OpenMS  2.8.0
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Ribonucleotide Class Reference

Representation of a ribonucleotide (modified or unmodified) More...

#include <OpenMS/CHEMISTRY/Ribonucleotide.h>

Collaboration diagram for Ribonucleotide:
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Public Types

enum  TermSpecificityNuc { ANYWHERE , FIVE_PRIME , THREE_PRIME , NUMBER_OF_TERM_SPECIFICITY }
 

Public Member Functions

Constructors
 Ribonucleotide (const String &name="unknown ribonucleotide", const String &code=".", const String &new_code="", const String &html_code=".", const EmpiricalFormula &formula=EmpiricalFormula(), char origin='.', double mono_mass=0.0, double avg_mass=0.0, enum TermSpecificityNuc term_spec=ANYWHERE, const EmpiricalFormula &baseloss_formula=default_baseloss_)
 Constructor. More...
 
 Ribonucleotide (const Ribonucleotide &ribo)=default
 Copy constructor. More...
 
virtual ~Ribonucleotide ()
 Destructor. More...
 
Assignment
Ribonucleotideoperator= (const Ribonucleotide &ribo)=default
 assignment operator More...
 

Friends

class RibonucleotideDB
 

Equality

std::ostream & operator<< (std::ostream &os, const Ribonucleotide &ribo)
 ostream iterator to write the residue to a stream More...
 
static const EmpiricalFormula default_baseloss_
 Default value for sum formula after nucleobase loss. More...
 
String name_
 full name More...
 
String code_
 short name More...
 
String new_code_
 Modomics code. More...
 
String html_code_
 RNAMods code. More...
 
EmpiricalFormula formula_
 sum formula More...
 
char origin_
 character of unmodified version of ribonucleotide More...
 
double mono_mass_
 monoisotopic mass More...
 
double avg_mass_
 average mass More...
 
enum TermSpecificityNuc term_spec_
 terminal specificity More...
 
EmpiricalFormula baseloss_formula_
 sum formula after loss of the nucleobase More...
 
bool operator== (const Ribonucleotide &ribonucleotide) const
 Equality operator. More...
 
const String getCode () const
 Return the short name. More...
 
void setCode (const String &code)
 Set the short name. More...
 
const String getName () const
 Get the name of the ribonucleotide. More...
 
void setName (const String &name)
 Set the name of the ribonucleotide. More...
 
const EmpiricalFormula getFormula () const
 Get formula for the ribonucleotide. More...
 
void setFormula (const EmpiricalFormula &formula)
 Set the empirical formula for the ribonucleotide. More...
 
double getMonoMass () const
 Get the monoisotopic mass of the ribonucleotide. More...
 
void setMonoMass (double mono_mass)
 Set the monoisotopic mass of the ribonucleotide. More...
 
double getAvgMass () const
 Set the average mass of the ribonucleotide. More...
 
void setAvgMass (double avg_mass)
 Get the average mass of the ribonucleotide. More...
 
const String getNewCode () const
 Get the "new" (Modomics) code. More...
 
void setNewCode (const String &new_code)
 Set the "new" (Modomics) code. More...
 
char getOrigin () const
 Get the code of the unmodified base (e.g., "A", "C", ...) More...
 
void setOrigin (char origin)
 Set the code of the unmodified base (e.g., "A", "C", ...) More...
 
String getHTMLCode () const
 Set the HTML (RNAMods) code. More...
 
void setHTMLCode (const String &html_code)
 Get the HTML (RNAMods) code. More...
 
enum TermSpecificityNuc getTermSpecificity () const
 Get the terminal specificity. More...
 
void setTermSpecificity (enum TermSpecificityNuc term_spec)
 Set the terminal specificity. More...
 
const EmpiricalFormula getBaselossFormula () const
 Get sum formula after loss of the nucleobase. More...
 
void setBaselossFormula (const EmpiricalFormula &formula)
 Set the sum formula after loss of the nucleobase. More...
 
bool isModified () const
 Return true if this is a modified ribonucleotide and false otherwise. More...
 
bool isAmbiguous () const
 Return whether this is an "ambiguous" modification (representing isobaric modifications on the base/ribose) More...
 

Detailed Description

Representation of a ribonucleotide (modified or unmodified)

The available information is based on the Modomics database (http://modomics.genesilico.pl/modifications/).

