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Residue Class Reference
[Chemistry]

#include <OpenMS/CHEMISTRY/Residue.h>

List of all members.


Detailed Description

Representation of a residue.

Typedefs and Constants

typedef std::vector
< EmpiricalFormula >
::const_iterator 
LowMassConstIterator
typedef std::vector
< EmpiricalFormula >::iterator 
LowMassIterator
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 EmpiricalFormulagetXIonToFull ()
static DoubleReal getXIonToFullAverageWeight ()
static DoubleReal getXIonToFullMonoWeight ()
static const EmpiricalFormulagetZIonToFull ()
static DoubleReal getZIonToFullAverageWeight ()
static DoubleReal getZIonToFullMonoWeight ()

Public Types

Enums
enum  ResidueType {
  Full = 0, Internal, NTerminal, CTerminal,
  AIon, BIon, CIon, XIon,
  YIon, ZIon
}

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, const EmpiricalFormula &neutral_loss)
 detailed constructor
virtual ~Residue ()
 destructor
Assignment
Residueoperator= (const Residue &residue)
 assignment operator
void setName (const String &name)
 sets the name of the residue
const StringgetName () 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 StringgetShortName () 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 StringgetThreeLetterCode () 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 StringgetOneLetterCode () const
 returns the name as one letter code
void setLossFormula (const EmpiricalFormula &)
 sets the neutral loss formula (if there is one)
const EmpiricalFormulagetLossFormula () const
 returns the neutral loss formula (or just an empty string if there is none)
void setLossAverageWeight (DoubleReal weight)
 sets the average weight of the neutral loss molecule
DoubleReal getLossAverageWeight () const
 return the average weight of the neutral loss molecule
void setLossMonoWeight (DoubleReal weight)
 sets the mono isotopic weight of the neutral loss molecule
DoubleReal getLossMonoWeight () const
 returns the mono isotopic weight of the neutral loss molecule
void setLossName (const String &name)
 set the neutral loss molecule weight (if there is one)
const StringgetLossName () const
 gets neutral loss name (if there is one, else returns an empty string)
void setFormula (const EmpiricalFormula &formula, ResidueType res_type=Full)
 set empirical formula of the residue
EmpiricalFormula getFormula (ResidueType res_type=Full) const
 returns the empirical formula of thre residue
void setAverageWeight (DoubleReal weight, ResidueType res_type=Full)
 sets average weight of the residue
DoubleReal getAverageWeight (ResidueType res_type=Full) const
 returns average weight of the residue
void setMonoWeight (DoubleReal weight, ResidueType res_type=Full)
 sets mono weight of the residue
DoubleReal getMonoWeight (ResidueType res_type=Full) const
 returns mono weight of the residue
void setModification (ResidueModification *modification)
 sets the modification pointer
const ResidueModificationgetModification () const
 returns a pointer to the modification, if the residue is unmodified, 0 is returned
void setUnmodifiedName (const String &name)
 sets the name of the unmodified residue
const StringgetUnmodifiedName () const
 returns the name of the unmodified residue
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
Predicates
bool hasNeutralLoss () const
 true if the residue has neutral loss
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

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_
ResidueModificationmodification_
String loss_name_
EmpiricalFormula loss_formula_
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_

Friends

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

Member Typedef Documentation

typedef std::vector<EmpiricalFormula>::const_iterator LowMassConstIterator

typedef std::vector<EmpiricalFormula>::iterator LowMassIterator


Member Enumeration Documentation

enum ResidueType

Enumerator:
Full 
Internal 
NTerminal 
CTerminal 
AIon 
BIon 
CIon 
XIon 
YIon 
ZIon 


