terminus)
EmpiricalFormula	getFormula (ResidueType res_type=Full) const
	returns the empirical formula of the residue
void	setAverageWeight (DoubleReal weight)
	sets average weight of the residue (must be full, with N and C-terminus)
DoubleReal	getAverageWeight (ResidueType res_type=Full) const
	returns average weight of the residue
void	setMonoWeight (DoubleReal weight)
	sets mono weight of the residue (must be full, with N and C-terminus)
DoubleReal	getMonoWeight (ResidueType res_type=Full) const
	returns mono weight of the residue
void	setModification (const String &name)
	sets by the name, this mod should be present in ModificationsDB
const String &	getModification () const
	returns the name of the modification to the modification
void	setLowMassIons (const std::vector< EmpiricalFormula > &low_mass_ions)
	sets the low mass marker ions as a vector of formulas
const std::vector < EmpiricalFormula > &	getLowMassIons () const
	returns a vector of formulas with the low mass markers of the residue
void	setResidueSets (const std::set< String > &residues_sets)
	sets the residue sets the amino acid is contained in
void	addResidueSet (const String &residue_sets)
	adds a residue set to the residue sets
const std::set< String > &	getResidueSets () const
	returns the residue sets this residue is contained in
Predicates

bool	hasNeutralLoss () const
	true if the residue has neutral loss
bool	hasNTermNeutralLosses () const
	true if N-terminal neutral losses are set
bool	operator== (const Residue &residue) const
	equality operator
bool	operator!= (const Residue &residue) const
	inequality operator
bool	operator== (char one_letter_code) const
	equality operator for one letter code
bool	operator!= (char one_letter_code) const
	equality operator for one letter code
DoubleReal	getPka () const
	returns the pka of the residue
DoubleReal	getPkb () const
	returns the pkb of the residue
DoubleReal	getPkc () const
	returns the pkc of the residue if it exists otherwise -1
DoubleReal	getPiValue () const
	calculates the isoelectric point using the pk* values
void	setPka (DoubleReal value)
	sets the pka of the residue
void	setPkb (DoubleReal value)
	sets the pkb of the residue
void	setPkc (DoubleReal value)
	sets the pkc of the residue
DoubleReal	getSideChainBasicity () const
	returns the side chain basicity
void	setSideChainBasicity (DoubleReal gb_sc)
	sets the side chain basicity
DoubleReal	getBackboneBasicityLeft () const
	returns the backbone basicitiy if located in N-terminal direction
void	setBackboneBasicityLeft (DoubleReal gb_bb_l)
	sets the N-terminal direction backbone basicitiy
DoubleReal	getBackboneBasicityRight () const
	returns the C-terminal direction backbone basicitiy
void	setBackboneBasicityRight (DoubleReal gb_bb_r)
	sets the C-terminal direction backbone basicity
bool	isModified () const
	true if the residue is a modified one
bool	isInResidueSet (const String &residue_set)
	true if the residue is contained in the set
Static Public Member Functions
static String	getResidueTypeName (const ResidueType res_type)
	returns the ion name given as a residue type
Typedefs and Constants

