Residue#

class pyopenms.Residue#

Bases: object

Cython implementation of _Residue

Original C++ documentation is available here

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: Residue) → None

Overload:

__init__(self, name: bytes | str | String, three_letter_code: bytes | str | String, one_letter_code: bytes | str | String, formula: EmpiricalFormula) → None

Methods

`__init__`	Overload:
`addLossFormula`(self, in_0)	Adds a neutral loss formula
`addLossName`(self, name)	Adds neutral loss molecule name
`addNTermLossFormula`(self, in_0)	Adds N-terminal losses
`addNTermLossName`(self, name)	Adds a N-terminal loss name
`addResidueSet`(self, residue_sets)	Adds a residue set to the residue sets
`addSynonym`(self, synonym)	Adds a synonym
`getAverageWeight`	Overload:
`getBackboneBasicityLeft`(self)	Returns the backbone basicitiy if located in N-terminal direction
`getBackboneBasicityRight`(self)	Returns the C-terminal direction backbone basicitiy
`getFormula`	Overload:
`getInternalToAIon`(self)
`getInternalToBIon`(self)
`getInternalToCIon`(self)
`getInternalToCTerm`(self)
`getInternalToFull`(self)
`getInternalToNTerm`(self)
`getInternalToXIon`(self)
`getInternalToYIon`(self)
`getInternalToZIon`(self)
`getLossFormulas`(self)	Returns the neutral loss formulas
`getLossNames`(self)	Gets neutral loss name (if there is one, else returns an empty string)
`getLowMassIons`(self)	Returns a vector of formulas with the low mass markers of the residue
`getModification`(self)
`getModificationName`(self)	Returns the name of the modification to the modification
`getMonoWeight`	Overload:
`getNTermLossFormulas`(self)	Returns N-terminal loss formulas
`getNTermLossNames`(self)	Returns the N-terminal loss names
`getName`(self)	Returns the name of the residue
`getOneLetterCode`(self)	Returns the name as one letter code
`getPiValue`(self)	Calculates the isoelectric point using the pk values
`getPka`(self)	Returns the pka of the residue
`getPkb`(self)	Returns the pkb of the residue
`getPkc`(self)	Returns the pkc of the residue if it exists otherwise -1
`getResidueSets`(self)	Returns the residue sets this residue is contained in
`getResidueTypeName`(self, res_type)	Returns the ion name given as a residue type
`getSideChainBasicity`(self)	Returns the side chain basicity
`getSynonyms`(self)	Returns the sysnonyms
`getThreeLetterCode`(self)	Returns the name of the residue as three letter code
`hasNTermNeutralLosses`(self)	True if N-terminal neutral losses are set
`hasNeutralLoss`(self)	True if the residue has neutral loss
`isInResidueSet`(self, residue_set)	True if the residue is contained in the set
`isModified`(self)	True if the residue is a modified one
`residueTypeToIonLetter`(self, res_type)	Helper for mapping residue types to letters for Text annotations and labels
`setAverageWeight`(self, weight)	Sets average weight of the residue (must be full, with N and C-terminus)
`setBackboneBasicityLeft`(self, gb_bb_l)	Sets the N-terminal direction backbone basicitiy
`setBackboneBasicityRight`(self, gb_bb_r)	Sets the C-terminal direction backbone basicity
`setFormula`(self, formula)	Sets empirical formula of the residue (must be full, with N and C-terminus)
`setLossFormulas`(self, in_0)	Sets the neutral loss formulas
`setLossNames`(self, name)	Sets the neutral loss molecule name
`setLowMassIons`(self, low_mass_ions)	Sets the low mass marker ions as a vector of formulas
`setModification`	Overload:
`setModificationByDiffMonoMass`(self, diffMonoMass)	Sets the modification by monoisotopic mass difference in Da; checks if present in ModificationsDB with tolerance and adds a "user-defined" modification if not (for later lookups).
`setMonoWeight`(self, weight)	Sets monoisotopic weight of the residue (must be full, with N and C-terminus)
`setNTermLossFormulas`(self, in_0)	Sets the N-terminal losses
`setNTermLossNames`(self, name)	Sets the N-terminal loss names
`setName`(self, name)	Sets the name of the residue
`setOneLetterCode`(self, one_letter_code)	Sets the name as one letter code
`setPka`(self, value)	Sets the pka of the residue
`setPkb`(self, value)	Sets the pkb of the residue
`setPkc`(self, value)	Sets the pkc of the residue
`setResidueSets`(self, residues_sets)	Sets the residue sets the amino acid is contained in
`setSideChainBasicity`(self, gb_sc)	Sets the side chain basicity
`setSynonyms`(self, synonyms)	Sets the synonyms
`setThreeLetterCode`(self, three_letter_code)	Sets the name of the residue as three letter code

