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::InconsistentInputError);
 480     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 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::InconsistentInputError);
 487     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 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::InconsistentInputError);
 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::InconsistentInputError);
 503     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 504 }
 505
 506 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 507 {
 508     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 509     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
 510                      gmx::InconsistentInputError);
 511     EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
 512 }
 513
 514 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 515 {
 516     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
 517     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 518     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 519 }
 520
 521 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 522 {
 523     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 524     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 525     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 526 }
 527
 528 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 529 {
 530     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 531     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 532     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 533 }
 534
 535 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 536 {
 537     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 538     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 539     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 540 }
 541
 542 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 543 {
 544     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 545     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 546     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 547 }
 548
 549 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 550 {
 551     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 552     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 553     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 554 }
 555
 556 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 557 {
 558     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 559     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 560     ASSERT_NO_THROW_GMX(sc_.compile());
 561     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 562 }
 563
 564 // TODO: Tests for evaluation errors
 565
 566
 567 /********************************************************************
 568  * Tests for selection keywords
 569  */
 570
 571 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 572 {
 573     static const char * const selections[] = {
 574         "all",
 575         "none"
 576     };
 577     runTest(10, selections);
 578 }
 579
 580 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 581 {
 582     static const char * const selections[] = {
 583         "atomnr 1 to 3 6 to 8",
 584         "atomnr 4 2 5 to 7",
 585         "atomnr <= 5"
 586     };
 587     runTest(10, selections);
 588 }
 589
 590 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 591 {
 592     static const char * const selections[] = {
 593         "resnr 1 2 5",
 594         "resid 4 to 3"
 595     };
 596     runTest("simple.gro", selections);
 597 }
 598
 599 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 600 {
 601     static const char * const selections[] = {
 602         "resindex 1 4",
 603         "residue 1 3"
 604     };
 605     runTest("simple.pdb", selections);
 606 }
 607
 608 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 609 {
 610     static const char * const selections[] = {
 611         "molindex 1 4",
 612         "molecule 2 3 5"
 613     };
 614     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 615     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 616     topManager_.initUniformMolecules(3);
 617     ASSERT_NO_FATAL_FAILURE(runCompiler());
 618 }
 619
 620 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 621 {
 622     static const char * const selections[] = {
 623         "name CB",
 624         "atomname S1 S2"
 625     };
 626     runTest("simple.gro", selections);
 627 }
 628
 629 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 630 {
 631     static const char * const selections[] = {
 632         "name HG21",
 633         "name 1HG2",
 634         "pdbname HG21 CB",
 635         "pdbatomname 1HG2"
 636     };
 637     runTest("simple.pdb", selections);
 638 }
 639
 640
 641 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 642 {
 643     static const char * const selections[] = {
 644         "atomtype CA"
 645     };
 646     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 647     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 648     const char *const types[] = { "CA", "SA", "SB" };
 649     topManager_.initAtomTypes(types);
 650     ASSERT_NO_FATAL_FAILURE(runCompiler());
 651 }
 652
 653 TEST_F(SelectionCollectionDataTest, HandlesChain)
 654 {
 655     static const char * const selections[] = {
 656         "chain A",
 657         "chain B"
 658     };
 659     runTest("simple.pdb", selections);
 660 }
 661
 662 TEST_F(SelectionCollectionDataTest, HandlesMass)
 663 {
 664     static const char * const selections[] = {
 665         "mass > 5"
 666     };
