OpenMS::ML Namespace Reference

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. Throws explicit OpenMS exceptions if the sequence is invalid, too long, or contains modifications.
std::vector< float >	generateUnmodifiedModXTensor (size_t batch_size, size_t sequence_length)
	Generates an empty mod_x tensor for unmodified peptides. Resolves to a flat vector of zeros of size (batch_size * sequence_length * 109).

Variables
constexpr int64_t	PEPTDEEP_MOD_ELEMENTS = 109
const std::string	PEPTDEEP_VALID_AAS = "ACDEFGHIKLMNPQRSTVWY"

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Class Documentation

OpenMS::ML::PeptDeepInputBatch

struct OpenMS::ML::PeptDeepInputBatch

Flat tensor buffers and dimensions for a PeptDeep ONNX batch.

Collaboration diagram for PeptDeepInputBatch:

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.

Collaboration diagram for PeptDeepInputConfig:

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

generateUnmodifiedModXTensor()

std::vector< float > generateUnmodifiedModXTensor ( size_t  batch_size, size_t  sequence_length  )

inline

Generates an empty mod_x tensor for unmodified peptides. Resolves to a flat vector of zeros of size (batch_size * sequence_length * 109).

References PEPTDEEP_MOD_ELEMENTS.

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. Throws explicit OpenMS exceptions if the sequence is invalid, too long, or contains modifications.

• Parameters

  peptide

  The raw peptide string to validate.

References PEPTDEEP_VALID_AAS.

Variable Documentation

PEPTDEEP_MOD_ELEMENTS

constexpr int64_t PEPTDEEP_MOD_ELEMENTS = 109

constexpr

Referenced by generateUnmodifiedModXTensor().

PEPTDEEP_VALID_AAS

const std::string PEPTDEEP_VALID_AAS = "ACDEFGHIKLMNPQRSTVWY"

Referenced by validatePeptide().