src/gromacs/selection/tests/selectioncollection.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests selection parsing and compilation.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include <gtest/gtest.h>
  43
  44 #include "gromacs/options/basicoptions.h"
  45 #include "gromacs/options/options.h"
  46 #include "gromacs/selection/indexutil.h"
  47 #include "gromacs/selection/selectioncollection.h"
  48 #include "gromacs/selection/selection.h"
  49 #include "gromacs/topology/topology.h"
  50 #include "gromacs/utility/arrayref.h"
  51 #include "gromacs/utility/exceptions.h"
  52 #include "gromacs/utility/flags.h"
  53 #include "gromacs/utility/gmxregex.h"
  54 #include "gromacs/utility/stringutil.h"
  55
  56 #include "testutils/refdata.h"
  57 #include "testutils/testasserts.h"
  58 #include "testutils/testfilemanager.h"
  59 #include "testutils/testoptions.h"
  60
  61 #include "toputils.h"
  62
  63 namespace
  64 {
  65
  66 /********************************************************************
  67  * Test fixture for selection testing
  68  */
  69
  70 class SelectionCollectionTest : public ::testing::Test
  71 {
  72     public:
  73         static int               s_debugLevel;
  74
  75         SelectionCollectionTest();
  76         ~SelectionCollectionTest();
  77
  78         void setAtomCount(int natoms)
  79         {
  80             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  81         }
  82         void loadTopology(const char *filename);
  83         void setTopology();
  84         void loadIndexGroups(const char *filename);
  85
  86         gmx::test::TopologyManager  topManager_;
  87         gmx::SelectionCollection    sc_;
  88         gmx::SelectionList          sel_;
  89         t_topology                 *top_;
  90         t_trxframe                 *frame_;
  91         gmx_ana_indexgrps_t        *grps_;
  92 };
  93
  94 int SelectionCollectionTest::s_debugLevel = 0;
  95
  96 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
  97 #ifndef DOXYGEN
  98 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  99 {
 100     options->addOption(gmx::IntegerOption("seldebug")
 101                            .store(&SelectionCollectionTest::s_debugLevel)
 102                            .description("Set selection debug level"));
 103 }
 104 #endif
 105
 106 SelectionCollectionTest::SelectionCollectionTest()
 107     : top_(NULL), frame_(NULL), grps_(NULL)
 108 {
 109     topManager_.requestFrame();
 110     sc_.setDebugLevel(s_debugLevel);
 111     sc_.setReferencePosType("atom");
 112     sc_.setOutputPosType("atom");
 113 }
 114
 115 SelectionCollectionTest::~SelectionCollectionTest()
 116 {
 117     if (grps_ != NULL)
 118     {
 119         gmx_ana_indexgrps_free(grps_);
 120     }
 121 }
 122
 123 void
 124 SelectionCollectionTest::loadTopology(const char *filename)
 125 {
 126     topManager_.loadTopology(filename);
 127     setTopology();
 128 }
 129
 130 void
 131 SelectionCollectionTest::setTopology()
 132 {
 133     top_   = topManager_.topology();
 134     frame_ = topManager_.frame();
 135
 136     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 137 }
 138
 139 void
 140 SelectionCollectionTest::loadIndexGroups(const char *filename)
 141 {
 142     GMX_RELEASE_ASSERT(grps_ == NULL,
 143                        "External groups can only be loaded once");
 144     std::string fullpath =
 145         gmx::test::TestFileManager::getInputFilePath(filename);
 146     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 147     sc_.setIndexGroups(grps_);
 148 }
 149
 150
 151 /********************************************************************
 152  * Test fixture for selection testing with reference data
 153  */
 154
 155 class SelectionCollectionDataTest : public SelectionCollectionTest
 156 {
 157     public:
 158         enum TestFlag
 159         {
 160             efTestEvaluation            = 1<<0,
 161             efTestPositionAtoms         = 1<<1,
 162             efTestPositionCoordinates   = 1<<2,
 163             efTestPositionMapping       = 1<<3,
 164             efTestPositionMasses        = 1<<4,
 165             efTestPositionCharges       = 1<<5,
 166             efTestSelectionNames        = 1<<6,
 167             efDontTestCompiledAtoms     = 1<<8
 168         };
 169         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 170
 171         SelectionCollectionDataTest()
 172             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 173         {
 174         }
 175
 176         void setFlags(TestFlags flags) { flags_ = flags; }
 177
 178         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 179         void runCompiler();
 180         void runEvaluate();
 181         void runEvaluateFinal();
 182
 183         void runTest(int                                     natoms,
 184                      const gmx::ConstArrayRef<const char *> &selections);
 185         void runTest(const char                             *filename,
 186                      const gmx::ConstArrayRef<const char *> &selections);
 187
 188     private:
 189         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 190                                    const gmx::Selection &sel, TestFlags flags);
 191
 192         void checkCompiled();
 193
 194         gmx::test::TestReferenceData    data_;
 195         gmx::test::TestReferenceChecker checker_;
 196         size_t                          count_;
 197         int                             framenr_;
