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UnimodTest.cpp File Reference
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "Unimod.hpp"
#include <cstring>

Go to the source code of this file.

Functions

void test ()
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 

Function Documentation

§ test()

void test ( )

Definition at line 39 of file UnimodTest.cpp.

References Alanine, pwiz::data::unimod::Any(), Asparagine, AsparticAcid, Cysteine, GlutamicAcid, Glutamine, Lysine, Methionine, pwiz::data::unimod::modification(), pwiz::data::unimod::modifications(), MS_matrix_assisted_laser_desorption_ionization, MS_modification_specificity_peptide_C_term, MS_modification_specificity_peptide_N_term, os_, pwiz::data::unimod::position(), Proline, pwiz::data::unimod::ProteinNTerminus(), Serine, pwiz::data::unimod::site(), Threonine, Tyrosine, UNIMOD_Acetyl, UNIMOD_Gln__pyro_Glu, UNIMOD_Met__Hse, UNIMOD_Oxidation, UNIMOD_Phospho, unit_assert, unit_assert_operator_equal, and unit_assert_throws_what.

Referenced by main().

40 {
41  if (os_) *os_ << "test()\n";
42 
45  unit_assert_operator_equal(Site::NTerminus, site('n'));
46  unit_assert_operator_equal(Site::CTerminus, site('c'));
51  unit_assert_throws_what(site('1'), invalid_argument, "[unimod::site] invalid symbol \"1\"");
52  unit_assert_throws_what(site('z'), invalid_argument, "[unimod::site] invalid symbol \"z\"");
53 
54 
55  unit_assert_operator_equal(Position::Anywhere, position());
58  unit_assert_throws_what(position(MS_matrix_assisted_laser_desorption_ionization), invalid_argument, "[unimod::position] invalid cvid \"MALDI\" (1000075)");
59 
60 
61  if (os_) *os_ << "Unimod entries: " << modifications().size() << endl;
62  unit_assert(modifications().size() > 500);
63 
64 
65  const Modification& acetyl = modification("Acetyl");
68  unit_assert_operator_equal("Acetyl", acetyl.name);
69  unit_assert(acetyl.approved);
70  unit_assert_operator_equal("C2H2O1", acetyl.deltaComposition.formula());
71  unit_assert_operator_equal(8, acetyl.specificities.size());
72 
73  unit_assert_operator_equal(Site::Lysine, acetyl.specificities[0].site);
74  unit_assert_operator_equal(Position::Anywhere, acetyl.specificities[0].position);
75  unit_assert_operator_equal(false, acetyl.specificities[0].hidden);
76  unit_assert_operator_equal(Classification::Multiple, acetyl.specificities[0].classification);
77 
78  unit_assert_operator_equal(Site::NTerminus, acetyl.specificities[1].site);
79  unit_assert_operator_equal(Position::AnyNTerminus, acetyl.specificities[1].position);
80  unit_assert_operator_equal(false, acetyl.specificities[1].hidden);
81  unit_assert_operator_equal(Classification::Multiple, acetyl.specificities[1].classification);
82 
83  unit_assert_operator_equal(Site::Cysteine, acetyl.specificities[2].site);
84  unit_assert_operator_equal(Position::Anywhere, acetyl.specificities[2].position);
85  unit_assert_operator_equal(true, acetyl.specificities[2].hidden);
86  unit_assert_operator_equal(Classification::PostTranslational, acetyl.specificities[2].classification);
87 
88  unit_assert_operator_equal(Site::NTerminus, acetyl.specificities[4].site);
89  unit_assert_operator_equal(Position::ProteinNTerminus, acetyl.specificities[4].position);
90  unit_assert_operator_equal(false, acetyl.specificities[4].hidden);
91  unit_assert_operator_equal(Classification::PostTranslational, acetyl.specificities[4].classification);
92 
93  unit_assert_operator_equal(UNIMOD_Acetyl, modifications(acetyl.deltaMonoisotopicMass(), 0)[0].cvid);
94  unit_assert_operator_equal(UNIMOD_Acetyl, modifications(acetyl.deltaAverageMass(), 0, false)[0].cvid);
95 
96  // test a position-only filter
97  unit_assert_operator_equal(1, modifications(acetyl.deltaMonoisotopicMass(), 0.0001,
98  indeterminate, indeterminate,
99  Site::Any, Position::AnyNTerminus).size());
100  unit_assert_operator_equal(UNIMOD_Acetyl, modifications(acetyl.deltaMonoisotopicMass(), 0.5,
101  indeterminate, indeterminate,
102  Site::Any, Position::AnyNTerminus)[0].cvid);
103 
104 
