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
Overload:
empty
(self)Check if sequence is empty
__static_AASequence_fromString(s: Union[bytes, str, String] ) -> AASequence
__static_AASequence_fromStringPermissive(s: Union[bytes, str, String] , permissive: bool ) -> AASequence
Overload:
getCTerminalModification
(self)Returns a copy of the name C-terminal modification object, or None
Returns the name (ID) of the C-terminal modification, or an empty string if none is set
Overload:
Overload:
Overload:
getNTerminalModification
(self)Returns a copy of the name N-terminal modification object, or None
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
Overload:
setCTerminalModificationByDiffMonoMass
(self, ...)Sets the C-terminal modification by the monoisotopic mass difference it introduces (creates a "user-defined" mod if not present)
Overload:
setModificationByDiffMonoMass
(self, index, ...)Modifies the residue at index in the sequence and potentially in the ResidueDB
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
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
- 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
- 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