Representation of a residue. More...

#include <OpenMS/CHEMISTRY/Residue.h>

Collaboration diagram for Residue:

Public Member Functions
Constructors
	Residue ()
	Default constructor. More...

	Residue (const Residue &)=default
	Copy constructor. More...

	Residue (Residue &&)=default
	Move 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 &)=default
	Assignment operator. More...

Residue &	operator= (Residue &&) &=default
	Move assignment operator. More...

Accessors
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 (String of size 3) More...

const String &	getThreeLetterCode () const
	returns the name of the residue as three letter code (String of size 3) More...

void	setOneLetterCode (const String &one_letter_code)
	sets the name as one letter code (String of size 1) More...

const String &	getOneLetterCode () const
	returns the name as one letter code (String of size 1) 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 monoisotopic weight of the residue (must be full, with N and C-terminus) More...

double	getMonoWeight (ResidueType res_type=Full) const
	returns monoisotopic weight of the residue More...

const ResidueModification *	getModification () const
	returns a pointer to the modification, or zero if none is set More...

void	setModification (const String &name)
	sets the modification by name; the mod should be present in ModificationsDB More...

void	setModification (const ResidueModification *mod)
	sets the modification by existing ResMod (make sure it exists in ModificationDB) More...

const String &	getModificationName () const
	returns the name (ID) of the modification, or an empty string if none is set 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...

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...

Static Public Member Functions
Formula conversion
Computes empirical formula required to add to the desired type Computes the empirical formula required to be added to convert an internal residue (inside an AA sequence) to that of a residue of the desired type. For example, to obtain the conversion formula for an internal ion to a "y ion", use getInternalToYTerm(). Formulae that need to be added to the internal residues to get to fragment type from http://www.matrixscience.com/help/fragmentation_help.html
static const EmpiricalFormula &	getInternalToFull ()

static const EmpiricalFormula &	getInternalToNTerm ()

static const EmpiricalFormula &	getInternalToCTerm ()

static const EmpiricalFormula &	getInternalToAIon ()

static const EmpiricalFormula &	getInternalToBIon ()

static const EmpiricalFormula &	getInternalToCIon ()

static const EmpiricalFormula &	getInternalToXIon ()

static const EmpiricalFormula &	getInternalToYIon ()

static const EmpiricalFormula &	getInternalToZIon ()

Friends
class	ResidueDB

Enums
enum	ResidueType { Full = 0, Internal, NTerminal, CTerminal, AIon, BIon, CIon, XIon, YIon, ZIon, Precursor, BIonMinusH20, YIonMinusH20, BIonMinusNH3, YIonMinusNH3, NonIdentified, Unannotated, SizeOfResidueType }

static String	getResidueTypeName (const ResidueType res_type)
	returns the ion name given as a residue type More...

Predicates
std::ostream &	operator<< (std::ostream &os, const Residue &residue)
	ostream iterator to write the residue to a stream More...

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_

const ResidueModification *	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_

double	internal_to_full_monoweight_ = getInternalToFull().getMonoWeight()

double	internal_to_nterm_monoweight_ = getInternalToNTerm().getMonoWeight()

double	internal_to_cterm_monoweight_ = getInternalToCTerm().getMonoWeight()

double	internal_to_a_monoweight_ = getInternalToAIon().getMonoWeight()

double	internal_to_b_monoweight_ = getInternalToBIon().getMonoWeight()

double	internal_to_c_monoweight_ = getInternalToCIon().getMonoWeight()

double	internal_to_x_monoweight_ = getInternalToXIon().getMonoWeight()

double	internal_to_y_monoweight_ = getInternalToYIon().getMonoWeight()

double	internal_to_z_monoweight_ = getInternalToZIon().getMonoWeight()

static char	residueTypeToIonLetter (const ResidueType &res_type)
	helper for mapping residue types to letters for Text annotations and labels More...

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...

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...

String	toString () const

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

◆ ResidueType

enum ResidueType

Enumerator
Full	with N-terminus and C-terminus
Internal	internal, without any termini
NTerminal	only N-terminus
CTerminal	only C-terminus
AIon	MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond.
BIon	MS:1001224 N-terminus up to the peptide bond.
CIon	MS:1001231 N-terminus up to the amide/C-alpha bond.
XIon	MS:1001228 amide/C-alpha bond up to the C-terminus.
YIon	MS:1001220 peptide bond up to the C-terminus.
ZIon	MS:1001230 C-alpha/carbonyl carbon bond.
Precursor	MS:1001523 Precursor ion.
BIonMinusH20	MS:1001222 b ion without water.
YIonMinusH20	MS:1001223 y ion without water.
BIonMinusNH3	MS:1001232 b ion without ammonia.
YIonMinusNH3	MS:1001233 y ion without ammonia.
NonIdentified	MS:1001240 Non-identified ion.
Unannotated	no stored annotation
SizeOfResidueType

Constructor & Destructor Documentation

◆ Residue() [1/4]

Residue ( )

Default constructor.

