AASequence#

class pyopenms.AASequence#

Bases: object

Cython implementation of _AASequence

Original C++ documentation is available here

Representation of a peptide/protein sequence This class represents amino acid sequences in OpenMS. An AASequence instance primarily contains a sequence of residues.

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: AASequence) → None

Methods

`__init__`	Overload:
`empty`(self)	Check if sequence is empty
`fromString`	__static_AASequence_fromString(s: Union[bytes, str, String] ) -> AASequence
`fromStringPermissive`	__static_AASequence_fromStringPermissive(s: Union[bytes, str, String] , permissive: bool ) -> AASequence
`getAAFrequencies`
`getAverageWeight`	Overload:
`getCTerminalModification`(self)	Returns a copy of the name C-terminal modification object, or None
`getCTerminalModificationName`(self)	Returns the name (ID) of the C-terminal modification, or an empty string if none is set
`getFormula`	Overload:
`getMZ`	Overload:
`getMonoWeight`	Overload:
`getNTerminalModification`(self)	Returns a copy of the name N-terminal modification object, or None
`getNTerminalModificationName`(self)	Returns the name (ID) of the N-terminal modification, or an empty string if none is set
`getPrefix`(self, index)	Returns a peptide sequence of the first index residues
`getResidue`(self, index)	Returns the residue at position index
`getSubsequence`(self, index, number)	Returns a peptide sequence of number residues, beginning at position index
`getSuffix`(self, index)	Returns a peptide sequence of the last index residues
`has`(self, residue)	Returns true if the peptide contains the given residue
`hasCTerminalModification`(self)	Predicate which is true if the peptide is C-term modified
`hasNTerminalModification`(self)	Predicate which is true if the peptide is N-term modified
`hasPrefix`(self, peptide)	Returns true if the peptide has the given prefix
`hasSubsequence`(self, peptide)	Returns true if the peptide contains the given peptide
`hasSuffix`(self, peptide)	Returns true if the peptide has the given suffix
`isModified`(self)	Returns true if any of the residues or termini are modified
`setCTerminalModification`	Overload:
`setCTerminalModificationByDiffMonoMass`(self, ...)	Sets the C-terminal modification by the monoisotopic mass difference it introduces (creates a "user-defined" mod if not present)
`setModification`	Overload:
`setModificationByDiffMonoMass`(self, index, ...)	Modifies the residue at index in the sequence and potentially in the ResidueDB
`setNTerminalModification`	Overload:
`setNTerminalModificationByDiffMonoMass`(self, ...)	Sets the N-terminal modification by the monoisotopic mass difference it introduces (creates a "user-defined" mod if not present)
`size`(self)	Returns the number of residues
`toBracketString`	Overload:
`toString`(self)	Returns the peptide as string with modifications embedded in brackets
`toUniModString`(self)	Returns the peptide as string with UniMod-style modifications embedded in brackets
`toUnmodifiedString`(self)	Returns the peptide as string without any modifications

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

fromString()#: __static_AASequence_fromString(s: Union[bytes, str, String] ) -> AASequence

fromStringPermissive()#: __static_AASequence_fromStringPermissive(s: Union[bytes, str, String] , permissive: bool ) -> AASequence

getAAFrequencies()#

getAverageWeight()#

Overload:

getAverageWeight(self) → float

Returns the average weight of the peptide

Overload:

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

getCTerminalModification(self) → ResidueModification#: Returns a copy of the name C-terminal modification object, or None

getCTerminalModificationName(self) → bytes | str | String#: Returns the name (ID) of the C-terminal modification, or an empty string if none is set

getFormula()#

Overload:

getFormula(self) → EmpiricalFormula

Convenience function with ResidueType=Full and charge = 0 by default

Overload:

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

getMZ()#

Overload:

getMZ(self, charge: int) → float

Returns the mass-to-charge ratio of the peptide

Overload:

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

getMonoWeight()#

Overload:

getMonoWeight(self) → float

Returns the mono isotopic weight of the peptide

Overload:

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

getNTerminalModification(self) → ResidueModification#: Returns a copy of the name N-terminal modification object, or None

getNTerminalModificationName(self) → bytes | str | String#: Returns the name (ID) of the N-terminal modification, or an empty string if none is set

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

getResidue(self, index: int) → Residue#: Returns the residue at position index

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

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

has(self, residue: Residue) → bool#: Returns true if the peptide contains the given residue

hasCTerminalModification(self) → bool#: Predicate which is true if the peptide is C-term modified

hasNTerminalModification(self) → bool#: Predicate which is true if the peptide is N-term modified

hasPrefix(self, peptide: AASequence) → bool#: Returns true if the peptide has the given prefix

hasSubsequence(self, peptide: AASequence) → bool#: Returns true if the peptide contains the given peptide

hasSuffix(self, peptide: AASequence) → bool#: Returns true if the peptide has the given suffix

isModified(self) → bool#: Returns true if any of the residues or termini are modified

setCTerminalModification()#

Overload:

setCTerminalModification(self, modification: bytes | str | String) → None

Sets the C-terminal modification (by lookup in the mod names of the ModificationsDB). Throws if nothing is found (since the name is not enough information to create a new mod)

Overload:

setCTerminalModification(self, mod: ResidueModification) → None

Sets the C-terminal modification (copies and adds to database if not present)

setCTerminalModificationByDiffMonoMass(self, diffMonoMass: float, protein_term: bool) → None#: Sets the C-terminal modification by the monoisotopic mass difference it introduces (creates a “user-defined” mod if not present)

setModification()#

Overload:

setModification(self, index: int, modification: bytes | str | String) → None

Sets the modification of the residue at position index. If an empty string is passed replaces the residue with its unmodified version

Overload:

setModification(self, index: int, modification: ResidueModification) → None

Sets the modification of AA at index by providing a ResidueModification object. Stricter than just looking for the name and adds the Modification to the DB if not present

setModificationByDiffMonoMass(self, index: int, diffMonoMass: float) → None#: Modifies the residue at index in the sequence and potentially in the ResidueDB

setNTerminalModification()#

Overload:

setNTerminalModification(self, modification: bytes | str | String) → None

Sets the N-terminal modification (by lookup in the mod names of the ModificationsDB). Throws if nothing is found (since the name is not enough information to create a new mod)

Overload:

setNTerminalModification(self, mod: ResidueModification) → None

Sets the N-terminal modification (copies and adds to database if not present)

setNTerminalModificationByDiffMonoMass(self, diffMonoMass: float, protein_term: bool) → None#: Sets the N-terminal modification by the monoisotopic mass difference it introduces (creates a “user-defined” mod if not present)

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

toBracketString()#

Overload:

toBracketString(self) → bytes | str | String

Create a TPP compatible string of the modified sequence using bracket notation. Uses integer mass by default

Overload:

toBracketString(self, integer_mass: bool) → bytes | str | String

Create a TPP compatible string of the modified sequence using bracket notation

Overload:

toBracketString(self, integer_mass: bool, mass_delta: bool) → bytes | str | String

Create a TPP compatible string of the modified sequence using bracket notation.

Overload:

toBracketString(self, integer_mass: bool, mass_delta: bool, fixed_modifications: List[bytes]) → bytes | str | String

Create a TPP compatible string of the modified sequence using bracket notation

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

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

toUnmodifiedString(self) → bytes | str | String#: Returns the peptide as string without any modifications