 667     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 668     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 669     for (int i = 0; i < top_->atoms.nr; ++i)
 670     {
 671         top_->atoms.atom[i].m = 1.0 + i;
 672     }
 673     ASSERT_NO_FATAL_FAILURE(runCompiler());
 674 }
 675
 676 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 677 {
 678     static const char * const selections[] = {
 679         "charge < 0.5"
 680     };
 681     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 682     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 683     for (int i = 0; i < top_->atoms.nr; ++i)
 684     {
 685         top_->atoms.atom[i].q = i / 10.0;
 686     }
 687     ASSERT_NO_FATAL_FAILURE(runCompiler());
 688 }
 689
 690 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 691 {
 692     static const char * const selections[] = {
 693         "altloc \" \"",
 694         "altloc A"
 695     };
 696     runTest("simple.pdb", selections);
 697 }
 698
 699 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 700 {
 701     static const char * const selections[] = {
 702         "insertcode \" \"",
 703         "insertcode A"
 704     };
 705     runTest("simple.pdb", selections);
 706 }
 707
 708 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 709 {
 710     static const char * const selections[] = {
 711         "occupancy 1",
 712         "occupancy < .5"
 713     };
 714     runTest("simple.pdb", selections);
 715 }
 716
 717 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 718 {
 719     static const char * const selections[] = {
 720         "beta 0",
 721         "beta >= 0.3"
 722     };
 723     runTest("simple.pdb", selections);
 724 }
 725
 726 TEST_F(SelectionCollectionDataTest, HandlesResname)
 727 {
 728     static const char * const selections[] = {
 729         "resname RA",
 730         "resname RB RC"
 731     };
 732     runTest("simple.gro", selections);
 733 }
 734
 735 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 736 {
 737     static const char * const selections[] = {
 738         "x < 3",
 739         "y >= 3",
 740         "x {-1 to 2}"
 741     };
 742     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 743     runTest("simple.gro", selections);
 744 }
 745
 746
 747 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 748 {
 749     static const char * const selections[] = {
 750         "same residue as atomnr 1 4 12"
 751     };
 752     runTest("simple.gro", selections);
 753 }
 754
 755
 756 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 757 {
 758     static const char * const selections[] = {
 759         "same resname as atomnr 1 14"
 760     };
 761     runTest("simple.gro", selections);
 762 }
 763
 764
 765 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 766 {
 767     static const char * const selections[] = {
 768         "cog of resnr 1 3",
 769         "res_cog of name CB and resnr 1 3",
 770         "whole_res_cog of name CB and resnr 1 3",
 771         "part_res_cog of x < 3",
 772         "dyn_res_cog of x < 3"
 773     };
 774     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 775              | efTestPositionAtoms);
 776     runTest("simple.gro", selections);
 777 }
 778
 779
 780 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 781 {
 782     static const char * const selections[] = {
 783         "distance from cog of resnr 1 < 2"
 784     };
 785     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 786     runTest("simple.gro", selections);
 787 }
 788
 789
 790 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 791 {
 792     static const char * const selections[] = {
 793         "mindistance from resnr 1 < 2"
 794     };
 795     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 796     runTest("simple.gro", selections);
 797 }
 798
 799
 800 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 801 {
 802     static const char * const selections[] = {
 803         "within 1 of resnr 2"
 804     };
 805     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 806     runTest("simple.gro", selections);
 807 }
 808
 809
 810 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 811 {
 812     // Both of these should evaluate to empty on a correct implementation.
 813     static const char * const selections[] = {
 814         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 815         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 816     };
 817     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 818     runTest("sphere.gro", selections);
 819 }
 820
 821
 822 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 823 {
 824     static const char * const selections[] = {
 825         "all permute 3 1 2",
 826         "res_cog of resnr 1 to 4 permute 2 1",
 827         "name CB S1 and res_cog x < 3 permute 2 1"
 828     };
 829     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 830              | efTestPositionAtoms | efTestPositionMapping);
 831     runTest("simple.gro", selections);
 832 }
 833
 834
 835 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 836 {
 837     static const char * const selections[] = {
 838         "name S2 plus name S1",
 839         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 840         "name S1 and y < 3 plus res_cog of x < 2.5"
 841     };
 842     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 843              | efTestPositionAtoms | efTestPositionMapping);
 844     runTest("simple.gro", selections);
 845 }
 846
 847
 848 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 849 {
 850     static const char * const selections[] = {
