src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp

   1 /*
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   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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/fileio/filetypes.h"
  47 #include "gromacs/utility/futil.h"
  48 #include "gromacs/utility/textreader.h"
  49
  50 #include "testutils/cmdlinetest.h"
  51 #include "testutils/conftest.h"
  52 #include "testutils/filematchers.h"
  53 #include "testutils/refdata.h"
  54 #include "testutils/testfilemanager.h"
  55 #include "testutils/textblockmatchers.h"
  56
  57 namespace gmx
  58 {
  59 namespace test
  60 {
  61 namespace
  62 {
  63
  64 using test::CommandLine;
  65
  66 //! Test parameter struct.
  67 using CommandLineOptionParams = std::tuple<std::string, std::string, std::string, std::string,
  68                                            std::string, std::string, int>;
  69
  70 /*! \brief Strings containing regular expressions for lines to skip
  71  * when matching.
  72  *
  73  * \todo It would be preferable to just scrub the content that actually
  74  * varies, but we don't use enough regular expression support for that
  75  * yet.
  76  *
  77  * Note that the "\n" are needed so these regular expressions match
  78  * Windows line endings. */
  79 std::vector<std::string>   c_regexStringsToSkip =
  80 {
  81     "^;[[:blank:]] *File '.*' was generated.*\n",
  82     "^;[[:blank:]]*By user:.*\n",
  83     "^;[[:blank:]]*On host:.*\n",
  84     "^;[[:blank:]]*At date:.*\n",
  85     "^;[[:blank:]]*:-\\).*\\(-:.*\n",
  86     "^;[[:blank:]]*Executable:.*\n",
  87     "^;[[:blank:]]*Data prefix:.*\n",
  88     "^;[[:blank:]]*Working dir:.*\n",
  89     "^;[[:blank:]]*pdb2gmx.*-test.*\n"
  90 };
  91 //! Compiled regular expressions for lines to skip when matching.
  92 FilteringExactTextMatch    c_textMatcher(c_regexStringsToSkip);
  93
  94 class Pdb2gmxTest : public test::CommandLineTestBase,
  95                     public ::testing::WithParamInterface<CommandLineOptionParams>
  96 {
  97     public:
  98         Pdb2gmxTest()
  99         {
 100             int outputFileType = std::get<6>(GetParam());
 101             if (outputFileType == efPDB)
 102             {
 103                 // If we're writing PDB output, we are interested in
 104                 // testing things like TER records and chain IDs.
 105                 std::string    outputfile = "conf.";
 106                 outputfile += ftp2ext(outputFileType);
 107                 ExactTextMatch settings;
 108                 setOutputFile("-o", outputfile.c_str(), TextFileMatch(settings));
 109             }
 110             else
 111             {
 112                 setOutputFile("-o", "conf.gro", ConfMatch());
 113             }
 114             setOutputFile("-p", "topol.top", TextFileMatch(c_textMatcher));
 115         }
 116
 117         void runTest(const CommandLine &args)
 118         {
 119             CommandLine &cmdline = commandLine();
 120             cmdline.merge(args);
 121
 122             TestReferenceChecker rootChecker(this->rootChecker());
 123
 124             ASSERT_EQ(0, CommandLineTestHelper::runModuleFactory(&pdb2gmxInfo::create, &cmdline));
 125
 126             checkOutputFiles();
 127         }
 128 };
 129
 130 TEST_P(Pdb2gmxTest, ProducesMatchingTopology)
 131 {
 132     const auto &params    = GetParam();
 133     std::string cmdline[] = {
 134         "pdb2gmx", "-ignh", "-ff", std::get<0>(params), "-water", std::get<1>(params), "-vsite", std::get<2>(params),
 135         "-chainsep", std::get<3>(params), "-merge", std::get<4>(params)
 136     };
 137     setInputFile("-f", std::get<5>(params));
 138     runTest(CommandLine(cmdline));
 139 }
 140
 141 // These tests are still rather slow when run with TSAN, so in the
 142 // CMakeLists.txt file we split them into separtae test binaries.
