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/arrayref.h"
  50 #include "gromacs/utility/exceptions.h"
  51 #include "gromacs/utility/flags.h"
  52 #include "gromacs/utility/gmxregex.h"
  53 #include "gromacs/utility/stringutil.h"
  54
  55 #include "testutils/refdata.h"
  56 #include "testutils/testasserts.h"
  57 #include "testutils/testfilemanager.h"
  58 #include "testutils/testoptions.h"
  59
  60 #include "toputils.h"
  61
  62 namespace
  63 {
  64
  65 /********************************************************************
  66  * Test fixture for selection testing
  67  */
  68
  69 class SelectionCollectionTest : public ::testing::Test
  70 {
  71     public:
  72         static int               s_debugLevel;
  73
  74         SelectionCollectionTest();
  75         ~SelectionCollectionTest();
  76
  77         void setAtomCount(int natoms)
  78         {
  79             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  80         }
  81         void loadTopology(const char *filename);
  82         void setTopology();
  83         void loadIndexGroups(const char *filename);
  84
  85         gmx::test::TopologyManager  topManager_;
  86         gmx::SelectionCollection    sc_;
  87         gmx::SelectionList          sel_;
  88         t_topology                 *top_;
  89         t_trxframe                 *frame_;
  90         gmx_ana_indexgrps_t        *grps_;
  91 };
  92
  93 int SelectionCollectionTest::s_debugLevel = 0;
  94
  95 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
  96 #ifndef DOXYGEN
  97 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  98 {
  99     options->addOption(gmx::IntegerOption("seldebug")
 100                            .store(&SelectionCollectionTest::s_debugLevel)
 101                            .description("Set selection debug level"));
 102 }
 103 #endif
 104
 105 SelectionCollectionTest::SelectionCollectionTest()
 106     : top_(NULL), frame_(NULL), grps_(NULL)
 107 {
 108     topManager_.requestFrame();
 109     sc_.setDebugLevel(s_debugLevel);
 110     sc_.setReferencePosType("atom");
 111     sc_.setOutputPosType("atom");
 112 }
 113
 114 SelectionCollectionTest::~SelectionCollectionTest()
 115 {
 116     if (grps_ != NULL)
 117     {
 118         gmx_ana_indexgrps_free(grps_);
 119     }
 120 }
 121
 122 void
 123 SelectionCollectionTest::loadTopology(const char *filename)
 124 {
 125     topManager_.loadTopology(filename);
 126     setTopology();
 127 }
 128
 129 void
 130 SelectionCollectionTest::setTopology()
 131 {
 132     top_   = topManager_.topology();
 133     frame_ = topManager_.frame();
 134
 135     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 136 }
 137
 138 void
 139 SelectionCollectionTest::loadIndexGroups(const char *filename)
 140 {
 141     GMX_RELEASE_ASSERT(grps_ == NULL,
 142                        "External groups can only be loaded once");
 143     std::string fullpath =
 144         gmx::test::TestFileManager::getInputFilePath(filename);
 145     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 146     sc_.setIndexGroups(grps_);
 147 }
 148
 149
 150 /********************************************************************
 151  * Test fixture for selection testing with reference data
 152  */
 153
 154 class SelectionCollectionDataTest : public SelectionCollectionTest
 155 {
 156     public:
 157         enum TestFlag
 158         {
 159             efTestEvaluation            = 1<<0,
 160             efTestPositionAtoms         = 1<<1,
 161             efTestPositionCoordinates   = 1<<2,
 162             efTestPositionMapping       = 1<<3,
 163             efTestPositionMasses        = 1<<4,
 164             efTestPositionCharges       = 1<<5,
 165             efTestSelectionNames        = 1<<6,
 166             efDontTestCompiledAtoms     = 1<<8
 167         };
 168         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 169
 170         SelectionCollectionDataTest()
 171             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 172         {
 173         }
 174
 175         void setFlags(TestFlags flags) { flags_ = flags; }
 176
 177         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 178         void runCompiler();
 179         void runEvaluate();
 180         void runEvaluateFinal();
 181
 182         void runTest(int                                     natoms,
 183                      const gmx::ConstArrayRef<const char *> &selections);
 184         void runTest(const char                             *filename,
 185                      const gmx::ConstArrayRef<const char *> &selections);
 186
 187     private:
 188         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 189                                    const gmx::Selection &sel, TestFlags flags);
 190
 191         void checkCompiled();
 192
 193         gmx::test::TestReferenceData    data_;
 194         gmx::test::TestReferenceChecker checker_;
 195         size_t                          count_;
 196         int                             framenr_;
 197         TestFlags                       flags_;
 198 };
 199
 200
 201 void
 202 SelectionCollectionDataTest::checkSelection(
 203         gmx::test::TestReferenceChecker *checker,
 204         const gmx::Selection &sel, TestFlags flags)
 205 {
