src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests for pdb2gmx
  38  *
  39  * \author Mark Abraham <mark.j.abraham@gmail.com>
  40  */
  41
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/gmxpreprocess/pdb2gmx.h"
  45
  46 #include "gromacs/utility/futil.h"
  47 #include "gromacs/utility/textreader.h"
  48
  49 #include "testutils/cmdlinetest.h"
  50 #include "testutils/conftest.h"
  51 #include "testutils/filematchers.h"
  52 #include "testutils/refdata.h"
  53 #include "testutils/testfilemanager.h"
  54 #include "testutils/textblockmatchers.h"
  55
  56 namespace gmx
  57 {
  58 namespace test
  59 {
  60 namespace
  61 {
  62
  63 using gmx::test::CommandLine;
  64 using gmx::test::ConfMatch;
  65
  66 //! Test parameter struct.
  67 using CommandLineOptionParams = std::tuple<std::string, std::string, std::string, std::string,
  68                                            std::string, std::string>;
  69
  70 class Pdb2gmxTest : public gmx::test::CommandLineTestBase,
  71                     public ::testing::WithParamInterface<CommandLineOptionParams>
  72 {
  73     public:
  74         Pdb2gmxTest()
  75         {
  76             // TODO It would be preferable to just scrub the content
  77             // that actually varies, but we don't have enough regular
  78             // expression support for that yet.
  79
  80             // Note that the "\n" are needed so these regular
  81             // expressions match Windows line endings.
  82             textMatcher_.addRegexToSkip("^;[[:blank:]] *File '.*' was generated.*\n");
  83             textMatcher_.addRegexToSkip("^;[[:blank:]]*By user:.*\n");
  84             textMatcher_.addRegexToSkip("^;[[:blank:]]*On host:.*\n");
  85             textMatcher_.addRegexToSkip("^;[[:blank:]]*At date:.*\n");
  86             textMatcher_.addRegexToSkip("^;[[:blank:]]*:-\\).*\\(-:.*\n");
  87             textMatcher_.addRegexToSkip("^;[[:blank:]]*Executable:.*\n");
  88             textMatcher_.addRegexToSkip("^;[[:blank:]]*Data prefix:.*\n");
  89             textMatcher_.addRegexToSkip("^;[[:blank:]]*Working dir:.*\n");
  90             textMatcher_.addRegexToSkip("^;[[:blank:]]*pdb2gmx-test.*\n");
  91             setOutputFile("-o", "conf.gro", ConfMatch());
  92             setOutputFile("-p", "topol.top", TextFileMatch(textMatcher_));
  93         }
  94
  95         void runTest(const CommandLine &args)
  96         {
  97             CommandLine &cmdline = commandLine();
  98             cmdline.merge(args);
  99
 100             ASSERT_EQ(0, gmx_pdb2gmx(cmdline.argc(), cmdline.argv()));
 101             checkOutputFiles();
 102         }
 103         FilteringExactTextMatch textMatcher_;
 104 };
 105
 106 TEST_P(Pdb2gmxTest, ProducesMatchingTopology)
 107 {
 108     const auto &params    = GetParam();
 109     std::string cmdline[] = {
 110         "pdb2gmx", "-ignh", "-ff", std::get<0>(params), "-water", std::get<1>(params), "-vsite", std::get<2>(params),
 111         "-chainsep", std::get<3>(params), "-merge", std::get<4>(params)
 112     };
 113     setInputFile("-f", std::get<5>(params));
 114     runTest(CommandLine(cmdline));
 115 }
 116
 117 INSTANTIATE_TEST_CASE_P(ForOplsaa, Pdb2gmxTest,
 118                             ::testing::Combine
 119                             (::testing::Values("oplsaa"),
 120                                 ::testing::Values("tip3p", "tip4p", "tip5p"),
 121                                 ::testing::Values("none", "h"),
 122                                 ::testing::Values("id_or_ter"),
 123                                 ::testing::Values("no"),
 124                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"))
 125                         );
 126
 127 INSTANTIATE_TEST_CASE_P(ForGromos43a1, Pdb2gmxTest,
 128                             ::testing::Combine
 129                             (::testing::Values("gromos43a1"),
 130                                 ::testing::Values("spc", "spce"),
 131                                 ::testing::Values("none", "h"),
 132                                 ::testing::Values("id_or_ter"),
 133                                 ::testing::Values("no"),
 134                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"))
 135                         );
 136
 137 INSTANTIATE_TEST_CASE_P(ForGromos53a6, Pdb2gmxTest,
 138                             ::testing::Combine
 139                             (::testing::Values("gromos53a6"),
 140                                 ::testing::Values("spc", "spce"),
 141                                 ::testing::Values("none", "h"),
 142                                 ::testing::Values("id_or_ter"),
 143                                 ::testing::Values("no"),
 144                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"))
 145                         );
 146
 147 INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildn, Pdb2gmxTest,
 148                             ::testing::Combine
 149                             (::testing::Values("amber99sb-ildn"),
 150                                 ::testing::Values("tip3p"),
 151                                 ::testing::Values("none", "h"),
 152                                 ::testing::Values("id_or_ter"),
 153                                 ::testing::Values("no"),
 154                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"))
 155                         );
 156
 157 INSTANTIATE_TEST_CASE_P(ForCharmm27, Pdb2gmxTest,
 158                             ::testing::Combine
 159                             (::testing::Values("charmm27"),
 160                                 ::testing::Values("tip3p"),
 161                                 ::testing::Values("none", "h"),
 162                                 ::testing::Values("id_or_ter"),
 163                                 ::testing::Values("no"),
 164                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"))
 165                         );
 166
 167
 168 INSTANTIATE_TEST_CASE_P(ChainSep, Pdb2gmxTest,
 169                             ::testing::Combine
 170                             (::testing::Values("charmm27"),
 171                                 ::testing::Values("tip3p"),
 172                                 ::testing::Values("none"),
 173                                 ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
 174                                 ::testing::Values("all", "no"),
 175                                 ::testing::Values("chainTer.pdb"))
 176                         );
 177
 178
 179 } // namespace
 180 } // namespace
 181 } // namespace