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 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 491 {
 492     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 493     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
 494                      gmx::InconsistentInputError);
 495     EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
 496 }
 497
 498 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 499 {
 500     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
 501     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 502     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 503 }
 504
 505 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 506 {
 507     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 508     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 509     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 510 }
 511
 512 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 513 {
 514     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 515     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 516     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 517 }
 518
 519 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 520 {
 521     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 522     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 523     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 524 }
 525
 526 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 527 {
 528     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 529     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 530     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 531 }
 532
 533 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 534 {
 535     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 536     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 537     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 538 }
 539
 540 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 541 {
 542     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 543     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 544     ASSERT_NO_THROW_GMX(sc_.compile());
 545     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 546 }
 547
 548 // TODO: Tests for evaluation errors
 549
 550
 551 /********************************************************************
 552  * Tests for selection keywords
 553  */
 554
 555 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 556 {
 557     static const char * const selections[] = {
 558         "all",
 559         "none"
 560     };
 561     runTest(10, selections);
 562 }
 563
 564 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 565 {
 566     static const char * const selections[] = {
 567         "atomnr 1 to 3 6 to 8",
 568         "atomnr 4 2 5 to 7",
 569         "atomnr <= 5"
 570     };
 571     runTest(10, selections);
 572 }
 573
 574 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 575 {
 576     static const char * const selections[] = {
 577         "resnr 1 2 5",
 578         "resid 4 to 3"
 579     };
 580     runTest("simple.gro", selections);
 581 }
 582
 583 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 584 {
 585     static const char * const selections[] = {
 586         "resindex 1 4",
 587         "residue 1 3"
 588     };
 589     runTest("simple.pdb", selections);
 590 }
 591
 592 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 593 {
 594     static const char * const selections[] = {
 595         "molindex 1 4",
 596         "molecule 2 3 5"
 597     };
 598     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 599     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 600     topManager_.initUniformMolecules(3);
 601     ASSERT_NO_FATAL_FAILURE(runCompiler());
 602 }
 603
 604 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 605 {
 606     static const char * const selections[] = {
 607         "name CB",
 608         "atomname S1 S2"
 609     };
 610     runTest("simple.gro", selections);
 611 }
 612
 613 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 614 {
 615     static const char * const selections[] = {
 616         "name HG21",
 617         "name 1HG2",
 618         "pdbname HG21 CB",
 619         "pdbatomname 1HG2"
 620     };
 621     runTest("simple.pdb", selections);
 622 }
 623
 624
 625 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 626 {
 627     static const char * const selections[] = {
 628         "atomtype CA"
 629     };
 630     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 631     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 632     const char *const types[] = { "CA", "SA", "SB" };
 633     topManager_.initAtomTypes(types);
 634     ASSERT_NO_FATAL_FAILURE(runCompiler());
 635 }
 636
 637 TEST_F(SelectionCollectionDataTest, HandlesChain)
 638 {
 639     static const char * const selections[] = {
 640         "chain A",
 641         "chain B"
 642     };
 643     runTest("simple.pdb", selections);
 644 }
 645
 646 TEST_F(SelectionCollectionDataTest, HandlesMass)
 647 {
 648     static const char * const selections[] = {
 649         "mass > 5"
 650     };
 651     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 652     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 653     for (int i = 0; i < top_->atoms.nr; ++i)
 654     {
 655         top_->atoms.atom[i].m = 1.0 + i;
 656     }
 657     ASSERT_NO_FATAL_FAILURE(runCompiler());
 658 }
 659
 660 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 661 {
 662     static const char * const selections[] = {
 663         "charge < 0.5"
 664     };
 665     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 666     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 667     for (int i = 0; i < top_->atoms.nr; ++i)
 668     {
 669         top_->atoms.atom[i].q = i / 10.0;
 670     }
 671     ASSERT_NO_FATAL_FAILURE(runCompiler());
 672 }
 673
 674 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 675 {
 676     static const char * const selections[] = {
 677         "altloc \" \"",
 678         "altloc A"
 679     };
 680     runTest("simple.pdb", selections);
 681 }
 682
 683 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 684 {
 685     static const char * const selections[] = {
 686         "insertcode \" \"",
 687         "insertcode A"
 688     };
 689     runTest("simple.pdb", selections);
 690 }
 691
 692 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 693 {
 694     static const char * const selections[] = {
 695         "occupancy 1",
 696         "occupancy < .5"
 697     };
 698     runTest("simple.pdb", selections);
 699 }
 700
 701 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 702 {
 703     static const char * const selections[] = {
 704         "beta 0",
 705         "beta >= 0.3"
 706     };
 707     runTest("simple.pdb", selections);
 708 }
 709
 710 TEST_F(SelectionCollectionDataTest, HandlesResname)
 711 {
 712     static const char * const selections[] = {
 713         "resname RA",
 714         "resname RB RC"
 715     };
 716     runTest("simple.gro", selections);
 717 }
 718
 719 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 720 {
 721     static const char * const selections[] = {
