PeptDeepLibraryPredictor.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Justin Sing $
// $Authors: Justin Sing $
// --------------------------------------------------------------------------
 
#pragma once
 
#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>
 
namespace OpenMS
{
  struct OPENMS_DLLAPI PeptDeepLibraryPrecursor
  {
    AASequence peptide;
    std::string id;
    Int charge = 0;
    float nce = 30.0f;
    Int64 instrument_index = 0;
    std::vector<std::string> protein_refs;
  };
 
  class OPENMS_DLLAPI PeptDeepLibraryPredictor
  {
  public:
    struct OPENMS_DLLAPI Config
    {
      std::string rt_model_path;
      std::string ccs_model_path;
      std::string ms2_model_path;
      int intra_op_threads = 4; 
      Size batch_size = 500;
      bool predict_ccs = true;
    };
 
    PeptDeepLibraryPredictor();
 
    explicit PeptDeepLibraryPredictor(const Config& config);
 
    OpenSwath::LightTargetedExperiment predict(const std::vector<PeptDeepLibraryPrecursor>& precursors);
 
  private:
    PeptDeepRTInference rt_predictor_;
    std::unique_ptr<PeptDeepCCSInference> ccs_predictor_;
    PeptDeepMS2Inference ms2_predictor_;
  };
} // namespace OpenMS