1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
|
//
// File: test_fragmentationcid.cpp
// Created by: Olivier Langella
// Created on: 10/3/2015
//
/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
// ./tests/catch2-only-tests [fragmentationcid] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <pappsomspp/core/pappsoexception.h>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/peptide/peptidefragmentionlistbase.h>
#include <iostream>
#include <QDebug>
#include <QString>
using namespace pappso;
using namespace std;
TEST_CASE("fragmentationcid test suite.", "[fragmentationcid]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: test fragmentationcid ::..", "[fragmentationcid]")
{
std::cout << std::endl << "..:: test ion direction ::.." << std::endl;
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::b) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::bstar) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::bo) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::a) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::astar) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::ao) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::bp) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::c) == PeptideDirection::Nter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::y) == PeptideDirection::Cter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::ystar) == PeptideDirection::Cter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::yo) == PeptideDirection::Cter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::z) == PeptideDirection::Cter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::yp) == PeptideDirection::Cter);
REQUIRE(getPeptideIonDirection(Enums::PeptideIon::x) == PeptideDirection::Cter);
INFO("..:: peptide fragment init ::..");
// http://proteus.moulon.inra.fr/w2dpage/proticdb/angular/#/peptide_hits/10053478
Peptide peptide("DSTIPDKQITASSFYK");
std::list<Enums::PeptideIon> cid_ion = PeptideFragmentIonListBase::getCIDionList();
PeptideFragmentIonListBase frag_cid(peptide.makePeptideSp(), cid_ion);
std::list<PeptideFragmentIonSp>::const_iterator it = frag_cid.begin();
while(it != frag_cid.end())
{
// unsigned int size = it->get()->size();
QString name = it->get()->getPeptideIonName();
std::cout << it->get()->getSequence().toStdString() << " "
<< it->get()->getPeptideIonName().toStdString() << " " << it->get()->getMz(1)
<< " " << it->get()->getFormula(1).toStdString() << std::endl;
it++;
}
auto ion_y_list = frag_cid.getPeptideFragmentIonSp(Enums::PeptideIon::y);
for(auto &fragment_ion_sp : ion_y_list)
{
std::size_t ion_number = fragment_ion_sp.get()->size();
switch(ion_number)
{
case 1:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 146.1055277001);
break;
case 2:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 309.1688562342);
break;
case 3:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 456.2372701487);
break;
case 4:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 543.2692985538);
break;
case 5:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 630.301326959);
break;
default:
break;
}
}
auto ion_b_list = frag_cid.getPeptideFragmentIonSp(Enums::PeptideIon::b);
for(auto &fragment_ion_sp : ion_b_list)
{
std::size_t ion_number = fragment_ion_sp.get()->size();
switch(ion_number)
{
case 1:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 115.0269430247);
break;
case 2:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 202.0589714298);
break;
case 3:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 303.1066498994);
break;
case 4:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 416.1907138784);
break;
case 5:
REQUIRE(Catch::Approx(fragment_ion_sp.get()->getMass()) == 513.2434777285);
break;
default:
break;
}
}
}
}
|
