Residue#

class pyopenms.Residue#

Bases: object

Cython implementation of _Residue

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1Residue.html

__init__()#

Cython signature: void Residue()
Cython signature: void Residue(Residue &)
Cython signature: void Residue(String name, String three_letter_code, String one_letter_code, EmpiricalFormula formula)

Methods

`__init__`	Cython signature: void Residue()
`addLossFormula`	Cython signature: void addLossFormula(EmpiricalFormula) Adds a neutral loss formula
`addLossName`	Cython signature: void addLossName(String name) Adds neutral loss molecule name
`addNTermLossFormula`	Cython signature: void addNTermLossFormula(EmpiricalFormula) Adds N-terminal losses
`addNTermLossName`	Cython signature: void addNTermLossName(String name) Adds a N-terminal loss name
`addResidueSet`	Cython signature: void addResidueSet(String residue_sets) Adds a residue set to the residue sets
`addSynonym`	Cython signature: void addSynonym(String synonym) Adds a synonym
`getAverageWeight`	Cython signature: double getAverageWeight()
`getBackboneBasicityLeft`	Cython signature: double getBackboneBasicityLeft() Returns the backbone basicitiy if located in N-terminal direction
`getBackboneBasicityRight`	Cython signature: double getBackboneBasicityRight() Returns the C-terminal direction backbone basicitiy
`getFormula`	Cython signature: EmpiricalFormula getFormula()
`getInternalToAIon`	Cython signature: EmpiricalFormula getInternalToAIon()
`getInternalToBIon`	Cython signature: EmpiricalFormula getInternalToBIon()
`getInternalToCIon`	Cython signature: EmpiricalFormula getInternalToCIon()
`getInternalToCTerm`	Cython signature: EmpiricalFormula getInternalToCTerm()
`getInternalToFull`	Cython signature: EmpiricalFormula getInternalToFull()
`getInternalToNTerm`	Cython signature: EmpiricalFormula getInternalToNTerm()
`getInternalToXIon`	Cython signature: EmpiricalFormula getInternalToXIon()
`getInternalToYIon`	Cython signature: EmpiricalFormula getInternalToYIon()
`getInternalToZIon`	Cython signature: EmpiricalFormula getInternalToZIon()
`getLossFormulas`	Cython signature: libcpp_vector[EmpiricalFormula] getLossFormulas() Returns the neutral loss formulas
`getLossNames`	Cython signature: libcpp_vector[String] getLossNames() Gets neutral loss name (if there is one, else returns an empty string)
`getLowMassIons`	Cython signature: libcpp_vector[EmpiricalFormula] getLowMassIons() Returns a vector of formulas with the low mass markers of the residue
`getModification`	Cython signature: const ResidueModification * getModification()
`getModificationName`	Cython signature: String getModificationName() Returns the name of the modification to the modification
`getMonoWeight`	Cython signature: double getMonoWeight()
`getNTermLossFormulas`	Cython signature: libcpp_vector[EmpiricalFormula] getNTermLossFormulas() Returns N-terminal loss formulas
`getNTermLossNames`	Cython signature: libcpp_vector[String] getNTermLossNames() Returns the N-terminal loss names
`getName`	Cython signature: String getName() Returns the name of the residue
`getOneLetterCode`	Cython signature: String getOneLetterCode() Returns the name as one letter code
`getPiValue`	Cython signature: double getPiValue() Calculates the isoelectric point using the pk values
`getPka`	Cython signature: double getPka() Returns the pka of the residue
`getPkb`	Cython signature: double getPkb() Returns the pkb of the residue
`getPkc`	Cython signature: double getPkc() Returns the pkc of the residue if it exists otherwise -1
`getResidueSets`	Cython signature: libcpp_set[String] getResidueSets() Returns the residue sets this residue is contained in
`getResidueTypeName`	Cython signature: String getResidueTypeName(ResidueType res_type) Returns the ion name given as a residue type
`getSideChainBasicity`	Cython signature: double getSideChainBasicity() Returns the side chain basicity
`getSynonyms`	Cython signature: libcpp_set[String] getSynonyms() Returns the sysnonyms
`getThreeLetterCode`	Cython signature: String getThreeLetterCode() Returns the name of the residue as three letter code
`hasNTermNeutralLosses`	Cython signature: bool hasNTermNeutralLosses() True if N-terminal neutral losses are set
`hasNeutralLoss`	Cython signature: bool hasNeutralLoss() True if the residue has neutral loss
`isInResidueSet`	Cython signature: bool isInResidueSet(String residue_set) True if the residue is contained in the set
`isModified`	Cython signature: bool isModified() True if the residue is a modified one
`residueTypeToIonLetter`	Cython signature: char residueTypeToIonLetter(ResidueType res_type) Helper for mapping residue types to letters for Text annotations and labels
`setAverageWeight`	Cython signature: void setAverageWeight(double weight) Sets average weight of the residue (must be full, with N and C-terminus)
`setBackboneBasicityLeft`	Cython signature: void setBackboneBasicityLeft(double gb_bb_l) Sets the N-terminal direction backbone basicitiy
`setBackboneBasicityRight`	Cython signature: void setBackboneBasicityRight(double gb_bb_r) Sets the C-terminal direction backbone basicity
`setFormula`	Cython signature: void setFormula(EmpiricalFormula formula) Sets empirical formula of the residue (must be full, with N and C-terminus)
`setLossFormulas`	Cython signature: void setLossFormulas(libcpp_vector[EmpiricalFormula]) Sets the neutral loss formulas
`setLossNames`	Cython signature: void setLossNames(libcpp_vector[String] name) Sets the neutral loss molecule name
`setLowMassIons`	Cython signature: void setLowMassIons(libcpp_vector[EmpiricalFormula] low_mass_ions) Sets the low mass marker ions as a vector of formulas
`setModification`	Cython signature: void setModification(String name)
`setModificationByDiffMonoMass`	Cython signature: void setModificationByDiffMonoMass(double 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`	Cython signature: void setMonoWeight(double weight) Sets monoisotopic weight of the residue (must be full, with N and C-terminus)
`setNTermLossFormulas`	Cython signature: void setNTermLossFormulas(libcpp_vector[EmpiricalFormula]) Sets the N-terminal losses
`setNTermLossNames`	Cython signature: void setNTermLossNames(libcpp_vector[String] name) Sets the N-terminal loss names
`setName`	Cython signature: void setName(String name) Sets the name of the residue
`setOneLetterCode`	Cython signature: void setOneLetterCode(String one_letter_code) Sets the name as one letter code
`setPka`	Cython signature: void setPka(double value) Sets the pka of the residue
`setPkb`	Cython signature: void setPkb(double value) Sets the pkb of the residue
`setPkc`	Cython signature: void setPkc(double value) Sets the pkc of the residue
`setResidueSets`	Cython signature: void setResidueSets(libcpp_set[String] residues_sets) Sets the residue sets the amino acid is contained in
`setSideChainBasicity`	Cython signature: void setSideChainBasicity(double gb_sc) Sets the side chain basicity
`setSynonyms`	Cython signature: void setSynonyms(libcpp_set[String] synonyms) Sets the synonyms
`setThreeLetterCode`	Cython signature: void setThreeLetterCode(String three_letter_code) Sets the name of the residue as three letter code

