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) → Union[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) → Union[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: Union[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: Union[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: Union[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) → Union[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) → Union[bytes, str, String]

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

Overload:

toBracketString(self, integer_mass: bool, mass_delta: bool) → Union[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]) → Union[bytes, str, String]

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

toString(self) → Union[bytes, str, String]

Returns the peptide as string with modifications embedded in brackets

toUniModString(self) → Union[bytes, str, String]

Returns the peptide as string with UniMod-style modifications embedded in brackets

toUnmodifiedString(self) → Union[bytes, str, String]

Returns the peptide as string without any modifications