 851         "name S2 merge name S1",
 852         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 853         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 854     };
 855     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 856              | efTestPositionAtoms | efTestPositionMapping);
 857     runTest("simple.gro", selections);
 858 }
 859
 860
 861 /********************************************************************
 862  * Tests for generic selection evaluation
 863  */
 864
 865 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 866 {
 867     static const char * const selections[] = {
 868         "name CB",
 869         "y > 2",
 870         "res_cog of y > 2"
 871     };
 872     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 873              | efTestPositionMasses | efTestPositionCharges);
 874     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 875     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 876     for (int i = 0; i < top_->atoms.nr; ++i)
 877     {
 878         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 879         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 880     }
 881     ASSERT_NO_FATAL_FAILURE(runCompiler());
 882     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 883     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 884 }
 885
 886 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 887 {
 888     static const char * const selections[] = {
 889         "atomnr 1 to 3 8 to 9",
 890         "y > 2",
 891         "cog of (y > 2)"
 892     };
 893     setFlags(TestFlags() | efTestPositionAtoms
 894              | efTestPositionMasses | efTestPositionCharges);
 895     runTest(10, selections);
 896 }
 897
 898
 899 /********************************************************************
 900  * Tests for selection syntactic constructs
 901  */
 902
 903 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 904 {
 905     static const char * const selections[] = {
 906         "\"GroupSelection\" group \"GrpA\"",
 907         "\"DynamicSelection\" x < 5",
 908         "y < 3"
 909     };
 910     setFlags(TestFlags() | efTestSelectionNames);
 911     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 912     runTest(10, selections);
 913 }
 914
 915 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 916 {
 917     static const char * const selections[] = {
 918         "group \"GrpA\"",
 919         "GrpB",
 920         "1",
 921         "group \"GrpB\" and resname RB"
 922     };
 923     setFlags(TestFlags() | efTestSelectionNames);
 924     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 925     runTest("simple.gro", selections);
 926 }
 927
 928 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 929 {
 930     static const char * const selections[] = {
 931         "group \"GrpA\"",
 932         "GrpB",
 933         "1",
 934         "group \"GrpB\" and resname RB"
 935     };
 936     setFlags(TestFlags() | efTestSelectionNames);
 937     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 938     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 939     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 940     ASSERT_NO_FATAL_FAILURE(runCompiler());
 941 }
 942
 943 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 944 {
 945     static const char * const selections[] = {
 946         "[1, -2, 3.5]"
 947     };
 948     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 949     runTest("simple.gro", selections);
 950 }
 951
 952
 953 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 954 {
 955     static const char * const selections[] = {
 956         "within 1 of [2, 1, 0]"
 957     };
 958     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 959     runTest("simple.gro", selections);
 960 }
 961
 962
 963 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 964 {
 965     static const char * const selections[] = {
 966         "name = S1 \"C?\"",
 967         "name ? S1 \"C?\""
 968     };
 969     runTest("simple.gro", selections);
 970 }
 971
 972
 973 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 974 {
 975     static const char * const selections[] = {
 976         "name \"S?\"",
 977         "name ? \"S?\""
 978     };
 979     runTest("simple.gro", selections);
 980 }
 981
 982
 983 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 984 {
 985     static const char * const selections[] = {
 986         "resname \"R[BD]\"",
 987         "resname ~ \"R[BD]\""
 988     };
 989     if (gmx::Regex::isSupported())
 990     {
 991         runTest("simple.gro", selections);
 992     }
 993 }
 994
 995
 996 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 997 {
 998     static const char * const selections[] = {
 999         "atomnr 1 to 5 and atomnr 2 to 7",
1000         "atomnr 1 to 5 or not atomnr 3 to 8",
1001         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1002         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1003         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1004     };
1005     runTest(10, selections);
1006 }
1007
1008
1009 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1010 {
1011     static const char * const selections[] = {
1012         "same residue as (atomnr 3 5 13 or y > 5)",
1013         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1014     };
1015     setFlags(TestFlags() | efTestEvaluation);
1016     runTest("simple.gro", selections);
1017 }
1018
1019
1020 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1021 {
1022     static const char * const selections[] = {
1023         "x > 2",
1024         "2 < x",
1025         "y > resnr",
