AASequence#

class pyopenms.AASequence#

Bases: object

Cython implementation of _AASequence

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1AASequence.html

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

__init__()#

Cython signature: void AASequence()
Cython signature: void AASequence(AASequence &)

Methods

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

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

fromString()#: Cython signature: AASequence fromString(String s)

fromStringPermissive()#: Cython signature: AASequence fromStringPermissive(String s, bool permissive)

getAAFrequencies()#

getAverageWeight()#

Cython signature: double getAverageWeight() Returns the average weight of the peptide
Cython signature: double getAverageWeight(ResidueType type_, int charge)

getCTerminalModification()#: Cython signature: const ResidueModification * getCTerminalModification() Returns a copy of the name C-terminal modification object, or None

getCTerminalModificationName()#: Cython signature: String getCTerminalModificationName() Returns the name (ID) of the C-terminal modification, or an empty string if none is set

getFormula()#

Cython signature: EmpiricalFormula getFormula() Convenience function with ResidueType=Full and charge = 0 by default
Cython signature: EmpiricalFormula getFormula(ResidueType type_, int charge)

getMZ()#

Cython signature: double getMZ(int charge) Returns the mass-to-charge ratio of the peptide
Cython signature: double getMZ(int charge, ResidueType type_)

getMonoWeight()#

Cython signature: double getMonoWeight() Returns the mono isotopic weight of the peptide
Cython signature: double getMonoWeight(ResidueType type_, int charge)

getNTerminalModification()#: Cython signature: const ResidueModification * getNTerminalModification() Returns a copy of the name N-terminal modification object, or None

getNTerminalModificationName()#: Cython signature: String getNTerminalModificationName() Returns the name (ID) of the N-terminal modification, or an empty string if none is set

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

getResidue()#: Cython signature: Residue getResidue(size_t index) Returns the residue at position index

getSubsequence()#: Cython signature: AASequence getSubsequence(size_t index, unsigned int number) Returns a peptide sequence of number residues, beginning at position index

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

has()#: Cython signature: bool has(Residue residue) Returns true if the peptide contains the given residue

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

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

hasPrefix()#: Cython signature: bool hasPrefix(AASequence peptide) Returns true if the peptide has the given prefix

hasSubsequence()#: Cython signature: bool hasSubsequence(AASequence peptide) Returns true if the peptide contains the given peptide

hasSuffix()#: Cython signature: bool hasSuffix(AASequence peptide) Returns true if the peptide has the given suffix

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

setCTerminalModification()#

Cython signature: void setCTerminalModification(String modification) 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)
Cython signature: void setCTerminalModification(const ResidueModification & mod) Sets the C-terminal modification (copies and adds to database if not present)

setCTerminalModificationByDiffMonoMass()#: Cython signature: void setCTerminalModificationByDiffMonoMass(double diffMonoMass, bool protein_term) Sets the C-terminal modification by the monoisotopic mass difference it introduces (creates a “user-defined” mod if not present)

setModification()#

Cython signature: void setModification(size_t index, const String & modification) Sets the modification of the residue at position index. If an empty string is passed replaces the residue with its unmodified version
Cython signature: void setModification(size_t index, const ResidueModification & modification) 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()#: Cython signature: void setModificationByDiffMonoMass(size_t index, double diffMonoMass) Modifies the residue at index in the sequence and potentially in the ResidueDB

setNTerminalModification()#

Cython signature: void setNTerminalModification(String modification) 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)
Cython signature: void setNTerminalModification(const ResidueModification & mod) Sets the N-terminal modification (copies and adds to database if not present)

setNTerminalModificationByDiffMonoMass()#: Cython signature: void setNTerminalModificationByDiffMonoMass(double diffMonoMass, bool protein_term) Sets the N-terminal modification by the monoisotopic mass difference it introduces (creates a “user-defined” mod if not present)

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

toBracketString()#

Cython signature: String toBracketString() Create a TPP compatible string of the modified sequence using bracket notation. Uses integer mass by default
Cython signature: String toBracketString(bool integer_mass) Create a TPP compatible string of the modified sequence using bracket notation
Cython signature: String toBracketString(bool integer_mass, bool mass_delta) Create a TPP compatible string of the modified sequence using bracket notation.
Cython signature: String toBracketString(bool integer_mass, bool mass_delta, libcpp_vector[String] fixed_modifications) Create a TPP compatible string of the modified sequence using bracket notation

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

toUniModString()#: Cython signature: String toUniModString() Returns the peptide as string with UniMod-style modifications embedded in brackets

toUnmodifiedString()#: Cython signature: String toUnmodifiedString() Returns the peptide as string without any modifications