 206     using gmx::test::TestReferenceChecker;
 207
 208     {
 209         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 210         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 211     }
 212     if (flags.test(efTestPositionAtoms)
 213         || flags.test(efTestPositionCoordinates)
 214         || flags.test(efTestPositionMapping)
 215         || flags.test(efTestPositionMasses)
 216         || flags.test(efTestPositionCharges))
 217     {
 218         TestReferenceChecker compound(
 219                 checker->checkSequenceCompound("Positions", sel.posCount()));
 220         for (int i = 0; i < sel.posCount(); ++i)
 221         {
 222             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 223             const gmx::SelectionPosition &p = sel.position(i);
 224             if (flags.test(efTestPositionAtoms))
 225             {
 226                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 227                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 228             }
 229             if (flags.test(efTestPositionCoordinates))
 230             {
 231                 poscompound.checkVector(p.x(), "Coordinates");
 232             }
 233             if (flags.test(efTestPositionMapping))
 234             {
 235                 poscompound.checkInteger(p.refId(), "RefId");
 236                 poscompound.checkInteger(p.mappedId(), "MappedId");
 237             }
 238             if (flags.test(efTestPositionMasses))
 239             {
 240                 poscompound.checkReal(p.mass(), "Mass");
 241             }
 242             if (flags.test(efTestPositionCharges))
 243             {
 244                 poscompound.checkReal(p.charge(), "Charge");
 245             }
 246         }
 247     }
 248 }
 249
 250
 251 void
 252 SelectionCollectionDataTest::runParser(
 253         const gmx::ConstArrayRef<const char *> &selections)
 254 {
 255     using gmx::test::TestReferenceChecker;
 256
 257     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 258     size_t               varcount = 0;
 259     count_ = 0;
 260     for (size_t i = 0; i < selections.size(); ++i)
 261     {
 262         SCOPED_TRACE(std::string("Parsing selection \"")
 263                      + selections[i] + "\"");
 264         gmx::SelectionList result;
 265         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 266         sel_.insert(sel_.end(), result.begin(), result.end());
 267         if (sel_.size() == count_)
 268         {
 269             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 270             TestReferenceChecker varcompound(
 271                     compound.checkCompound("ParsedVariable", id.c_str()));
 272             varcompound.checkString(selections[i], "Input");
 273             ++varcount;
 274         }
 275         else
 276         {
 277             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 278             TestReferenceChecker selcompound(
 279                     compound.checkCompound("ParsedSelection", id.c_str()));
 280             selcompound.checkString(selections[i], "Input");
 281             if (flags_.test(efTestSelectionNames))
 282             {
 283                 selcompound.checkString(sel_[count_].name(), "Name");
 284             }
 285             selcompound.checkString(sel_[count_].selectionText(), "Text");
 286             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 287             ++count_;
 288         }
 289     }
 290 }
 291
 292
 293 void
 294 SelectionCollectionDataTest::runCompiler()
 295 {
 296     ASSERT_NO_THROW_GMX(sc_.compile());
 297     ASSERT_EQ(count_, sel_.size());
 298     checkCompiled();
 299 }
 300
 301
 302 void
 303 SelectionCollectionDataTest::checkCompiled()
 304 {
 305     using gmx::test::TestReferenceChecker;
 306     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 307
 308     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 309     for (size_t i = 0; i < count_; ++i)
 310     {
 311         SCOPED_TRACE(std::string("Checking selection \"") +
 312                      sel_[i].selectionText() + "\"");
 313         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 314         TestReferenceChecker selcompound(
 315                 compound.checkCompound("Selection", id.c_str()));
 316         if (flags_.test(efTestSelectionNames))
 317         {
 318             selcompound.checkString(sel_[i].name(), "Name");
 319         }
 320         if (!flags_.test(efDontTestCompiledAtoms))
 321         {
 322             checkSelection(&selcompound, sel_[i], flags_ & mask);
 323         }
 324     }
 325 }
 326
 327
 328 void
 329 SelectionCollectionDataTest::runEvaluate()
 330 {
 331     using gmx::test::TestReferenceChecker;
 332
 333     ++framenr_;
 334     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 335     std::string          frame = gmx::formatString("Frame%d", framenr_);
 336     TestReferenceChecker compound(
 337             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 338     for (size_t i = 0; i < count_; ++i)
 339     {
 340         SCOPED_TRACE(std::string("Checking selection \"") +
 341                      sel_[i].selectionText() + "\"");
 342         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 343         TestReferenceChecker selcompound(
