PrecursorIonSelectionPreprocessing

class pyopenms.PrecursorIonSelectionPreprocessing

Bases: object

Cython implementation of _PrecursorIonSelectionPreprocessing

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PrecursorIonSelectionPreprocessing.html

– Inherits from [‘DefaultParamHandler’]

__init__()

• Cython signature: void PrecursorIonSelectionPreprocessing()

• Cython signature: void PrecursorIonSelectionPreprocessing(PrecursorIonSelectionPreprocessing &)

Methods

__init__	Cython signature: void PrecursorIonSelectionPreprocessing()
dbPreprocessing	Cython signature: void dbPreprocessing(String db_path, bool save)
getDefaults	Cython signature: Param getDefaults() Returns the default parameters
getGaussMu	Cython signature: double getGaussMu() Returns the Gauss Mu value
getGaussSigma	Cython signature: double getGaussSigma() Returns the Gauss Sigma value
getMasses	Cython signature: libcpp_vector[double] getMasses(String acc)
getName	Cython signature: String getName() Returns the name
getPT	Cython signature: double getPT(String prot_id, size_t peptide_index) Returns the PT value
getParameters	Cython signature: Param getParameters() Returns the parameters
getRT	Cython signature: double getRT(String prot_id, size_t peptide_index) Returns the RT value
getRTProbability	Cython signature: double getRTProbability(String prot_id, size_t peptide_index, Feature & feature)
getSubsections	Cython signature: libcpp_vector[String] getSubsections()
getWeight	Cython signature: double getWeight(double mass) Returns the weighted frequency of a mass
loadPreprocessing	Cython signature: void loadPreprocessing() Loads tryptic peptide masses of a given database
setFixedModifications	Cython signature: void setFixedModifications(StringList & modifications)
setGaussianParameters	Cython signature: void setGaussianParameters(double mu, double sigma)
setName	Cython signature: void setName(const String &) Sets the name
setParameters	Cython signature: void setParameters(Param & param) Sets the parameters

dbPreprocessing()

• Cython signature: void dbPreprocessing(String db_path, bool save)

Parameters

• db_path – Path to database file (fasta)

• save – Flag if preprocessing should be stored

Raises

Exception: FileNotFound is thrown if the file could not be found

Raises

Exception: UnableToCreateFile if preprocessing file can’t be written

• Cython signature: void dbPreprocessing(String db_path, String rt_model_path, String dt_model_path, bool save)

Parameters

db_path – Path to database file (fasta)

:param rt_model_path :param dt_model_path :param save: Flag if preprocessing should be stored —– :raises:

Exception: FileNotFound is thrown if the file could not be found

Raises

Exception: UnableToCreateFile if preprocessing file can’t be written

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getGaussMu()

Cython signature: double getGaussMu() Returns the Gauss Mu value

getGaussSigma()

Cython signature: double getGaussSigma() Returns the Gauss Sigma value

getMasses()

Cython signature: libcpp_vector[double] getMasses(String acc)

getName()

Cython signature: String getName() Returns the name

getPT()

Cython signature: double getPT(String prot_id, size_t peptide_index) Returns the PT value

getParameters()

Cython signature: Param getParameters() Returns the parameters

getRT()

Cython signature: double getRT(String prot_id, size_t peptide_index) Returns the RT value

getRTProbability()

• Cython signature: double getRTProbability(String prot_id, size_t peptide_index, Feature & feature)

• Cython signature: double getRTProbability(double pred_rt, Feature & feature)

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

getWeight()

Cython signature: double getWeight(double mass) Returns the weighted frequency of a mass

loadPreprocessing()

Cython signature: void loadPreprocessing() Loads tryptic peptide masses of a given database

setFixedModifications()

Cython signature: void setFixedModifications(StringList & modifications)

setGaussianParameters()

Cython signature: void setGaussianParameters(double mu, double sigma)

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters