PeptDeepLibraryPredictor.h File Reference

#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/ML/PEPTDEEP/PeptDeepCCSInference.h>
#include <OpenMS/ML/PEPTDEEP/PeptDeepMS2Inference.h>
#include <OpenMS/ML/PEPTDEEP/PeptDeepRTInference.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/config.h>
#include <memory>
#include <string>
#include <vector>

Go to the source code of this file.

Classes
struct	PeptDeepLibraryPrecursor
	Input precursor for native PeptDeep spectral-library prediction. More...
class	PeptDeepLibraryPredictor
	Convert peptide precursors into an OpenSWATH assay batch using native PeptDeep ONNX models. More...
struct	PeptDeepLibraryPredictor::Config

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::PeptDeepLibraryPrecursor

struct OpenMS::PeptDeepLibraryPrecursor

Input precursor for native PeptDeep spectral-library prediction.

The caller owns precursor identity. In particular, id must be unique across the complete library, not only within one prediction batch. This keeps IDs stable when the same predictor is later used for bounded/on-demand library generation.

Class Members
Int	charge = 0
string	id
Int64	instrument_index = 0
float	nce = 30.0f
AASequence	peptide
vector< string >	protein_refs

OpenMS::PeptDeepLibraryPredictor::Config

struct OpenMS::PeptDeepLibraryPredictor::Config

Class Members
Size	batch_size = 500
string	ccs_model_path
int	intra_op_threads = 4	threads of each predictor: its model runs that run at once, each on one thread (ONNXPredictorBase::forEachBatch())
string	ms2_model_path
bool	predict_ccs = true
string	rt_model_path