 198         TestFlags                       flags_;
 199 };
 200
 201
 202 void
 203 SelectionCollectionDataTest::checkSelection(
 204         gmx::test::TestReferenceChecker *checker,
 205         const gmx::Selection &sel, TestFlags flags)
 206 {
 207     using gmx::test::TestReferenceChecker;
 208
 209     {
 210         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 211         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 212     }
 213     if (flags.test(efTestPositionAtoms)
 214         || flags.test(efTestPositionCoordinates)
 215         || flags.test(efTestPositionMapping)
 216         || flags.test(efTestPositionMasses)
 217         || flags.test(efTestPositionCharges))
 218     {
 219         TestReferenceChecker compound(
 220                 checker->checkSequenceCompound("Positions", sel.posCount()));
 221         for (int i = 0; i < sel.posCount(); ++i)
 222         {
 223             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 224             const gmx::SelectionPosition &p = sel.position(i);
 225             if (flags.test(efTestPositionAtoms))
 226             {
 227                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 228                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 229             }
 230             if (flags.test(efTestPositionCoordinates))
 231             {
 232                 poscompound.checkVector(p.x(), "Coordinates");
 233             }
 234             if (flags.test(efTestPositionMapping))
 235             {
 236                 poscompound.checkInteger(p.refId(), "RefId");
 237                 poscompound.checkInteger(p.mappedId(), "MappedId");
 238             }
 239             if (flags.test(efTestPositionMasses))
 240             {
 241                 poscompound.checkReal(p.mass(), "Mass");
 242             }
 243             if (flags.test(efTestPositionCharges))
 244             {
 245                 poscompound.checkReal(p.charge(), "Charge");
 246             }
 247         }
 248     }
 249 }
 250
 251
 252 void
 253 SelectionCollectionDataTest::runParser(
 254         const gmx::ConstArrayRef<const char *> &selections)
 255 {
 256     using gmx::test::TestReferenceChecker;
 257
 258     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 259     size_t               varcount = 0;
 260     count_ = 0;
 261     for (size_t i = 0; i < selections.size(); ++i)
 262     {
 263         SCOPED_TRACE(std::string("Parsing selection \"")
 264                      + selections[i] + "\"");
 265         gmx::SelectionList result;
 266         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 267         sel_.insert(sel_.end(), result.begin(), result.end());
 268         if (sel_.size() == count_)
 269         {
 270             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 271             TestReferenceChecker varcompound(
 272                     compound.checkCompound("ParsedVariable", id.c_str()));
 273             varcompound.checkString(selections[i], "Input");
 274             ++varcount;
 275         }
 276         else
 277         {
 278             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 279             TestReferenceChecker selcompound(
 280                     compound.checkCompound("ParsedSelection", id.c_str()));
 281             selcompound.checkString(selections[i], "Input");
 282             if (flags_.test(efTestSelectionNames))
 283             {
 284                 selcompound.checkString(sel_[count_].name(), "Name");
 285             }
 286             selcompound.checkString(sel_[count_].selectionText(), "Text");
 287             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 288             ++count_;
 289         }
 290     }
 291 }
 292
 293
 294 void
 295 SelectionCollectionDataTest::runCompiler()
 296 {
 297     ASSERT_NO_THROW_GMX(sc_.compile());
 298     ASSERT_EQ(count_, sel_.size());
 299     checkCompiled();
 300 }
 301
 302
 303 void
 304 SelectionCollectionDataTest::checkCompiled()
 305 {
 306     using gmx::test::TestReferenceChecker;
 307     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 308
 309     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 310     for (size_t i = 0; i < count_; ++i)
 311     {
 312         SCOPED_TRACE(std::string("Checking selection \"") +
 313                      sel_[i].selectionText() + "\"");
 314         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 315         TestReferenceChecker selcompound(
 316                 compound.checkCompound("Selection", id.c_str()));
 317         if (flags_.test(efTestSelectionNames))
 318         {
 319             selcompound.checkString(sel_[i].name(), "Name");
 320         }
 321         if (!flags_.test(efDontTestCompiledAtoms))
 322         {
 323             checkSelection(&selcompound, sel_[i], flags_ & mask);
 324         }
 325     }
 326 }
 327
 328
 329 void
 330 SelectionCollectionDataTest::runEvaluate()
 331 {
 332     using gmx::test::TestReferenceChecker;
 333
 334     ++framenr_;
 335     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 336     std::string          frame = gmx::formatString("Frame%d", framenr_);
 337     TestReferenceChecker compound(
 338             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 339     for (size_t i = 0; i < count_; ++i)
 340     {
 341         SCOPED_TRACE(std::string("Checking selection \"") +
 342                      sel_[i].selectionText() + "\"");
 343         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 344         TestReferenceChecker selcompound(