 344                 compound.checkCompound("Selection", id.c_str()));
 345         checkSelection(&selcompound, sel_[i], flags_);
 346     }
 347 }
 348
 349
 350 void
 351 SelectionCollectionDataTest::runEvaluateFinal()
 352 {
 353     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 354     checkCompiled();
 355 }
 356
 357
 358 void
 359 SelectionCollectionDataTest::runTest(
 360         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 361 {
 362     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 363     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 364     ASSERT_NO_FATAL_FAILURE(runCompiler());
 365 }
 366
 367
 368 void
 369 SelectionCollectionDataTest::runTest(
 370         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 371 {
 372     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 373     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 374     ASSERT_NO_FATAL_FAILURE(runCompiler());
 375     if (flags_.test(efTestEvaluation))
 376     {
 377         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 378         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 379     }
 380 }
 381
 382
 383 /********************************************************************
 384  * Tests for SelectionCollection functionality without reference data
 385  */
 386
 387 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 388 {
 389     EXPECT_FALSE(sc_.requiresTopology());
 390     EXPECT_NO_THROW_GMX(sc_.compile());
 391 }
 392
 393 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 394 {
 395     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 396     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 397     ASSERT_EQ(2U, sel_.size());
 398     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 399     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 400     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 401     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 402     ASSERT_NO_THROW_GMX(sc_.compile());
 403     EXPECT_TRUE(sel_[0].hasVelocities());
 404     EXPECT_TRUE(sel_[1].hasVelocities());
 405     EXPECT_TRUE(sel_[0].hasForces());
 406     EXPECT_TRUE(sel_[1].hasForces());
 407 }
 408
 409 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 410 {
 411     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 412                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 413     // These should match the contents of selfile.dat
 414     ASSERT_EQ(2U, sel_.size());
 415     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 416     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 417 }
 418
 419 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 420 {
 421     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 422     EXPECT_THROW_GMX({
 423                          sc_.parseFromString("resname ~ \"R[A\"");
 424                          sc_.compile();
 425                      }, gmx::InvalidInputError);
 426 }
 427
 428 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 429 {
 430     if (!gmx::Regex::isSupported())
 431     {
 432         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 433         EXPECT_THROW_GMX({
 434                              sc_.parseFromString("resname \"R[AD]\"");
 435                              sc_.compile();
 436                          }, gmx::InvalidInputError);
 437     }
 438 }
 439
 440 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 441 {
 442     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 443                      gmx::InvalidInputError);
 444 }
 445
 446 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 447 {
 448     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 449                      gmx::InvalidInputError);
 450 }
 451
 452 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 453 {
 454     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 455                      gmx::InvalidInputError);
 456 }
 457
 458 // TODO: Tests for more parser errors
 459
 460 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 461 {
 462     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 463     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 464     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 465 }
 466
 467 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 468 {
 469     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 470     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 471     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 472 }
 473
 474 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 475 {
 476     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 477     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 478     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 479     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 480 }
 481
 482 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 483 {
 484     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 485     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 486     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 487     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 488 }
 489
 490 // TODO: Make the check less eager so that it doesn't break other tests, and
 491 // adapt these tests accordingly.
