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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 contructor 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
Residueoperator= (const Residue &residue)
 assignment operator More...
 
void setName (const String &name)
 sets the name of the residue More...
 
const StringgetName () 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 StringgetShortName () 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 sysnonyms More...
 
void setThreeLetterCode (const String &three_letter_code)
 sets the name of the residue as three letter code More...
 
const StringgetThreeLetterCode () 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 StringgetOneLetterCode () 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 (DoubleReal weight)
 sets average weight of the residue (must be full, with N and C-terminus) More...
 
DoubleReal getAverageWeight (ResidueType res_type=Full) const
 returns average weight of the residue More...
 
void setMonoWeight (DoubleReal weight)
 sets mono weight of the residue (must be full, with N and C-terminus) More...
 
DoubleReal 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 StringgetModification () 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...
 
DoubleReal getPka () const
 returns the pka of the residue More...
 
DoubleReal getPkb () const
 returns the pkb of the residue More...
 
DoubleReal getPkc () const
 returns the pkc of the residue if it exists otherwise -1 More...
 
DoubleReal getPiValue () const
 calculates the isoelectric point using the pk* values More...
 
void setPka (DoubleReal value)
 sets the pka of the residue More...
 
void setPkb (DoubleReal value)
 sets the pkb of the residue More...
 
void setPkc (DoubleReal value)
 sets the pkc of the residue More...
 
DoubleReal getSideChainBasicity () const
 returns the side chain basicity More...
 
void setSideChainBasicity (DoubleReal gb_sc)
 sets the side chain basicity More...
 
DoubleReal getBackboneBasicityLeft () const
 returns the backbone basicitiy if located in N-terminal direction More...
 
void setBackboneBasicityLeft (DoubleReal gb_bb_l)
 sets the N-terminal direction backbone basicitiy More...
 
DoubleReal getBackboneBasicityRight () const
 returns the C-terminal direction backbone basicitiy More...
 
void setBackboneBasicityRight (DoubleReal 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 EmpiricalFormulagetInternalToFull ()
 
static DoubleReal getInternalToFullAverageWeight ()
 
static DoubleReal getInternalToFullMonoWeight ()
 
static const EmpiricalFormulagetNTerminalToFull ()
 
static DoubleReal getNTerminalToFullAverageWeight ()
 
static DoubleReal getNTerminalToFullMonoWeight ()
 
static const EmpiricalFormulagetCTerminalToFull ()
 
static DoubleReal getCTerminalToFullAverageWeight ()
 
static DoubleReal getCTerminalToFullMonoWeight ()
 
static const EmpiricalFormulagetBIonToFull ()
 
static DoubleReal getBIonToFullAverageWeight ()
 
static DoubleReal getBIonToFullMonoWeight ()
 
static const EmpiricalFormulagetAIonToFull ()
 
static DoubleReal getAIonToFullAverageWeight ()
 
static DoubleReal getAIonToFullMonoWeight ()
 
static const EmpiricalFormulagetYIonToFull ()
 
static DoubleReal getYIonToFullAverageWeight ()
 
static DoubleReal getYIonToFullMonoWeight ()
 
static const EmpiricalFormulagetCIonToFull ()
 
static DoubleReal getCIonToFullAverageWeight ()
 
static DoubleReal getCIonToFullMonoWeight ()
 
static const EmpiricalFormulagetCIonMinusOneToFull ()
 
static DoubleReal getCIonMinusOneToFullAverageWeight ()
 
static DoubleReal getCIonMinusOneToFullMonoWeight ()
 
static const EmpiricalFormulagetCIonPlusOneToFull ()
 
static DoubleReal getCIonPlusOneToFullAverageWeight ()
 
static DoubleReal getCIonPlusOneToFullMonoWeight ()
 
static const EmpiricalFormulagetCIonPlusTwoToFull ()
 
static DoubleReal getCIonPlusTwoToFullAverageWeight ()
 
static DoubleReal getCIonPlusTwoToFullMonoWeight ()
 
static const EmpiricalFormulagetXIonToFull ()
 
static DoubleReal getXIonToFullAverageWeight ()
 
static DoubleReal getXIonToFullMonoWeight ()
 
static const EmpiricalFormulagetZIonToFull ()
 
static DoubleReal getZIonToFullAverageWeight ()
 
static DoubleReal getZIonToFullMonoWeight ()
 