◆ Residue() [2/4]

Residue ( const Residue & )

default

Copy constructor.

◆ Residue() [3/4]

Residue ( Residue && )

default

Move constructor.

◆ Residue() [4/4]

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

Detailed constructor.

◆ ~Residue()

virtual ~Residue ( )

virtual

Destructor.

Member Function Documentation

◆ addLossFormula()

void addLossFormula ( const EmpiricalFormula & )

adds a neutral loss formula

◆ addLossName()

void addLossName ( const String & name )

add neutral loss molecule name

◆ addNTermLossFormula()

void addNTermLossFormula ( const EmpiricalFormula & )

adds N-terminal losses

◆ addNTermLossName()

void addNTermLossName ( const String & name )

adds a N-terminal loss name

◆ addResidueSet()

void addResidueSet ( const String & residue_sets )

adds a residue set to the residue sets

◆ addSynonym()

void addSynonym ( const String & synonym )

adds a synonym

◆ getAverageWeight()

double getAverageWeight ( ResidueType res_type = Full ) const

returns average weight of the residue

◆ getBackboneBasicityLeft()

double getBackboneBasicityLeft ( ) const

returns the backbone basicitiy if located in N-terminal direction

◆ getBackboneBasicityRight()

double getBackboneBasicityRight ( ) const

returns the C-terminal direction backbone basicitiy

◆ getFormula()

EmpiricalFormula getFormula ( ResidueType res_type = Full ) const

returns the empirical formula of the residue

◆ getInternalToAIon()

static const EmpiricalFormula& getInternalToAIon ( )

inlinestatic

◆ getInternalToBIon()

static const EmpiricalFormula& getInternalToBIon ( )

inlinestatic

◆ getInternalToCIon()

static const EmpiricalFormula& getInternalToCIon ( )

inlinestatic

◆ getInternalToCTerm()

static const EmpiricalFormula& getInternalToCTerm ( )

inlinestatic

◆ getInternalToFull()

static const EmpiricalFormula& getInternalToFull ( )

inlinestatic

◆ getInternalToNTerm()

static const EmpiricalFormula& getInternalToNTerm ( )

inlinestatic

◆ getInternalToXIon()

static const EmpiricalFormula& getInternalToXIon ( )

inlinestatic

◆ getInternalToYIon()

static const EmpiricalFormula& getInternalToYIon ( )

inlinestatic

◆ getInternalToZIon()

static const EmpiricalFormula& getInternalToZIon ( )

inlinestatic

◆ getLossFormulas()

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

returns the neutral loss formulas

◆ getLossNames()

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

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

◆ getLowMassIons()

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

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

◆ getModification()

const ResidueModification* getModification ( ) const

returns a pointer to the modification, or zero if none is set

◆ getModificationName()

const String& getModificationName ( ) const

returns the name (ID) of the modification, or an empty string if none is set

◆ getMonoWeight()

double getMonoWeight ( ResidueType res_type = Full ) const

returns monoisotopic weight of the residue

◆ getName()

const String& getName ( ) const

returns the name of the residue

◆ getNTermLossFormulas()

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

returns N-terminal loss formulas

◆ getNTermLossNames()

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

returns the N-terminal loss names

◆ getOneLetterCode()

const String& getOneLetterCode ( ) const

returns the name as one letter code (String of size 1)

Referenced by AAIndex::calculateGB().

