OpenMS  2.8.0
AdductInfo.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Erhan Kenar, Chris Bielow $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42  class OPENMS_DLLAPI AdductInfo
43  {
44  public:
54  AdductInfo(const String& name, const EmpiricalFormula& adduct, int charge, UInt mol_multiplier = 1);
55 
57  double getNeutralMass(double observed_mz) const;
58 
60  double getMZ(double neutral_mass) const;
61 
63  double getMassShift(bool use_avg_mass = false) const;
64 
67  bool isCompatible(EmpiricalFormula db_entry) const;
68 
70  int getCharge() const;
71 
73  const String& getName() const;
74 
77 
80 
84  static AdductInfo parseAdductString(const String& adduct);
85 
87  bool operator==(const AdductInfo& other) const;
88 
89  private:
93  double mass_;
94  int charge_;
96  };
97 }
Definition: AdductInfo.h:43
double getMassShift(bool use_avg_mass=false) const
returns the mass shift caused by this adduct if charges are compensated with protons
AdductInfo(const String &name, const EmpiricalFormula &adduct, int charge, UInt mol_multiplier=1)
double mass_
computed from ef_.getMonoWeight(), but stored explicitly for efficiency
Definition: AdductInfo.h:93
EmpiricalFormula ef_
Sum formula for the actual adduct e.g. 'H' in 2M+H;+1.
Definition: AdductInfo.h:92
const EmpiricalFormula & getEmpiricalFormula() const
sum formula of adduct itself. Useful for comparison with feature adduct annotation
String name_
members
Definition: AdductInfo.h:91
UInt getMolMultiplier() const
get molecular multiplier
bool operator==(const AdductInfo &other) const
equality operator
double getNeutralMass(double observed_mz) const
returns the neutral mass of the small molecule without adduct (creates monomer from nmer,...
int getCharge() const
get charge of adduct
static AdductInfo parseAdductString(const String &adduct)
UInt mol_multiplier_
Mol multiplier, e.g. 2 in 2M+H;+1.
Definition: AdductInfo.h:95
int charge_
negative or positive charge; must not be 0
Definition: AdductInfo.h:94
const String & getName() const
original string used for parsing
bool isCompatible(EmpiricalFormula db_entry) const
double getMZ(double neutral_mass) const
returns the m/z of the small molecule with neutral mass neutral_mass if the adduct is added (given ma...
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47