Classes
struct	PeptDeepInputBatch
	Flat tensor buffers and dimensions for a PeptDeep ONNX batch. More...

class	PeptDeepInputBuilder
	Shared featurization for PeptDeep RT, CCS, and MS2 ONNX predictors. More...

struct	PeptDeepInputConfig
	Sequence-padding policy for PeptDeep ONNX inputs. More...

Functions
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.

Class Documentation

◆ OpenMS::ML::PeptDeepInputBatch

struct OpenMS::ML::PeptDeepInputBatch

Flat tensor buffers and dimensions for a PeptDeep ONNX batch.

Class Members
vector< int64_t >	aa_indices
size_t	batch_size = 0
vector< float >	charges
vector< int64_t >	instrument_indices
vector< float >	mod_x
vector< float >	nces
size_t	sequence_length = 0

◆ OpenMS::ML::PeptDeepInputConfig

struct OpenMS::ML::PeptDeepInputConfig

Sequence-padding policy for PeptDeep ONNX inputs.

Class Members
bool	add_terminal_tokens = true	Add PeptDeep terminal padding tokens around each peptide.
size_t	fixed_sequence_length = 0	If non-zero, pad every batch to this fixed sequence length. If zero, pad only to the longest encoded peptide in the batch.

Function Documentation

◆ getAAIndex()

OpenMS::Int64 getAAIndex ( char aa )

inline

Maps amino acid characters to 1-based token indices for PeptDeep models.

Converts uppercase and lowercase letters A-Z to indices 1-26 using canonical ord-offset encoding. Non-alphabetic characters map to 0, which serves as the padding and unknown token in PeptDeep ONNX input tensors.

Parameters

aa	Amino acid character (case-insensitive)

Returns: Token index: 1-26 for A-Z/a-z, 0 for padding/unknown

◆ validatePeptide()

void validatePeptide ( const std::string & peptide )

inline

Validates a peptide sequence for PeptDeep inference. Complex character validation and modification parsing is handled downstream by AASequence.

Parameters

peptide The raw peptide string to validate.

Variable Documentation

◆ ALPHAPEPTDEEP_MOD_ELEMENTS

constexpr std::array<std::string_view, 109> ALPHAPEPTDEEP_MOD_ELEMENTS

inlineconstexpr

Initial value:

= {
    "C", "H", "N", "O", "P", "S", "B", "F", "I", "K", "U", "V", "W", "X", "Y",
    "Ac", "Ag", "Al", "Am", "Ar", "As", "At", "Au", "Ba", "Be", "Bi", "Bk",
    "Br", "Ca", "Cd", "Ce", "Cf", "Cl", "Cm", "Co", "Cr", "Cs", "Cu", "Dy",
    "Er", "Es", "Eu", "Fe", "Fm", "Fr", "Ga", "Gd", "Ge", "He", "Hf", "Hg",
    "Ho", "In", "Ir", "Kr", "La", "Li", "Lr", "Lu", "Md", "Mg", "Mn", "Mo",
    "Na", "Nb", "Nd", "Ne", "Ni", "No", "Np", "Os", "Pa", "Pb", "Pd", "Pm",
    "Po", "Pr", "Pt", "Pu", "Ra", "Rb", "Re", "Rh", "Rn", "Ru", "Sb", "Sc",
    "Se", "Si", "Sm", "Sn", "Sr", "Ta", "Tb", "Tc", "Te", "Th", "Ti", "Tl",
    "Tm", "Xe", "Yb", "Zn", "Zr", "2H", "13C", "15N", "18O", "?"
    }

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.

◆ PEPTDEEP_MOD_ELEMENTS

constexpr int64_t PEPTDEEP_MOD_ELEMENTS = 109

constexpr

Classes

Functions

Variables