src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  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 =
  68         std::tuple<std::string, std::string, std::string, std::string, std::string, std::string, int, bool>;
  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 = { "^;[[:blank:]] *File '.*' was generated.*\n",
  80                                                   "^;[[:blank:]]*By user:.*\n",
  81                                                   "^;[[:blank:]]*On host:.*\n",
  82                                                   "^;[[:blank:]]*At date:.*\n",
  83                                                   "^;[[:blank:]]*:-\\).*\\(-:.*\n",
  84                                                   "^;[[:blank:]]*Executable:.*\n",
  85                                                   "^;[[:blank:]]*Data prefix:.*\n",
  86                                                   "^;[[:blank:]]*Working dir:.*\n",
  87                                                   "^;[[:blank:]]*pdb2gmx.*-test.*\n" };
  88 //! Compiled regular expressions for lines to skip when matching.
  89 FilteringExactTextMatch c_textMatcher(c_regexStringsToSkip);
  90
  91 class Pdb2gmxTest : public test::CommandLineTestBase, public ::testing::WithParamInterface<CommandLineOptionParams>
  92 {
  93 public:
  94     Pdb2gmxTest()
  95     {
  96         int outputFileType = std::get<6>(GetParam());
  97         // If the file type of the output configuration is one
  98         // commonly used (ie. pdb, gro), then check its content.
  99         if (outputFileType == efPDB)
 100         {
 101             // If we're writing PDB output, we are interested in
 102             // testing things like TER records and chain IDs.
 103             std::string outputfile = "conf.";
 104             outputfile += ftp2ext(outputFileType);
 105             ExactTextMatch settings;
 106             setOutputFile("-o", outputfile.c_str(), TextFileMatch(settings));
 107         }
 108         else if (outputFileType == efGRO)
 109         {
 110             setOutputFile("-o", "conf.gro", ConfMatch().matchFullConfiguration(std::get<7>(GetParam())));
 111         }
 112         setOutputFile("-p", "topol.top", TextFileMatch(c_textMatcher));
 113     }
 114
 115     void runTest(const CommandLine& args)
 116     {
 117         CommandLine& cmdline = commandLine();
 118         cmdline.merge(args);
 119
 120         TestReferenceChecker rootChecker(this->rootChecker());
 121
 122         ASSERT_EQ(0, CommandLineTestHelper::runModuleFactory(&pdb2gmxInfo::create, &cmdline));
 123
 124         checkOutputFiles();
 125     }
 126 };
 127
 128 TEST_P(Pdb2gmxTest, ProducesMatchingTopology)
 129 {
 130     const auto& params    = GetParam();
 131     std::string cmdline[] = { "pdb2gmx",   "-ignh",
 132                               "-ff",       std::get<0>(params),
 133                               "-water",    std::get<1>(params),
 134                               "-vsite",    std::get<2>(params),
 135                               "-chainsep", std::get<3>(params),
 136                               "-merge",    std::get<4>(params) };
 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,
 146                         Pdb2gmxTest,
 147                         ::testing::Combine(::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",
 153                                                              "fragment2.pdb",
 154                                                              "fragment3.pdb",
 155                                                              "fragment4.pdb"),
 156                                            ::testing::Values(efGRO),
 157                                            ::testing::Values(false)));
 158 #endif
 159
 160 #if GROMOS
 161 INSTANTIATE_TEST_CASE_P(ForGromos43a1,
 162                         Pdb2gmxTest,
 163                         ::testing::Combine(::testing::Values("gromos43a1"),
 164                                            ::testing::Values("spc", "spce"),
 165                                            ::testing::Values("none", "h"),
 166                                            ::testing::Values("id_or_ter"),
 167                                            ::testing::Values("no"),
 168                                            ::testing::Values("fragment1.pdb",
 169                                                              "fragment2.pdb",
 170                                                              "fragment3.pdb",
 171                                                              "fragment4.pdb"),
 172                                            ::testing::Values(efGRO),
 173                                            ::testing::Values(false)));
 174
 175 INSTANTIATE_TEST_CASE_P(ForGromos53a6,
 176                         Pdb2gmxTest,
 177                         ::testing::Combine(::testing::Values("gromos53a6"),
 178                                            ::testing::Values("spc", "spce"),
 179                                            ::testing::Values("none", "h"),
 180                                            ::testing::Values("id_or_ter"),
 181                                            ::testing::Values("no"),
 182                                            ::testing::Values("fragment1.pdb",
 183                                                              "fragment2.pdb",