static const EmpiricalFormulagetZIonMinusOneToFull ()
 
static DoubleReal getZIonMinusOneToFullAverageWeight ()
 
static DoubleReal getZIonMinusOneToFullMonoWeight ()
 
static const EmpiricalFormulagetZIonPlusOneToFull ()
 
static DoubleReal getZIonPlusOneToFullAverageWeight ()
 
static DoubleReal getZIonPlusOneToFullMonoWeight ()
 
static const EmpiricalFormulagetZIonPlusTwoToFull ()
 
static DoubleReal getZIonPlusTwoToFullAverageWeight ()
 
static DoubleReal getZIonPlusTwoToFullMonoWeight ()
 

Protected Attributes

String name_
 
String short_name_
 
std::set< Stringsynonyms_
 
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< Stringloss_names_
 
std::vector< EmpiricalFormulaloss_formulas_
 
std::vector< StringNTerm_loss_names_
 
std::vector< EmpiricalFormulaNTerm_loss_formulas_
 
DoubleReal loss_average_weight_
 
DoubleReal loss_mono_weight_
 
std::vector< EmpiricalFormulalow_mass_ions_
 
DoubleReal pka_
 
DoubleReal pkb_
 
DoubleReal pkc_
 
DoubleReal gb_sc_
 
DoubleReal gb_bb_l_
 
DoubleReal gb_bb_r_
 
std::set< Stringresidue_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.

Member Enumeration Documentation

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 ( )
inlinestatic
static DoubleReal getAIonToFullAverageWeight ( )
inlinestatic
static DoubleReal getAIonToFullMonoWeight ( )
inlinestatic
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 ( )
inlinestatic
static DoubleReal getBIonToFullAverageWeight ( )
inlinestatic
static DoubleReal getBIonToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getCIonMinusOneToFull ( )
inlinestatic
static DoubleReal getCIonMinusOneToFullAverageWeight ( )
inlinestatic
static DoubleReal getCIonMinusOneToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getCIonPlusOneToFull ( )
inlinestatic
static DoubleReal getCIonPlusOneToFullAverageWeight ( )
inlinestatic
static DoubleReal getCIonPlusOneToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getCIonPlusTwoToFull ( )
inlinestatic
static DoubleReal getCIonPlusTwoToFullAverageWeight ( )
inlinestatic
static DoubleReal getCIonPlusTwoToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getCIonToFull ( )
inlinestatic
static DoubleReal getCIonToFullAverageWeight ( )
inlinestatic
static DoubleReal getCIonToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getCTerminalToFull ( )
inlinestatic
static DoubleReal getCTerminalToFullAverageWeight ( )
inlinestatic
static DoubleReal getCTerminalToFullMonoWeight ( )
inlinestatic
EmpiricalFormula getFormula ( ResidueType  res_type = Full) const

returns the empirical formula of the residue

static const EmpiricalFormula& getInternalToFull ( )
inlinestatic
static DoubleReal getInternalToFullAverageWeight ( )
inlinestatic
static DoubleReal 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

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 ( )
inlinestatic
static DoubleReal getNTerminalToFullAverageWeight ( )
inlinestatic
static DoubleReal 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().

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 ( )
inlinestatic
static DoubleReal getXIonToFullAverageWeight ( )
inlinestatic
static DoubleReal getXIonToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getYIonToFull ( )
inlinestatic
static DoubleReal getYIonToFullAverageWeight ( )
inlinestatic
static DoubleReal getYIonToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getZIonMinusOneToFull ( )
inlinestatic
static DoubleReal getZIonMinusOneToFullAverageWeight ( )
inlinestatic
static DoubleReal getZIonMinusOneToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getZIonPlusOneToFull ( )
inlinestatic
static DoubleReal getZIonPlusOneToFullAverageWeight ( )
inlinestatic
static DoubleReal getZIonPlusOneToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getZIonPlusTwoToFull ( )
inlinestatic
static DoubleReal getZIonPlusTwoToFullAverageWeight ( )
inlinestatic
static DoubleReal getZIonPlusTwoToFullMonoWeight ( )
inlinestatic
static const EmpiricalFormula& getZIonToFull ( )
inlinestatic
static DoubleReal getZIonToFullAverageWeight ( )
inlinestatic
static DoubleReal 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 ( 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

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5