| OpenMS 2.5.0

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

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

`#include <OpenMS/CHEMISTRY/Ribonucleotide.h>`

## Public Types

enum | TermSpecificityNuc { ANYWHERE, FIVE_PRIME, THREE_PRIME, NUMBER_OF_TERM_SPECIFICITY }

## Public Member Functions

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...
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
Ribonucleotide & | operator= (const Ribonucleotide &ribo)=default
| assignment operator More...
Equality
bool | operator== (const Ribonucleotide &ribonucleotide) const
| Equality operator. More...

## Protected Attributes

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...

## Static Protected Attributes

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

## Friends

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

## 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 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_

static protected

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