ResidueType#: alias of pyopenms.pyopenms_8.__ResidueType

addLossFormula()#: Cython signature: void addLossFormula(EmpiricalFormula) Adds a neutral loss formula

addLossName()#: Cython signature: void addLossName(String name) Adds neutral loss molecule name

addNTermLossFormula()#: Cython signature: void addNTermLossFormula(EmpiricalFormula) Adds N-terminal losses

addNTermLossName()#: Cython signature: void addNTermLossName(String name) Adds a N-terminal loss name

addResidueSet()#: Cython signature: void addResidueSet(String residue_sets) Adds a residue set to the residue sets

addSynonym()#: Cython signature: void addSynonym(String synonym) Adds a synonym

getAverageWeight()#

Cython signature: double getAverageWeight() Returns average weight of the residue
Cython signature: double getAverageWeight(ResidueType res_type)

getBackboneBasicityLeft()#: Cython signature: double getBackboneBasicityLeft() Returns the backbone basicitiy if located in N-terminal direction

getBackboneBasicityRight()#: Cython signature: double getBackboneBasicityRight() Returns the C-terminal direction backbone basicitiy

getFormula()#

Cython signature: EmpiricalFormula getFormula() Returns the empirical formula of the residue
Cython signature: EmpiricalFormula getFormula(ResidueType res_type)

getInternalToAIon()#: Cython signature: EmpiricalFormula getInternalToAIon()

getInternalToBIon()#: Cython signature: EmpiricalFormula getInternalToBIon()

getInternalToCIon()#: Cython signature: EmpiricalFormula getInternalToCIon()

getInternalToCTerm()#: Cython signature: EmpiricalFormula getInternalToCTerm()

getInternalToFull()#: Cython signature: EmpiricalFormula getInternalToFull()

getInternalToNTerm()#: Cython signature: EmpiricalFormula getInternalToNTerm()

getInternalToXIon()#: Cython signature: EmpiricalFormula getInternalToXIon()

getInternalToYIon()#: Cython signature: EmpiricalFormula getInternalToYIon()

getInternalToZIon()#: Cython signature: EmpiricalFormula getInternalToZIon()

getLossFormulas()#: Cython signature: libcpp_vector[EmpiricalFormula] getLossFormulas() Returns the neutral loss formulas

getLossNames()#: Cython signature: libcpp_vector[String] getLossNames() Gets neutral loss name (if there is one, else returns an empty string)

getLowMassIons()#: Cython signature: libcpp_vector[EmpiricalFormula] getLowMassIons() Returns a vector of formulas with the low mass markers of the residue