◆ getPiValue()

double getPiValue ( ) const

calculates the isoelectric point using the pk* values

◆ getPka()

double getPka ( ) const

returns the pka of the residue

◆ getPkb()

double getPkb ( ) const

returns the pkb of the residue

◆ getPkc()

double getPkc ( ) const

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

◆ getResidueSets()

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

returns the residue sets this residue is contained in

◆ getResidueTypeName()

static String getResidueTypeName ( const ResidueType res_type )

static

returns the ion name given as a residue type

◆ getShortName()

const String& getShortName ( ) const

returns the short name of the residue

◆ getSideChainBasicity()

double getSideChainBasicity ( ) const

returns the side chain basicity

◆ getSynonyms()

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

returns the synonyms

◆ getThreeLetterCode()

const String& getThreeLetterCode ( ) const

returns the name of the residue as three letter code (String of size 3)

◆ hasNeutralLoss()

bool hasNeutralLoss ( ) const

true if the residue has neutral loss

◆ hasNTermNeutralLosses()

bool hasNTermNeutralLosses ( ) const

true if N-terminal neutral losses are set

◆ isInResidueSet()

bool isInResidueSet ( const String & residue_set )

true if the residue is contained in the set

◆ isModified()

bool isModified ( ) const

true if the residue is a modified one

◆ operator!=() [1/2]

bool operator!= ( char one_letter_code ) const

equality operator for one letter code

◆ operator!=() [2/2]

bool operator!= ( const Residue & residue ) const

inequality operator

◆ operator=() [1/2]

Residue& operator= ( const Residue & )

default

Assignment operator.

◆ operator=() [2/2]

Residue& operator= ( Residue && ) &

default

Move assignment operator.

◆ operator==() [1/2]

bool operator== ( char one_letter_code ) const

equality operator for one letter code

◆ operator==() [2/2]

bool operator== ( const Residue & residue ) const

equality operator

◆ residueTypeToIonLetter()

static char residueTypeToIonLetter ( const ResidueType & res_type )

static

helper for mapping residue types to letters for Text annotations and labels

◆ setAverageWeight()

void setAverageWeight ( double weight )

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

◆ setBackboneBasicityLeft()

void setBackboneBasicityLeft ( double gb_bb_l )

sets the N-terminal direction backbone basicitiy

◆ setBackboneBasicityRight()

void setBackboneBasicityRight ( double gb_bb_r )

sets the C-terminal direction backbone basicity

◆ setFormula()

void setFormula ( const EmpiricalFormula & formula )

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

◆ setLossFormulas()

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

sets the neutral loss formulas

◆ setLossNames()

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

set the neutral loss molecule name

◆ setLowMassIons()

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

sets the low mass marker ions as a vector of formulas

◆ setModification() [1/2]

void setModification ( const ResidueModification * mod )

sets the modification by existing ResMod (make sure it exists in ModificationDB)

◆ setModification() [2/2]

void setModification ( const String & name )

sets the modification by name; the mod should be present in ModificationsDB

◆ setMonoWeight()

void setMonoWeight ( double weight )

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

◆ setName()

void setName ( const String & name )

sets the name of the residue

◆ setNTermLossFormulas()

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

sets the N-terminal losses

◆ setNTermLossNames()

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

sets the N-terminal loss names

◆ setOneLetterCode()

void setOneLetterCode ( const String & one_letter_code )

sets the name as one letter code (String of size 1)

◆ setPka()

void setPka ( double value )

sets the pka of the residue

◆ setPkb()

void setPkb ( double value )

sets the pkb of the residue

◆ setPkc()

void setPkc ( double value )

sets the pkc of the residue

◆ setResidueSets()

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

sets the residue sets the amino acid is contained in

◆ setShortName()

void setShortName ( const String & short_name )

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

◆ setSideChainBasicity()

void setSideChainBasicity ( double gb_sc )

sets the side chain basicity

◆ setSynonyms()

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

sets the synonyms

◆ setThreeLetterCode()

void setThreeLetterCode ( const String & three_letter_code )

sets the name of the residue as three letter code (String of size 3)

◆ toString()

String toString ( ) const

Write as Origin+Modification, e.g. M(Oxidation), or X[945.34] or N[+14.54] for user-defined mods. This requires the Residue to have a valid OneLetterCode and an optional (but valid) ResidueModification (see ResidueModification::toString())