 492 TEST_F(SelectionCollectionTest, DISABLED_HandlesUnsortedGroupReference)
 493 {
 494     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 495     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
 496                      gmx::InconsistentInputError);
 497     EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
 498 }
 499
 500 TEST_F(SelectionCollectionTest, DISABLED_HandlesUnsortedGroupReferenceDelayed)
 501 {
 502     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
 503     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 504     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 505 }
 506
 507 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 508 {
 509     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 510     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 511     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 512 }
 513
 514 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 515 {
 516     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 517     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 518     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 519 }
 520
 521 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 522 {
 523     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 524     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 525     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 526 }
 527
 528 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 529 {
 530     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 531     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 532     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 533 }
 534
 535 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 536 {
 537     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 538     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 539     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 540 }
 541
 542 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 543 {
 544     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 545     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 546     ASSERT_NO_THROW_GMX(sc_.compile());
 547     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 548 }
 549
 550 // TODO: Tests for evaluation errors
 551
 552
 553 /********************************************************************
 554  * Tests for selection keywords
 555  */
 556
 557 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 558 {
 559     static const char * const selections[] = {
 560         "all",
 561         "none"
 562     };
 563     runTest(10, selections);
 564 }
 565
 566 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 567 {
 568     static const char * const selections[] = {
 569         "atomnr 1 to 3 6 to 8",
 570         "atomnr 4 2 5 to 7",
 571         "atomnr <= 5"
 572     };
 573     runTest(10, selections);
 574 }
 575
 576 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 577 {
 578     static const char * const selections[] = {
 579         "resnr 1 2 5",
 580         "resid 4 to 3"
 581     };
 582     runTest("simple.gro", selections);
 583 }
 584
 585 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 586 {
 587     static const char * const selections[] = {
 588         "resindex 1 4",
 589         "residue 1 3"
 590     };
 591     runTest("simple.pdb", selections);
 592 }
 593
 594 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 595 {
 596     static const char * const selections[] = {
 597         "molindex 1 4",
 598         "molecule 2 3 5"
 599     };
 600     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 601     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 602     topManager_.initUniformMolecules(3);
 603     ASSERT_NO_FATAL_FAILURE(runCompiler());
 604 }
 605
 606 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 607 {
 608     static const char * const selections[] = {
 609         "name CB",
 610         "atomname S1 S2"
 611     };
 612     runTest("simple.gro", selections);
 613 }
 614
 615 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 616 {
 617     static const char * const selections[] = {
 618         "name HG21",
 619         "name 1HG2",
 620         "pdbname HG21 CB",
 621         "pdbatomname 1HG2"
 622     };
 623     runTest("simple.pdb", selections);
 624 }
 625
 626
 627 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 628 {
 629     static const char * const selections[] = {
 630         "atomtype CA"
 631     };
 632     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 633     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 634     const char *const types[] = { "CA", "SA", "SB" };
 635     topManager_.initAtomTypes(types);
 636     ASSERT_NO_FATAL_FAILURE(runCompiler());
 637 }
 638
 639 TEST_F(SelectionCollectionDataTest, HandlesChain)
 640 {
 641     static const char * const selections[] = {
 642         "chain A",
 643         "chain B"
 644     };
 645     runTest("simple.pdb", selections);
 646 }
 647
 648 TEST_F(SelectionCollectionDataTest, HandlesMass)
 649 {
 650     static const char * const selections[] = {
 651         "mass > 5"
 652     };
 653     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 654     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 655     for (int i = 0; i < top_->atoms.nr; ++i)
 656     {
 657         top_->atoms.atom[i].m = 1.0 + i;
 658     }
 659     ASSERT_NO_FATAL_FAILURE(runCompiler());
 660 }
 661
 662 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 663 {
 664     static const char * const selections[] = {
 665         "charge < 0.5"
 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].q = i / 10.0;