 345                 compound.checkCompound("Selection", id.c_str()));
 346         checkSelection(&selcompound, sel_[i], flags_);
 347     }
 348 }
 349
 350
 351 void
 352 SelectionCollectionDataTest::runEvaluateFinal()
 353 {
 354     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 355     checkCompiled();
 356 }
 357
 358
 359 void
 360 SelectionCollectionDataTest::runTest(
 361         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 362 {
 363     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 364     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 365     ASSERT_NO_FATAL_FAILURE(runCompiler());
 366 }
 367
 368
 369 void
 370 SelectionCollectionDataTest::runTest(
 371         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 372 {
 373     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 374     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 375     ASSERT_NO_FATAL_FAILURE(runCompiler());
 376     if (flags_.test(efTestEvaluation))
 377     {
 378         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 379         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 380     }
 381 }
 382
 383
 384 /********************************************************************
 385  * Tests for SelectionCollection functionality without reference data
 386  */
 387
 388 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 389 {
 390     EXPECT_FALSE(sc_.requiresTopology());
 391     EXPECT_NO_THROW_GMX(sc_.compile());
 392 }
 393
 394 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 395 {
 396     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 397     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 398     ASSERT_EQ(2U, sel_.size());
 399     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 400     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 401     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 402     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 403     ASSERT_NO_THROW_GMX(sc_.compile());
 404     EXPECT_TRUE(sel_[0].hasVelocities());
 405     EXPECT_TRUE(sel_[1].hasVelocities());
 406     EXPECT_TRUE(sel_[0].hasForces());
 407     EXPECT_TRUE(sel_[1].hasForces());
 408 }
 409
 410 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 411 {
 412     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 413                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 414     // These should match the contents of selfile.dat
 415     ASSERT_EQ(2U, sel_.size());
 416     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 417     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 418 }
 419
 420 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 421 {
 422     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 423     EXPECT_THROW_GMX({
 424                          sc_.parseFromString("resname ~ \"R[A\"");
 425                          sc_.compile();
 426                      }, gmx::InvalidInputError);
 427 }
 428
 429 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 430 {
 431     if (!gmx::Regex::isSupported())
 432     {
 433         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 434         EXPECT_THROW_GMX({
 435                              sc_.parseFromString("resname \"R[AD]\"");
 436                              sc_.compile();
 437                          }, gmx::InvalidInputError);
 438     }
 439 }
 440
 441 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 442 {
 443     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 444                      gmx::InvalidInputError);
 445 }
 446
 447 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 448 {
 449     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 450                      gmx::InvalidInputError);
 451 }
 452
 453 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 454 {
 455     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 456                      gmx::InvalidInputError);
 457 }
 458
 459 // TODO: Tests for more parser errors
 460
 461 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 462 {
 463     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 464     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 465     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 466 }
 467
 468 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 469 {
 470     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 471     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 472     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 473 }
 474
 475 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 476 {
 477     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 478     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 479     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 480     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 481 }
 482
 483 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 484 {
 485     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 486     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 487     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 488     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 489 }
 490
 491 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 492 {
 493     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 494     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
 495                      gmx::InconsistentInputError);
 496     EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
