src/gromacs/fileio/tests/confio.cpp

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   4  * Copyright (c) 2015, by the GROMACS development team, led by
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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/fileio/tpxio.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/math/vectypes.h"
  56 #include "gromacs/topology/atoms.h"
  57 #include "gromacs/topology/symtab.h"
  58 #include "gromacs/topology/topology.h"
  59 #include "gromacs/utility/cstringutil.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 #include "testutils/stringtest.h"
  63 #include "testutils/testfilemanager.h"
  64
  65 // TODO: These should really appear somewhere centralized.
  66 /*! \brief
  67  * Google Test formatter for GromacsFileType values.
  68  */
  69 void PrintTo(const GromacsFileType &ftp, std::ostream *os)
  70 {
  71     *os << "'" << ftp2ext(ftp) << "'";
  72 }
  73
  74 namespace
  75 {
  76
  77 class StructureIORoundtripTest : public gmx::test::StringTestBase,
  78                                  public ::testing::WithParamInterface<GromacsFileType>
  79 {
  80     public:
  81         StructureIORoundtripTest()
  82         {
  83             generateReferenceTopology();
  84             generateReferenceCoordinates();
  85             testTop_ = NULL;
  86             testX_   = NULL;
  87             clear_mat(testBox_);
  88             referenceFilename_ =
  89                 fileManager_.getTemporaryFilePath(getFileSuffix("ref"));
  90             testFilename_ =
  91                 fileManager_.getTemporaryFilePath(getFileSuffix("test"));
  92         }
  93         ~StructureIORoundtripTest()
  94         {
  95             if (testTop_ != NULL)
  96             {
  97                 free_t_atoms(&testTop_->atoms, TRUE);
  98                 done_top(testTop_);
  99                 sfree(testTop_);
 100             }
 101             sfree(testX_);
 102             done_top(refTop_);
 103             sfree(refTop_);
 104         }
 105
 106         void writeReferenceFile()
 107         {
 108             write_sto_conf(referenceFilename_.c_str(), *refTop_->name,
 109                            &refTop_->atoms, as_rvec_array(&refX_[0]), NULL, -1,
 110                            refBox_);
 111         }
 112
 113         void readReferenceFileStx()
 114         {
 115             int natoms = -1;
 116             get_stx_coordnum(referenceFilename_.c_str(), &natoms);
 117             ASSERT_EQ(refTop_->atoms.nr, natoms)
 118             << "get_stx_coordnum() returned unexpected number of atoms";
 119             char title[STRLEN];
 120             snew(testTop_, 1);
 121             init_t_atoms(&testTop_->atoms, natoms, GetParam() == efPDB);
 122             snew(testX_, natoms);
 123             read_stx_conf(referenceFilename_.c_str(), title, &testTop_->atoms,
 124                           testX_, NULL, NULL, testBox_);
 125             testTop_->name = put_symtab(&testTop_->symtab, title);
 126         }
 127
 128         void readReferenceFileTps()
 129         {
 130             snew(testTop_, 1);
 131             int  ePBC = -2;
 132             char title[STRLEN];
 133             read_tps_conf(referenceFilename_.c_str(), title, testTop_,
 134                           &ePBC, &testX_, NULL, testBox_, FALSE);
 135             testTop_->name = put_symtab(&testTop_->symtab, title);
 136         }
 137
 138         void testTopologies()
 139         {
 140             // TODO: Compare the topologies.
 141         }
 142
 143         void writeTestFileAndTest()
 144         {
 145             write_sto_conf(testFilename_.c_str(), *testTop_->name,
 146                            &testTop_->atoms, testX_, NULL, -1, testBox_);
 147             testFilesEqual(referenceFilename_, testFilename_);
 148         }
 149
 150     private:
 151         std::string getFileSuffix(const char *type)
 152         {
 153             return std::string(type) + "." + ftp2ext(GetParam());
 154         }
 155
 156         void generateReferenceTopology()
 157         {
 158             snew(refTop_, 1);
 159             open_symtab(&refTop_->symtab);
 160             if (GetParam() == efESP)
 161             {
 162                 // Titles cannot be read from an .esp file...
 163                 refTop_->name = put_symtab(&refTop_->symtab, "");
 164             }
 165             else
 166             {
 167                 refTop_->name = put_symtab(&refTop_->symtab, "Test title");
 168             }
 169             const int atomCount = 10;
 170             init_t_atoms(&refTop_->atoms, atomCount, FALSE);
 171             for (int i = 0; i < atomCount; ++i)
 172             {
 173                 char name[3];
 174                 name[0]                       = 'A';
 175                 name[1]                       = 'A' + i%3;
 176                 name[2]                       = '\0';
 177                 refTop_->atoms.atomname[i]    = put_symtab(&refTop_->symtab, name);
 178                 refTop_->atoms.atom[i].resind = i/3;
 179                 if (i%3 == 0)
 180                 {
 181                     char resname[3];
 182                     resname[0] = 'R';
 183                     resname[1] = 'A' + i/3;
 184                     resname[2] = '\0';
 185                     t_atoms_set_resinfo(&refTop_->atoms, i, &refTop_->symtab,
 186                                         resname, i/3 + 1, ' ', 0, ' ');
 187                 }
 188             }
 189             refTop_->atoms.nres = 4;
 190             close_symtab(&refTop_->symtab);
 191         }
 192
 193         void generateReferenceCoordinates()
 194         {
 195             clear_mat(refBox_);
 196             refBox_[XX][XX] = 1;
 197             refBox_[YY][YY] = 2;
 198             refBox_[ZZ][ZZ] = 3;
 199             const int atomCount = refTop_->atoms.nr;
 200             refX_.reserve(atomCount);
 201             for (int i = 0; i < atomCount; ++i)
 202             {
 203                 refX_.push_back(gmx::RVec(i%4, i/4, (i/2)%3));
 204             }
 205         }
 206
 207         gmx::test::TestFileManager      fileManager_;
 208         std::string                     referenceFilename_;
 209         std::string                     testFilename_;
 210         t_topology                     *refTop_;
 211         std::vector<gmx::RVec>          refX_;
 212         matrix                          refBox_;
 213         t_topology                     *testTop_;
 214         rvec                           *testX_;
 215         matrix                          testBox_;
 216 };
 217
 218 TEST_P(StructureIORoundtripTest, ReadWriteStxConf)
 219 {
 220     writeReferenceFile();
 221     readReferenceFileStx();
 222     testTopologies();
 223     writeTestFileAndTest();
 224 }
 225
 226 TEST_P(StructureIORoundtripTest, ReadWriteTpsConf)
 227 {
 228     writeReferenceFile();
 229     readReferenceFileTps();
 230     testTopologies();
 231     writeTestFileAndTest();
 232 }
 233
 234 INSTANTIATE_TEST_CASE_P(WithDifferentFormats,
 235                         StructureIORoundtripTest,
 236                             ::testing::Values(efGRO, efG96, efPDB, efESP));
 237
 238 } // namespace