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/utility/exceptions.h"
  50 #include "gromacs/utility/flags.h"
  51 #include "gromacs/utility/gmxregex.h"
  52 #include "gromacs/utility/stringutil.h"
  53
  54 #include "testutils/refdata.h"
  55 #include "testutils/testasserts.h"
  56 #include "testutils/testfilemanager.h"
  57 #include "testutils/testoptions.h"
  58
  59 #include "toputils.h"
  60
  61 namespace
  62 {
  63
  64 /********************************************************************
  65  * Test fixture for selection testing
  66  */
  67
  68 class SelectionCollectionTest : public ::testing::Test
  69 {
  70     public:
  71         static int               s_debugLevel;
  72
  73         SelectionCollectionTest();
  74         ~SelectionCollectionTest();
  75
  76         void setAtomCount(int natoms)
  77         {
  78             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  79         }
  80         void loadTopology(const char *filename);
  81         void setTopology();
  82         void loadIndexGroups(const char *filename);
  83
  84         gmx::test::TopologyManager  topManager_;
  85         gmx::SelectionCollection    sc_;
  86         gmx::SelectionList          sel_;
  87         t_topology                 *top_;
  88         t_trxframe                 *frame_;
  89         gmx_ana_indexgrps_t        *grps_;
  90 };
  91
  92 int SelectionCollectionTest::s_debugLevel = 0;
  93
  94 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  95 {
  96     options->addOption(gmx::IntegerOption("seldebug")
  97                            .store(&SelectionCollectionTest::s_debugLevel)
  98                            .description("Set selection debug level"));
  99 }
 100
 101 SelectionCollectionTest::SelectionCollectionTest()
 102     : top_(NULL), frame_(NULL), grps_(NULL)
 103 {
 104     topManager_.requestFrame();
 105     sc_.setDebugLevel(s_debugLevel);
 106     sc_.setReferencePosType("atom");
 107     sc_.setOutputPosType("atom");
 108 }
 109
 110 SelectionCollectionTest::~SelectionCollectionTest()
 111 {
 112     if (grps_ != NULL)
 113     {
 114         gmx_ana_indexgrps_free(grps_);
 115     }
 116 }
 117
 118 void
 119 SelectionCollectionTest::loadTopology(const char *filename)
 120 {
 121     topManager_.loadTopology(filename);
 122     setTopology();
 123 }
 124
 125 void
 126 SelectionCollectionTest::setTopology()
 127 {
 128     top_   = topManager_.topology();
 129     frame_ = topManager_.frame();
 130
 131     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 132 }
 133
 134 void
 135 SelectionCollectionTest::loadIndexGroups(const char *filename)
 136 {
 137     GMX_RELEASE_ASSERT(grps_ == NULL,
 138                        "External groups can only be loaded once");
 139     std::string fullpath =
 140         gmx::test::TestFileManager::getInputFilePath(filename);
 141     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 142     sc_.setIndexGroups(grps_);
 143 }
 144
 145
 146 /********************************************************************
 147  * Test fixture for selection testing with reference data
 148  */
 149
 150 class SelectionCollectionDataTest : public SelectionCollectionTest
 151 {
 152     public:
 153         enum TestFlag
 154         {
 155             efTestEvaluation            = 1<<0,
 156             efTestPositionAtoms         = 1<<1,
 157             efTestPositionCoordinates   = 1<<2,
 158             efTestPositionMapping       = 1<<3,
 159             efTestPositionMasses        = 1<<4,
 160             efTestPositionCharges       = 1<<5,
 161             efTestSelectionNames        = 1<<6,
 162             efDontTestCompiledAtoms     = 1<<8
 163         };
 164         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 165
 166         SelectionCollectionDataTest()
 167             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 168         {
 169         }
 170
 171         void setFlags(TestFlags flags) { flags_ = flags; }
 172
 173         template <size_t count>
 174         void runTest(int natoms, const char *const (&selections)[count])
 175         {
 176             runTest(natoms, selections, count);
 177         }
 178         template <size_t count>
 179         void runTest(const char *filename, const char *const (&selections)[count])
 180         {
 181             runTest(filename, selections, count);
 182         }
 183
 184         template <size_t count>
 185         void runParser(const char *const (&selections)[count])
 186         {
 187             runParser(selections, count);
 188         }
 189
 190         void runCompiler();
 191         void runEvaluate();
 192         void runEvaluateFinal();
 193
 194     private:
 195         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 196                                    const gmx::Selection &sel, TestFlags flags);
 197
 198         void runTest(int natoms, const char *const *selections, size_t count);
 199         void runTest(const char *filename, const char *const *selections,
 200                      size_t count);
 201         void runParser(const char *const *selections, size_t count);
 202
 203         void checkCompiled();
 204
 205         gmx::test::TestReferenceData    data_;
 206         gmx::test::TestReferenceChecker checker_;
 207         size_t                          count_;
 208         int                             framenr_;
 209         TestFlags                       flags_;
 210 };
 211
 212
 213 void
 214 SelectionCollectionDataTest::checkSelection(
 215         gmx::test::TestReferenceChecker *checker,
