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, CIon, XIon,   YIon, ZIon, Precursor, BIonMinusH20,   YIonMinusH20, BIonMinusNH3, YIonMinusNH3, NonIdentified,   Unannotated, 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...
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...
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...
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...
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...
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 ()

Protected Member Functions
void	setModification_ (const ResidueModification &mod)
	sets the modification (helper function) More...

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_
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_

Friends
class	ResidueDB
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.

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() [1/3]

Residue

(

)

default constructor

Residue() [2/3]

Residue

(

const Residue &

residue

)

copy constructor

Residue() [3/3]

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!=

(

const Residue &

residue

)

const

inequality operator

operator!=() [2/2]

bool operator!=

(

char

one_letter_code

)

const

equality operator for one letter code

operator=()

Residue& operator=

(

const Residue &

residue

)

assignment operator

operator==() [1/2]

bool operator==

(

const Residue &

residue

)

const

equality operator

operator==() [2/2]

bool operator==

(

char

one_letter_code

)

const

equality operator for one letter code

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()

void setModification

(

const String &

name

)

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

setModification_()

void setModification_ ( const ResidueModification &  mod )

protected

sets the modification (helper function)

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)

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

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