Feature#

class pyopenms.Feature#

Bases: object

Cython implementation of _Feature

Original C++ documentation is available here: – Inherits from [‘UniqueIdInterface’, ‘RichPeak2D’]

An LC-MS feature representing a detected analyte signal

The Feature class represents a two-dimensional (RT and m/z) signal from an analyte in LC-MS data. It is one of the core data structures in OpenMS for representing detected peaks or compounds.

A Feature stores:

Position: retention time (RT) and mass-to-charge ratio (m/z)
Intensity: the signal strength (typically total ion count)
Quality metrics: scores indicating detection confidence
Charge state: the charge of the ion
Convex hulls: the 2D area occupied by the feature in RT-m/z space
Peptide identifications: for identified peptides (optional)
Subordinate features: for isotopic peaks or related signals

By convention, the feature’s position is at the maximum of the elution profile (RT dimension) and at the monoisotopic peak (m/z dimension).

Example usage:

feature = oms.Feature()
feature.setRT(1234.5)  # Set retention time in seconds
feature.setMZ(445.678)  # Set m/z value
feature.setIntensity(100000.0)  # Set intensity
feature.setCharge(2)  # Set charge state
feature.setOverallQuality(0.95)  # Set quality score (0-1)
# Access the values
print(f"RT: {feature.getRT()}, m/z: {feature.getMZ()}, charge: {feature.getCharge()}")

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: Feature) → None

Methods

`__init__`
`clearMetaInfo`(self)	Removes all meta values
`clearUniqueId`(self)	Clear the unique id.
`encloses`(self, rt, mz)	Checks if the feature's convex hulls enclose a given position
`ensureUniqueId`(self)	Assigns a valid unique id, but only if the present one is invalid.
`getAnnotationState`(self)	Returns the annotation state of the feature
`getCharge`(self)	Returns the charge state of the feature
`getConvexHull`(self)	Returns the overall convex hull of the feature
`getConvexHulls`(self)	Returns the convex hulls of individual mass traces
`getIntensity`(self)	Returns the data point intensity (height)
`getKeys`(self, keys)	Fills the given vector with a list of all keys for which a value is set
`getMZ`(self)	Returns the m/z coordinate (index 1)
`getMetaValue`(self, in_0)	Returns the value corresponding to a string, or
`getOverallQuality`(self)	Returns the overall quality score of the feature
`getPeptideIdentifications`(self)	Returns the peptide identifications associated with this feature
`getQuality`(self, index)	Returns the quality score in a specific dimension
`getRT`(self)	Returns the RT coordinate (index 0)
`getSubordinates`(self)	Returns subordinate features (e.g., isotopic peaks)
`getUniqueId`(self)	Returns the unique id
`getWidth`(self)	Returns the width (FWHM) of the feature in RT dimension
`hasInvalidUniqueId`(self)	Returns whether the unique id is invalid.
`hasValidUniqueId`(self)	Returns whether the unique id is valid.
`isMetaEmpty`(self)	Returns if the MetaInfo is empty
`isValid`(self, unique_id)	Returns true if the unique_id is valid, false otherwise
`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
`setCharge`(self, q)	Sets the charge state of the feature
`setConvexHulls`(self, in_0)	Sets the convex hulls for individual mass traces
`setIntensity`(self, in_0)	Returns the data point intensity (height)
`setMZ`(self, in_0)	Returns the m/z coordinate (index 1)
`setMetaValue`(self, in_0, in_1)	Sets the DataValue corresponding to a name
`setOverallQuality`(self, q)	Sets the overall quality score of the feature
`setPeptideIdentifications`(self, peptides)	Sets the peptide identifications for this feature
`setQuality`(self, index, q)	Sets the quality score for a specific dimension
`setRT`(self, in_0)	Returns the RT coordinate (index 0)
`setSubordinates`(self, in_0)	Sets the subordinate features
`setUniqueId`(self, rhs)	Assigns a new, valid unique id.
`setWidth`(self, q)	Sets the width (FWHM) of the feature in RT dimension

clearMetaInfo(self) → None#: Removes all meta values

clearUniqueId(self) → int#: Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise

encloses(self, rt: float, mz: float) → bool#

Checks if the feature’s convex hulls enclose a given position

Parameters:

rt – Retention time in seconds
mz – Mass-to-charge ratio

Returns:

