| OpenMS 2.5.0

Public Member Functions | Protected Attributes | List of all members
DigestionEnzymeRNA Class Reference
Chemistry

Representation of a digestion enzyme for RNA (RNase) More...

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

Inheritance diagram for DigestionEnzymeRNA:

## Public Member Functions

void | setCutsAfterRegEx (const String &value)
| sets the "cuts after ..." regular expression More...
String | getCutsAfterRegEx () const
| returns the "cuts after ..." regular expression More...
void | setCutsBeforeRegEx (const String &value)
| sets the "cuts before ..." regular expression More...
String | getCutsBeforeRegEx () const
| returns the "cuts before ..." regular expression More...
void | setThreePrimeGain (const String &value)
| sets the 3' gain (as a nucleotide modification code) More...
String | getThreePrimeGain () const
| returns the 3' gain (as a nucleotide modification code) More...
void | setFivePrimeGain (const String &value)
| sets the 5' gain (as a nucleotide modification code) More...
String | getFivePrimeGain () const
| returns the 5' gain (as a nucleotide modification code) More...
bool | setValueFromFile (const String &key, const String &value) override
| Set the value of a member variable based on an entry from an input file. More...
Public Member Functions inherited from DigestionEnzyme
| DigestionEnzyme (const DigestionEnzyme &)=default
| Copy constructor. More...
| DigestionEnzyme (DigestionEnzyme &&)=default
| Move constructor. More...
| DigestionEnzyme (const String &name, const String &cleavage_regex, const std::set< String > &synonyms=std::set< String >(), String regex_description="")
| Detailed constructor. More...
virtual | ~DigestionEnzyme ()
| Destructor. More...
DigestionEnzyme & | operator= (const DigestionEnzyme &)=default
| Assignment operator. More...
DigestionEnzyme & | operator= (DigestionEnzyme &&) &=default
| Move assignment operator. More...
void | setName (const String &name)
| sets the name of the enzyme More...
String | getName () const
| returns the name of the enzyme 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 | setRegEx (const String &cleavage_regex)
| sets the cleavage regex More...
String | getRegEx () const
| returns the cleavage regex More...
void | setRegExDescription (const String &value)
| sets the regex description More...
String | getRegExDescription () const
| returns the regex description More...
bool | operator== (const DigestionEnzyme &enzyme) const
| equality operator More...
bool | operator!= (const DigestionEnzyme &enzyme) const
| inequality operator More...
bool | operator== (const String &cleavage_regex) const
| equality operator for regex More...
bool | operator!= (const String &cleavage_regex) const
| equality operator for regex More...
bool | operator< (const DigestionEnzyme &enzyme) const
| order operator More...

## Protected Attributes

String | three_prime_gain_
String | five_prime_gain_
String | cuts_after_regex_
String | cuts_before_regex_
Protected Attributes inherited from DigestionEnzyme
String | name_
String | cleavage_regex_
std::set< String > | synonyms_
String | regex_description_

## Additional Inherited Members

Protected Member Functions inherited from DigestionEnzyme
| DigestionEnzyme ()
| default constructor More...

## Detailed Description

Representation of a digestion enzyme for RNA (RNase)

The cutting sites of these enzymes are defined using two different mechanisms: First, a single regular expression that is applied to strings of unmodified RNA sequence and defines cutting sites via zero-length matches (using lookahead/lookbehind assertions). This is the same mechanism that is used for proteases (

See also
  ProteaseDigestion). However, due to the complex notation involved, this approach is not practical for modification-aware digestion. Thus, the second mechanism uses two regular expressions ("cuts after"/"cuts before"), which are applied to the short codes (e.g. "m6A") of sequential ribonucleotides. If both expressions match, then there is a cutting site between the two ribonucleotides.

There is support for terminal (5'/3') modifications that may be generated on fragments as a result of RNase cleavage. A typical example is 3'-phosphate, resulting from cleavage of the phosphate backbone.

## Member Function Documentation

## ◆ getCutsAfterRegEx()

String getCutsAfterRegEx | ( |  | ) | const

returns the "cuts after ..." regular expression

## ◆ getCutsBeforeRegEx()

String getCutsBeforeRegEx | ( |  | ) | const

returns the "cuts before ..." regular expression

## ◆ getFivePrimeGain()

String getFivePrimeGain | ( |  | ) | const

returns the 5' gain (as a nucleotide modification code)

## ◆ getThreePrimeGain()

String getThreePrimeGain | ( |  | ) | const

returns the 3' gain (as a nucleotide modification code)

## ◆ setCutsAfterRegEx()

void setCutsAfterRegEx | ( | const String & | value | ) |

sets the "cuts after ..." regular expression

## ◆ setCutsBeforeRegEx()

void setCutsBeforeRegEx | ( | const String & | value | ) |

sets the "cuts before ..." regular expression

## ◆ setFivePrimeGain()

void setFivePrimeGain | ( | const String & | value | ) |

sets the 5' gain (as a nucleotide modification code)

## ◆ setThreePrimeGain()

void setThreePrimeGain | ( | const String & | value | ) |

sets the 3' gain (as a nucleotide modification code)

## ◆ setValueFromFile()

bool setValueFromFile | ( | const String & | key,
|  | const String & | value
| ) |  |

override virtual

Set the value of a member variable based on an entry from an input file.

Returns whether the key was recognized and the value set successfully.

Reimplemented from DigestionEnzyme.

## Member Data Documentation

## ◆ cuts_after_regex_

String cuts_after_regex_

protected

## ◆ cuts_before_regex_

String cuts_before_regex_

protected

## ◆ five_prime_gain_

String five_prime_gain_

protected

## ◆ three_prime_gain_

String three_prime_gain_

protected