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DigestionEnzymeRNA Class Reference

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

#include <OpenMS/CHEMISTRY/DigestionEnzymeRNA.h>

Inheritance diagram for DigestionEnzymeRNA:
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Collaboration diagram for DigestionEnzymeRNA:
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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...
 
 DigestionEnzyme (const String &name, String cut_before, const String &nocut_after="", String sense="C", const std::set< String > &synonyms=std::set< String >(), String regex_description="")
 Detailed constructor 2. More...
 
virtual ~DigestionEnzyme ()
 Destructor. More...
 
DigestionEnzymeoperator= (const DigestionEnzyme &)=default
 Assignment operator. More...
 
DigestionEnzymeoperator= (DigestionEnzyme &&) &=default
 Move assignment operator. More...
 
void setName (const String &name)
 sets the name of the enzyme More...
 
const StringgetName () 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...
 
const StringgetRegEx () const
 returns the cleavage regex More...
 
void setRegExDescription (const String &value)
 sets the regex description More...
 
const StringgetRegExDescription () 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< Stringsynonyms_
 
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 
)
overridevirtual

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