 497 }
 498
 499 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 500 {
 501     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
 502     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 503     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 504 }
 505
 506 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 507 {
 508     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 509     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 510     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 511 }
 512
 513 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 514 {
 515     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 516     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 517     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 518 }
 519
 520 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 521 {
 522     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 523     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 524     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 525 }
 526
 527 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 528 {
 529     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 530     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 531     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 532 }
 533
 534 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 535 {
 536     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 537     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 538     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 539 }
 540
 541 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 542 {
 543     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 544     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 545     ASSERT_NO_THROW_GMX(sc_.compile());
 546     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 547 }
 548
 549 // TODO: Tests for evaluation errors
 550
 551
 552 /********************************************************************
 553  * Tests for selection keywords
 554  */
 555
 556 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 557 {
 558     static const char * const selections[] = {
 559         "all",
 560         "none"
 561     };
 562     runTest(10, selections);
 563 }
 564
 565 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 566 {
 567     static const char * const selections[] = {
 568         "atomnr 1 to 3 6 to 8",
 569         "atomnr 4 2 5 to 7",
 570         "atomnr <= 5"
 571     };
 572     runTest(10, selections);
 573 }
 574
 575 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 576 {
 577     static const char * const selections[] = {
 578         "resnr 1 2 5",
 579         "resid 4 to 3"
 580     };
 581     runTest("simple.gro", selections);
 582 }
 583
 584 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 585 {
 586     static const char * const selections[] = {
 587         "resindex 1 4",
 588         "residue 1 3"
 589     };
 590     runTest("simple.pdb", selections);
 591 }
 592
 593 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 594 {
 595     static const char * const selections[] = {
 596         "molindex 1 4",
 597         "molecule 2 3 5"
 598     };
 599     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 600     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 601     topManager_.initUniformMolecules(3);
 602     ASSERT_NO_FATAL_FAILURE(runCompiler());
 603 }
 604
 605 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 606 {
 607     static const char * const selections[] = {
 608         "name CB",
 609         "atomname S1 S2"
 610     };
 611     runTest("simple.gro", selections);
 612 }
 613
 614 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 615 {
 616     static const char * const selections[] = {
 617         "name HG21",
 618         "name 1HG2",
 619         "pdbname HG21 CB",
 620         "pdbatomname 1HG2"
 621     };
 622     runTest("simple.pdb", selections);
 623 }
 624
 625
 626 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 627 {
 628     static const char * const selections[] = {
 629         "atomtype CA"
 630     };
 631     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 632     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 633     const char *const types[] = { "CA", "SA", "SB" };
 634     topManager_.initAtomTypes(types);
 635     ASSERT_NO_FATAL_FAILURE(runCompiler());
 636 }
 637
 638 TEST_F(SelectionCollectionDataTest, HandlesChain)
 639 {
 640     static const char * const selections[] = {
 641         "chain A",
 642         "chain B"
 643     };
 644     runTest("simple.pdb", selections);
 645 }
 646
 647 TEST_F(SelectionCollectionDataTest, HandlesMass)
 648 {
 649     static const char * const selections[] = {
 650         "mass > 5"
 651     };
 652     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 653     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 654     for (int i = 0; i < top_->atoms.nr; ++i)
 655     {
 656         top_->atoms.atom[i].m = 1.0 + i;
 657     }
 658     ASSERT_NO_FATAL_FAILURE(runCompiler());
 659 }
 660
 661 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 662 {
 663     static const char * const selections[] = {
 664         "charge < 0.5"
 665     };
 666     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 667     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 668     for (int i = 0; i < top_->atoms.nr; ++i)
 669     {
 670         top_->atoms.atom[i].q = i / 10.0;
