src/gromacs/trajectoryanalysis/tests/sasa.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests for functionality of the "sasa" trajectory analysis module.
  38  *
  39  * These tests test the basic functionality of the tool itself, but currently
  40  * the tests related to -odg output are missing.  This would require a full tpr
  41  * file, and some investigation on what kind of tpr it should be to produce
  42  * reasonable output.
  43  *
  44  * The actual surface area algorithm is tested separately in surfacearea.cpp.
  45  *
  46  * \author Teemu Murtola <teemu.murtola@gmail.com>
  47  * \ingroup module_trajectoryanalysis
  48  */
  49 #include "gmxpre.h"
  50
  51 #include "gromacs/trajectoryanalysis/modules/sasa.h"
  52
  53 #include <gtest/gtest.h>
  54
  55 #include "testutils/cmdlinetest.h"
  56 #include "testutils/testasserts.h"
  57 #include "testutils/textblockmatchers.h"
  58 #include "testutils/xvgtest.h"
  59
  60 #include "moduletest.h"
  61
  62 namespace
  63 {
  64
  65 using gmx::test::CommandLine;
  66 using gmx::test::ExactTextMatch;
  67 using gmx::test::NoTextMatch;
  68 using gmx::test::XvgMatch;
  69
  70 /********************************************************************
  71  * Tests for gmx::analysismodules::Sasa.
  72  */
  73
  74 //! Test fixture for the `sasa` analysis module.
  75 typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::SasaInfo>
  76     SasaModuleTest;
  77
  78 TEST_F(SasaModuleTest, BasicTest)
  79 {
  80     const char *const cmdline[] = {
  81         "sasa",
  82         "-surface", "all",
  83         "-output", "name N CA C O H"
  84     };
  85     setTopology("lysozyme.gro");
  86     setOutputFile("-o", ".xvg", XvgMatch().testData(false));
  87     setOutputFile("-or", ".xvg", XvgMatch());
  88     setOutputFile("-oa", ".xvg", XvgMatch());
  89     setOutputFile("-tv", ".xvg", XvgMatch().testData(false));
  90     excludeDataset("dgsolv");
  91     setDatasetTolerance("area", gmx::test::ulpTolerance(8));
  92     setDatasetTolerance("volume", gmx::test::ulpTolerance(8));
  93     runTest(CommandLine(cmdline));
  94 }
  95
  96 TEST_F(SasaModuleTest, HandlesSelectedResidues)
  97 {
  98     const char *const cmdline[] = {
  99         "sasa",
 100         "-surface", "resnr 2 4 to 5 8"
 101     };
 102     setTopology("lysozyme.gro");
 103     setOutputFile("-o", ".xvg", XvgMatch().testData(false));
 104     setOutputFile("-or", ".xvg", XvgMatch());
 105     setOutputFile("-oa", ".xvg", XvgMatch());
 106     excludeDataset("dgsolv");
 107     excludeDataset("volume");
 108     setDatasetTolerance("area", gmx::test::ulpTolerance(8));
 109     runTest(CommandLine(cmdline));
 110 }
 111
 112 TEST_F(SasaModuleTest, WritesConnollySurfaceWithSolute)
 113 {
 114     const char *const cmdline[] = {
 115         "sasa",
 116         "-surface", "atomnr 1"
 117     };
 118     setTopology("lysozyme.gro");
 119     setOutputFile("-o", ".xvg", NoTextMatch());
 120     setOutputFile("-q", "connolly.pdb", ExactTextMatch());
 121     includeDataset("area");
 122     runTest(CommandLine(cmdline));
 123 }
 124
 125 // The CONECT records written to the output make this very difficult to test
 126 // without parsing the output file, since by construction, there are a lot of
 127 // dot pairs that are at exactly the same distance from each other in exact
 128 // arithmetic, and depending on rounding etc., different pairs get picked into
 129 // the output for single and double precision.
 130 #if 0
 131 TEST_F(SasaModuleTest, WritesConnollySurfaceWithoutSolute)
 132 {
 133     const char *const cmdline[] = {
 134         "sasa",
 135         "-surface", "atomnr 1",
 136         "-noprot"
 137     };
 138     setTopology("lysozyme.gro");
 139     setOutputFileNoTest("-o", "xvg");
 140     setOutputFile("-q", "connolly.pdb");
 141     includeDataset("area");
 142     runTest(CommandLine(cmdline));
 143 }
 144 #endif
 145
 146 TEST_F(SasaModuleTest, HandlesDynamicOutputGroup)
 147 {
 148     const char *const cmdline[] = {
 149         "sasa",
 150         "-surface", "all",
 151         "-output", "y > 1.5"
 152     };
 153     setTopology("lysozyme.gro");
 154     setOutputFile("-o", ".xvg", NoTextMatch());
 155     setOutputFile("-or", ".xvg", NoTextMatch());
 156     setOutputFile("-oa", ".xvg", NoTextMatch());
 157     excludeDataset("volume");
 158     excludeDataset("dgsolv");
 159     setDatasetTolerance("area", gmx::test::ulpTolerance(8));
 160     runTest(CommandLine(cmdline));
 161 }
 162
 163 TEST_F(SasaModuleTest, HandlesDynamicCalculationGroup)
 164 {
 165     const char *const cmdline[] = {
 166         "sasa",
 167         "-surface", "y > 1.5",
 168         "-output", "y > 1.5 and z > 0"
 169     };
 170     setTopology("lysozyme.gro");
 171     setOutputFile("-o", ".xvg", NoTextMatch());
 172     setOutputFile("-or", ".xvg", NoTextMatch());
 173     setOutputFile("-oa", ".xvg", NoTextMatch());
 174     excludeDataset("volume");
 175     excludeDataset("dgsolv");
 176     setDatasetTolerance("area", gmx::test::ulpTolerance(8));
 177     runTest(CommandLine(cmdline));
 178 }
 179
 180 } // namespace