True if the position (rt, mz) is within the feature’s convex hulls, False otherwise

This uses the feature’s convex hull representation to determine spatial containment

ensureUniqueId(self) → int#: Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise

getAnnotationState(self) → int#

Returns the annotation state of the feature

Returns:: Enum indicating the annotation status of this feature

getCharge(self) → int#

Returns the charge state of the feature

Returns:: Charge state (e.g., 2 for doubly charged ions, 0 if unknown)

getConvexHull(self) → ConvexHull2D#

Returns the overall convex hull of the feature

Returns:: The overall 2D convex hull encompassing all mass traces

This is the union of all individual mass trace convex hulls

getConvexHulls(self) → List[ConvexHull2D]#

Returns the convex hulls of individual mass traces

Returns:: List of convex hulls, one for each isotopic mass trace

Each isotopic peak typically has its own convex hull in RT-m/z space

getIntensity(self) → float#: Returns the data point intensity (height)

getKeys(self, keys: List[bytes]) → None#: Fills the given vector with a list of all keys for which a value is set

getMZ(self) → float#: Returns the m/z coordinate (index 1)

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

getOverallQuality(self) → float#

Returns the overall quality score of the feature

Returns:: Overall quality score (typically 0-1, where 1 is highest quality)

This score represents the overall confidence in the feature detection

getPeptideIdentifications(self) → PeptideIdentificationList#

Returns the peptide identifications associated with this feature

Returns:: List of peptide identifications from database search

Only relevant for peptide features. Contains results from peptide identification tools

getQuality(self, index: int) → float#

Returns the quality score in a specific dimension

Parameters:: index – The dimension index (0 for RT, 1 for m/z)
Returns:: Quality score for the specified dimension (typically 0-1 range)

getRT(self) → float#: Returns the RT coordinate (index 0)

getSubordinates(self) → List[Feature]#

Returns subordinate features (e.g., isotopic peaks)

Returns:: List of subordinate features associated with this feature

Subordinate features often represent individual isotopic peaks of the same compound

getUniqueId(self) → int#: Returns the unique id

getWidth(self) → float#

Returns the width (FWHM) of the feature in RT dimension

Returns:: Full Width at Half Maximum (FWHM) in seconds

Represents the elution peak width

hasInvalidUniqueId(self) → int#: Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise

hasValidUniqueId(self) → int#: Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise

isMetaEmpty(self) → bool#: Returns if the MetaInfo is empty

isValid(self, unique_id: int) → bool#: Returns true if the unique_id is valid, false otherwise

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

setCharge(self, q: int) → None#

Sets the charge state of the feature

Parameters:: q – Charge state (e.g., 2 for doubly charged ions)

setConvexHulls(self, in_0: List[ConvexHull2D]) → None#

Sets the convex hulls for individual mass traces

Parameters:: hulls – List of convex hulls to set for this feature

setIntensity(self, in_0: float) → None#: Returns the data point intensity (height)

setMZ(self, in_0: float) → None#: Returns the m/z coordinate (index 1)

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

setOverallQuality(self, q: float) → None#

Sets the overall quality score of the feature

Parameters:: q – Overall quality score (typically 0-1, where 1 is highest quality)

setPeptideIdentifications(self, peptides: PeptideIdentificationList) → None#

Sets the peptide identifications for this feature

Parameters:: peptides – List of peptide identifications to associate with this feature

setQuality(self, index: int, q: float) → None#

Sets the quality score for a specific dimension

Parameters:

index – The dimension index (0 for RT, 1 for m/z)
q – Quality score to set (typically 0-1 range)

setRT(self, in_0: float) → None#: Returns the RT coordinate (index 0)

setSubordinates(self, in_0: List[Feature]) → None#

Sets the subordinate features

Parameters:: subordinates – List of subordinate features to associate with this feature

setUniqueId(self, rhs: int) → None#: Assigns a new, valid unique id. Always returns 1

setWidth(self, q: float) → None#

Sets the width (FWHM) of the feature in RT dimension

Parameters:: q – Full Width at Half Maximum in seconds