PeptDeepUtils.h File Reference

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <string>
#include <vector>
#include <array>
#include <string_view>

Go to the source code of this file.

Namespaces
namespace	OpenMS
	Main OpenMS namespace.
namespace	OpenMS::ML

Functions
int64_t	instrumentIndex (std::string_view name)
	Instrument index for name, mirroring peptdeep's parse_instrument_indices().
void	validateInstrumentIndices (const std::vector< int64_t > &instrument_indices)
	Validates instrument indices for PeptDeep MS2 inference.
OpenMS::Int64	getAAIndex (char aa)
	Maps amino acid characters to 1-based token indices for PeptDeep models.
void	validatePeptide (const std::string &peptide)
	Validates a peptide sequence for PeptDeep inference. Complex character validation and modification parsing is handled downstream by AASequence.

Variables
constexpr int64_t	PEPTDEEP_MOD_ELEMENTS = 109
constexpr std::array< std::string_view, 109 >	ALPHAPEPTDEEP_MOD_ELEMENTS
	AlphaPeptDeep's exact 109-element array for modification tensor mapping. Elements missing from this list are binned into the final "Other" channel ("?"). Heavy isotopes (2H, 13C, 15N, 18O) map strictly to their dedicated channels.
constexpr int64_t	PEPTDEEP_MAX_INSTRUMENT_NUM = 8
	Width of the instrument one-hot in AlphaPeptDeep's MS2 model.
constexpr int64_t	PEPTDEEP_UNKNOWN_INSTRUMENT_INDEX = PEPTDEEP_MAX_INSTRUMENT_NUM - 1
	Index peptdeep gives an instrument it does not recognise (featurize.py: max_instrument_num - 1).
constexpr std::array< std::string_view, 5 >	ALPHAPEPTDEEP_INSTRUMENTS
	AlphaPeptDeep's instrument names, in the order that is their encoding.