static const EmpiricalFormula &	getInternalToFull ()
static DoubleReal	getInternalToFullAverageWeight ()
static DoubleReal	getInternalToFullMonoWeight ()
static const EmpiricalFormula &	getNTerminalToFull ()
static DoubleReal	getNTerminalToFullAverageWeight ()
static DoubleReal	getNTerminalToFullMonoWeight ()
static const EmpiricalFormula &	getCTerminalToFull ()
static DoubleReal	getCTerminalToFullAverageWeight ()
static DoubleReal	getCTerminalToFullMonoWeight ()
static const EmpiricalFormula &	getBIonToFull ()
static DoubleReal	getBIonToFullAverageWeight ()
static DoubleReal	getBIonToFullMonoWeight ()
static const EmpiricalFormula &	getAIonToFull ()
static DoubleReal	getAIonToFullAverageWeight ()
static DoubleReal	getAIonToFullMonoWeight ()
static const EmpiricalFormula &	getYIonToFull ()
static DoubleReal	getYIonToFullAverageWeight ()
static DoubleReal	getYIonToFullMonoWeight ()
static const EmpiricalFormula &	getCIonToFull ()
static DoubleReal	getCIonToFullAverageWeight ()
static DoubleReal	getCIonToFullMonoWeight ()
static const EmpiricalFormula &	getCIonMinusOneToFull ()
static DoubleReal	getCIonMinusOneToFullAverageWeight ()
static DoubleReal	getCIonMinusOneToFullMonoWeight ()
static const EmpiricalFormula &	getCIonPlusOneToFull ()
static DoubleReal	getCIonPlusOneToFullAverageWeight ()
static DoubleReal	getCIonPlusOneToFullMonoWeight ()
static const EmpiricalFormula &	getCIonPlusTwoToFull ()
static DoubleReal	getCIonPlusTwoToFullAverageWeight ()
static DoubleReal	getCIonPlusTwoToFullMonoWeight ()
static const EmpiricalFormula &	getXIonToFull ()
static DoubleReal	getXIonToFullAverageWeight ()
static DoubleReal	getXIonToFullMonoWeight ()
static const EmpiricalFormula &	getZIonToFull ()
static DoubleReal	getZIonToFullAverageWeight ()
static DoubleReal	getZIonToFullMonoWeight ()
static const EmpiricalFormula &	getZIonMinusOneToFull ()
static DoubleReal	getZIonMinusOneToFullAverageWeight ()
static DoubleReal	getZIonMinusOneToFullMonoWeight ()
static const EmpiricalFormula &	getZIonPlusOneToFull ()
static DoubleReal	getZIonPlusOneToFullAverageWeight ()
static DoubleReal	getZIonPlusOneToFullMonoWeight ()
static const EmpiricalFormula &	getZIonPlusTwoToFull ()
static DoubleReal	getZIonPlusTwoToFullAverageWeight ()
static DoubleReal	getZIonPlusTwoToFullMonoWeight ()
Protected Attributes
String	name_
String	short_name_
std::set< String >	synonyms_
String	three_letter_code_
String	one_letter_code_
EmpiricalFormula	formula_
EmpiricalFormula	internal_formula_
DoubleReal	average_weight_
DoubleReal	mono_weight_
bool	is_modified_
String	pre_mod_name_
String	modification_
std::vector< String >	loss_names_
std::vector< EmpiricalFormula >	loss_formulas_
std::vector< String >	NTerm_loss_names_
std::vector< EmpiricalFormula >	NTerm_loss_formulas_
DoubleReal	loss_average_weight_
DoubleReal	loss_mono_weight_
std::vector< EmpiricalFormula >	low_mass_ions_
DoubleReal	pka_
DoubleReal	pkb_
DoubleReal	pkc_
DoubleReal	gb_sc_
DoubleReal	gb_bb_l_
DoubleReal	gb_bb_r_
std::set< String >	residue_sets_
Friends
std::ostream &	operator<< (std::ostream &os, const Residue &residue)
	ostream iterator to write the residue to a stream

Detailed Description

Representation of a residue.

This class represents residues. Residues can have many different attributes, like the formula physico-chemical values of properties and so on.

A very important property of residues are their modifications. By default no modification is present. Any modification which is present in the ModificationsDB can be applied, if appropriate.

Member Enumeration Documentation

enum ResidueType

Enumerator:

Full
Internal
NTerminal
CTerminal
AIon
BIon
CIonMinusOne
CIon
CIonPlusOne
CIonPlusTwo
XIon
YIon
ZIonMinusOne
ZIon
ZIonPlusOne
ZIonPlusTwo
SizeOfResidueType	Todo: add c+1, z+1, z+2 ion types (Andreas)

Constructor & Destructor Documentation

Residue ( )

default contructor

Residue ( const Residue & residue )

copy constructor

Residue	(	const String &	name,
		const String &	three_letter_code,
		const String &	one_letter_code,
		const EmpiricalFormula &	formula
	)

detailed constructor

virtual ~Residue ( ) [virtual]

destructor

Member Function Documentation

void addLossFormula ( const EmpiricalFormula & )

adds a neutral loss formula

void addLossName ( const String & name )

add neutral loss molecule name

void addNTermLossFormula ( const EmpiricalFormula & )

adds N-terminal losses

void addNTermLossName ( const String & name )

adds a N-terminal loss name

void addResidueSet ( const String & residue_sets )

adds a residue set to the residue sets

void addSynonym ( const String & synonym )

adds a synonym

static const EmpiricalFormula& getAIonToFull ( ) [inline, static]

static DoubleReal getAIonToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getAIonToFullMonoWeight ( ) [inline, static]