 216         const gmx::Selection &sel, TestFlags flags)
 217 {
 218     using gmx::test::TestReferenceChecker;
 219
 220     {
 221         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 222         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 223     }
 224     if (flags.test(efTestPositionAtoms)
 225         || flags.test(efTestPositionCoordinates)
 226         || flags.test(efTestPositionMapping)
 227         || flags.test(efTestPositionMasses)
 228         || flags.test(efTestPositionCharges))
 229     {
 230         TestReferenceChecker compound(
 231                 checker->checkSequenceCompound("Positions", sel.posCount()));
 232         for (int i = 0; i < sel.posCount(); ++i)
 233         {
 234             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 235             const gmx::SelectionPosition &p = sel.position(i);
 236             if (flags.test(efTestPositionAtoms))
 237             {
 238                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 239                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 240             }
 241             if (flags.test(efTestPositionCoordinates))
 242             {
 243                 poscompound.checkVector(p.x(), "Coordinates");
 244             }
 245             if (flags.test(efTestPositionMapping))
 246             {
 247                 poscompound.checkInteger(p.refId(), "RefId");
 248                 poscompound.checkInteger(p.mappedId(), "MappedId");
 249             }
 250             if (flags.test(efTestPositionMasses))
 251             {
 252                 poscompound.checkReal(p.mass(), "Mass");
 253             }
 254             if (flags.test(efTestPositionCharges))
 255             {
 256                 poscompound.checkReal(p.charge(), "Charge");
 257             }
 258         }
 259     }
 260 }
 261
 262
 263 void
 264 SelectionCollectionDataTest::runParser(const char *const *selections,
 265                                        size_t             count)
 266 {
 267     using gmx::test::TestReferenceChecker;
 268
 269     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 270     size_t               varcount = 0;
 271     count_ = 0;
 272     for (size_t i = 0; i < count; ++i)
 273     {
 274         SCOPED_TRACE(std::string("Parsing selection \"")
 275                      + selections[i] + "\"");
 276         gmx::SelectionList result;
 277         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 278         sel_.insert(sel_.end(), result.begin(), result.end());
 279         if (sel_.size() == count_)
 280         {
 281             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 282             TestReferenceChecker varcompound(
 283                     compound.checkCompound("ParsedVariable", id.c_str()));
 284             varcompound.checkString(selections[i], "Input");
 285             ++varcount;
 286         }
 287         else
 288         {
 289             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 290             TestReferenceChecker selcompound(
 291                     compound.checkCompound("ParsedSelection", id.c_str()));
 292             selcompound.checkString(selections[i], "Input");
 293             selcompound.checkString(sel_[count_].name(), "Name");
 294             selcompound.checkString(sel_[count_].selectionText(), "Text");
 295             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 296             ++count_;
 297         }
 298     }
 299 }
 300
 301
 302 void
 303 SelectionCollectionDataTest::runCompiler()
 304 {
 305     ASSERT_NO_THROW_GMX(sc_.compile());
 306     ASSERT_EQ(count_, sel_.size());
 307     checkCompiled();
 308 }
 309
 310
 311 void
 312 SelectionCollectionDataTest::checkCompiled()
 313 {
 314     using gmx::test::TestReferenceChecker;
 315     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 316
 317     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 318     for (size_t i = 0; i < count_; ++i)
 319     {
 320         SCOPED_TRACE(std::string("Checking selection \"") +
 321                      sel_[i].selectionText() + "\"");
 322         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 323         TestReferenceChecker selcompound(
 324                 compound.checkCompound("Selection", id.c_str()));
 325         if (flags_.test(efTestSelectionNames))
 326         {
 327             selcompound.checkString(sel_[i].name(), "Name");
 328         }
 329         if (!flags_.test(efDontTestCompiledAtoms))
 330         {
 331             checkSelection(&selcompound, sel_[i], flags_ & mask);
 332         }
 333     }
 334 }
 335
 336
 337 void
 338 SelectionCollectionDataTest::runEvaluate()
 339 {
 340     using gmx::test::TestReferenceChecker;
 341
 342     ++framenr_;
 343     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 344     std::string          frame = gmx::formatString("Frame%d", framenr_);
 345     TestReferenceChecker compound(
 346             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 347     for (size_t i = 0; i < count_; ++i)
 348     {
 349         SCOPED_TRACE(std::string("Checking selection \"") +
 350                      sel_[i].selectionText() + "\"");
 351         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 352         TestReferenceChecker selcompound(
 353                 compound.checkCompound("Selection", id.c_str()));
 354         checkSelection(&selcompound, sel_[i], flags_);
 355     }
 356 }
 357
 358
 359 void
 360 SelectionCollectionDataTest::runEvaluateFinal()
 361 {