 671     }
 672     ASSERT_NO_FATAL_FAILURE(runCompiler());
 673 }
 674
 675 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 676 {
 677     static const char * const selections[] = {
 678         "altloc \" \"",
 679         "altloc A"
 680     };
 681     runTest("simple.pdb", selections);
 682 }
 683
 684 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 685 {
 686     static const char * const selections[] = {
 687         "insertcode \" \"",
 688         "insertcode A"
 689     };
 690     runTest("simple.pdb", selections);
 691 }
 692
 693 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 694 {
 695     static const char * const selections[] = {
 696         "occupancy 1",
 697         "occupancy < .5"
 698     };
 699     runTest("simple.pdb", selections);
 700 }
 701
 702 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 703 {
 704     static const char * const selections[] = {
 705         "beta 0",
 706         "beta >= 0.3"
 707     };
 708     runTest("simple.pdb", selections);
 709 }
 710
 711 TEST_F(SelectionCollectionDataTest, HandlesResname)
 712 {
 713     static const char * const selections[] = {
 714         "resname RA",
 715         "resname RB RC"
 716     };
 717     runTest("simple.gro", selections);
 718 }
 719
 720 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 721 {
 722     static const char * const selections[] = {
 723         "x < 3",
 724         "y >= 3",
 725         "x {-1 to 2}"
 726     };
 727     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 728     runTest("simple.gro", selections);
 729 }
 730
 731
 732 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 733 {
 734     static const char * const selections[] = {
 735         "same residue as atomnr 1 4 12"
 736     };
 737     runTest("simple.gro", selections);
 738 }
 739
 740
 741 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 742 {
 743     static const char * const selections[] = {
 744         "same resname as atomnr 1 14"
 745     };
 746     runTest("simple.gro", selections);
 747 }
 748
 749
 750 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 751 {
 752     static const char * const selections[] = {
 753         "cog of resnr 1 3",
 754         "res_cog of name CB and resnr 1 3",
 755         "whole_res_cog of name CB and resnr 1 3",
 756         "part_res_cog of x < 3",
 757         "dyn_res_cog of x < 3"
 758     };
 759     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 760              | efTestPositionAtoms);
 761     runTest("simple.gro", selections);
 762 }
 763
 764
 765 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 766 {
 767     static const char * const selections[] = {
 768         "distance from cog of resnr 1 < 2"
 769     };
 770     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 771     runTest("simple.gro", selections);
 772 }
 773
 774
 775 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 776 {
 777     static const char * const selections[] = {
 778         "mindistance from resnr 1 < 2"
 779     };
 780     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 781     runTest("simple.gro", selections);
 782 }
 783
 784
 785 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 786 {
 787     static const char * const selections[] = {
 788         "within 1 of resnr 2"
 789     };
 790     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 791     runTest("simple.gro", selections);
 792 }
 793
 794
 795 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 796 {
 797     // Both of these should evaluate to empty on a correct implementation.
 798     static const char * const selections[] = {
 799         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 800         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 801     };
 802     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 803     runTest("sphere.gro", selections);
 804 }
 805
 806
 807 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 808 {
 809     static const char * const selections[] = {
 810         "all permute 3 1 2",
 811         "res_cog of resnr 1 to 4 permute 2 1",
 812         "name CB S1 and res_cog x < 3 permute 2 1"
 813     };
 814     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 815              | efTestPositionAtoms | efTestPositionMapping);
 816     runTest("simple.gro", selections);
 817 }
 818
 819
 820 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 821 {
 822     static const char * const selections[] = {
 823         "name S2 plus name S1",
 824         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 825         "name S1 and y < 3 plus res_cog of x < 2.5"
 826     };
 827     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 828              | efTestPositionAtoms | efTestPositionMapping);
 829     runTest("simple.gro", selections);
 830 }
 831
 832
 833 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 834 {
 835     static const char * const selections[] = {
 836         "name S2 merge name S1",
 837         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 838         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 839     };
 840     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 841              | efTestPositionAtoms | efTestPositionMapping);
 842     runTest("simple.gro", selections);
 843 }
 844
 845
 846 /********************************************************************
 847  * Tests for generic selection evaluation
 848  */
 849
 850 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 851 {
