NASequence#

class pyopenms.NASequence#

Bases: object

Cython implementation of _NASequence

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1NASequence.html

Representation of an RNA sequence This class represents nucleic acid sequences in OpenMS. An NASequence instance primarily contains a sequence of ribonucleotides.

__init__()#

  • Cython signature: void NASequence()

  • Cython signature: void NASequence(NASequence &)

Methods

__init__

  • Cython signature: void NASequence()

empty

Cython signature: bool empty() Check if sequence is empty

fromString

Cython signature: NASequence fromString(const String & s)

get

Cython signature: const Ribonucleotide * get(size_t index) Returns the residue at position index

getAverageWeight

  • Cython signature: double getAverageWeight()

getFivePrimeMod

Cython signature: const Ribonucleotide * getFivePrimeMod() Returns the name (ID) of the N-terminal modification, or an empty string if none is set

getFormula

  • Cython signature: EmpiricalFormula getFormula()

getMonoWeight

  • Cython signature: double getMonoWeight()

getPrefix

Cython signature: NASequence getPrefix(size_t length) Returns a peptide sequence of the first index residues

getSequence

Cython signature: libcpp_vector[const Ribonucleotide *] getSequence()

getSubsequence

Cython signature: NASequence getSubsequence(size_t start, size_t length) Returns a peptide sequence of number residues, beginning at position index

getSuffix

Cython signature: NASequence getSuffix(size_t length) Returns a peptide sequence of the last index residues

getThreePrimeMod

Cython signature: const Ribonucleotide * getThreePrimeMod()

set

Cython signature: void set(size_t index, const Ribonucleotide * r) Sets the residue at position index

setFivePrimeMod

Cython signature: void setFivePrimeMod(const Ribonucleotide * modification) Sets the 5' modification

setSequence

Cython signature: void setSequence(const libcpp_vector[const Ribonucleotide *] & seq)

setThreePrimeMod

Cython signature: void setThreePrimeMod(const Ribonucleotide * modification) Sets the 3' modification

size

Cython signature: size_t size() Returns the number of residues

toString

Cython signature: String toString() Returns the peptide as string with modifications embedded in brackets
NASFragmentType#

alias of pyopenms.pyopenms_3.__NASFragmentType

empty()#

Cython signature: bool empty() Check if sequence is empty

fromString()#

Cython signature: NASequence fromString(const String & s)

get()#

Cython signature: const Ribonucleotide * get(size_t index) Returns the residue at position index

getAverageWeight()#

  • Cython signature: double getAverageWeight() Returns the average weight of the peptide

  • Cython signature: double getAverageWeight(NASFragmentType type_, int charge)

getFivePrimeMod()#

Cython signature: const Ribonucleotide * getFivePrimeMod() Returns the name (ID) of the N-terminal modification, or an empty string if none is set

getFormula()#

  • Cython signature: EmpiricalFormula getFormula() Returns the formula of the peptide

  • Cython signature: EmpiricalFormula getFormula(NASFragmentType type_, int charge)

getMonoWeight()#

  • Cython signature: double getMonoWeight() Returns the mono isotopic weight of the peptide

  • Cython signature: double getMonoWeight(NASFragmentType type_, int charge)

getPrefix()#

Cython signature: NASequence getPrefix(size_t length) Returns a peptide sequence of the first index residues

getSequence()#

Cython signature: libcpp_vector[const Ribonucleotide *] getSequence()

getSubsequence()#

Cython signature: NASequence getSubsequence(size_t start, size_t length) Returns a peptide sequence of number residues, beginning at position index

getSuffix()#

Cython signature: NASequence getSuffix(size_t length) Returns a peptide sequence of the last index residues

getThreePrimeMod()#

Cython signature: const Ribonucleotide * getThreePrimeMod()

set()#

Cython signature: void set(size_t index, const Ribonucleotide * r) Sets the residue at position index

setFivePrimeMod()#

Cython signature: void setFivePrimeMod(const Ribonucleotide * modification) Sets the 5’ modification

setSequence()#

Cython signature: void setSequence(const libcpp_vector[const Ribonucleotide *] & seq)

setThreePrimeMod()#

Cython signature: void setThreePrimeMod(const Ribonucleotide * modification) Sets the 3’ modification

size()#

Cython signature: size_t size() Returns the number of residues

toString()#

Cython signature: String toString() Returns the peptide as string with modifications embedded in brackets