PeptDeepUtils.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Satyam Yadav $
// --------------------------------------------------------------------------
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <string>
#include <vector>
 
namespace OpenMS {
  namespace ML {
 
    // --- Shared PeptDeep Architecture Constants ---
    constexpr int64_t PEPTDEEP_MOD_ELEMENTS = 109;
    const std::string PEPTDEEP_VALID_AAS = "ACDEFGHIKLMNPQRSTVWY";
 
    inline OpenMS::Int64 getAAIndex(char aa) {
      if (aa >= 'A' && aa <= 'Z') return aa - 'A' + 1;
      if (aa >= 'a' && aa <= 'z') return aa - 'a' + 1;
      return 0; // 0 serves as the padding and unknown token
    }
 
    inline void validatePeptide(const std::string& peptide) {
        if (peptide.empty()) {
            throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Peptide sequence cannot be empty.");
        }
        if (peptide.find_first_of("[]()") != std::string::npos) {
            throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Modified peptides are not currently supported in this engine.");
        }
        if (peptide.find_first_not_of(PEPTDEEP_VALID_AAS) != std::string::npos) {
            throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Unsupported residue encountered.", peptide);
        }
    }
 
    inline std::vector<float> generateUnmodifiedModXTensor(size_t batch_size, size_t sequence_length) {
        return std::vector<float>(batch_size * sequence_length * PEPTDEEP_MOD_ELEMENTS, 0.0f);
    }
 
  }
}