Residue Class Reference

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 constructor More...
	Residue (const Residue &residue)
	copy constructor More...
	Residue (const String &name, const String &three_letter_code, const String &one_letter_code, const EmpiricalFormula &formula)
	detailed constructor More...
virtual	~Residue ()
	destructor More...
Assignment
Residue &	operator= (const Residue &residue)
	assignment operator More...
void	setName (const String &name)
	sets the name of the residue More...
const String &	getName () const
	returns the name of the residue More...
void	setShortName (const String &short_name)
	sets the short name of the residue, this name is used in the PeptideSequence for output More...
const String &	getShortName () const
	returns the short name of the residue More...
void	setSynonyms (const std::set< String > &synonyms)
	sets the synonyms More...
void	addSynonym (const String &synonym)
	adds a synonym More...
const std::set< String > &	getSynonyms () const
	returns the synonyms More...
void	setThreeLetterCode (const String &three_letter_code)
	sets the name of the residue as three letter code More...
const String &	getThreeLetterCode () const
	returns the name of the residue as three letter code More...
void	setOneLetterCode (const String &one_letter_code)
	sets the name as one letter code More...
const String &	getOneLetterCode () const
	returns the name as one letter code More...
void	addLossFormula (const EmpiricalFormula &)
	adds a neutral loss formula More...
void	setLossFormulas (const std::vector< EmpiricalFormula > &)
	sets the neutral loss formulas More...
void	addNTermLossFormula (const EmpiricalFormula &)
	adds N-terminal losses More...
void	setNTermLossFormulas (const std::vector< EmpiricalFormula > &)
	sets the N-terminal losses More...
const std::vector< EmpiricalFormula > &	getLossFormulas () const
	returns the neutral loss formulas More...
const std::vector< EmpiricalFormula > &	getNTermLossFormulas () const
	returns N-terminal loss formulas More...
void	setLossNames (const std::vector< String > &name)
	set the neutral loss molecule name More...
void	setNTermLossNames (const std::vector< String > &name)
	sets the N-terminal loss names More...
void	addLossName (const String &name)
	add neutral loss molecule name More...
void	addNTermLossName (const String &name)
	adds a N-terminal loss name More...
const std::vector< String > &	getLossNames () const
	gets neutral loss name (if there is one, else returns an empty string) More...
const std::vector< String > &	getNTermLossNames () const
	returns the N-terminal loss names More...
void	setFormula (const EmpiricalFormula &formula)
	set empirical formula of the residue (must be full, with N and C-terminus) More...
EmpiricalFormula	getFormula (ResidueType res_type=Full) const
	returns the empirical formula of the residue More...
void	setAverageWeight (double weight)
	sets average weight of the residue (must be full, with N and C-terminus) More...
double	getAverageWeight (ResidueType res_type=Full) const
	returns average weight of the residue More...
void	setMonoWeight (double weight)
	sets mono weight of the residue (must be full, with N and C-terminus) More...
double	getMonoWeight (ResidueType res_type=Full) const
	returns mono weight of the residue More...
void	setModification (const String &name)
	sets by the name, this mod should be present in ModificationsDB More...
const String &	getModification () const
	returns the name of the modification to the modification More...
void	setLowMassIons (const std::vector< EmpiricalFormula > &low_mass_ions)
	sets the low mass marker ions as a vector of formulas More...
const std::vector< EmpiricalFormula > &	getLowMassIons () const
	returns a vector of formulas with the low mass markers of the residue More...
void	setResidueSets (const std::set< String > &residues_sets)
	sets the residue sets the amino acid is contained in More...
void	addResidueSet (const String &residue_sets)
	adds a residue set to the residue sets More...
const std::set< String > &	getResidueSets () const
	returns the residue sets this residue is contained in More...
Predicates
bool	hasNeutralLoss () const
	true if the residue has neutral loss More...
bool	hasNTermNeutralLosses () const
	true if N-terminal neutral losses are set More...
bool	operator== (const Residue &residue) const
	equality operator More...
bool	operator!= (const Residue &residue) const
	inequality operator More...
bool	operator== (char one_letter_code) const
	equality operator for one letter code More...
bool	operator!= (char one_letter_code) const
	equality operator for one letter code More...
double	getPka () const
	returns the pka of the residue More...
double	getPkb () const
	returns the pkb of the residue More...
double	getPkc () const
	returns the pkc of the residue if it exists otherwise -1 More...
double	getPiValue () const
	calculates the isoelectric point using the pk* values More...
void	setPka (double value)
	sets the pka of the residue More...
void	setPkb (double value)
	sets the pkb of the residue More...
void	setPkc (double value)
	sets the pkc of the residue More...
double	getSideChainBasicity () const
	returns the side chain basicity More...
void	setSideChainBasicity (double gb_sc)
	sets the side chain basicity More...
double	getBackboneBasicityLeft () const
	returns the backbone basicitiy if located in N-terminal direction More...
void	setBackboneBasicityLeft (double gb_bb_l)
	sets the N-terminal direction backbone basicitiy More...
double	getBackboneBasicityRight () const
	returns the C-terminal direction backbone basicitiy More...
void	setBackboneBasicityRight (double gb_bb_r)
	sets the C-terminal direction backbone basicity More...
bool	isModified () const
	true if the residue is a modified one More...
bool	isInResidueSet (const String &residue_set)
	true if the residue is contained in the set More...

