DigestionEnzymeRNA#

class pyopenms.DigestionEnzymeRNA#

Bases: object

Cython implementation of _DigestionEnzymeRNA

Original C++ documentation is available here

– Inherits from [‘DigestionEnzyme’]

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 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.

__init__()#

Overload:

__init__(self) None

Overload:

__init__(self, in_0: DigestionEnzymeRNA) None

Methods

__init__

Overload:

addSynonym(self, synonym)

Adds a synonym

getCutsAfterRegEx(self)

Returns the "cuts after ..." regular expression

getCutsBeforeRegEx(self)

Returns the "cuts before ..." regular expression

getFivePrimeGain(self)

Returns the 5' gain

getName(self)

Returns the name of the enzyme

getRegEx(self)

Returns the cleavage regex

getRegExDescription(self)

Returns the regex description

getSynonyms(self)

Returns the synonyms

getThreePrimeGain(self)

Returns the 3' gain

setCutsAfterRegEx(self, value)

Sets the "cuts after ..." regular expression

setCutsBeforeRegEx(self, value)

Sets the "cuts before ..." regular expression

setFivePrimeGain(self, value)

Sets the 5' gain

setName(self, name)

Sets the name of the enzyme

setRegEx(self, cleavage_regex)

Sets the cleavage regex

setRegExDescription(self, value)

Sets the regex description

setSynonyms(self, synonyms)

Sets the synonyms

setThreePrimeGain(self, value)

Sets the 3' gain

setValueFromFile(self, key, value)

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

addSynonym(self, synonym: bytes | str | String) None#

Adds a synonym

getCutsAfterRegEx(self) bytes | str | String#

Returns the “cuts after …” regular expression

getCutsBeforeRegEx(self) bytes | str | String#

Returns the “cuts before …” regular expression

getFivePrimeGain(self) bytes | str | String#

Returns the 5’ gain

getName(self) bytes | str | String#

Returns the name of the enzyme

getRegEx(self) bytes | str | String#

Returns the cleavage regex

getRegExDescription(self) bytes | str | String#

Returns the regex description

getSynonyms(self) Set[bytes]#

Returns the synonyms

getThreePrimeGain(self) bytes | str | String#

Returns the 3’ gain

setCutsAfterRegEx(self, value: bytes | str | String) None#

Sets the “cuts after …” regular expression

setCutsBeforeRegEx(self, value: bytes | str | String) None#

Sets the “cuts before …” regular expression

setFivePrimeGain(self, value: bytes | str | String) None#

Sets the 5’ gain

setName(self, name: bytes | str | String) None#

Sets the name of the enzyme

setRegEx(self, cleavage_regex: bytes | str | String) None#

Sets the cleavage regex

setRegExDescription(self, value: bytes | str | String) None#

Sets the regex description

setSynonyms(self, synonyms: Set[bytes]) None#

Sets the synonyms

setThreePrimeGain(self, value: bytes | str | String) None#

Sets the 3’ gain

setValueFromFile(self, key: bytes | str | String, value: bytes | str | String) bool#

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