| OpenMS 2.5.0

Static Public Member Functions | Static Protected Member Functions | List of all members
SiriusFragmentAnnotation Class Reference

`#include <OpenMS/FORMAT/DATAACCESS/SiriusFragmentAnnotation.h>`

## Static Public Member Functions

static void | extractSiriusFragmentAnnotationMapping (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
| extractSiriusFragmentAnnotationMapping Extract native id (./spectrum.ms) and fragment annotation (./spectra/1_sumformula.ms) from SIRIUS output (per compound). More...

## Static Protected Member Functions

static OpenMS::String | extractNativeIDFromSiriusMS_ (const OpenMS::String &path_to_sirius_workspace)
| extractNativeIDFromSiriusMS Extract native id from SIRIUS output (./spectrum.ms). More...
static OpenMS::String | extractMIDFromSiriusMS_ (const String &path_to_sirius_workspace)
| extractMIDFromSiriusMS Extract mid from SIRIUS output (./spectrum.ms). Mid is the native id + an index, which is incremented based on the number of possible identifications (accurate mass search). More...
static void | extractAnnotationFromSiriusFile_ (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
| extractAnnotationFromSiriusFile Extract fragment annotation from SIRIUS (./spectra/1_sumformula.ms). More...

## Member Function Documentation

## ◆ extractAnnotationFromSiriusFile_()

static void extractAnnotationFromSiriusFile_ | ( | const String & | path_to_sirius_workspace,
|  | MSSpectrum & | msspectrum_to_fill,
|  | bool | use_exact_mass = `false`
| ) |  |

static protected

extractAnnotationFromSiriusFile Extract fragment annotation from SIRIUS (./spectra/1_sumformula.ms).

Returns
  annotated (consensus) MSSpectrum (mz, int, exact mass, fragment explanation).

MetaValues: peak_mz: indicates which mass input was used in Peak1D (mz or exact_mass). annotated_sumformula annotated_adduct

Parameters

  path_to_sirius_workspace | Path to SIRIUS workspace.
  use_exact_mass | Option to use exact mass instead of peak mz in MSSpectrum.

## ◆ extractMIDFromSiriusMS_()

static OpenMS::String extractMIDFromSiriusMS_ | ( | const String & | path_to_sirius_workspace | ) |

static protected

extractMIDFromSiriusMS Extract mid from SIRIUS output (./spectrum.ms). Mid is the native id + an index, which is incremented based on the number of possible identifications (accurate mass search).

Returns
  String mid of current SIRIUS compound

Parameters

  path_to_sirius_workspace | Path to SIRIUS workspace.

## ◆ extractNativeIDFromSiriusMS_()

static OpenMS::String extractNativeIDFromSiriusMS_ | ( | const OpenMS::String & | path_to_sirius_workspace | ) |

static protected

extractNativeIDFromSiriusMS Extract native id from SIRIUS output (./spectrum.ms).

Returns
  String native id of current SIRIUS compound

Parameters

  path_to_sirius_workspace | Path to SIRIUS workspace.

## ◆ extractSiriusFragmentAnnotationMapping()

static void extractSiriusFragmentAnnotationMapping | ( | const String & | path_to_sirius_workspace,
|  | MSSpectrum & | msspectrum_to_fill,
|  | bool | use_exact_mass = `false`
| ) |  |

static

extractSiriusFragmentAnnotationMapping Extract native id (./spectrum.ms) and fragment annotation (./spectra/1_sumformula.ms) from SIRIUS output (per compound).

Returns
  annotated (consensus) MSSpectrum with associated native id

MetaValues: peak_mz: indicates which mass input was used in Peak1D (mass or exact_mass). annotated_sumformula annotated_adduct

The data is stored in a MSSpectrum, which contains a Peak1D (mz, int), a FloatDataArry (exact mass), and a StringDataArry (explanation).

MSSpectrum
Peak1D |  | FloatDataArray | StringDataArray
--- | --- | --- | ---
mz | intensity | exact_mass | explanation
56.050855 | 20794.85 | 56.049476 | C3H5N

Parameters

  path_to_sirius_workspace | Path to SIRIUS workspace.
  use_exact_mass | Option to use exact mass instead of peak mz in MSSpectrum.