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 pyopenms._pyopenms_3.__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) → Union[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: Union[bytes, str, String]) → Union[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) → Union[bytes, str, String]: Returns the protein score type

getSearchEngine(self) → Union[bytes, str, String]: Returns the type of search engine used

getSearchEngineVersion(self) → Union[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: Union[bytes, str, String]) → bool: Returns whether an entry with the given name exists

removeMetaValue(self, in_0: Union[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_: Union[bytes, str, String]) → None: Sets the identifier

setMetaValue(self, in_0: Union[bytes, str, String], in_1: Union[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: Union[bytes, str, String]) → None: Sets the protein score type

setSearchEngine(self, search_engine: Union[bytes, str, String]) → None: Sets the search engine type

setSearchEngineVersion(self, search_engine_version: Union[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