ResidueType#: alias of __ResidueType

addLossFormula(self, in_0: EmpiricalFormula) → None#: Adds a neutral loss formula

addLossName(self, name: bytes | str | String) → None#: Adds neutral loss molecule name

addNTermLossFormula(self, in_0: EmpiricalFormula) → None#: Adds N-terminal losses

addNTermLossName(self, name: bytes | str | String) → None#: Adds a N-terminal loss name

addResidueSet(self, residue_sets: bytes | str | String) → None#: Adds a residue set to the residue sets

addSynonym(self, synonym: bytes | str | String) → None#: Adds a synonym

getAverageWeight()#

Overload:

getAverageWeight(self) → float

Returns average weight of the residue

Overload:

getAverageWeight(self, res_type: int) → float

getBackboneBasicityLeft(self) → float#: Returns the backbone basicitiy if located in N-terminal direction

getBackboneBasicityRight(self) → float#: Returns the C-terminal direction backbone basicitiy

getFormula()#

Overload:

getFormula(self) → EmpiricalFormula

Returns the empirical formula of the residue

Overload:

getFormula(self, res_type: int) → EmpiricalFormula

getInternalToAIon(self) → EmpiricalFormula#

getInternalToBIon(self) → EmpiricalFormula#

getInternalToCIon(self) → EmpiricalFormula#

getInternalToCTerm(self) → EmpiricalFormula#

getInternalToFull(self) → EmpiricalFormula#

getInternalToNTerm(self) → EmpiricalFormula#

getInternalToXIon(self) → EmpiricalFormula#

getInternalToYIon(self) → EmpiricalFormula#

getInternalToZIon(self) → EmpiricalFormula#

getLossFormulas(self) → List[EmpiricalFormula]#: Returns the neutral loss formulas

getLossNames(self) → List[bytes]#: Gets neutral loss name (if there is one, else returns an empty string)

getLowMassIons(self) → List[EmpiricalFormula]#: Returns a vector of formulas with the low mass markers of the residue

getModification(self) → ResidueModification#

getModificationName(self) → bytes | str | String#: Returns the name of the modification to the modification

getMonoWeight()#

Overload:

getMonoWeight(self) → float

Returns monoisotopic weight of the residue

Overload:

getMonoWeight(self, res_type: int) → float

getNTermLossFormulas(self) → List[EmpiricalFormula]#: Returns N-terminal loss formulas

getNTermLossNames(self) → List[bytes]#: Returns the N-terminal loss names

getName(self) → bytes | str | String#: Returns the name of the residue

getOneLetterCode(self) → bytes | str | String#: Returns the name as one letter code

getPiValue(self) → float#: Calculates the isoelectric point using the pk values

getPka(self) → float#: Returns the pka of the residue

getPkb(self) → float#: Returns the pkb of the residue

getPkc(self) → float#: Returns the pkc of the residue if it exists otherwise -1

getResidueSets(self) → Set[bytes]#: Returns the residue sets this residue is contained in

getResidueTypeName(self, res_type: int) → bytes | str | String#: Returns the ion name given as a residue type

getSideChainBasicity(self) → float#: Returns the side chain basicity

getSynonyms(self) → Set[bytes]#: Returns the sysnonyms

getThreeLetterCode(self) → bytes | str | String#: Returns the name of the residue as three letter code

hasNTermNeutralLosses(self) → bool#: True if N-terminal neutral losses are set

hasNeutralLoss(self) → bool#: True if the residue has neutral loss

isInResidueSet(self, residue_set: bytes | str | String) → bool#: True if the residue is contained in the set

isModified(self) → bool#: True if the residue is a modified one

residueTypeToIonLetter(self, res_type: int) → bytes#: Helper for mapping residue types to letters for Text annotations and labels

setAverageWeight(self, weight: float) → None#: Sets average weight of the residue (must be full, with N and C-terminus)

setBackboneBasicityLeft(self, gb_bb_l: float) → None#: Sets the N-terminal direction backbone basicitiy

setBackboneBasicityRight(self, gb_bb_r: float) → None#: Sets the C-terminal direction backbone basicity

setFormula(self, formula: EmpiricalFormula) → None#: Sets empirical formula of the residue (must be full, with N and C-terminus)

setLossFormulas(self, in_0: List[EmpiricalFormula]) → None#: Sets the neutral loss formulas

setLossNames(self, name: List[bytes]) → None#: Sets the neutral loss molecule name

setLowMassIons(self, low_mass_ions: List[EmpiricalFormula]) → None#: Sets the low mass marker ions as a vector of formulas

setModification()#

Overload:

setModification(self, name: bytes | str | String) → None

Sets the modification by name; the mod should be present in ModificationsDB

Overload:

setModification(self, mod: ResidueModification) → None

Sets the modification by a ResidueModification object; checks if present in ModificationsDB and adds if not.

setModificationByDiffMonoMass(self, diffMonoMass: float) → None#: Sets the modification by monoisotopic mass difference in Da; checks if present in ModificationsDB with tolerance and adds a “user-defined” modification if not (for later lookups).

setMonoWeight(self, weight: float) → None#: Sets monoisotopic weight of the residue (must be full, with N and C-terminus)

setNTermLossFormulas(self, in_0: List[EmpiricalFormula]) → None#: Sets the N-terminal losses

setNTermLossNames(self, name: List[bytes]) → None#: Sets the N-terminal loss names

setName(self, name: bytes | str | String) → None#: Sets the name of the residue

setOneLetterCode(self, one_letter_code: bytes | str | String) → None#: Sets the name as one letter code

setPka(self, value: float) → None#: Sets the pka of the residue

setPkb(self, value: float) → None#: Sets the pkb of the residue

setPkc(self, value: float) → None#: Sets the pkc of the residue

setResidueSets(self, residues_sets: Set[bytes]) → None#: Sets the residue sets the amino acid is contained in

setSideChainBasicity(self, gb_sc: float) → None#: Sets the side chain basicity

setSynonyms(self, synonyms: Set[bytes]) → None#: Sets the synonyms

setThreeLetterCode(self, three_letter_code: bytes | str | String) → None#: Sets the name of the residue as three letter code