 852     static const char * const selections[] = {
 853         "name CB",
 854         "y > 2",
 855         "res_cog of y > 2"
 856     };
 857     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 858              | efTestPositionMasses | efTestPositionCharges);
 859     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 860     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 861     for (int i = 0; i < top_->atoms.nr; ++i)
 862     {
 863         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 864         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 865     }
 866     ASSERT_NO_FATAL_FAILURE(runCompiler());
 867     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 868     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 869 }
 870
 871 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 872 {
 873     static const char * const selections[] = {
 874         "atomnr 1 to 3 8 to 9",
 875         "y > 2",
 876         "cog of (y > 2)"
 877     };
 878     setFlags(TestFlags() | efTestPositionAtoms
 879              | efTestPositionMasses | efTestPositionCharges);
 880     runTest(10, selections);
 881 }
 882
 883
 884 /********************************************************************
 885  * Tests for selection syntactic constructs
 886  */
 887
 888 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 889 {
 890     static const char * const selections[] = {
 891         "\"GroupSelection\" group \"GrpA\"",
 892         "\"DynamicSelection\" x < 5",
 893         "y < 3"
 894     };
 895     setFlags(TestFlags() | efTestSelectionNames);
 896     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 897     runTest(10, selections);
 898 }
 899
 900 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 901 {
 902     static const char * const selections[] = {
 903         "group \"GrpA\"",
 904         "GrpB",
 905         "1",
 906         "group \"GrpB\" and resname RB"
 907     };
 908     setFlags(TestFlags() | efTestSelectionNames);
 909     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 910     runTest("simple.gro", selections);
 911 }
 912
 913 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 914 {
 915     static const char * const selections[] = {
 916         "group \"GrpA\"",
 917         "GrpB",
 918         "1",
 919         "group \"GrpB\" and resname RB"
 920     };
 921     setFlags(TestFlags() | efTestSelectionNames);
 922     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 923     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 924     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 925     ASSERT_NO_FATAL_FAILURE(runCompiler());
 926 }
 927
 928 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 929 {
 930     static const char * const selections[] = {
 931         "[1, -2, 3.5]"
 932     };
 933     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 934     runTest("simple.gro", selections);
 935 }
 936
 937
 938 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 939 {
 940     static const char * const selections[] = {
 941         "within 1 of [2, 1, 0]"
 942     };
 943     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 944     runTest("simple.gro", selections);
 945 }
 946
 947
 948 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 949 {
 950     static const char * const selections[] = {
 951         "name = S1 \"C?\"",
 952         "name ? S1 \"C?\""
 953     };
 954     runTest("simple.gro", selections);
 955 }
 956
 957
 958 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 959 {
 960     static const char * const selections[] = {
 961         "name \"S?\"",
 962         "name ? \"S?\""
 963     };
 964     runTest("simple.gro", selections);
 965 }
 966
 967
 968 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 969 {
 970     static const char * const selections[] = {
 971         "resname \"R[BD]\"",
 972         "resname ~ \"R[BD]\""
 973     };
 974     if (gmx::Regex::isSupported())
 975     {
 976         runTest("simple.gro", selections);
 977     }
 978 }
 979
 980
 981 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 982 {
 983     static const char * const selections[] = {
 984         "atomnr 1 to 5 and atomnr 2 to 7",
 985         "atomnr 1 to 5 or not atomnr 3 to 8",
 986         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 987         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 988         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 989     };
 990     runTest(10, selections);
 991 }
 992
 993
 994 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
 995 {
 996     static const char * const selections[] = {
 997         "same residue as (atomnr 3 5 13 or y > 5)",
 998         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
 999     };
1000     setFlags(TestFlags() | efTestEvaluation);
1001     runTest("simple.gro", selections);
1002 }
1003
1004
1005 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1006 {
1007     static const char * const selections[] = {
1008         "none and x > 2",
1009         "none and same resname as resnr 2"
1010     };
1011     runTest("simple.gro", selections);
1012 }
1013
1014
1015 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1016 {
1017     static const char * const selections[] = {
1018         "x > 2",
1019         "2 < x",
1020         "y > resnr",
1021         "resnr < 2.5",
1022         "2.5 > resnr"
1023     };
1024     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1025     runTest("simple.gro", selections);
