ProteinHit

class pyopenms.ProteinHit

Bases: object

Cython implementation of _ProteinHit

Original C++ documentation is available here

– Inherits from [‘MetaInfoInterface’]

Represents a single protein identification hit from a database search

A ProteinHit stores information about a protein that was identified based on peptide evidence. Each hit contains:

• Protein accession (database identifier)

• Score from protein inference

• Rank among protein candidates

• Protein sequence (optional)

• Sequence coverage percentage

Multiple ProteinHit objects are stored in a ProteinIdentification, typically sorted by score to show the most confident identifications first.

Example usage:

protein_hit = oms.ProteinHit()
protein_hit.setAccession("P12345")
protein_hit.setScore(150.5)
protein_hit.setRank(1)
protein_hit.setCoverage(45.2)  # 45.2% coverage
protein_hit.setDescription("Example protein")
# Access information
print(f"Accession: {protein_hit.getAccession()}")
print(f"Score: {protein_hit.getScore()}, Coverage: {protein_hit.getCoverage()}%")

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, score: float, rank: int, accession: bytes | str | String, sequence: bytes | str | String) → None

Overload:

__init__(self, in_0: ProteinHit) → None

Methods

__init__
clearMetaInfo(self)	Removes all meta values
getAccession(self)	Returns the protein accession
getCoverage(self)	Returns the sequence coverage percentage
getDescription(self)	Returns the protein description
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
getRank(self)	Returns the rank of this protein hit
getScore(self)	Returns the protein inference score
getSequence(self)	Returns the protein sequence
isDecoy(self)	Checks if this is a decoy protein hit
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
setAccession(self, in_0)	Sets the protein accession
setCoverage(self, in_0)	Sets the sequence coverage percentage
setDescription(self, description)	Sets the protein description
setMetaValue(self, in_0, in_1)	Sets the DataValue corresponding to a name
setRank(self, in_0)	Sets the rank
setScore(self, in_0)	Sets the protein inference score
setSequence(self, in_0)	Sets the protein sequence

clearMetaInfo(self) → None

Removes all meta values

getAccession(self) → bytes | str | String

Returns the protein accession

Returns:

Database accession/identifier (e.g., “P12345” for UniProt)

getCoverage(self) → float

Returns the sequence coverage percentage

Returns:

Percentage of protein sequence covered by identified peptides

Value is in range 0-100 (e.g., 45.2 means 45.2% coverage)

getDescription(self) → bytes | str | String

Returns the protein description

Returns:

Human-readable protein name/description from database

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

getRank(self) → int

Returns the rank of this protein hit

Returns:

Rank (1 = best hit, 2 = second best, etc.)

getScore(self) → float

Returns the protein inference score

Returns:

Score from protein inference algorithm

getSequence(self) → bytes | str | String

Returns the protein sequence

Returns:

Full amino acid sequence of the protein (if available)

isDecoy(self) → bool

Checks if this is a decoy protein hit

Returns:

True if this is a decoy hit from target-decoy search

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

setAccession(self, in_0: bytes | str | String) → None

Sets the protein accession

Parameters:

accession – Database accession/identifier

setCoverage(self, in_0: float) → None

Sets the sequence coverage percentage

Parameters:

coverage – Percentage (0-100) of sequence covered by peptides

setDescription(self, description: bytes | str | String) → None

Sets the protein description

Parameters:

description – Human-readable protein name/description

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

setRank(self, in_0: int) → None

Sets the rank

Parameters:

rank – Rank among all protein candidates

setScore(self, in_0: float) → None

Sets the protein inference score

Parameters:

score – Score to set

setSequence(self, in_0: bytes | str | String) → None

Sets the protein sequence

Parameters:

sequence – Full amino acid sequence