| OpenMS 2.5.0

Static Public Member Functions | Protected Member Functions | Protected Attributes | Friends | List of all members
Residue Class Reference
Chemistry

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

## 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() [1/4]

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 | ( |  | ) |

inline static

## ◆ getInternalToBIon()

static const EmpiricalFormula& getInternalToBIon | ( |  | ) |

inline static

## ◆ getInternalToCIon()

static const EmpiricalFormula& getInternalToCIon | ( |  | ) |

inline static

## ◆ getInternalToCTerm()

static const EmpiricalFormula& getInternalToCTerm | ( |  | ) |

inline static

## ◆ getInternalToFull()

static const EmpiricalFormula& getInternalToFull | ( |  | ) |

inline static

## ◆ getInternalToNTerm()

static const EmpiricalFormula& getInternalToNTerm | ( |  | ) |

inline static

## ◆ getInternalToXIon()

static const EmpiricalFormula& getInternalToXIon | ( |  | ) |

inline static

## ◆ getInternalToYIon()

static const EmpiricalFormula& getInternalToYIon | ( |  | ) |

inline static

## ◆ getInternalToZIon()

static const EmpiricalFormula& getInternalToZIon | ( |  | ) |

inline static

## ◆ 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=() [1/2]

Residue& operator= | ( | const Residue & |  | ) |

default

Assignment operator.

## ◆ operator=() [2/2]

Residue& operator= | ( | Residue && |  | ) | &

default

Move 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

## ◆ 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()

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

## ◆ 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