 672     }
 673     ASSERT_NO_FATAL_FAILURE(runCompiler());
 674 }
 675
 676 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 677 {
 678     static const char * const selections[] = {
 679         "altloc \" \"",
 680         "altloc A"
 681     };
 682     runTest("simple.pdb", selections);
 683 }
 684
 685 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 686 {
 687     static const char * const selections[] = {
 688         "insertcode \" \"",
 689         "insertcode A"
 690     };
 691     runTest("simple.pdb", selections);
 692 }
 693
 694 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 695 {
 696     static const char * const selections[] = {
 697         "occupancy 1",
 698         "occupancy < .5"
 699     };
 700     runTest("simple.pdb", selections);
 701 }
 702
 703 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 704 {
 705     static const char * const selections[] = {
 706         "beta 0",
 707         "beta >= 0.3"
 708     };
 709     runTest("simple.pdb", selections);
 710 }
 711
 712 TEST_F(SelectionCollectionDataTest, HandlesResname)
 713 {
 714     static const char * const selections[] = {
 715         "resname RA",
 716         "resname RB RC"
 717     };
 718     runTest("simple.gro", selections);
 719 }
 720
 721 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 722 {
 723     static const char * const selections[] = {
 724         "x < 3",
 725         "y >= 3",
 726         "x {-1 to 2}"
 727     };
 728     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 729     runTest("simple.gro", selections);
 730 }
 731
 732
 733 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 734 {
 735     static const char * const selections[] = {
 736         "same residue as atomnr 1 4 12"
 737     };
 738     runTest("simple.gro", selections);
 739 }
 740
 741
 742 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 743 {
 744     static const char * const selections[] = {
 745         "same resname as atomnr 1 14"
 746     };
 747     runTest("simple.gro", selections);
 748 }
 749
 750
 751 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 752 {
 753     static const char * const selections[] = {
 754         "cog of resnr 1 3",
 755         "res_cog of name CB and resnr 1 3",
 756         "whole_res_cog of name CB and resnr 1 3",
 757         "part_res_cog of x < 3",
 758         "dyn_res_cog of x < 3"
 759     };
 760     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 761              | efTestPositionAtoms);
 762     runTest("simple.gro", selections);
 763 }
 764
 765
 766 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 767 {
 768     static const char * const selections[] = {
 769         "distance from cog of resnr 1 < 2"
 770     };
 771     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 772     runTest("simple.gro", selections);
 773 }
 774
 775
 776 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 777 {
 778     static const char * const selections[] = {
 779         "mindistance from resnr 1 < 2"
 780     };
 781     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 782     runTest("simple.gro", selections);
 783 }
 784
 785
 786 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 787 {
 788     static const char * const selections[] = {
 789         "within 1 of resnr 2"
 790     };
 791     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 792     runTest("simple.gro", selections);
 793 }
 794
 795
 796 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 797 {
 798     // Both of these should evaluate to empty on a correct implementation.
 799     static const char * const selections[] = {
 800         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 801         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 802     };
 803     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 804     runTest("sphere.gro", selections);
 805 }
 806
 807
 808 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 809 {
 810     static const char * const selections[] = {
 811         "all permute 3 1 2",
 812         "res_cog of resnr 1 to 4 permute 2 1",
 813         "name CB S1 and res_cog x < 3 permute 2 1"
 814     };
 815     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 816              | efTestPositionAtoms | efTestPositionMapping);
 817     runTest("simple.gro", selections);
 818 }
 819
 820
 821 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 822 {
 823     static const char * const selections[] = {
 824         "name S2 plus name S1",
 825         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 826         "name S1 and y < 3 plus res_cog of x < 2.5"
 827     };
 828     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 829              | efTestPositionAtoms | efTestPositionMapping);
 830     runTest("simple.gro", selections);
 831 }
 832
 833
 834 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 835 {
 836     static const char * const selections[] = {
 837         "name S2 merge name S1",
 838         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 839         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 840     };
 841     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 842              | efTestPositionAtoms | efTestPositionMapping);
 843     runTest("simple.gro", selections);
 844 }
 845
 846
 847 /********************************************************************
 848  * Tests for generic selection evaluation
 849  */
 850
 851 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 852 {
 853     static const char * const selections[] = {
 854         "name CB",
 855         "y > 2",
 856         "res_cog of y > 2"
 857     };