105  const Modification& hse = modification("Met->Hse");
107  unit_assert_operator_equal("Met->Hse", hse.name);
108  unit_assert(hse.approved);
109  unit_assert_operator_equal("C-1H-2O1S-1", hse.deltaComposition.formula());
110  unit_assert_operator_equal(Site::Methionine, hse.specificities[0].site);
111  unit_assert_operator_equal(Position::AnyCTerminus, hse.specificities[0].position);
112  unit_assert_operator_equal(false, hse.specificities[0].hidden);
113  unit_assert_operator_equal(Classification::ChemicalDerivative, hse.specificities[0].classification);
114 
115 
116  const Modification& oxidation = modification(UNIMOD_Oxidation);
117 
118  // 3 mods have the same mass as oxidation
119  unit_assert_operator_equal(3, modifications(oxidation.deltaMonoisotopicMass(), 0, true, indeterminate).size());
120  unit_assert_operator_equal(3, modifications(oxidation.deltaAverageMass(), 0, false, indeterminate).size());
121 
122  // only one of those mods happen on Methionine
123  unit_assert_operator_equal(1, modifications(oxidation.deltaMonoisotopicMass(), 0, true, indeterminate, Site::Methionine).size());
124  unit_assert_operator_equal(1, modifications(oxidation.deltaAverageMass(), 0, false, indeterminate, Site::Methionine).size());
125 
126  // oxidation also happens on Proline (test multi-bit Site mask)
127  unit_assert_operator_equal(1, modifications(oxidation.deltaAverageMass(), 0, false, indeterminate, Site::Methionine | Site::Proline).size());
128 
129  // add Alanine as a site and it could be a substitution
130  unit_assert_operator_equal(2, modifications(oxidation.deltaAverageMass(), 0, false, indeterminate, Site::Methionine | Site::Alanine).size());
131 
132 
133  // 18 mods are 28 +/- 1
134  unit_assert_operator_equal(18, modifications(28, 1, true, indeterminate).size());
135 
136  // only two of those mods happen post-translationally on protein N-termini
137  unit_assert_operator_equal(2, modifications(28, 1, true, indeterminate, Site::Any,
139  Classification::PostTranslational).size());
140 
141 
142  const Modification& phospho = modification(UNIMOD_Phospho);
143 
144  // phospho on S and T are grouped (property names are duplicated)
145  unit_assert_operator_equal(UNIMOD_Phospho, modifications(phospho.deltaMonoisotopicMass(), 0, true, true, Site::Serine)[0].cvid);
146  unit_assert_operator_equal(UNIMOD_Phospho, modifications(phospho.deltaMonoisotopicMass(), 0, true, true, Site::Threonine)[0].cvid);
147  unit_assert_operator_equal(UNIMOD_Phospho, modifications(phospho.deltaMonoisotopicMass(), 0, true, true, Site::Tyrosine)[0].cvid);
148 
149  // test multi-bit Site mask
150  unit_assert_operator_equal(UNIMOD_Phospho, modifications(phospho.deltaMonoisotopicMass(), 0, true, true, Site::Serine | Site::Tyrosine)[0].cvid);
151 
152  // there are no unapproved mods at phospho's mass
153  unit_assert_operator_equal(0, modifications(phospho.deltaMonoisotopicMass(), 0, true, false).size());
154 
155  // phospho and sulfo are only distinguishable with PPM mass accuracy
156  double mass_2000Da_1ppm = 2000 - (2000 - MZTolerance(1, MZTolerance::PPM));
157  unit_assert_operator_equal(2, modifications(phospho.deltaMonoisotopicMass(), 0.5, true, true, Site::Serine).size());
158  unit_assert_operator_equal(1, modifications(phospho.deltaMonoisotopicMass(), mass_2000Da_1ppm, true, true, Site::Serine).size());
159 
160  // test indeterminate and average mass
161  unit_assert_operator_equal(2, modifications(phospho.deltaMonoisotopicMass(), 0.1, indeterminate, true, Site::Serine).size());
162  unit_assert_operator_equal(2, modifications(phospho.deltaAverageMass(), 0.1, indeterminate, true, Site::Serine).size());
163  unit_assert_operator_equal(2, modifications(phospho.deltaAverageMass(), 0.1, false, true, Site::Serine).size());
164 
165  // test negative mass
167  mass_2000Da_1ppm,
168  true, true,
170  Position::AnyNTerminus)[0].cvid);
171 
172 
173  // at 14.5 +/- 0.5 there are 3 approved mods and 6 unapproved
174  unit_assert_operator_equal(3, modifications(14.5, 0.5, true, true).size());
