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 <tuple>
  47
  48 #include "gromacs/fileio/filetypes.h"
  49 #include "gromacs/utility/futil.h"
  50 #include "gromacs/utility/stringutil.h"
  51 #include "gromacs/utility/textreader.h"
  52
  53 #include "testutils/cmdlinetest.h"
  54 #include "testutils/conftest.h"
  55 #include "testutils/filematchers.h"
  56 #include "testutils/refdata.h"
  57 #include "testutils/testfilemanager.h"
  58 #include "testutils/textblockmatchers.h"
  59
  60 namespace gmx
  61 {
  62 namespace test
  63 {
  64 namespace
  65 {
  66
  67 using test::CommandLine;
  68
  69 //! Test parameter struct.
  70 using CommandLineOptionParams =
  71         std::tuple<std::string, std::string, std::string, std::string, std::string, std::string, int, bool>;
  72
  73 /*! \brief Strings containing regular expressions for lines to skip
  74  * when matching.
  75  *
  76  * \todo It would be preferable to just scrub the content that actually
  77  * varies, but we don't use enough regular expression support for that
  78  * yet.
  79  *
  80  * Note that the "\n" are needed so these regular expressions match
  81  * Windows line endings. */
  82 std::vector<std::string> c_regexStringsToSkip = { "^;[[:blank:]] *File '.*' was generated.*\n",
  83                                                   "^;[[:blank:]]*By user:.*\n",
  84                                                   "^;[[:blank:]]*On host:.*\n",
  85                                                   "^;[[:blank:]]*At date:.*\n",
  86                                                   "^;[[:blank:]]*:-\\).*\\(-:.*\n",
  87                                                   "^;[[:blank:]]*Executable:.*\n",
  88                                                   "^;[[:blank:]]*Data prefix:.*\n",
  89                                                   "^;[[:blank:]]*Working dir:.*\n",
  90                                                   "^;[[:blank:]]*pdb2gmx.*-test.*\n" };
  91 //! Compiled regular expressions for lines to skip when matching.
  92 FilteringExactTextMatch c_textMatcher(c_regexStringsToSkip);
  93
  94 class Pdb2gmxTest : public test::CommandLineTestBase, public ::testing::WithParamInterface<CommandLineOptionParams>
  95 {
  96 public:
  97     Pdb2gmxTest()
  98     {
  99         int outputFileType = std::get<6>(GetParam());
 100         // If the file type of the output configuration is one
 101         // commonly used (ie. pdb, gro), then check its content.
 102         if (outputFileType == efPDB)
 103         {
 104             // If we're writing PDB output, we are interested in
 105             // testing things like TER records and chain IDs.
 106             std::string outputfile = "conf.";
 107             outputfile += ftp2ext(outputFileType);
 108             ExactTextMatch settings;
 109             setOutputFile("-o", outputfile.c_str(), TextFileMatch(settings));
 110         }
 111         else if (outputFileType == efGRO)
 112         {
 113             setOutputFile("-o", "conf.gro", ConfMatch().matchFullConfiguration(std::get<7>(GetParam())));
 114         }
 115         setOutputFile("-p", "topol.top", TextFileMatch(c_textMatcher));
 116     }
 117
 118     void runTest(const CommandLine& args)
 119     {
 120         CommandLine& cmdline = commandLine();
 121         cmdline.merge(args);
 122
 123         TestReferenceChecker rootChecker(this->rootChecker());
 124
 125         ASSERT_EQ(0, CommandLineTestHelper::runModuleFactory(&pdb2gmxInfo::create, &cmdline));
 126
 127         checkOutputFiles();
 128     }
 129 };
 130
 131 TEST_P(Pdb2gmxTest, ProducesMatchingTopology)
 132 {
 133     const auto& params    = GetParam();
 134     std::string cmdline[] = { "pdb2gmx",   "-ignh",
 135                               "-ff",       std::get<0>(params),
 136                               "-water",    std::get<1>(params),
 137                               "-vsite",    std::get<2>(params),
 138                               "-chainsep", std::get<3>(params),
 139                               "-merge",    std::get<4>(params) };
 140     setInputFile("-f", std::get<5>(params));
 141     runTest(CommandLine(cmdline));
 142 }
 143
 144 //! Help GoogleTest name our test cases
 145 std::string namesOfTests(const testing::TestParamInfo<Pdb2gmxTest::ParamType>& info)
 146 {
 147     const auto& param = info.param;
 148
 149     std::string testName = formatString(
 150             "ff_%s_"
 151             "water_%s_"
 152             "vsite_%s_"
 153             "chainsep_%s_"
 154             "merge_%s_"
 155             "input_%s_"
 156             "format_%s_"
 157             "matchfullconfiguration_%s_",
 158             std::get<0>(param).c_str(),