1026 }
1027
1028
1029 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1030 {
1031     static const char * const selections[] = {
1032         "x+1 > 3",
1033         "(y-1)^2 <= 1",
1034         "x+--1 > 3",
1035         "-x+-1 < -3"
1036     };
1037     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1038     runTest("simple.gro", selections);
1039 }
1040
1041
1042 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1043 {
1044     static const char * const selections[] = {
1045         "value = x + y",
1046         "value <= 4",
1047         "index = resnr",
1048         "index < 3"
1049     };
1050     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1051     runTest("simple.gro", selections);
1052 }
1053
1054
1055 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1056 {
1057     static const char * const selections[] = {
1058         "value = x + y",
1059         "resname RA and value <= 4",
1060         "resname RA RB and x < 3 and value <= 4",
1061         "index = atomnr",
1062         "resname RA and index < 3",
1063         "resname RB and y < 3 and index < 6"
1064     };
1065     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1066     runTest("simple.gro", selections);
1067 }
1068
1069
1070 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1071 {
1072     static const char * const selections[] = {
1073         "foo = res_cog of resname RA",
1074         "foo",
1075         "within 1 of foo",
1076         "bar = cog of resname RA",
1077         "bar",
1078         "within 1 of bar"
1079     };
1080     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1081     runTest("simple.gro", selections);
1082 }
1083
1084
1085 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1086 {
1087     static const char * const selections[] = {
1088         "constpos = [1.0, 2.5, 0.5]",
1089         "constpos",
1090         "within 2 of constpos"
1091     };
1092     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1093              | efTestPositionAtoms);
1094     runTest("simple.gro", selections);
1095 }
1096
1097
1098 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1099 {
1100     static const char * const selections[] = {
1101         "constint = 4",
1102         "constreal1 = 0.5",
1103         "constreal2 = 2.7",
1104         "resnr < constint",
1105         "x + constreal1 < constreal2"
1106     };
1107     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1108     runTest("simple.gro", selections);
1109 }
1110
1111
1112 /********************************************************************
1113  * Tests for complex boolean syntax
1114  */
1115
1116 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1117 {
1118     static const char * const selections[] = {
1119         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1120         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1121         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1122         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1123         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1124     };
1125     runTest(10, selections);
1126 }
1127
1128
1129 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1130 {
1131     static const char * const selections[] = {
1132         "foo = atomnr 4 to 7 or x < 2",
1133         "atomnr 1 to 4 and foo",
1134         "atomnr 2 to 6 and y < 3 and foo",
1135         "atomnr 6 to 10 and not foo"
1136     };
1137     runTest(10, selections);
1138 }
1139
1140
1141 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1142 {
1143     static const char * const selections[] = {
1144         "foo = atomnr 4 to 7",
1145         "bar = foo and x < 2",
1146         "bar2 = foo and y < 2",
1147         "atomnr 1 to 4 and bar",
1148         "atomnr 2 to 6 and y < 3 and bar2",
1149         "atomnr 6 to 10 and not foo"
1150     };
1151     runTest(10, selections);
1152 }
1153
1154
1155 /********************************************************************
1156  * Tests for complex subexpression cases
1157  *
1158  * These tests use some knowledge of the implementation to trigger different
1159  * paths in the code.
1160  */
1161
1162 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1163 {
1164     static const char * const selections[] = {
1165         "unused1 = atomnr 1 to 3",
1166         "foo = atomnr 4 to 7",
1167         "atomnr 1 to 6 and foo",
1168         "unused2 = atomnr 3 to 5"
1169     };
1170     runTest(10, selections);
1171 }
1172
1173
1174 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1175 {
1176     static const char * const selections[] = {
1177         "foo = atomnr 4 to 7 and x < 2",
1178         "atomnr 1 to 5 and foo",
1179         "atomnr 3 to 7 and foo"
1180     };
1181     runTest(10, selections);
1182 }
1183
1184
1185 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1186 {
1187     static const char * const selections[] = {
1188         "foo = atomnr 4 to 7 and x < 2",
1189         "atomnr 1 to 6 and foo",
1190         "within 1 of foo",
1191         "foo"
1192     };
1193     runTest(10, selections);
1194 }
1195
1196
1197 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1198 {
1199     static const char * const selections[] = {
1200         "foo = atomnr 1 to 8 and x < 10",
1201         "atomnr 1 to 5 and y < 10 and foo",
1202         "foo"
1203     };
1204     setFlags(TestFlags() | efTestEvaluation);
1205     runTest("simple.gro", selections);
1206 }
1207
1208
1209 } // namespace