Static Public Member Functions
static String	getResidueTypeName (const ResidueType res_type)
	returns the ion name given as a residue type More...
Typedefs and Constants
static const EmpiricalFormula &	getInternalToFull ()
static double	getInternalToFullAverageWeight ()
static double	getInternalToFullMonoWeight ()
static const EmpiricalFormula &	getNTerminalToFull ()
static double	getNTerminalToFullAverageWeight ()
static double	getNTerminalToFullMonoWeight ()
static const EmpiricalFormula &	getCTerminalToFull ()
static double	getCTerminalToFullAverageWeight ()
static double	getCTerminalToFullMonoWeight ()
static const EmpiricalFormula &	getBIonToFull ()
static double	getBIonToFullAverageWeight ()
static double	getBIonToFullMonoWeight ()
static const EmpiricalFormula &	getAIonToFull ()
static double	getAIonToFullAverageWeight ()
static double	getAIonToFullMonoWeight ()
static const EmpiricalFormula &	getYIonToFull ()
static double	getYIonToFullAverageWeight ()
static double	getYIonToFullMonoWeight ()
static const EmpiricalFormula &	getCIonToFull ()
static double	getCIonToFullAverageWeight ()
static double	getCIonToFullMonoWeight ()
static const EmpiricalFormula &	getCIonMinusOneToFull ()
static double	getCIonMinusOneToFullAverageWeight ()
static double	getCIonMinusOneToFullMonoWeight ()
static const EmpiricalFormula &	getCIonPlusOneToFull ()
static double	getCIonPlusOneToFullAverageWeight ()
static double	getCIonPlusOneToFullMonoWeight ()
static const EmpiricalFormula &	getCIonPlusTwoToFull ()
static double	getCIonPlusTwoToFullAverageWeight ()
static double	getCIonPlusTwoToFullMonoWeight ()
static const EmpiricalFormula &	getXIonToFull ()
static double	getXIonToFullAverageWeight ()
static double	getXIonToFullMonoWeight ()
static const EmpiricalFormula &	getZIonToFull ()
static double	getZIonToFullAverageWeight ()
static double	getZIonToFullMonoWeight ()
static const EmpiricalFormula &	getZIonMinusOneToFull ()
static double	getZIonMinusOneToFullAverageWeight ()
static double	getZIonMinusOneToFullMonoWeight ()
static const EmpiricalFormula &	getZIonPlusOneToFull ()
static double	getZIonPlusOneToFullAverageWeight ()
static double	getZIonPlusOneToFullMonoWeight ()
static const EmpiricalFormula &	getZIonPlusTwoToFull ()
static double	getZIonPlusTwoToFullAverageWeight ()
static double	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_
double	average_weight_
double	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_
double	loss_average_weight_
double	loss_mono_weight_
std::vector< EmpiricalFormula >	low_mass_ions_
double	pka_
double	pkb_
double	pkc_
double	gb_sc_
double	gb_bb_l_
double	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 More...

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.

