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 
)
staticprotected

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_workspacePath to SIRIUS workspace.
use_exact_massOption to use exact mass instead of peak mz in MSSpectrum.

◆ extractMIDFromSiriusMS_()

static OpenMS::String extractMIDFromSiriusMS_ ( const String path_to_sirius_workspace)
staticprotected

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_workspacePath to SIRIUS workspace.

◆ extractNativeIDFromSiriusMS_()

static OpenMS::String extractNativeIDFromSiriusMS_ ( const OpenMS::String path_to_sirius_workspace)
staticprotected

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

Returns
String native id of current SIRIUS compound
Parameters
path_to_sirius_workspacePath 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_workspacePath to SIRIUS workspace.
use_exact_massOption to use exact mass instead of peak mz in MSSpectrum.