ProteinIdentification#

class pyopenms.ProteinIdentification#

Bases: object

Cython implementation of _ProteinIdentification

Original C++ documentation is available here

– Inherits from [‘MetaInfoInterface’]

__init__()#

Overload:

__init__(self) None

Overload:

__init__(self, in_0: ProteinIdentification) None

Methods

__init__

Overload:

addPrimaryMSRunPath

Overload:

assignRanks(self)

Sorts the protein hits by score and assigns ranks (best score has rank 1)

clearMetaInfo(self)

Removes all meta values

computeCoverage(self, pep_ids)

Compute the coverage (in percent) of all ProteinHits given PeptideHits

getDateTime(self)

Returns the date of the protein identification run

getHits(self)

Returns the protein hits

getIdentifier(self)

Returns the identifier

getIndistinguishableProteins(self)

Returns the indistinguishable proteins

getKeys(self, keys)

Fills the given vector with a list of all keys for which a value is set

getMetaValue(self, in_0)

Returns the value corresponding to a string, or

getPrimaryMSRunPath

Overload:

getProteinGroups(self)

Returns the protein groups

getScoreType(self)

Returns the protein score type

getSearchEngine(self)

Returns the type of search engine used

getSearchEngineVersion(self)

Returns the search engine version

getSearchParameters(self)

Returns the search parameters

getSignificanceThreshold(self)

Returns the protein significance threshold value

insertHit(self, input)

Appends a protein hit

insertIndistinguishableProteins(self, group)

Appends new indistinguishable proteins

insertProteinGroup(self, group)

Appends a new protein group

isHigherScoreBetter(self)

Returns true if a higher score represents a better score

isMetaEmpty(self)

Returns if the MetaInfo is empty

metaRegistry(self)

Returns a reference to the MetaInfoRegistry

metaValueExists(self, in_0)

Returns whether an entry with the given name exists

removeMetaValue(self, in_0)

Removes the DataValue corresponding to name if it exists

setDateTime(self, date)

Sets the date of the protein identification run

setHigherScoreBetter(self, higher_is_better)

Sets the orientation of the score (is higher better?)

setHits(self, hits)

Sets the protein hits

setIdentifier(self, id_)

Sets the identifier

setMetaValue(self, in_0, in_1)

Sets the DataValue corresponding to a name

setPrimaryMSRunPath

Overload:

setScoreType(self, type)

Sets the protein score type

setSearchEngine(self, search_engine)

Sets the search engine type

setSearchEngineVersion(self, ...)

Sets the search engine version

setSearchParameters(self, search_parameters)

Sets the search parameters

setSignificanceThreshold(self, value)

Sets the protein significance threshold value

sort(self)

Sorts the protein hits according to their score

PeakMassType#

alias of __PeakMassType

addPrimaryMSRunPath()#

Overload:

addPrimaryMSRunPath(self, s: List[bytes]) None

Overload:

addPrimaryMSRunPath(self, s: List[bytes], raw: bool) None
assignRanks(self) None#

Sorts the protein hits by score and assigns ranks (best score has rank 1)

clearMetaInfo(self) None#

Removes all meta values

computeCoverage(self, pep_ids: List[PeptideIdentification]) None#

Compute the coverage (in percent) of all ProteinHits given PeptideHits

getDateTime(self) DateTime#

Returns the date of the protein identification run

getHits(self) List[ProteinHit]#

Returns the protein hits

getIdentifier(self) bytes | str | String#

Returns the identifier

getIndistinguishableProteins(self) List[ProteinGroup]#

Returns the indistinguishable proteins

getKeys(self, keys: List[bytes]) None#

Fills the given vector with a list of all keys for which a value is set

getMetaValue(self, in_0: bytes | str | String) int | float | bytes | str | List[int] | List[float] | List[bytes]#

Returns the value corresponding to a string, or

getPrimaryMSRunPath()#

Overload:

getPrimaryMSRunPath(self, output: List[bytes]) None

Overload:

getPrimaryMSRunPath(self, output: List[bytes], raw: bool) None
getProteinGroups(self) List[ProteinGroup]#

Returns the protein groups

getScoreType(self) bytes | str | String#

Returns the protein score type

getSearchEngine(self) bytes | str | String#

Returns the type of search engine used

getSearchEngineVersion(self) bytes | str | String#

Returns the search engine version

getSearchParameters(self) SearchParameters#

Returns the search parameters

getSignificanceThreshold(self) float#

Returns the protein significance threshold value

insertHit(self, input: ProteinHit) None#

Appends a protein hit

insertIndistinguishableProteins(self, group: ProteinGroup) None#

Appends new indistinguishable proteins

insertProteinGroup(self, group: ProteinGroup) None#

Appends a new protein group

isHigherScoreBetter(self) bool#

Returns true if a higher score represents a better score

isMetaEmpty(self) bool#

Returns if the MetaInfo is empty

metaRegistry(self) MetaInfoRegistry#

Returns a reference to the MetaInfoRegistry

metaValueExists(self, in_0: bytes | str | String) bool#

Returns whether an entry with the given name exists

removeMetaValue(self, in_0: bytes | str | String) None#

Removes the DataValue corresponding to name if it exists

setDateTime(self, date: DateTime) None#

Sets the date of the protein identification run

setHigherScoreBetter(self, higher_is_better: bool) None#

Sets the orientation of the score (is higher better?)

setHits(self, hits: List[ProteinHit]) None#

Sets the protein hits

setIdentifier(self, id_: bytes | str | String) None#

Sets the identifier

setMetaValue(self, in_0: bytes | str | String, in_1: int | float | bytes | str | List[int] | List[float] | List[bytes]) None#

Sets the DataValue corresponding to a name

setPrimaryMSRunPath()#

Overload:

setPrimaryMSRunPath(self, s: List[bytes]) None

Set the file paths to the primary MS runs (usually the mzML files obtained after data conversion from raw files)

Parameters:

raw – Store paths to the raw files (or equivalent) rather than mzMLs

Overload:

setPrimaryMSRunPath(self, s: List[bytes], raw: bool) None
setScoreType(self, type: bytes | str | String) None#

Sets the protein score type

setSearchEngine(self, search_engine: bytes | str | String) None#

Sets the search engine type

setSearchEngineVersion(self, search_engine_version: bytes | str | String) None#

Sets the search engine version

setSearchParameters(self, search_parameters: SearchParameters) None#

Sets the search parameters

setSignificanceThreshold(self, value: float) None#

Sets the protein significance threshold value

sort(self) None#

Sorts the protein hits according to their score