 858     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 859              | efTestPositionMasses | efTestPositionCharges);
 860     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 861     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 862     for (int i = 0; i < top_->atoms.nr; ++i)
 863     {
 864         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 865         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 866     }
 867     ASSERT_NO_FATAL_FAILURE(runCompiler());
 868     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 869     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 870 }
 871
 872 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 873 {
 874     static const char * const selections[] = {
 875         "atomnr 1 to 3 8 to 9",
 876         "y > 2",
 877         "cog of (y > 2)"
 878     };
 879     setFlags(TestFlags() | efTestPositionAtoms
 880              | efTestPositionMasses | efTestPositionCharges);
 881     runTest(10, selections);
 882 }
 883
 884
 885 /********************************************************************
 886  * Tests for selection syntactic constructs
 887  */
 888
 889 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 890 {
 891     static const char * const selections[] = {
 892         "\"GroupSelection\" group \"GrpA\"",
 893         "\"DynamicSelection\" x < 5",
 894         "y < 3"
 895     };
 896     setFlags(TestFlags() | efTestSelectionNames);
 897     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 898     runTest(10, selections);
 899 }
 900
 901 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 902 {
 903     static const char * const selections[] = {
 904         "group \"GrpA\"",
 905         "GrpB",
 906         "1",
 907         "group \"GrpB\" and resname RB"
 908     };
 909     setFlags(TestFlags() | efTestSelectionNames);
 910     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 911     runTest("simple.gro", selections);
 912 }
 913
 914 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 915 {
 916     static const char * const selections[] = {
 917         "group \"GrpA\"",
 918         "GrpB",
 919         "1",
 920         "group \"GrpB\" and resname RB"
 921     };
 922     setFlags(TestFlags() | efTestSelectionNames);
 923     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 924     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 925     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 926     ASSERT_NO_FATAL_FAILURE(runCompiler());
 927 }
 928
 929 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
 930 {
 931     static const char * const selections[] = {
 932         "group \"GrpUnsorted\"",
 933         "GrpUnsorted",
 934         "2",
 935         "res_cog of group \"GrpUnsorted\"",
 936         "group \"GrpUnsorted\" permute 2 1"
 937     };
 938     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
 939              | efTestSelectionNames);
 940     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 941     runTest("simple.gro", selections);
 942 }
 943
 944 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 945 {
 946     static const char * const selections[] = {
 947         "[1, -2, 3.5]"
 948     };
 949     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 950     runTest("simple.gro", selections);
 951 }
 952
 953
 954 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 955 {
 956     static const char * const selections[] = {
 957         "within 1 of [2, 1, 0]"
 958     };
 959     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 960     runTest("simple.gro", selections);
 961 }
 962
 963
 964 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 965 {
 966     static const char * const selections[] = {
 967         "name = S1 \"C?\"",
 968         "name ? S1 \"C?\""
 969     };
 970     runTest("simple.gro", selections);
 971 }
 972
 973
 974 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 975 {
 976     static const char * const selections[] = {
 977         "name \"S?\"",
 978         "name ? \"S?\""
 979     };
 980     runTest("simple.gro", selections);
 981 }
 982
 983
 984 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 985 {
 986     static const char * const selections[] = {
 987         "resname \"R[BD]\"",
 988         "resname ~ \"R[BD]\""
 989     };
 990     if (gmx::Regex::isSupported())
 991     {
 992         runTest("simple.gro", selections);
 993     }
 994 }
 995
 996
 997 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 998 {
 999     static const char * const selections[] = {
1000         "atomnr 1 to 5 and atomnr 2 to 7",
1001         "atomnr 1 to 5 or not atomnr 3 to 8",
1002         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1003         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1004         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1005     };
1006     runTest(10, selections);
1007 }
1008
1009
1010 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1011 {
1012     static const char * const selections[] = {
1013         "same residue as (atomnr 3 5 13 or y > 5)",
1014         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1015     };
1016     setFlags(TestFlags() | efTestEvaluation);
1017     runTest("simple.gro", selections);
1018 }
1019
1020
1021 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1022 {
1023     static const char * const selections[] = {
1024         "none and x > 2",
1025         "none and same resname as resnr 2"
1026     };
1027     runTest("simple.gro", selections);
1028 }
1029
1030
1031 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1032 {
1033     static const char * const selections[] = {
1034         "x > 2",