1026         "resnr < 2.5",
1027         "2.5 > resnr"
1028     };
1029     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1030     runTest("simple.gro", selections);
1031 }
1032
1033
1034 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1035 {
1036     static const char * const selections[] = {
1037         "x+1 > 3",
1038         "(y-1)^2 <= 1",
1039         "x+--1 > 3",
1040         "-x+-1 < -3"
1041     };
1042     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1043     runTest("simple.gro", selections);
1044 }
1045
1046
1047 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1048 {
1049     static const char * const selections[] = {
1050         "value = x + y",
1051         "value <= 4",
1052         "index = resnr",
1053         "index < 3"
1054     };
1055     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1056     runTest("simple.gro", selections);
1057 }
1058
1059
1060 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1061 {
1062     static const char * const selections[] = {
1063         "value = x + y",
1064         "resname RA and value <= 4",
1065         "resname RA RB and x < 3 and value <= 4",
1066         "index = atomnr",
1067         "resname RA and index < 3",
1068         "resname RB and y < 3 and index < 6"
1069     };
1070     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1071     runTest("simple.gro", selections);
1072 }
1073
1074
1075 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1076 {
1077     static const char * const selections[] = {
1078         "foo = res_cog of resname RA",
1079         "foo",
1080         "within 1 of foo",
1081         "bar = cog of resname RA",
1082         "bar",
1083         "within 1 of bar"
1084     };
1085     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1086     runTest("simple.gro", selections);
1087 }
1088
1089
1090 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1091 {
1092     static const char * const selections[] = {
1093         "constpos = [1.0, 2.5, 0.5]",
1094         "constpos",
1095         "within 2 of constpos"
1096     };
1097     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1098              | efTestPositionAtoms);
1099     runTest("simple.gro", selections);
1100 }
1101
1102
1103 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1104 {
1105     static const char * const selections[] = {
1106         "constint = 4",
1107         "constreal1 = 0.5",
1108         "constreal2 = 2.7",
1109         "resnr < constint",
1110         "x + constreal1 < constreal2"
1111     };
1112     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1113     runTest("simple.gro", selections);
1114 }
1115
1116
1117 /********************************************************************
1118  * Tests for complex boolean syntax
1119  */
1120
1121 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1122 {
1123     static const char * const selections[] = {
1124         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1125         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1126         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1127         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1128         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1129     };
1130     runTest(10, selections);
1131 }
1132
1133
1134 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1135 {
1136     static const char * const selections[] = {
1137         "foo = atomnr 4 to 7 or x < 2",
1138         "atomnr 1 to 4 and foo",
1139         "atomnr 2 to 6 and y < 3 and foo",
1140         "atomnr 6 to 10 and not foo"
1141     };
1142     runTest(10, selections);
1143 }
1144
1145
1146 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1147 {
1148     static const char * const selections[] = {
1149         "foo = atomnr 4 to 7",
1150         "bar = foo and x < 2",
1151         "bar2 = foo and y < 2",
1152         "atomnr 1 to 4 and bar",
1153         "atomnr 2 to 6 and y < 3 and bar2",
1154         "atomnr 6 to 10 and not foo"
1155     };
1156     runTest(10, selections);
1157 }
1158
1159
1160 /********************************************************************
1161  * Tests for complex subexpression cases
1162  *
1163  * These tests use some knowledge of the implementation to trigger different
1164  * paths in the code.
1165  */
1166
1167 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1168 {
1169     static const char * const selections[] = {
1170         "unused1 = atomnr 1 to 3",
1171         "foo = atomnr 4 to 7",
1172         "atomnr 1 to 6 and foo",
1173         "unused2 = atomnr 3 to 5"
1174     };
1175     runTest(10, selections);
1176 }
1177
1178
1179 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1180 {
1181     static const char * const selections[] = {
1182         "foo = atomnr 4 to 7 and x < 2",
1183         "atomnr 1 to 5 and foo",
1184         "atomnr 3 to 7 and foo"
1185     };
1186     runTest(10, selections);
1187 }
1188
1189
1190 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1191 {
1192     static const char * const selections[] = {
1193         "foo = atomnr 4 to 7 and x < 2",
1194         "atomnr 1 to 6 and foo",
1195         "within 1 of foo",
1196         "foo"
1197     };
1198     runTest(10, selections);
1199 }
1200
1201
1202 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1203 {
1204     static const char * const selections[] = {
1205         "foo = atomnr 1 to 8 and x < 10",
1206         "atomnr 1 to 5 and y < 10 and foo",
1207         "foo"
1208     };
1209     setFlags(TestFlags() | efTestEvaluation);
1210     runTest("simple.gro", selections);
1211 }
1212
1213
1214 } // namespace