Inference engine for PeptDeep MS2 Fragment Intensity prediction. More...

#include <OpenMS/ML/PEPTDEEP/PeptDeepMS2Inference.h>

Collaboration diagram for PeptDeepMS2Inference:

Public Member Functions
	PeptDeepMS2Inference (const std::string &model_path, int intra_op_threads=4, size_t batch_size=500)
	Constructor initializes the ONNX session with the specified model graph.

	~PeptDeepMS2Inference ()
	Destructor.

std::vector< std::vector< float > >	predictMS2 (const std::vector< std::string > &peptides, const std::vector< float > &charges, const std::vector< float > &nces, const std::vector< int64_t > &instrument_indices)
	Predicts MS2 fragment intensities for a batch of peptide sequences.

Private Attributes
ONNXPredictorBase	model_

size_t	batch_size_

Detailed Description

Inference engine for PeptDeep MS2 Fragment Intensity prediction.

This class parses and tokenizes raw peptide string sequences into structural integer arrays and evaluates them through the ONNX Runtime backend to predict fragment intensities.

Constructor & Destructor Documentation

◆ PeptDeepMS2Inference()

PeptDeepMS2Inference	(	const std::string &	model_path,
		int	intra_op_threads = `4`,
		size_t	batch_size = `500`
	)

explicit

Constructor initializes the ONNX session with the specified model graph.

Parameters

model_path	Absolute or relative path to the PeptDeep MS2 ONNX model file.
intra_op_threads	Number of ONNX execution threads (default 4).
batch_size	Maximum number of peptides to process in a single ONNX run (default 500).

Exceptions

Exception::BaseException if the model file cannot be found or loaded by the runtime.

◆ ~PeptDeepMS2Inference()

~PeptDeepMS2Inference ( )

Destructor.

Member Function Documentation

◆ predictMS2()

std::vector< std::vector< float > > predictMS2	(	const std::vector< std::string > &	peptides,
		const std::vector< float > &	charges,
		const std::vector< float > &	nces,
		const std::vector< int64_t > &	instrument_indices
	)

Predicts MS2 fragment intensities for a batch of peptide sequences.

Parameters

peptides	A vector of raw uppercase peptide strings.
charges	A vector of precursor charge states (must match peptides size).
nces	A vector of normalized collision energies (must match peptides size).
instrument_indices	A vector of categorical integers representing MS instruments (e.g., 0=Lumos, 1=QE, 2=timsTOF, 3=Sciex).

Returns: A vector of flattened fragment intensity arrays, one for each peptide. Native shape ordering is contiguous by fragment and ion type [b_1, y_1, b_2, y_2...].

Exceptions

std::invalid_argument if the sequence string is empty, too long, or contains unmapped characters.

Member Data Documentation

◆ batch_size_

size_t batch_size_

private

◆ model_

ONNXPredictorBase model_