AASequence
- class pyopenms.AASequence
Bases:
objectCython 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
Cython signature: void AASequence()
Cython signature: bool empty() Check if sequence is empty
Cython signature: AASequence fromString(String s)
Cython signature: AASequence fromStringPermissive(String s, bool permissive)
Cython signature: double getAverageWeight()
Cython signature: const ResidueModification * getCTerminalModification() Returns a copy of the name C-terminal modification object, or None
Cython signature: String getCTerminalModificationName() Returns the name (ID) of the C-terminal modification, or an empty string if none is set
Cython signature: EmpiricalFormula getFormula()
Cython signature: double getMZ(int charge)
Cython signature: double getMonoWeight()
Cython signature: const ResidueModification * getNTerminalModification() Returns a copy of the name N-terminal modification object, or None
Cython signature: String getNTerminalModificationName() Returns the name (ID) of the N-terminal modification, or an empty string if none is set
Cython signature: AASequence getPrefix(size_t index) Returns a peptide sequence of the first index residues
Cython signature: Residue getResidue(size_t index) Returns the residue at position index
Cython signature: AASequence getSubsequence(size_t index, unsigned int number) Returns a peptide sequence of number residues, beginning at position index
Cython signature: AASequence getSuffix(size_t index) Returns a peptide sequence of the last index residues
Cython signature: bool has(Residue residue) Returns true if the peptide contains the given residue
Cython signature: bool hasCTerminalModification() Predicate which is true if the peptide is C-term modified
Cython signature: bool hasNTerminalModification() Predicate which is true if the peptide is N-term modified
Cython signature: bool hasPrefix(AASequence peptide) Returns true if the peptide has the given prefix
Cython signature: bool hasSubsequence(AASequence peptide) Returns true if the peptide contains the given peptide
Cython signature: bool hasSuffix(AASequence peptide) Returns true if the peptide has the given suffix
Cython signature: bool isModified() Returns true if any of the residues or termini are modified
Cython signature: void setCTerminalModification(String modification)
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)
Cython signature: void setModification(size_t index, const String & modification)
Cython signature: void setModificationByDiffMonoMass(size_t index, double diffMonoMass) Modifies the residue at index in the sequence and potentially in the ResidueDB
Cython signature: void setNTerminalModification(String modification)
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)
Cython signature: size_t size() Returns the number of residues
Cython signature: String toBracketString()
Cython signature: String toString() Returns the peptide as string with modifications embedded in brackets
Cython signature: String toUniModString() Returns the peptide as string with UniMod-style modifications embedded in brackets
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