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

#include <OpenMS/CHEMISTRY/Ribonucleotide.h>

Collaboration diagram for Ribonucleotide:

Public Types
enum	TermSpecificityNuc { ANYWHERE , FIVE_PRIME , THREE_PRIME , NUMBER_OF_TERM_SPECIFICITY }

Public Member Functions
Constructors
	Ribonucleotide (const std::string &name="unknown ribonucleotide", const std::string &code=".", const std::string &new_code="", const std::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 (const Ribonucleotide &ribo)=default
	Copy constructor.

virtual	~Ribonucleotide ()
	Destructor.

Assignment
Ribonucleotide &	operator= (const Ribonucleotide &ribo)=default
	assignment operator

Friends
class	RibonucleotideDB

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

static const EmpiricalFormula	default_baseloss_
	Default value for sum formula after nucleobase loss.

std::string	name_
	full name

std::string	code_
	short name

std::string	new_code_
	Modomics code.

std::string	html_code_
	RNAMods code.

EmpiricalFormula	formula_
	sum formula

char	origin_
	character of unmodified version of ribonucleotide

double	mono_mass_
	monoisotopic mass

double	avg_mass_
	average mass

enum TermSpecificityNuc	term_spec_
	terminal specificity

EmpiricalFormula	baseloss_formula_
	sum formula after loss of the nucleobase

bool	operator== (const Ribonucleotide &ribonucleotide) const
	Equality operator.

const std::string	getCode () const
	Return the short name.

void	setCode (const std::string &code)
	Set the short name.

const std::string	getName () const
	Get the name of the ribonucleotide.

void	setName (const std::string &name)
	Set the name of the ribonucleotide.

const EmpiricalFormula	getFormula () const
	Get formula for the ribonucleotide.

void	setFormula (const EmpiricalFormula &formula)
	Set the empirical formula for the ribonucleotide.

double	getMonoMass () const
	Get the monoisotopic mass of the ribonucleotide.

void	setMonoMass (double mono_mass)
	Set the monoisotopic mass of the ribonucleotide.

double	getAvgMass () const
	Set the average mass of the ribonucleotide.

void	setAvgMass (double avg_mass)
	Get the average mass of the ribonucleotide.

const std::string	getNewCode () const
	Get the "new" (Modomics) code.

void	setNewCode (const std::string &new_code)
	Set the "new" (Modomics) code.

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

void	setOrigin (char origin)
	Set the code of the unmodified base (e.g., "A", "C", ...)

std::string	getHTMLCode () const
	Set the HTML (RNAMods) code.

void	setHTMLCode (const std::string &html_code)
	Get the HTML (RNAMods) code.

enum TermSpecificityNuc	getTermSpecificity () const
	Get the terminal specificity.

void	setTermSpecificity (enum TermSpecificityNuc term_spec)
	Set the terminal specificity.

const EmpiricalFormula	getBaselossFormula () const
	Get sum formula after loss of the nucleobase.

void	setBaselossFormula (const EmpiricalFormula &formula)
	Set the sum formula after loss of the nucleobase.

bool	isModified () const
	Return true if this is a modified ribonucleotide and false otherwise.

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

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

enum TermSpecificityNuc

Enumerator
ANYWHERE
FIVE_PRIME
THREE_PRIME
NUMBER_OF_TERM_SPECIFICITY

Constructor & Destructor Documentation

◆ Ribonucleotide() [1/2]

Ribonucleotide	(	const std::string &	name = `"unknown ribonucleotide"`,
		const std::string &	code = `"."`,
		const std::string &	new_code = `""`,
		const std::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 std::string getCode ( ) const

Return the short name.

Accessors

Referenced by hash< OpenMS::NASequence >::operator()().

◆ getFormula()

const EmpiricalFormula getFormula ( ) const

Get formula for the ribonucleotide.

◆ getHTMLCode()

std::string getHTMLCode ( ) const

Set the HTML (RNAMods) code.

◆ getMonoMass()

double getMonoMass ( ) const

Get the monoisotopic mass of the ribonucleotide.

◆ getName()

const std::string getName ( ) const

Get the name of the ribonucleotide.

◆ getNewCode()

const std::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 std::string & code )

Set the short name.

◆ setFormula()

void setFormula ( const EmpiricalFormula & formula )

Set the empirical formula for the ribonucleotide.

◆ setHTMLCode()

void setHTMLCode ( const std::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 std::string & name )

Set the name of the ribonucleotide.

◆ setNewCode()

void setNewCode ( const std::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 Symbol 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_

std::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_

std::string html_code_

protected

RNAMods code.

◆ mono_mass_

double mono_mass_

protected

monoisotopic mass

◆ name_

std::string name_

protected

full name

◆ new_code_

std::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

Public Types

Public Member Functions

Friends

Equality

Detailed Description

Member Enumeration Documentation

◆ TermSpecificityNuc

Constructor & Destructor Documentation

◆ Ribonucleotide() [1/2]

◆ Ribonucleotide() [2/2]

◆ ~Ribonucleotide()

Member Function Documentation

◆ getAvgMass()

◆ getBaselossFormula()

◆ getCode()

◆ getFormula()

◆ getHTMLCode()

◆ getMonoMass()

◆ getName()

◆ getNewCode()

◆ getOrigin()

◆ getTermSpecificity()

◆ isAmbiguous()

◆ isModified()

◆ operator=()

◆ operator==()

◆ setAvgMass()

◆ setBaselossFormula()

◆ setCode()

◆ setFormula()

◆ setHTMLCode()

◆ setMonoMass()

◆ setName()

◆ setNewCode()

◆ setOrigin()

◆ setTermSpecificity()

Friends And Related Symbol Documentation

◆ operator<<

◆ RibonucleotideDB

Member Data Documentation

◆ avg_mass_

◆ baseloss_formula_

◆ code_

◆ default_baseloss_

◆ formula_

◆ html_code_

◆ mono_mass_

◆ name_

◆ new_code_

◆ origin_

◆ term_spec_