 362     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 363     checkCompiled();
 364 }
 365
 366
 367 void
 368 SelectionCollectionDataTest::runTest(int natoms, const char * const *selections,
 369                                      size_t count)
 370 {
 371     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 372     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 373     ASSERT_NO_FATAL_FAILURE(runCompiler());
 374 }
 375
 376
 377 void
 378 SelectionCollectionDataTest::runTest(const char         *filename,
 379                                      const char * const *selections,
 380                                      size_t              count)
 381 {
 382     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 383     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 384     ASSERT_NO_FATAL_FAILURE(runCompiler());
 385     if (flags_.test(efTestEvaluation))
 386     {
 387         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 388         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 389     }
 390 }
 391
 392
 393 /********************************************************************
 394  * Tests for SelectionCollection functionality without reference data
 395  */
 396
 397 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 398 {
 399     EXPECT_FALSE(sc_.requiresTopology());
 400     EXPECT_NO_THROW_GMX(sc_.compile());
 401 }
 402
 403 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 404 {
 405     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 406     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 407     ASSERT_EQ(2U, sel_.size());
 408     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 409     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 410     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 411     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 412     ASSERT_NO_THROW_GMX(sc_.compile());
 413     EXPECT_TRUE(sel_[0].hasVelocities());
 414     EXPECT_TRUE(sel_[1].hasVelocities());
 415     EXPECT_TRUE(sel_[0].hasForces());
 416     EXPECT_TRUE(sel_[1].hasForces());
 417 }
 418
 419 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 420 {
 421     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 422                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 423     // These should match the contents of selfile.dat
 424     ASSERT_EQ(2U, sel_.size());
 425     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 426     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 427 }
 428
 429 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 430 {
 431     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 432     EXPECT_THROW_GMX({
 433                          sc_.parseFromString("resname ~ \"R[A\"");
 434                          sc_.compile();
 435                      }, gmx::InvalidInputError);
 436 }
 437
 438 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 439 {
 440     if (!gmx::Regex::isSupported())
 441     {
 442         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 443         EXPECT_THROW_GMX({
 444                              sc_.parseFromString("resname \"R[AD]\"");
 445                              sc_.compile();
 446                          }, gmx::InvalidInputError);
 447     }
 448 }
 449
 450 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 451 {
 452     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 453                      gmx::InvalidInputError);
 454 }
 455
 456 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 457 {
 458     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 459                      gmx::InvalidInputError);
 460 }
 461
 462 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 463 {
 464     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 465                      gmx::InvalidInputError);
 466 }
 467
 468 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 469 {
 470     EXPECT_THROW_GMX(sc_.parseFromString("resname help"),
 471                      gmx::InvalidInputError);
 472 }
 473
 474 // TODO: Tests for more parser errors
 475
 476 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 477 {
 478     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 479     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InvalidInputError);
 480     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InvalidInputError);
 481 }
 482
 483 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 484 {
 485     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 486     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InvalidInputError);
 487     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InvalidInputError);
 488 }
 489
 490 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 491 {
 492     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 493     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 494     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
 495     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 496 }
 497
 498 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 499 {
 500     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 501     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 502     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InvalidInputError);
 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, HandlesNumericComparisons)
1006 {
1007     static const char * const selections[] = {
1008         "x > 2",
1009         "2 < x",
1010         "y > resnr",
1011         "resnr < 2.5",
1012         "2.5 > resnr"
1013     };