175  unit_assert_operator_equal(9, modifications(14.5, 0.5, true, false).size());
176 
177  // all 9 unapproved mods are hidden
178  unit_assert_operator_equal(0, modifications(14.5, 0.5, true, false, Site::Any,
179  Position::Anywhere, Classification::Any, false).size());
180 
181  // test ambiguous residue; this mod could be a Q->P substitution
182  unit_assert_operator_equal(1, modifications(-31, 0.01, true, indeterminate, site('Z')).size());
183 }
PWIZ_API_DECL const Modification & modification(CVID cvid)
find a modification by CVID
#define unit_assert_throws_what(x, exception, whatStr)
Definition: unit.hpp:119
MS_matrix_assisted_laser_desorption_ionization
matrix-assisted laser desorption ionization: The formation of gas-phase ions from molecules that are ...
Definition: cv.hpp:358
MS_modification_specificity_peptide_C_term
modification specificity peptide C-term: As parameter for search engine: apply the modification only ...
Definition: cv.hpp:3853
Glutamine
Definition: AminoAcid.hpp:45
AsparticAcid
Definition: AminoAcid.hpp:45
() Anywhere() AnyNTerminus() AnyCTerminus()() Any(1<< 0)(Artifact)(1<< 1)(ChemicalDerivative)(1<< 2)(CoTranslational)(1<< 3)(IsotopicLabel)(1<< 4)(Multiple)(1<< 5)(NLinkedGlycosylation)(1<< 6)(NonStandardResidue)(1<< 7)(OLinkedGlycosylation)(1<< 8)(OtherGlycosylation)(1<< 9)(Other)(1<< 10)(PostTranslational)(1<< 11)(PreTranslational)(1<< 12)(Substitution)(1<< 13)(SynthPepProtectGP)(1<< 14)) struct PWIZ_API_DECL Modification
a modification from Unimod
Definition: Unimod.hpp:81
Methionine
Definition: AminoAcid.hpp:45
UNIMOD_Acetyl
Acetyl: Acetylation.
Definition: cv.hpp:8422
PWIZ_API_DECL const std::vector< Modification > & modifications()
the entire list of Unimod modifications
Threonine
Definition: AminoAcid.hpp:45
Cysteine
Definition: AminoAcid.hpp:45
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:92
Proline
Definition: AminoAcid.hpp:45
Asparagine
Definition: AminoAcid.hpp:45
Tyrosine
Definition: AminoAcid.hpp:45
UNIMOD_Met__Hse
Met->Hse: Homoserine.
Definition: cv.hpp:8449
Lysine
Definition: AminoAcid.hpp:45
PWIZ_API_DECL Position position(CVID cvid=CVID_Unknown)
returns a Position corresponding to one of the following CVIDs: CVID_Unknown: Position::Anywhere MS_m...
MS_modification_specificity_peptide_N_term
modification specificity peptide N-term: As parameter for search engine: apply the modification only ...
Definition: cv.hpp:3850
GlutamicAcid
Definition: AminoAcid.hpp:45
UNIMOD_Phospho
Phospho: Phosphorylation.
Definition: cv.hpp:8467
struct for expressing m/z tolerance in either amu or ppm
Definition: MZTolerance.hpp:38
UNIMOD_Gln__pyro_Glu
Gln->pyro-Glu: Pyro-glu from Q.
Definition: cv.hpp:8485
Alanine
Definition: AminoAcid.hpp:45
ostream * os_
Definition: UnimodTest.cpp:36
() Anywhere() AnyNTerminus() AnyCTerminus() ProteinNTerminus(ProteinCTerminus)) BOOST_BITFIELD_EX(Classification
UNIMOD_Oxidation
Oxidation: Oxidation or Hydroxylation.
Definition: cv.hpp:8500
#define unit_assert(x)
Definition: unit.hpp:85
PWIZ_API_DECL Site site(char symbol)
returns the Site given a one-letter residue code, or: &#39;x&#39; for Site::Any, &#39;n&#39; for Site::NTerminus, &#39;c&#39; for Site::CTerminus
Serine
Definition: AminoAcid.hpp:45

§ main()

int main ( int  argc,
char *  argv[] 
)

Definition at line 186 of file UnimodTest.cpp.

References os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG.

187 {
188  TEST_PROLOG(argc, argv)
189 
190  try
191  {
192  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
193  test();
194  }
195  catch (exception& e)
196  {
197  TEST_FAILED(e.what())
198  }
199  catch (...)
200  {
201  TEST_FAILED("Caught unknown exception.")
202  }
203 
205 }
#define TEST_EPILOG
Definition: unit.hpp:182
#define TEST_FAILED(x)
Definition: unit.hpp:176
void test()
Definition: UnimodTest.cpp:39
#define TEST_PROLOG(argc, argv)
Definition: unit.hpp:174
ostream * os_
Definition: UnimodTest.cpp:36

Variable Documentation

§ os_

ostream* os_ = 0

Definition at line 36 of file UnimodTest.cpp.

Referenced by main(), and test().