EnzymaticDigestion

class pyopenms.EnzymaticDigestion

Bases: object

Cython implementation of _EnzymaticDigestion

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1EnzymaticDigestion.html

Digestion can be performed using simple regular expressions, e.g. [KR] | [^P] for trypsin. Also missed cleavages can be modeled, i.e. adjacent peptides are not cleaved due to enzyme malfunction/access restrictions. If n missed cleavages are allowed, all possible resulting peptides (cleaved and uncleaved) with up to n missed cleavages are returned. Thus no random selection of just n specific missed cleavage sites is performed.

__init__()

  • Cython signature: void EnzymaticDigestion()

  • Cython signature: void EnzymaticDigestion(EnzymaticDigestion &)

Methods

__init__

  • Cython signature: void EnzymaticDigestion()

digestUnmodified

Cython signature: size_t digestUnmodified(StringView sequence, libcpp_vector[StringView] & output, size_t min_length, size_t max_length)

getEnzymeName

Cython signature: String getEnzymeName() Returns the enzyme for the digestion

getMissedCleavages

Cython signature: size_t getMissedCleavages() Returns the number of missed cleavages for the digestion

getSpecificity

Cython signature: Specificity getSpecificity() Returns the specificity for the digestion

getSpecificityByName

Cython signature: Specificity getSpecificityByName(String name) Returns the specificity by name.

isValidProduct

Cython signature: bool isValidProduct(String sequence, int pos, int length, bool ignore_missed_cleavages)

setEnzyme

Cython signature: void setEnzyme(DigestionEnzyme * enzyme) Sets the enzyme for the digestion

setMissedCleavages

Cython signature: void setMissedCleavages(size_t missed_cleavages) Sets the number of missed cleavages for the digestion (default is 0).

setSpecificity

Cython signature: void setSpecificity(Specificity spec) Sets the specificity for the digestion (default is SPEC_FULL)
Specificity

alias of pyopenms.pyopenms_1.__Specificity

digestUnmodified()

Cython signature: size_t digestUnmodified(StringView sequence, libcpp_vector[StringView] & output, size_t min_length, size_t max_length)

Parameters

  • sequence – Sequence to digest

  • output – Digestion products

  • min_length – Minimal length of reported products

  • max_length – Maximal length of reported products (0 = no restriction)

Returns

Number of discarded digestion products (which are not matching length restrictions)

getEnzymeName()

Cython signature: String getEnzymeName() Returns the enzyme for the digestion

getMissedCleavages()

Cython signature: size_t getMissedCleavages() Returns the number of missed cleavages for the digestion

getSpecificity()

Cython signature: Specificity getSpecificity() Returns the specificity for the digestion

getSpecificityByName()

Cython signature: Specificity getSpecificityByName(String name) Returns the specificity by name. Returns SPEC_UNKNOWN if name is not valid

isValidProduct()

Cython signature: bool isValidProduct(String sequence, int pos, int length, bool ignore_missed_cleavages)

Parameters

  • protein – Protein sequence

  • pep_pos – Starting index of potential peptide

  • pep_length – Length of potential peptide

  • ignore_missed_cleavages – Do not compare MC’s of potential peptide to the maximum allowed MC’s

Returns

True if peptide has correct n/c terminals (according to enzyme, specificity and missed cleavages)

setEnzyme()

Cython signature: void setEnzyme(DigestionEnzyme * enzyme) Sets the enzyme for the digestion

setMissedCleavages()

Cython signature: void setMissedCleavages(size_t missed_cleavages) Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used

setSpecificity()

Cython signature: void setSpecificity(Specificity spec) Sets the specificity for the digestion (default is SPEC_FULL)