NASequence#

class pyopenms.NASequence#

Bases: object

Cython implementation of _NASequence

Original C++ documentation is available here

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

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: NASequence) → None

Methods

`__init__`	Overload:
`empty`(self)	Check if sequence is empty
`fromString`	__static_NASequence_fromString(s: Union[bytes, str, String] ) -> NASequence
`get`(self, index)	Returns the residue at position index
`getAverageWeight`	Overload:
`getFivePrimeMod`(self)	Returns the name (ID) of the N-terminal modification, or an empty string if none is set
`getFormula`	Overload:
`getMonoWeight`	Overload:
`getPrefix`(self, length)	Returns a peptide sequence of the first index residues
`getSequence`(self)
`getSubsequence`(self, start, length)	Returns a peptide sequence of number residues, beginning at position index
`getSuffix`(self, length)	Returns a peptide sequence of the last index residues
`getThreePrimeMod`(self)
`set`(self, index, r)	Sets the residue at position index
`setFivePrimeMod`(self, modification)	Sets the 5' modification
`setSequence`(self, seq)
`setThreePrimeMod`(self, modification)	Sets the 3' modification
`size`(self)	Returns the number of residues
`toString`(self)	Returns the peptide as string with modifications embedded in brackets

NASFragmentType#: alias of __NASFragmentType

empty(self) → bool#: Check if sequence is empty

fromString()#: __static_NASequence_fromString(s: Union[bytes, str, String] ) -> NASequence

get(self, index: int) → Ribonucleotide#: Returns the residue at position index

getAverageWeight()#

Overload:

getAverageWeight(self) → float

Returns the average weight of the peptide

Overload:

getAverageWeight(self, type_: int, charge: int) → float

getFivePrimeMod(self) → Ribonucleotide#: Returns the name (ID) of the N-terminal modification, or an empty string if none is set

getFormula()#

Overload:

getFormula(self) → EmpiricalFormula

Returns the formula of the peptide

Overload:

getFormula(self, type_: int, charge: int) → EmpiricalFormula

getMonoWeight()#

Overload:

getMonoWeight(self) → float

Returns the mono isotopic weight of the peptide

Overload:

getMonoWeight(self, type_: int, charge: int) → float

getPrefix(self, length: int) → NASequence#: Returns a peptide sequence of the first index residues

getSequence(self) → List[Ribonucleotide]#

getSubsequence(self, start: int, length: int) → NASequence#: Returns a peptide sequence of number residues, beginning at position index

getSuffix(self, length: int) → NASequence#: Returns a peptide sequence of the last index residues

getThreePrimeMod(self) → Ribonucleotide#

set(self, index: int, r: Ribonucleotide) → None#: Sets the residue at position index

setFivePrimeMod(self, modification: Ribonucleotide) → None#: Sets the 5’ modification

setSequence(self, seq: List[Ribonucleotide]) → None#

setThreePrimeMod(self, modification: Ribonucleotide) → None#: Sets the 3’ modification

size(self) → int#: Returns the number of residues

toString(self) → bytes | str | String#: Returns the peptide as string with modifications embedded in brackets