 159             std::get<1>(param).c_str(),
 160             std::get<2>(param).c_str(),
 161             std::get<3>(param).c_str(),
 162             std::get<4>(param).c_str(),
 163             std::get<5>(param).c_str(),
 164             ftp2ext(std::get<6>(param)),
 165             std::get<7>(param) ? "true" : "false");
 166
 167     // Note that the returned names must be unique and may use only
 168     // alphanumeric ASCII characters. It's not supposed to contain
 169     // underscores (see the GoogleTest FAQ
 170     // why-should-test-suite-names-and-test-names-not-contain-underscore),
 171     // but doing so works for now, is likely to remain so, and makes
 172     // such test names much more readable.
 173     testName = replaceAll(testName, "-", "");
 174     testName = replaceAll(testName, ".", "");
 175     return testName;
 176 }
 177
 178 // These tests are still rather slow when run with TSAN, so in the
 179 // CMakeLists.txt file we split them into separtae test binaries.
 180
 181 #if OPLSAA
 182 INSTANTIATE_TEST_CASE_P(ForOplsaa,
 183                         Pdb2gmxTest,
 184                         ::testing::Combine(::testing::Values("oplsaa"),
 185                                            ::testing::Values("tip3p", "tip4p", "tip5p"),
 186                                            ::testing::Values("none", "h"),
 187                                            ::testing::Values("id_or_ter"),
 188                                            ::testing::Values("no"),
 189                                            ::testing::Values("fragment1.pdb",
 190                                                              "fragment2.pdb",
 191                                                              "fragment3.pdb",
 192                                                              "fragment4.pdb"),
 193                                            ::testing::Values(efGRO),
 194                                            ::testing::Values(false)),
 195                         namesOfTests);
 196 #endif
 197
 198 #if GROMOS
 199 INSTANTIATE_TEST_CASE_P(ForGromos43a1,
 200                         Pdb2gmxTest,
 201                         ::testing::Combine(::testing::Values("gromos43a1"),
 202                                            ::testing::Values("spc", "spce"),
 203                                            ::testing::Values("none", "h"),
 204                                            ::testing::Values("id_or_ter"),
 205                                            ::testing::Values("no"),
 206                                            ::testing::Values("fragment1.pdb",
 207                                                              "fragment2.pdb",
 208                                                              "fragment3.pdb",
 209                                                              "fragment4.pdb"),
 210                                            ::testing::Values(efGRO),
 211                                            ::testing::Values(false)),
 212                         namesOfTests);
 213
 214 INSTANTIATE_TEST_CASE_P(ForGromos53a6,
 215                         Pdb2gmxTest,
 216                         ::testing::Combine(::testing::Values("gromos53a6"),
 217                                            ::testing::Values("spc", "spce"),
 218                                            ::testing::Values("none", "h"),
 219                                            ::testing::Values("id_or_ter"),
 220                                            ::testing::Values("no"),
 221                                            ::testing::Values("fragment1.pdb",
 222                                                              "fragment2.pdb",
 223                                                              "fragment3.pdb",
 224                                                              "fragment4.pdb"),
 225                                            ::testing::Values(efGRO),
 226                                            ::testing::Values(false)),
 227                         namesOfTests);
 228 #endif
 229
 230 #if AMBER
 231 INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildn,
 232                         Pdb2gmxTest,
 233                         ::testing::Combine(::testing::Values("amber99sb-ildn"),
 234                                            ::testing::Values("tip3p"),
 235                                            ::testing::Values("none", "h"),
 236                                            ::testing::Values("id_or_ter"),
 237                                            ::testing::Values("no"),
 238                                            ::testing::Values("fragment1.pdb",