1035         "2 < x",
1036         "y > resnr",
1037         "resnr < 2.5",
1038         "2.5 > resnr"
1039     };
1040     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1041     runTest("simple.gro", selections);
1042 }
1043
1044
1045 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1046 {
1047     static const char * const selections[] = {
1048         "x+1 > 3",
1049         "(y-1)^2 <= 1",
1050         "x+--1 > 3",
1051         "-x+-1 < -3"
1052     };
1053     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1054     runTest("simple.gro", selections);
1055 }
1056
1057
1058 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1059 {
1060     static const char * const selections[] = {
1061         "value = x + y",
1062         "value <= 4",
1063         "index = resnr",
1064         "index < 3"
1065     };
1066     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1067     runTest("simple.gro", selections);
1068 }
1069
1070
1071 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1072 {
1073     static const char * const selections[] = {
1074         "value = x + y",
1075         "resname RA and value <= 4",
1076         "resname RA RB and x < 3 and value <= 4",
1077         "index = atomnr",
1078         "resname RA and index < 3",
1079         "resname RB and y < 3 and index < 6"
1080     };
1081     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1082     runTest("simple.gro", selections);
1083 }
1084
1085
1086 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1087 {
1088     static const char * const selections[] = {
1089         "foo = res_cog of resname RA",
1090         "foo",
1091         "within 1 of foo",
1092         "bar = cog of resname RA",
1093         "bar",
1094         "within 1 of bar"
1095     };
1096     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1097     runTest("simple.gro", selections);
1098 }
1099
1100
1101 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1102 {
1103     static const char * const selections[] = {
1104         "constpos = [1.0, 2.5, 0.5]",
1105         "constpos",
1106         "within 2 of constpos"
1107     };
1108     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1109              | efTestPositionAtoms);
1110     runTest("simple.gro", selections);
1111 }
1112
1113
1114 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1115 {
1116     static const char * const selections[] = {
1117         "constint = 4",
1118         "constreal1 = 0.5",
1119         "constreal2 = 2.7",
1120         "resnr < constint",
1121         "x + constreal1 < constreal2"
1122     };
1123     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1124     runTest("simple.gro", selections);
1125 }
1126
1127
1128 /********************************************************************
1129  * Tests for complex boolean syntax
1130  */
1131
1132 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1133 {
1134     static const char * const selections[] = {
1135         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1136         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1137         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1138         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1139         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1140     };
1141     runTest(10, selections);
1142 }
1143
1144
1145 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1146 {
1147     static const char * const selections[] = {
1148         "foo = atomnr 4 to 7 or x < 2",
1149         "atomnr 1 to 4 and foo",
1150         "atomnr 2 to 6 and y < 3 and foo",
1151         "atomnr 6 to 10 and not foo"
1152     };
1153     runTest(10, selections);
1154 }
1155
1156
1157 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1158 {
1159     static const char * const selections[] = {
1160         "foo = atomnr 4 to 7",
1161         "bar = foo and x < 2",
1162         "bar2 = foo and y < 2",
1163         "atomnr 1 to 4 and bar",
1164         "atomnr 2 to 6 and y < 3 and bar2",
1165         "atomnr 6 to 10 and not foo"
1166     };
1167     runTest(10, selections);
1168 }
1169
1170
1171 /********************************************************************
1172  * Tests for complex subexpression cases
1173  *
1174  * These tests use some knowledge of the implementation to trigger different
1175  * paths in the code.
1176  */
1177
1178 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1179 {
1180     static const char * const selections[] = {
1181         "unused1 = atomnr 1 to 3",
1182         "foo = atomnr 4 to 7",
1183         "atomnr 1 to 6 and foo",
1184         "unused2 = atomnr 3 to 5"
1185     };
1186     runTest(10, selections);
1187 }
1188
1189
1190 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1191 {
1192     static const char * const selections[] = {
1193         "foo = atomnr 4 to 7 and x < 2",
1194         "atomnr 1 to 5 and foo",
1195         "atomnr 3 to 7 and foo"
1196     };
1197     runTest(10, selections);
1198 }
1199
1200
1201 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1202 {
1203     static const char * const selections[] = {
1204         "foo = atomnr 4 to 7 and x < 2",
1205         "atomnr 1 to 6 and foo",
1206         "within 1 of foo",
1207         "foo"
1208     };
1209     runTest(10, selections);
1210 }
1211
1212
1213 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1214 {
1215     static const char * const selections[] = {
1216         "foo = atomnr 1 to 8 and x < 10",
1217         "atomnr 1 to 5 and y < 10 and foo",
1218         "foo"
1219     };
1220     setFlags(TestFlags() | efTestEvaluation);
1221     runTest("simple.gro", selections);
1222 }
1223
1224
1225 } // namespace