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_3.__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