DoubleReal getAverageWeight ( ResidueType res_type = Full ) const

returns average weight of the residue

DoubleReal getBackboneBasicityLeft ( ) const

returns the backbone basicitiy if located in N-terminal direction

DoubleReal getBackboneBasicityRight ( ) const

returns the C-terminal direction backbone basicitiy

static const EmpiricalFormula& getBIonToFull ( ) [inline, static]

static DoubleReal getBIonToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getBIonToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getCIonMinusOneToFull ( ) [inline, static]

static DoubleReal getCIonMinusOneToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getCIonMinusOneToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getCIonPlusOneToFull ( ) [inline, static]

static DoubleReal getCIonPlusOneToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getCIonPlusOneToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getCIonPlusTwoToFull ( ) [inline, static]

static DoubleReal getCIonPlusTwoToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getCIonPlusTwoToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getCIonToFull ( ) [inline, static]

static DoubleReal getCIonToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getCIonToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getCTerminalToFull ( ) [inline, static]

static DoubleReal getCTerminalToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getCTerminalToFullMonoWeight ( ) [inline, static]

EmpiricalFormula getFormula ( ResidueType res_type = Full ) const

returns the empirical formula of the residue

static const EmpiricalFormula& getInternalToFull ( ) [inline, static]

static DoubleReal getInternalToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getInternalToFullMonoWeight ( ) [inline, static]

const std::vector<EmpiricalFormula>& getLossFormulas ( ) const

returns the neutral loss formulas

const std::vector<String>& getLossNames ( ) const

gets neutral loss name (if there is one, else returns an empty string)

const std::vector<EmpiricalFormula>& getLowMassIons ( ) const

returns a vector of formulas with the low mass markers of the residue

const String& getModification ( ) const

returns the name of the modification to the modification

DoubleReal getMonoWeight ( ResidueType res_type = Full ) const

returns mono weight of the residue

const String& getName ( ) const

returns the name of the residue

static const EmpiricalFormula& getNTerminalToFull ( ) [inline, static]

static DoubleReal getNTerminalToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getNTerminalToFullMonoWeight ( ) [inline, static]

const std::vector<EmpiricalFormula>& getNTermLossFormulas ( ) const

returns N-terminal loss formulas

const std::vector<String>& getNTermLossNames ( ) const

returns the N-terminal loss names

const String& getOneLetterCode ( ) const

returns the name as one letter code

Referenced by AAIndex::calculateGB().

DoubleReal getPiValue ( ) const

calculates the isoelectric point using the pk* values

DoubleReal getPka ( ) const

returns the pka of the residue

DoubleReal getPkb ( ) const

returns the pkb of the residue

DoubleReal getPkc ( ) const

returns the pkc of the residue if it exists otherwise -1

const std::set<String>& getResidueSets ( ) const

returns the residue sets this residue is contained in

static String getResidueTypeName ( const ResidueType res_type ) [static]

returns the ion name given as a residue type

const String& getShortName ( ) const

returns the short name of the residue

DoubleReal getSideChainBasicity ( ) const

returns the side chain basicity

const std::set<String>& getSynonyms ( ) const

returns the sysnonyms

const String& getThreeLetterCode ( ) const

returns the name of the residue as three letter code

static const EmpiricalFormula& getXIonToFull ( ) [inline, static]

static DoubleReal getXIonToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getXIonToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getYIonToFull ( ) [inline, static]

static DoubleReal getYIonToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getYIonToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getZIonMinusOneToFull ( ) [inline, static]

static DoubleReal getZIonMinusOneToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getZIonMinusOneToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getZIonPlusOneToFull ( ) [inline, static]

static DoubleReal getZIonPlusOneToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getZIonPlusOneToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getZIonPlusTwoToFull ( ) [inline, static]

static DoubleReal getZIonPlusTwoToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getZIonPlusTwoToFullMonoWeight ( ) [inline, static]

static const EmpiricalFormula& getZIonToFull ( ) [inline, static]

static DoubleReal getZIonToFullAverageWeight ( ) [inline, static]

