libpappsomspp
Library for mass spectrometry
peptiderawfragmentmasses.h
Go to the documentation of this file.
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/**
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* \file pappsomspp/peptide/peptiderawfragmentmasses.h
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* \date 16/7/2016
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* \author Olivier Langella
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* \brief class dedicated to raw mass computations of peptide products
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* (fragments)
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*/
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/*******************************************************************************
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* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
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*
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* This file is part of the PAPPSOms++ library.
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*
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* PAPPSOms++ is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PAPPSOms++ is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
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*
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* Contributors:
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* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
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*implementation
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******************************************************************************/
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#pragma once
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#include "
peptide.h
"
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#include "../massspectrum/massspectrum.h"
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namespace
pappso
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{
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enum class
RawFragmentationMode
: std::int8_t
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{
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full = 0,
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proline_effect
= 1
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};
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struct
SimplePeakIonMatch
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{
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DataPoint
peak
;
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PeptideIon
ion_type
;
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unsigned
int
ion_size
;
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unsigned
int
ion_charge
;
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pappso_double
ion_mz
;
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};
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class
PMSPP_LIB_DECL
PeptideRawFragmentMasses
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{
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using
ionDeltatMzMassMap
=
pappso_double
[20];
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private
:
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static
ionDeltatMzMassMap
m_ionDeltaMz
;
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/** \brief cumulative Nter masses (without internal Nter modification)
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* */
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std::vector<pappso_double>
m_cumulativeNterMasses
;
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/** \brief cumulative Cter masses (without internal Cter modification)
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* */
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std::vector<pappso_double>
m_cumulativeCterMasses
;
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public
:
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PeptideRawFragmentMasses
(
const
Peptide
&peptide,
RawFragmentationMode
mode);
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~
PeptideRawFragmentMasses
();
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void
pushBackIonMasses(std::vector<pappso_double> &mass_list,
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PeptideIon
ion_type)
const
;
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void
pushBackIonMz(std::vector<pappso_double> &mass_list,
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PeptideIon
ion_type,
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unsigned
int
charge)
const
;
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void
pushBackMatchSpectrum(std::vector<SimplePeakIonMatch> &peak_match_list,
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const
MassSpectrum
&spectrum,
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PrecisionPtr
precision,
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PeptideIon
ion_type,
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unsigned
int
charge)
const
;
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static
pappso_double
getDeltaMass(
PeptideIon
ion_type);
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};
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}
// namespace pappso
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition:
types.h:48
pappso::PeptideRawFragmentMasses::m_ionDeltaMz
static ionDeltatMzMassMap m_ionDeltaMz
Definition:
peptiderawfragmentmasses.h:64
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition:
exportinmportconfig.h:14
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
Definition:
aa.cpp:39
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition:
massspectrum.h:71
pappso::PeptideRawFragmentMasses::m_cumulativeCterMasses
std::vector< pappso_double > m_cumulativeCterMasses
cumulative Cter masses (without internal Cter modification)
Definition:
peptiderawfragmentmasses.h:72
pappso::DataPoint
Definition:
datapoint.h:21
pappso::SimplePeakIonMatch::ion_charge
unsigned int ion_charge
Definition:
peptiderawfragmentmasses.h:54
peptide.h
peptide model
pappso::PeptideIon
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition:
types.h:334
pappso::Peptide
Definition:
peptide.h:93
pappso::RawFragmentationMode::full
@ full
pappso::SimplePeakIonMatch::peak
DataPoint peak
Definition:
peptiderawfragmentmasses.h:51
pappso::PeptideRawFragmentMasses::ionDeltatMzMassMap
pappso_double[20] ionDeltatMzMassMap
Definition:
peptiderawfragmentmasses.h:61
pappso::PeptideRawFragmentMasses::m_cumulativeNterMasses
std::vector< pappso_double > m_cumulativeNterMasses
cumulative Nter masses (without internal Nter modification)
Definition:
peptiderawfragmentmasses.h:68
pappso::SimplePeakIonMatch::ion_mz
pappso_double ion_mz
Definition:
peptiderawfragmentmasses.h:55
pappso::SimplePeakIonMatch::ion_type
PeptideIon ion_type
Definition:
peptiderawfragmentmasses.h:52
pappso::PrecisionBase
Definition:
precision.h:44
pappso::SimplePeakIonMatch::ion_size
unsigned int ion_size
Definition:
peptiderawfragmentmasses.h:53
pappso::PeptideRawFragmentMasses
Definition:
peptiderawfragmentmasses.h:60
pappso::RawFragmentationMode
RawFragmentationMode
Definition:
peptiderawfragmentmasses.h:43
pappso::SimplePeakIonMatch
Definition:
peptiderawfragmentmasses.h:50
pappsomspp
peptide
peptiderawfragmentmasses.h
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