1014     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1015     runTest("simple.gro", selections);
1016 }
1017
1018
1019 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1020 {
1021     static const char * const selections[] = {
1022         "x+1 > 3",
1023         "(y-1)^2 <= 1",
1024         "x+--1 > 3",
1025         "-x+-1 < -3"
1026     };
1027     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1028     runTest("simple.gro", selections);
1029 }
1030
1031
1032 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1033 {
1034     static const char * const selections[] = {
1035         "value = x + y",
1036         "value <= 4",
1037         "index = resnr",
1038         "index < 3"
1039     };
1040     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1041     runTest("simple.gro", selections);
1042 }
1043
1044
1045 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1046 {
1047     static const char * const selections[] = {
1048         "value = x + y",
1049         "resname RA and value <= 4",
1050         "resname RA RB and x < 3 and value <= 4",
1051         "index = atomnr",
1052         "resname RA and index < 3",
1053         "resname RB and y < 3 and index < 6"
1054     };
1055     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1056     runTest("simple.gro", selections);
1057 }
1058
1059
1060 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1061 {
1062     static const char * const selections[] = {
1063         "foo = res_cog of resname RA",
1064         "foo",
1065         "within 1 of foo",
1066         "bar = cog of resname RA",
1067         "bar",
1068         "within 1 of bar"
1069     };
1070     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1071     runTest("simple.gro", selections);
1072 }
1073
1074
1075 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1076 {
1077     static const char * const selections[] = {
1078         "constpos = [1.0, 2.5, 0.5]",
1079         "constpos",
1080         "within 2 of constpos"
1081     };
1082     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1083              | efTestPositionAtoms);
1084     runTest("simple.gro", selections);
1085 }
1086
1087
1088 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1089 {
1090     static const char * const selections[] = {
1091         "constint = 4",
1092         "constreal1 = 0.5",
1093         "constreal2 = 2.7",
1094         "resnr < constint",
1095         "x + constreal1 < constreal2"
1096     };
1097     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1098     runTest("simple.gro", selections);
1099 }
1100
1101
1102 /********************************************************************
1103  * Tests for complex boolean syntax
1104  */
1105
1106 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1107 {
1108     static const char * const selections[] = {
1109         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1110         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1111         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1112         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1113         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1114     };
1115     runTest(10, selections);
1116 }
1117
1118
1119 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1120 {
1121     static const char * const selections[] = {
1122         "foo = atomnr 4 to 7 or x < 2",
1123         "atomnr 1 to 4 and foo",
1124         "atomnr 2 to 6 and y < 3 and foo",
1125         "atomnr 6 to 10 and not foo"
1126     };
1127     runTest(10, selections);
1128 }
1129
1130
1131 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1132 {
1133     static const char * const selections[] = {
1134         "foo = atomnr 4 to 7",
1135         "bar = foo and x < 2",
1136         "bar2 = foo and y < 2",
1137         "atomnr 1 to 4 and bar",
1138         "atomnr 2 to 6 and y < 3 and bar2",
1139         "atomnr 6 to 10 and not foo"
1140     };
1141     runTest(10, selections);
1142 }
1143
1144
1145 /********************************************************************
1146  * Tests for complex subexpression cases
1147  *
1148  * These tests use some knowledge of the implementation to trigger different
1149  * paths in the code.
1150  */
1151
1152 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1153 {
1154     static const char * const selections[] = {
1155         "unused1 = atomnr 1 to 3",
1156         "foo = atomnr 4 to 7",
1157         "atomnr 1 to 6 and foo",
1158         "unused2 = atomnr 3 to 5"
1159     };
1160     runTest(10, selections);
1161 }
1162
1163
1164 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1165 {
1166     static const char * const selections[] = {
1167         "foo = atomnr 4 to 7 and x < 2",
1168         "atomnr 1 to 5 and foo",
1169         "atomnr 3 to 7 and foo"
1170     };
1171     runTest(10, selections);
1172 }
1173
1174
1175 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1176 {
1177     static const char * const selections[] = {
1178         "foo = atomnr 4 to 7 and x < 2",
1179         "atomnr 1 to 6 and foo",
1180         "within 1 of foo",
1181         "foo"
1182     };
1183     runTest(10, selections);
1184 }
1185
1186
1187 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1188 {
1189     static const char * const selections[] = {
1190         "foo = atomnr 1 to 8 and x < 10",
1191         "atomnr 1 to 5 and y < 10 and foo",
1192         "foo"
1193     };
1194     setFlags(TestFlags() | efTestEvaluation);
1195     runTest("simple.gro", selections);
1196 }
1197
1198
1199 } // namespace