Constructor & Destructor Documentation

Residue

(

)

default constructor

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 ( )

inlinestatic

static double getAIonToFullAverageWeight ( )

inlinestatic

static double getAIonToFullMonoWeight ( )

inlinestatic

double getAverageWeight

(

ResidueType

res_type = Full

)

const

returns average weight of the residue

double getBackboneBasicityLeft

(

)

const

returns the backbone basicitiy if located in N-terminal direction

double getBackboneBasicityRight

(

)

const

returns the C-terminal direction backbone basicitiy

static const EmpiricalFormula& getBIonToFull ( )

inlinestatic

static double getBIonToFullAverageWeight ( )

inlinestatic

static double getBIonToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getCIonMinusOneToFull ( )

inlinestatic

static double getCIonMinusOneToFullAverageWeight ( )

inlinestatic

static double getCIonMinusOneToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getCIonPlusOneToFull ( )

inlinestatic

static double getCIonPlusOneToFullAverageWeight ( )

inlinestatic

static double getCIonPlusOneToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getCIonPlusTwoToFull ( )

inlinestatic

static double getCIonPlusTwoToFullAverageWeight ( )

inlinestatic

static double getCIonPlusTwoToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getCIonToFull ( )

inlinestatic

static double getCIonToFullAverageWeight ( )

inlinestatic

static double getCIonToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getCTerminalToFull ( )

inlinestatic

static double getCTerminalToFullAverageWeight ( )

inlinestatic

static double getCTerminalToFullMonoWeight ( )

inlinestatic

EmpiricalFormula getFormula

(

ResidueType

res_type = Full

)

const

returns the empirical formula of the residue

static const EmpiricalFormula& getInternalToFull ( )

inlinestatic

static double getInternalToFullAverageWeight ( )

inlinestatic

static double getInternalToFullMonoWeight ( )

inlinestatic

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

double 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 ( )

inlinestatic

static double getNTerminalToFullAverageWeight ( )

inlinestatic

static double getNTerminalToFullMonoWeight ( )

inlinestatic

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().

double getPiValue

(

)

const

calculates the isoelectric point using the pk* values

double getPka

(

)

const

returns the pka of the residue

double getPkb

(

)

const

returns the pkb of the residue

double 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

double getSideChainBasicity

(

)

const

returns the side chain basicity

const std::set<String>& getSynonyms

(

)

const

returns the synonyms

const String& getThreeLetterCode

(

)

const

returns the name of the residue as three letter code

static const EmpiricalFormula& getXIonToFull ( )

inlinestatic

static double getXIonToFullAverageWeight ( )

inlinestatic

static double getXIonToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getYIonToFull ( )

inlinestatic

static double getYIonToFullAverageWeight ( )

inlinestatic

static double getYIonToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getZIonMinusOneToFull ( )

inlinestatic

static double getZIonMinusOneToFullAverageWeight ( )

inlinestatic

static double getZIonMinusOneToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getZIonPlusOneToFull ( )

inlinestatic

static double getZIonPlusOneToFullAverageWeight ( )

inlinestatic

static double getZIonPlusOneToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getZIonPlusTwoToFull ( )

inlinestatic

static double getZIonPlusTwoToFullAverageWeight ( )

inlinestatic

static double getZIonPlusTwoToFullMonoWeight ( )

inlinestatic

static const EmpiricalFormula& getZIonToFull ( )

inlinestatic

static double getZIonToFullAverageWeight ( )

inlinestatic

static double getZIonToFullMonoWeight ( )

inlinestatic

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==

(

const Residue &

residue

)

const

equality operator

bool operator==

(

char

one_letter_code

)

const

equality operator for one letter code

void setAverageWeight

(

double

weight

)

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

void setBackboneBasicityLeft

(

double

gb_bb_l

)

sets the N-terminal direction backbone basicitiy

void setBackboneBasicityRight

(

double

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

(

double

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

(

double

value

)

sets the pka of the residue

void setPkb

(

double

value

)

sets the pkb of the residue

void setPkc

(

double

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

(

double

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

double average_weight_

protected

EmpiricalFormula formula_

protected

double gb_bb_l_

protected

double gb_bb_r_

protected

double gb_sc_

protected

EmpiricalFormula internal_formula_

protected

bool is_modified_

protected

double loss_average_weight_

protected

std::vector<EmpiricalFormula> loss_formulas_

protected

double loss_mono_weight_

protected

std::vector<String> loss_names_

protected

std::vector<EmpiricalFormula> low_mass_ions_

protected

String modification_

protected

double 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

double pka_

protected

double pkb_

protected

double 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