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const Residue &	residue
	)

friend

ostream iterator to write the residue to a stream

◆ ResidueDB

friend class ResidueDB

friend

Member Data Documentation

◆ average_weight_

double average_weight_

protected

◆ formula_

EmpiricalFormula formula_

protected

◆ gb_bb_l_

double gb_bb_l_

protected

◆ gb_bb_r_

double gb_bb_r_

protected

◆ gb_sc_

double gb_sc_

protected

◆ internal_formula_

EmpiricalFormula internal_formula_

protected

◆ internal_to_a_monoweight_

double internal_to_a_monoweight_ = getInternalToAIon().getMonoWeight()

protected

◆ internal_to_b_monoweight_

double internal_to_b_monoweight_ = getInternalToBIon().getMonoWeight()

protected

◆ internal_to_c_monoweight_

double internal_to_c_monoweight_ = getInternalToCIon().getMonoWeight()

protected

◆ internal_to_cterm_monoweight_

double internal_to_cterm_monoweight_ = getInternalToCTerm().getMonoWeight()

protected

◆ internal_to_full_monoweight_

double internal_to_full_monoweight_ = getInternalToFull().getMonoWeight()

protected

◆ internal_to_nterm_monoweight_

double internal_to_nterm_monoweight_ = getInternalToNTerm().getMonoWeight()

protected

◆ internal_to_x_monoweight_

double internal_to_x_monoweight_ = getInternalToXIon().getMonoWeight()

protected

◆ internal_to_y_monoweight_

double internal_to_y_monoweight_ = getInternalToYIon().getMonoWeight()

protected

◆ internal_to_z_monoweight_

double internal_to_z_monoweight_ = getInternalToZIon().getMonoWeight()

protected

◆ loss_average_weight_

double loss_average_weight_

protected

◆ loss_formulas_

std::vector<EmpiricalFormula> loss_formulas_

protected

◆ loss_mono_weight_

double loss_mono_weight_

protected

◆ loss_names_

std::vector<String> loss_names_

protected

◆ low_mass_ions_

std::vector<EmpiricalFormula> low_mass_ions_

protected

◆ modification_

const ResidueModification* modification_

protected

◆ mono_weight_

double mono_weight_

protected

◆ name_

String name_

protected

◆ NTerm_loss_formulas_

std::vector<EmpiricalFormula> NTerm_loss_formulas_

protected

◆ NTerm_loss_names_

std::vector<String> NTerm_loss_names_

protected

◆ one_letter_code_

String one_letter_code_

protected

◆ pka_

double pka_

protected

◆ pkb_

double pkb_

protected

◆ pkc_

double pkc_

protected

◆ residue_sets_

std::set<String> residue_sets_

protected

◆ short_name_

String short_name_

protected

◆ synonyms_

std::set<String> synonyms_

protected

◆ three_letter_code_

String three_letter_code_

protected

Public Member Functions

Static Public Member Functions

Friends

Enums

Predicates

Detailed Description

Member Enumeration Documentation

◆ ResidueType

Constructor & Destructor Documentation

◆ Residue() [1/4]

◆ Residue() [2/4]

◆ Residue() [3/4]

◆ Residue() [4/4]

◆ ~Residue()

Member Function Documentation

◆ addLossFormula()

◆ addLossName()

◆ addNTermLossFormula()

◆ addNTermLossName()

◆ addResidueSet()

◆ addSynonym()

◆ getAverageWeight()

◆ getBackboneBasicityLeft()

◆ getBackboneBasicityRight()

◆ getFormula()

◆ getInternalToAIon()

◆ getInternalToBIon()

◆ getInternalToCIon()

◆ getInternalToCTerm()

◆ getInternalToFull()

◆ getInternalToNTerm()

◆ getInternalToXIon()

◆ getInternalToYIon()

◆ getInternalToZIon()

◆ getLossFormulas()

◆ getLossNames()

◆ getLowMassIons()

◆ getModification()

◆ getModificationName()

◆ getMonoWeight()

◆ getName()

◆ getNTermLossFormulas()

◆ getNTermLossNames()

◆ getOneLetterCode()

◆ getPiValue()

◆ getPka()

◆ getPkb()

◆ getPkc()

◆ getResidueSets()

◆ getResidueTypeName()

◆ getShortName()

◆ getSideChainBasicity()

◆ getSynonyms()

◆ getThreeLetterCode()

◆ hasNeutralLoss()

◆ hasNTermNeutralLosses()

◆ isInResidueSet()

◆ isModified()

◆ operator!=() [1/2]

◆ operator!=() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==() [1/2]

◆ operator==() [2/2]

◆ residueTypeToIonLetter()

◆ setAverageWeight()

◆ setBackboneBasicityLeft()

◆ setBackboneBasicityRight()

◆ setFormula()

◆ setLossFormulas()

◆ setLossNames()

◆ setLowMassIons()

◆ setModification() [1/2]

◆ setModification() [2/2]

◆ setMonoWeight()

◆ setName()

◆ setNTermLossFormulas()

◆ setNTermLossNames()

◆ setOneLetterCode()

◆ setPka()