References EmpiricalFormula::getAverageWeight().

static DoubleReal getZIonToFullMonoWeight ( ) [inline, static]

bool hasNeutralLoss ( ) const

true if the residue has neutral loss

bool hasNTermNeutralLosses ( ) const

true if N-terminal neutral losses are set

bool isInResidueSet ( const String & residue_set )

true if the residue is contained in the set

bool isModified ( ) const

true if the residue is a modified one

bool operator!= ( const Residue & residue ) const

inequality operator

bool operator!= ( char one_letter_code ) const

equality operator for one letter code

Residue& operator= ( const Residue & residue )

assignment operator

bool operator== ( char one_letter_code ) const

equality operator for one letter code

bool operator== ( const Residue & residue ) const

equality operator

void setAverageWeight ( DoubleReal weight )

sets average weight of the residue (must be full, with N and C-terminus)

void setBackboneBasicityLeft ( DoubleReal gb_bb_l )

sets the N-terminal direction backbone basicitiy

void setBackboneBasicityRight ( DoubleReal gb_bb_r )

sets the C-terminal direction backbone basicity

void setFormula ( const EmpiricalFormula & formula )

set empirical formula of the residue (must be full, with N and C-terminus)

void setLossFormulas ( const std::vector< EmpiricalFormula > & )

sets the neutral loss formulas

void setLossNames ( const std::vector< String > & name )

set the neutral loss molecule name

void setLowMassIons ( const std::vector< EmpiricalFormula > & low_mass_ions )

sets the low mass marker ions as a vector of formulas

void setModification ( const String & name )

sets by the name, this mod should be present in ModificationsDB

void setMonoWeight ( DoubleReal weight )

sets mono weight of the residue (must be full, with N and C-terminus)

void setName ( const String & name )

sets the name of the residue

Accessors

void setNTermLossFormulas ( const std::vector< EmpiricalFormula > & )

sets the N-terminal losses

void setNTermLossNames ( const std::vector< String > & name )

sets the N-terminal loss names

void setOneLetterCode ( const String & one_letter_code )

sets the name as one letter code

void setPka ( DoubleReal value )

sets the pka of the residue

void setPkb ( DoubleReal value )

sets the pkb of the residue

void setPkc ( DoubleReal value )

sets the pkc of the residue

void setResidueSets ( const std::set< String > & residues_sets )

sets the residue sets the amino acid is contained in

void setShortName ( const String & short_name )

sets the short name of the residue, this name is used in the PeptideSequence for output

void setSideChainBasicity ( DoubleReal gb_sc )

sets the side chain basicity

void setSynonyms ( const std::set< String > & synonyms )

sets the synonyms

void setThreeLetterCode ( const String & three_letter_code )

sets the name of the residue as three letter code

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const Residue &	residue
	)			`[friend]`

ostream iterator to write the residue to a stream

Member Data Documentation

DoubleReal average_weight_ [protected]

EmpiricalFormula formula_ [protected]

DoubleReal gb_bb_l_ [protected]

DoubleReal gb_bb_r_ [protected]

DoubleReal gb_sc_ [protected]

EmpiricalFormula internal_formula_ [protected]

bool is_modified_ [protected]

DoubleReal loss_average_weight_ [protected]

std::vector<EmpiricalFormula> loss_formulas_ [protected]

DoubleReal loss_mono_weight_ [protected]

std::vector<String> loss_names_ [protected]

std::vector<EmpiricalFormula> low_mass_ions_ [protected]

String modification_ [protected]

DoubleReal mono_weight_ [protected]

String name_ [protected]

std::vector<EmpiricalFormula> NTerm_loss_formulas_ [protected]

std::vector<String> NTerm_loss_names_ [protected]

String one_letter_code_ [protected]

DoubleReal pka_ [protected]

DoubleReal pkb_ [protected]

DoubleReal pkc_ [protected]

String pre_mod_name_ [protected]

std::set<String> residue_sets_ [protected]

String short_name_ [protected]

std::set<String> synonyms_ [protected]

String three_letter_code_ [protected]

Residue Class Reference [Chemistry]

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Friends

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

Residue Class Reference
[Chemistry]