src/gromacs/fileio/tests/confio.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests for reading/writing different structure file formats.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_fileio
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/fileio/confio.h"
  45
  46 #include <iostream>
  47 #include <string>
  48 #include <vector>
  49
  50 #include <gtest/gtest.h>
  51
  52 #include "gromacs/fileio/filenm.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/math/vectypes.h"
  55 #include "gromacs/topology/atoms.h"
  56 #include "gromacs/topology/symtab.h"
  57 #include "gromacs/topology/topology.h"
  58 #include "gromacs/utility/cstringutil.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 #include "testutils/stringtest.h"
  62 #include "testutils/testfilemanager.h"
  63
  64 // TODO: These should really appear somewhere centralized.
  65 /*! \brief
  66  * Google Test formatter for GromacsFileType values.
  67  */
  68 void PrintTo(const GromacsFileType &ftp, std::ostream *os)
  69 {
  70     *os << "'" << ftp2ext(ftp) << "'";
  71 }
  72
  73 namespace
  74 {
  75
  76 class StructureIORoundtripTest : public gmx::test::StringTestBase,
  77                                  public ::testing::WithParamInterface<GromacsFileType>
  78 {
  79     public:
  80         StructureIORoundtripTest()
  81         {
  82             generateReferenceTopology();
  83             generateReferenceCoordinates();
  84             testTop_ = NULL;
  85             testX_   = NULL;
  86             clear_mat(testBox_);
  87             referenceFilename_ =
  88                 fileManager_.getTemporaryFilePath(getFileSuffix("ref"));
  89             testFilename_ =
  90                 fileManager_.getTemporaryFilePath(getFileSuffix("test"));
  91         }
  92         ~StructureIORoundtripTest()
  93         {
  94             if (testTop_ != NULL)
  95             {
  96                 free_t_atoms(&testTop_->atoms, TRUE);
  97                 done_top(testTop_);
  98                 sfree(testTop_);
  99             }
 100             sfree(testX_);
 101             done_top(refTop_);
 102             sfree(refTop_);
 103         }
 104
 105         void writeReferenceFile()
 106         {
 107             write_sto_conf(referenceFilename_.c_str(), *refTop_->name,
 108                            &refTop_->atoms, as_rvec_array(&refX_[0]), NULL, -1,
 109                            refBox_);
 110         }
 111
 112         void readReferenceFileStx()
 113         {
 114             int natoms = -1;
 115             get_stx_coordnum(referenceFilename_.c_str(), &natoms);
 116             ASSERT_EQ(refTop_->atoms.nr, natoms)
 117             << "get_stx_coordnum() returned unexpected number of atoms";
 118             char title[STRLEN];
 119             snew(testTop_, 1);
 120             init_t_atoms(&testTop_->atoms, natoms, GetParam() == efPDB);
 121             snew(testX_, natoms);
 122             read_stx_conf(referenceFilename_.c_str(), title, &testTop_->atoms,
 123                           testX_, NULL, NULL, testBox_);
 124             testTop_->name = put_symtab(&testTop_->symtab, title);
 125         }
 126
 127         void readReferenceFileTps()
 128         {
 129             snew(testTop_, 1);
 130             int  ePBC = -2;
 131             char title[STRLEN];
 132             read_tps_conf(referenceFilename_.c_str(), title, testTop_,
 133                           &ePBC, &testX_, NULL, testBox_, FALSE);
 134             testTop_->name = put_symtab(&testTop_->symtab, title);
 135         }
 136
 137         void testTopologies()
 138         {
 139             // TODO: Compare the topologies.
 140         }
 141
 142         void writeTestFileAndTest()
 143         {
 144             write_sto_conf(testFilename_.c_str(), *testTop_->name,
 145                            &testTop_->atoms, testX_, NULL, -1, testBox_);
 146             testFilesEqual(referenceFilename_, testFilename_);
 147         }
 148
 149     private:
 150         std::string getFileSuffix(const char *type)
 151         {
 152             return std::string(type) + "." + ftp2ext(GetParam());
 153         }
 154
 155         void generateReferenceTopology()
 156         {
 157             snew(refTop_, 1);
 158             open_symtab(&refTop_->symtab);
 159             if (GetParam() == efESP)
 160             {
 161                 // Titles cannot be read from an .esp file...
 162                 refTop_->name = put_symtab(&refTop_->symtab, "");
 163             }
 164             else
 165             {
 166                 refTop_->name = put_symtab(&refTop_->symtab, "Test title");
 167             }
 168             const int atomCount = 10;
 169             init_t_atoms(&refTop_->atoms, atomCount, FALSE);
 170             for (int i = 0; i < atomCount; ++i)
 171             {
 172                 char name[3];
 173                 name[0]                       = 'A';
 174                 name[1]                       = 'A' + i%3;
 175                 name[2]                       = '\0';
 176                 refTop_->atoms.atomname[i]    = put_symtab(&refTop_->symtab, name);
 177                 refTop_->atoms.atom[i].resind = i/3;
 178                 if (i%3 == 0)
 179                 {
 180                     char resname[3];
 181                     resname[0] = 'R';
 182                     resname[1] = 'A' + i/3;
 183                     resname[2] = '\0';
 184                     t_atoms_set_resinfo(&refTop_->atoms, i, &refTop_->symtab,
 185                                         resname, i/3 + 1, ' ', 0, ' ');
 186                 }
 187             }
 188             refTop_->atoms.nres = 4;
 189             close_symtab(&refTop_->symtab);
 190         }
 191
 192         void generateReferenceCoordinates()
 193         {
 194             clear_mat(refBox_);
 195             refBox_[XX][XX] = 1;
 196             refBox_[YY][YY] = 2;
 197             refBox_[ZZ][ZZ] = 3;
 198             const int atomCount = refTop_->atoms.nr;
 199             refX_.reserve(atomCount);
 200             for (int i = 0; i < atomCount; ++i)
 201             {
 202                 refX_.push_back(gmx::RVec(i%4, i/4, (i/2)%3));
 203             }
 204         }
 205
 206         gmx::test::TestFileManager      fileManager_;
 207         std::string                     referenceFilename_;
 208         std::string                     testFilename_;
 209         t_topology                     *refTop_;
 210         std::vector<gmx::RVec>          refX_;
 211         matrix                          refBox_;
 212         t_topology                     *testTop_;
 213         rvec                           *testX_;
 214         matrix                          testBox_;
 215 };
 216
 217 TEST_P(StructureIORoundtripTest, ReadWriteStxConf)
 218 {
 219     writeReferenceFile();
 220     readReferenceFileStx();
 221     testTopologies();
 222     writeTestFileAndTest();
 223 }
 224
 225 TEST_P(StructureIORoundtripTest, ReadWriteTpsConf)
 226 {
 227     writeReferenceFile();
 228     readReferenceFileTps();
 229     testTopologies();
 230     writeTestFileAndTest();
 231 }
 232
 233 INSTANTIATE_TEST_CASE_P(WithDifferentFormats,
 234                         StructureIORoundtripTest,
 235                             ::testing::Values(efGRO, efG96, efPDB, efESP));
 236
 237 } // namespace