See also
RibonucleotideDB

Member Enumeration Documentation

◆ TermSpecificityNuc

Enumerator
ANYWHERE 
FIVE_PRIME 
THREE_PRIME 
NUMBER_OF_TERM_SPECIFICITY 

Constructor & Destructor Documentation

◆ Ribonucleotide() [1/2]

Ribonucleotide ( const String name = "unknown ribonucleotide",
const String code = ".",
const String new_code = "",
const String html_code = ".",
const EmpiricalFormula formula = EmpiricalFormula(),
char  origin = '.',
double  mono_mass = 0.0,
double  avg_mass = 0.0,
enum TermSpecificityNuc  term_spec = ANYWHERE,
const EmpiricalFormula baseloss_formula = default_baseloss_ 
)

Constructor.

◆ Ribonucleotide() [2/2]

Ribonucleotide ( const Ribonucleotide ribo)
default

Copy constructor.

◆ ~Ribonucleotide()

virtual ~Ribonucleotide ( )
virtual

Destructor.

Member Function Documentation

◆ getAvgMass()

double getAvgMass ( ) const

Set the average mass of the ribonucleotide.

◆ getBaselossFormula()

const EmpiricalFormula getBaselossFormula ( ) const

Get sum formula after loss of the nucleobase.

◆ getCode()

const String getCode ( ) const

Return the short name.

Accessors

◆ getFormula()

const EmpiricalFormula getFormula ( ) const

Get formula for the ribonucleotide.

◆ getHTMLCode()

String getHTMLCode ( ) const

Set the HTML (RNAMods) code.

◆ getMonoMass()

double getMonoMass ( ) const

Get the monoisotopic mass of the ribonucleotide.

◆ getName()

const String getName ( ) const

Get the name of the ribonucleotide.

◆ getNewCode()

const String getNewCode ( ) const

Get the "new" (Modomics) code.

◆ getOrigin()

char getOrigin ( ) const

Get the code of the unmodified base (e.g., "A", "C", ...)

◆ getTermSpecificity()

enum TermSpecificityNuc getTermSpecificity ( ) const

Get the terminal specificity.

◆ isAmbiguous()

bool isAmbiguous ( ) const

Return whether this is an "ambiguous" modification (representing isobaric modifications on the base/ribose)

Referenced by NucleicAcidSearchEngine::getModifications_().

◆ isModified()

bool isModified ( ) const

Return true if this is a modified ribonucleotide and false otherwise.

◆ operator=()

Ribonucleotide& operator= ( const Ribonucleotide ribo)
default

assignment operator

◆ operator==()

bool operator== ( const Ribonucleotide ribonucleotide) const

Equality operator.

◆ setAvgMass()

void setAvgMass ( double  avg_mass)

Get the average mass of the ribonucleotide.

◆ setBaselossFormula()

void setBaselossFormula ( const EmpiricalFormula formula)

Set the sum formula after loss of the nucleobase.

◆ setCode()

void setCode ( const String code)

Set the short name.

◆ setFormula()

void setFormula ( const EmpiricalFormula formula)

Set the empirical formula for the ribonucleotide.

◆ setHTMLCode()

void setHTMLCode ( const String html_code)

Get the HTML (RNAMods) code.

◆ setMonoMass()

void setMonoMass ( double  mono_mass)

Set the monoisotopic mass of the ribonucleotide.

◆ setName()

void setName ( const String name)

Set the name of the ribonucleotide.

◆ setNewCode()

void setNewCode ( const String new_code)

Set the "new" (Modomics) code.

◆ setOrigin()

void setOrigin ( char  origin)

Set the code of the unmodified base (e.g., "A", "C", ...)

◆ setTermSpecificity()

void setTermSpecificity ( enum TermSpecificityNuc  term_spec)

Set the terminal specificity.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<< ( std::ostream &  os,
const Ribonucleotide ribo 
)
friend

ostream iterator to write the residue to a stream

◆ RibonucleotideDB

friend class RibonucleotideDB
friend

Member Data Documentation

◆ avg_mass_

double avg_mass_
protected

average mass

◆ baseloss_formula_

EmpiricalFormula baseloss_formula_
protected

sum formula after loss of the nucleobase

◆ code_

String code_
protected

short name

◆ default_baseloss_

const EmpiricalFormula default_baseloss_
staticprotected

Default value for sum formula after nucleobase loss.

◆ formula_

EmpiricalFormula formula_
protected

sum formula

◆ html_code_

String html_code_
protected

RNAMods code.

◆ mono_mass_

double mono_mass_
protected

monoisotopic mass

◆ name_

String name_
protected

full name

◆ new_code_

String new_code_
protected

Modomics code.

◆ origin_

char origin_
protected

character of unmodified version of ribonucleotide

◆ term_spec_

enum TermSpecificityNuc term_spec_
protected

terminal specificity