 239                                                              "fragment2.pdb",
 240                                                              "fragment3.pdb",
 241                                                              "fragment4.pdb"),
 242                                            ::testing::Values(efGRO),
 243                                            ::testing::Values(false)),
 244                         namesOfTests);
 245 INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildnWithTip4p,
 246                         Pdb2gmxTest,
 247                         ::testing::Combine(::testing::Values("amber99sb-ildn"),
 248                                            ::testing::Values("tip4p"),
 249                                            ::testing::Values("none"),
 250                                            ::testing::Values("id_or_ter"),
 251                                            ::testing::Values("no"),
 252                                            ::testing::Values("tip4p.pdb"),
 253                                            ::testing::Values(efGRO),
 254                                            ::testing::Values(true)),
 255                         namesOfTests);
 256 #endif
 257
 258 #if CHARMM
 259 INSTANTIATE_TEST_CASE_P(ForCharmm27,
 260                         Pdb2gmxTest,
 261                         ::testing::Combine(::testing::Values("charmm27"),
 262                                            ::testing::Values("tip3p"),
 263                                            ::testing::Values("none", "h"),
 264                                            ::testing::Values("id_or_ter"),
 265                                            ::testing::Values("no"),
 266                                            ::testing::Values("fragment1.pdb",
 267                                                              "fragment2.pdb",
 268                                                              "fragment3.pdb",
 269                                                              "fragment4.pdb",
 270                                                              "single-residue.pdb"),
 271                                            ::testing::Values(efGRO),
 272                                            ::testing::Values(false)),
 273                         namesOfTests);
 274
 275
 276 INSTANTIATE_TEST_CASE_P(ChainSep,
 277                         Pdb2gmxTest,
 278                         ::testing::Combine(::testing::Values("charmm27"),
 279                                            ::testing::Values("tip3p"),
 280                                            ::testing::Values("none"),
 281                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
 282                                            ::testing::Values("all", "no"),
 283                                            ::testing::Values("chainTer.pdb"),
 284                                            ::testing::Values(efGRO),
 285                                            ::testing::Values(false)),
 286                         namesOfTests);
 287
 288 INSTANTIATE_TEST_CASE_P(ChainChanges,
 289                         Pdb2gmxTest,
 290                         ::testing::Combine(::testing::Values("charmm27"),
 291                                            ::testing::Values("tip3p"),
 292                                            ::testing::Values("none"),
 293                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
 294                                            ::testing::Values("no"),
 295                                            ::testing::Values("two-fragments.pdb"),
 296                                            ::testing::Values(efPDB),
 297                                            ::testing::Values(false)),
 298                         namesOfTests);
 299
 300 INSTANTIATE_TEST_CASE_P(ForCharmm27CyclicSystem,
 301                         Pdb2gmxTest,
 302                         ::testing::Combine(::testing::Values("charmm27"),
 303                                            ::testing::Values("tip3p"),
 304                                            ::testing::Values("none"),
 305                                            ::testing::Values("id_or_ter"),
 306                                            ::testing::Values("no", "all"),
 307                                            ::testing::Values("cyclic-rna.pdb",
 308                                                              "cyclic-protein-small.pdb"),
 309                                            ::testing::Values(efGRO),
 310                                            ::testing::Values(false)),
 311                         namesOfTests);
 312 #endif
 313
 314 } // namespace
 315 } // namespace test
 316 } // namespace gmx