libpappsomspp
Library for mass spectrometry
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peptideinterface.cpp
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1
2/*******************************************************************************
3 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
4 *
5 * This file is part of the PAPPSOms++ library.
6 *
7 * PAPPSOms++ is free software: you can redistribute it and/or modify
8 * it under the terms of the GNU General Public License as published by
9 * the Free Software Foundation, either version 3 of the License, or
10 * (at your option) any later version.
11 *
12 * PAPPSOms++ is distributed in the hope that it will be useful,
13 * but WITHOUT ANY WARRANTY; without even the implied warranty of
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 * GNU General Public License for more details.
16 *
17 * You should have received a copy of the GNU General Public License
18 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
19 *
20 * Contributors:
21 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
22 *implementation
23 ******************************************************************************/
24
25#include "peptideinterface.h"
26
27namespace pappso
28{
29
30const QString
32{
33 return QString(this->getSequence()).replace("L", "I");
34}
35const QString
36PeptideInterface::getFormula(unsigned int charge) const
37{
38 QString carbon(
39 QString("C %1").arg(this->getNumberOfAtom(AtomIsotopeSurvey::C) -
41 if(this->getNumberOfIsotope(Isotope::C13) > 0)
42 {
43 carbon.append(
44 QString(" (13)C %1").arg(this->getNumberOfIsotope(Isotope::C13)));
45 }
46 QString hydrogen(
47 QString("H %1").arg(this->getNumberOfAtom(AtomIsotopeSurvey::H) + charge -
49 if(this->getNumberOfIsotope(Isotope::H2) > 0)
50 {
51 hydrogen.append(
52 QString(" (2)H %1").arg(this->getNumberOfIsotope(Isotope::H2)));
53 }
54 QString oxygen(
55 QString("O %1").arg(this->getNumberOfAtom(AtomIsotopeSurvey::O) -
58 if(this->getNumberOfIsotope(Isotope::O17) > 0)
59 {
60 oxygen.append(
61 QString(" (17)O %1").arg(this->getNumberOfIsotope(Isotope::O17)));
62 }
63 if(this->getNumberOfIsotope(Isotope::O18) > 0)
64 {
65 oxygen.append(
66 QString(" (18)O %1").arg(this->getNumberOfIsotope(Isotope::O18)));
67 }
68 QString nitrogen(
69 QString("N %1").arg(this->getNumberOfAtom(AtomIsotopeSurvey::N) -
71 if(this->getNumberOfIsotope(Isotope::N15) > 0)
72 {
73 nitrogen.append(
74 QString(" (15)N %1").arg(this->getNumberOfIsotope(Isotope::N15)));
75 }
76
77 QString sulfur(
78 QString("S %1").arg(this->getNumberOfAtom(AtomIsotopeSurvey::S) -
82 if(this->getNumberOfIsotope(Isotope::S33) > 0)
83 {
84 sulfur.append(
85 QString(" (33)S %1").arg(this->getNumberOfIsotope(Isotope::S33)));
86 }
87 if(this->getNumberOfIsotope(Isotope::S34) > 0)
88 {
89 sulfur.append(
90 QString(" (34)S %1").arg(this->getNumberOfIsotope(Isotope::S34)));
91 }
92 if(this->getNumberOfIsotope(Isotope::S36) > 0)
93 {
94 sulfur.append(
95 QString(" (36)S %1").arg(this->getNumberOfIsotope(Isotope::S36)));
96 }
97 return QString("%1 %2 %3 %4 %5")
98 .arg(carbon)
99 .arg(hydrogen)
100 .arg(oxygen)
101 .arg(nitrogen)
102 .arg(sulfur);
103}
104} // namespace pappso
virtual int getNumberOfIsotope(Isotope isotope) const =0
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const =0
get the number of atom C, O, N, H in the molecule
virtual const QString getSequence() const =0
amino acid sequence without modification
virtual const QString getSequenceLi() const
amino acid sequence without modification where L are replaced by I
virtual const QString getFormula(unsigned int charge) const final
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39