 143
 144 #if OPLSAA
 145 INSTANTIATE_TEST_CASE_P(ForOplsaa, Pdb2gmxTest,
 146                             ::testing::Combine
 147                             (::testing::Values("oplsaa"),
 148                                 ::testing::Values("tip3p", "tip4p", "tip5p"),
 149                                 ::testing::Values("none", "h"),
 150                                 ::testing::Values("id_or_ter"),
 151                                 ::testing::Values("no"),
 152                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"),
 153                                 ::testing::Values(efGRO))
 154                         );
 155 #endif
 156
 157 #if GROMOS
 158 INSTANTIATE_TEST_CASE_P(ForGromos43a1, Pdb2gmxTest,
 159                             ::testing::Combine
 160                             (::testing::Values("gromos43a1"),
 161                                 ::testing::Values("spc", "spce"),
 162                                 ::testing::Values("none", "h"),
 163                                 ::testing::Values("id_or_ter"),
 164                                 ::testing::Values("no"),
 165                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"),
 166                                 ::testing::Values(efGRO))
 167                         );
 168
 169 INSTANTIATE_TEST_CASE_P(ForGromos53a6, Pdb2gmxTest,
 170                             ::testing::Combine
 171                             (::testing::Values("gromos53a6"),
 172                                 ::testing::Values("spc", "spce"),
 173                                 ::testing::Values("none", "h"),
 174                                 ::testing::Values("id_or_ter"),
 175                                 ::testing::Values("no"),
 176                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"),
 177                                 ::testing::Values(efGRO))
 178                         );
 179 #endif
 180
 181 #if AMBER
 182 INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildn, Pdb2gmxTest,
 183                             ::testing::Combine
 184                             (::testing::Values("amber99sb-ildn"),
 185                                 ::testing::Values("tip3p"),
 186                                 ::testing::Values("none", "h"),
 187                                 ::testing::Values("id_or_ter"),
 188                                 ::testing::Values("no"),
 189                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"),
 190                                 ::testing::Values(efGRO))
 191                         );
 192 #endif
 193
 194 #if CHARMM
 195 INSTANTIATE_TEST_CASE_P(ForCharmm27, Pdb2gmxTest,
 196                             ::testing::Combine
 197                             (::testing::Values("charmm27"),
 198                                 ::testing::Values("tip3p"),
 199                                 ::testing::Values("none", "h"),
 200                                 ::testing::Values("id_or_ter"),
 201                                 ::testing::Values("no"),
 202                                 ::testing::Values("fragment1.pdb", "fragment2.pdb", "fragment3.pdb", "fragment4.pdb"),
 203                                 ::testing::Values(efGRO))
 204                         );
 205
 206
 207 INSTANTIATE_TEST_CASE_P(ChainSep, Pdb2gmxTest,
 208                             ::testing::Combine
 209                             (::testing::Values("charmm27"),
 210                                 ::testing::Values("tip3p"),
 211                                 ::testing::Values("none"),
 212                                 ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
 213                                 ::testing::Values("all", "no"),
 214                                 ::testing::Values("chainTer.pdb"),
 215                                 ::testing::Values(efGRO))
 216                         );
 217
 218 INSTANTIATE_TEST_CASE_P(ChainChanges, Pdb2gmxTest,
 219                             ::testing::Combine
 220                             (::testing::Values("charmm27"),
 221                                 ::testing::Values("tip3p"),
 222                                 ::testing::Values("none"),
 223                                 ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
 224                                 ::testing::Values("no"),
 225                                 ::testing::Values("two-fragments.pdb"),
 226                                 ::testing::Values(efPDB))
 227                         );
 228 #endif
 229
 230 } // namespace
 231 } // namespace test
 232 } // namespace gmx