 184                                                              "fragment3.pdb",
 185                                                              "fragment4.pdb"),
 186                                            ::testing::Values(efGRO),
 187                                            ::testing::Values(false)));
 188 #endif
 189
 190 #if AMBER
 191 INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildn,
 192                         Pdb2gmxTest,
 193                         ::testing::Combine(::testing::Values("amber99sb-ildn"),
 194                                            ::testing::Values("tip3p"),
 195                                            ::testing::Values("none", "h"),
 196                                            ::testing::Values("id_or_ter"),
 197                                            ::testing::Values("no"),
 198                                            ::testing::Values("fragment1.pdb",
 199                                                              "fragment2.pdb",
 200                                                              "fragment3.pdb",
 201                                                              "fragment4.pdb"),
 202                                            ::testing::Values(efGRO),
 203                                            ::testing::Values(false)));
 204 INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildnWithTip4p,
 205                         Pdb2gmxTest,
 206                         ::testing::Combine(::testing::Values("amber99sb-ildn"),
 207                                            ::testing::Values("tip4p"),
 208                                            ::testing::Values("none"),
 209                                            ::testing::Values("id_or_ter"),
 210                                            ::testing::Values("no"),
 211                                            ::testing::Values("tip4p.pdb"),
 212                                            ::testing::Values(efGRO),
 213                                            ::testing::Values(true)));
 214 #endif
 215
 216 #if CHARMM
 217 INSTANTIATE_TEST_CASE_P(ForCharmm27,
 218                         Pdb2gmxTest,
 219                         ::testing::Combine(::testing::Values("charmm27"),
 220                                            ::testing::Values("tip3p"),
 221                                            ::testing::Values("none", "h"),
 222                                            ::testing::Values("id_or_ter"),
 223                                            ::testing::Values("no"),
 224                                            ::testing::Values("fragment1.pdb",
 225                                                              "fragment2.pdb",
 226                                                              "fragment3.pdb",
 227                                                              "fragment4.pdb"),
 228                                            ::testing::Values(efGRO),
 229                                            ::testing::Values(false)));
 230
 231
 232 INSTANTIATE_TEST_CASE_P(ChainSep,
 233                         Pdb2gmxTest,
 234                         ::testing::Combine(::testing::Values("charmm27"),
 235                                            ::testing::Values("tip3p"),
 236                                            ::testing::Values("none"),
 237                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
 238                                            ::testing::Values("all", "no"),
 239                                            ::testing::Values("chainTer.pdb"),
 240                                            ::testing::Values(efGRO),
 241                                            ::testing::Values(false)));
 242
 243 INSTANTIATE_TEST_CASE_P(ChainChanges,
 244                         Pdb2gmxTest,
 245                         ::testing::Combine(::testing::Values("charmm27"),
 246                                            ::testing::Values("tip3p"),
 247                                            ::testing::Values("none"),
 248                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
 249                                            ::testing::Values("no"),
 250                                            ::testing::Values("two-fragments.pdb"),
 251                                            ::testing::Values(efPDB),
 252                                            ::testing::Values(false)));
 253
 254 INSTANTIATE_TEST_CASE_P(ForCharmm27CyclicSystem,
 255                         Pdb2gmxTest,
 256                         ::testing::Combine(::testing::Values("charmm27"),
 257                                            ::testing::Values("tip3p"),
 258                                            ::testing::Values("none"),
 259                                            ::testing::Values("id_or_ter"),
 260                                            ::testing::Values("no", "all"),
 261                                            ::testing::Values("cyclic-rna.pdb",
 262                                                              "cyclic-protein-small.pdb"),
 263                                            ::testing::Values(efGRO),
 264                                            ::testing::Values(false)));
 265 #endif
 266
 267 } // namespace
 268 } // namespace test
 269 } // namespace gmx