getModification()#: Cython signature: const ResidueModification * getModification()

getModificationName()#: Cython signature: String getModificationName() Returns the name of the modification to the modification

getMonoWeight()#

Cython signature: double getMonoWeight() Returns monoisotopic weight of the residue
Cython signature: double getMonoWeight(ResidueType res_type)

getNTermLossFormulas()#: Cython signature: libcpp_vector[EmpiricalFormula] getNTermLossFormulas() Returns N-terminal loss formulas

getNTermLossNames()#: Cython signature: libcpp_vector[String] getNTermLossNames() Returns the N-terminal loss names

getName()#: Cython signature: String getName() Returns the name of the residue

getOneLetterCode()#: Cython signature: String getOneLetterCode() Returns the name as one letter code

getPiValue()#: Cython signature: double getPiValue() Calculates the isoelectric point using the pk values

getPka()#: Cython signature: double getPka() Returns the pka of the residue

getPkb()#: Cython signature: double getPkb() Returns the pkb of the residue

getPkc()#: Cython signature: double getPkc() Returns the pkc of the residue if it exists otherwise -1

getResidueSets()#: Cython signature: libcpp_set[String] getResidueSets() Returns the residue sets this residue is contained in

getResidueTypeName()#: Cython signature: String getResidueTypeName(ResidueType res_type) Returns the ion name given as a residue type

getSideChainBasicity()#: Cython signature: double getSideChainBasicity() Returns the side chain basicity

getSynonyms()#: Cython signature: libcpp_set[String] getSynonyms() Returns the sysnonyms

getThreeLetterCode()#: Cython signature: String getThreeLetterCode() Returns the name of the residue as three letter code

hasNTermNeutralLosses()#: Cython signature: bool hasNTermNeutralLosses() True if N-terminal neutral losses are set

hasNeutralLoss()#: Cython signature: bool hasNeutralLoss() True if the residue has neutral loss

isInResidueSet()#: Cython signature: bool isInResidueSet(String residue_set) True if the residue is contained in the set

isModified()#: Cython signature: bool isModified() True if the residue is a modified one

residueTypeToIonLetter()#: Cython signature: char residueTypeToIonLetter(ResidueType res_type) Helper for mapping residue types to letters for Text annotations and labels

setAverageWeight()#: Cython signature: void setAverageWeight(double weight) Sets average weight of the residue (must be full, with N and C-terminus)

setBackboneBasicityLeft()#: Cython signature: void setBackboneBasicityLeft(double gb_bb_l) Sets the N-terminal direction backbone basicitiy

setBackboneBasicityRight()#: Cython signature: void setBackboneBasicityRight(double gb_bb_r) Sets the C-terminal direction backbone basicity

setFormula()#: Cython signature: void setFormula(EmpiricalFormula formula) Sets empirical formula of the residue (must be full, with N and C-terminus)

setLossFormulas()#: Cython signature: void setLossFormulas(libcpp_vector[EmpiricalFormula]) Sets the neutral loss formulas

setLossNames()#: Cython signature: void setLossNames(libcpp_vector[String] name) Sets the neutral loss molecule name

setLowMassIons()#: Cython signature: void setLowMassIons(libcpp_vector[EmpiricalFormula] low_mass_ions) Sets the low mass marker ions as a vector of formulas

setModification()#

Cython signature: void setModification(String name) Sets the modification by name; the mod should be present in ModificationsDB
Cython signature: void setModification(const ResidueModification & mod) Sets the modification by a ResidueModification object; checks if present in ModificationsDB and adds if not.

setModificationByDiffMonoMass()#: Cython signature: void setModificationByDiffMonoMass(double 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()#: Cython signature: void setMonoWeight(double weight) Sets monoisotopic weight of the residue (must be full, with N and C-terminus)

setNTermLossFormulas()#: Cython signature: void setNTermLossFormulas(libcpp_vector[EmpiricalFormula]) Sets the N-terminal losses

setNTermLossNames()#: Cython signature: void setNTermLossNames(libcpp_vector[String] name) Sets the N-terminal loss names

setName()#: Cython signature: void setName(String name) Sets the name of the residue

setOneLetterCode()#: Cython signature: void setOneLetterCode(String one_letter_code) Sets the name as one letter code

setPka()#: Cython signature: void setPka(double value) Sets the pka of the residue

setPkb()#: Cython signature: void setPkb(double value) Sets the pkb of the residue

setPkc()#: Cython signature: void setPkc(double value) Sets the pkc of the residue

setResidueSets()#: Cython signature: void setResidueSets(libcpp_set[String] residues_sets) Sets the residue sets the amino acid is contained in

setSideChainBasicity()#: Cython signature: void setSideChainBasicity(double gb_sc) Sets the side chain basicity

setSynonyms()#: Cython signature: void setSynonyms(libcpp_set[String] synonyms) Sets the synonyms

setThreeLetterCode()#: Cython signature: void setThreeLetterCode(String three_letter_code) Sets the name of the residue as three letter code