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,
const EmpiricalFormula neutral_loss 
)

detailed constructor

virtual ~Residue (  )  [virtual]

destructor


Member Function Documentation

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

static DoubleReal getInternalToFullAverageWeight (  )  [inline, static]

static DoubleReal getInternalToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getNTerminalToFullAverageWeight (  )  [inline, static]

static DoubleReal getNTerminalToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getCTerminalToFullAverageWeight (  )  [inline, static]

static DoubleReal getCTerminalToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getBIonToFullAverageWeight (  )  [inline, static]

static DoubleReal getBIonToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getAIonToFullAverageWeight (  )  [inline, static]

static DoubleReal getAIonToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getYIonToFullAverageWeight (  )  [inline, static]

static DoubleReal getYIonToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getCIonToFullAverageWeight (  )  [inline, static]

static DoubleReal getCIonToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getXIonToFullAverageWeight (  )  [inline, static]

static DoubleReal getXIonToFullMonoWeight (  )  [inline, static]

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

static DoubleReal getZIonToFullAverageWeight (  )  [inline, static]

static DoubleReal getZIonToFullMonoWeight (  )  [inline, static]

Residue& operator= ( const Residue residue  ) 

assignment operator

void setName ( const String name  ) 

sets the name of the residue

Accessors

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 setLossFormula ( const EmpiricalFormula  ) 

sets the neutral loss formula (if there is one)

const EmpiricalFormula& getLossFormula (  )  const

returns the neutral loss formula (or just an empty string if there is none)

void setLossAverageWeight ( DoubleReal  weight  ) 

sets the average weight of the neutral loss molecule

DoubleReal getLossAverageWeight (  )  const

return the average weight of the neutral loss molecule

void setLossMonoWeight ( DoubleReal  weight  ) 

sets the mono isotopic weight of the neutral loss molecule

DoubleReal getLossMonoWeight (  )  const

returns the mono isotopic weight of the neutral loss molecule

void setLossName ( const String name  ) 

set the neutral loss molecule weight (if there is one)

const String& getLossName (  )  const

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

void setFormula ( const EmpiricalFormula formula,
ResidueType  res_type = Full 
)

set empirical formula of the residue

EmpiricalFormula getFormula ( ResidueType  res_type = Full  )  const

returns the empirical formula of thre residue

void setAverageWeight ( DoubleReal  weight,
ResidueType  res_type = Full 
)

sets average weight of the residue

DoubleReal getAverageWeight ( ResidueType  res_type = Full  )  const

returns average weight of the residue

void setMonoWeight ( DoubleReal  weight,
ResidueType  res_type = Full 
)

sets mono weight of the residue

DoubleReal getMonoWeight ( ResidueType  res_type = Full  )  const

returns mono weight of the residue

void setModification ( ResidueModification modification  ) 

sets the modification pointer

const ResidueModification* getModification (  )  const

returns a pointer to the modification, if the residue is unmodified, 0 is returned

void setUnmodifiedName ( const String name  ) 

sets the name of the unmodified residue

const String& getUnmodifiedName (  )  const

returns the name of the unmodified residue

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

bool hasNeutralLoss (  )  const

true if the residue has neutral loss

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


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

String name_ [protected]

String short_name_ [protected]

std::set<String> synonyms_ [protected]

String three_letter_code_ [protected]

String one_letter_code_ [protected]

EmpiricalFormula formula_ [protected]

EmpiricalFormula internal_formula_ [protected]

DoubleReal average_weight_ [protected]

DoubleReal mono_weight_ [protected]

bool is_modified_ [protected]

String pre_mod_name_ [protected]

ResidueModification* modification_ [protected]

String loss_name_ [protected]

EmpiricalFormula loss_formula_ [protected]

DoubleReal loss_average_weight_ [protected]

DoubleReal loss_mono_weight_ [protected]

std::vector<EmpiricalFormula> low_mass_ions_ [protected]

DoubleReal pka_ [protected]

DoubleReal pkb_ [protected]

DoubleReal pkc_ [protected]

DoubleReal gb_sc_ [protected]

DoubleReal gb_bb_l_ [protected]

DoubleReal gb_bb_r_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1