 722         "x < 3",
 723         "y >= 3",
 724         "x {-1 to 2}"
 725     };
 726     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 727     runTest("simple.gro", selections);
 728 }
 729
 730
 731 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 732 {
 733     static const char * const selections[] = {
 734         "same residue as atomnr 1 4 12"
 735     };
 736     runTest("simple.gro", selections);
 737 }
 738
 739
 740 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 741 {
 742     static const char * const selections[] = {
 743         "same resname as atomnr 1 14"
 744     };
 745     runTest("simple.gro", selections);
 746 }
 747
 748
 749 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 750 {
 751     static const char * const selections[] = {
 752         "cog of resnr 1 3",
 753         "res_cog of name CB and resnr 1 3",
 754         "whole_res_cog of name CB and resnr 1 3",
 755         "part_res_cog of x < 3",
 756         "dyn_res_cog of x < 3"
 757     };
 758     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 759              | efTestPositionAtoms);
 760     runTest("simple.gro", selections);
 761 }
 762
 763
 764 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 765 {
 766     static const char * const selections[] = {
 767         "distance from cog of resnr 1 < 2"
 768     };
 769     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 770     runTest("simple.gro", selections);
 771 }
 772
 773
 774 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 775 {
 776     static const char * const selections[] = {
 777         "mindistance from resnr 1 < 2"
 778     };
 779     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 780     runTest("simple.gro", selections);
 781 }
 782
 783
 784 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 785 {
 786     static const char * const selections[] = {
 787         "within 1 of resnr 2"
 788     };
 789     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 790     runTest("simple.gro", selections);
 791 }
 792
 793
 794 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 795 {
 796     // Both of these should evaluate to empty on a correct implementation.
 797     static const char * const selections[] = {
 798         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 799         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 800     };
 801     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 802     runTest("sphere.gro", selections);
 803 }
 804
 805
 806 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 807 {
 808     static const char * const selections[] = {
 809         "all permute 3 1 2",
 810         "res_cog of resnr 1 to 4 permute 2 1",
 811         "name CB S1 and res_cog x < 3 permute 2 1"
 812     };
 813     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 814              | efTestPositionAtoms | efTestPositionMapping);
 815     runTest("simple.gro", selections);
 816 }
 817
 818
 819 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 820 {
 821     static const char * const selections[] = {
 822         "name S2 plus name S1",
 823         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 824         "name S1 and y < 3 plus res_cog of x < 2.5"
 825     };
 826     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 827              | efTestPositionAtoms | efTestPositionMapping);
 828     runTest("simple.gro", selections);
 829 }
 830
 831
 832 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 833 {
 834     static const char * const selections[] = {
 835         "name S2 merge name S1",
 836         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 837         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 838     };
 839     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 840              | efTestPositionAtoms | efTestPositionMapping);
 841     runTest("simple.gro", selections);
 842 }
 843
 844
 845 /********************************************************************
 846  * Tests for generic selection evaluation
 847  */
 848
 849 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 850 {
 851     static const char * const selections[] = {
 852         "name CB",
 853         "y > 2",
 854         "res_cog of y > 2"
 855     };
 856     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 857              | efTestPositionMasses | efTestPositionCharges);
 858     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 859     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 860     for (int i = 0; i < top_->atoms.nr; ++i)
 861     {
 862         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 863         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 864     }
 865     ASSERT_NO_FATAL_FAILURE(runCompiler());
 866     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 867     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 868 }
 869
 870 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 871 {
 872     static const char * const selections[] = {
 873         "atomnr 1 to 3 8 to 9",
 874         "y > 2",
 875         "cog of (y > 2)"
 876     };
 877     setFlags(TestFlags() | efTestPositionAtoms
 878              | efTestPositionMasses | efTestPositionCharges);
 879     runTest(10, selections);
 880 }
 881
 882
 883 /********************************************************************
 884  * Tests for selection syntactic constructs
 885  */
 886
 887 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 888 {
 889     static const char * const selections[] = {
 890         "\"GroupSelection\" group \"GrpA\"",
 891         "\"DynamicSelection\" x < 5",
 892         "y < 3"
 893     };
 894     setFlags(TestFlags() | efTestSelectionNames);
 895     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 896     runTest(10, selections);
 897 }
 898
 899 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 900 {
 901     static const char * const selections[] = {
 902         "group \"GrpA\"",
 903         "GrpB",
 904         "1",
 905         "group \"GrpB\" and resname RB"
 906     };
 907     setFlags(TestFlags() | efTestSelectionNames);
 908     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 909     runTest("simple.gro", selections);
 910 }
 911
 912 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 913 {
 914     static const char * const selections[] = {
 915         "group \"GrpA\"",
 916         "GrpB",
 917         "1",
 918         "group \"GrpB\" and resname RB"
 919     };
 920     setFlags(TestFlags() | efTestSelectionNames);
 921     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 922     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 923     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 924     ASSERT_NO_FATAL_FAILURE(runCompiler());
 925 }
 926
 927 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 928 {
 929     static const char * const selections[] = {
 930         "[1, -2, 3.5]"
 931     };
 932     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 933     runTest("simple.gro", selections);
 934 }
 935
 936
 937 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 938 {
 939     static const char * const selections[] = {
 940         "within 1 of [2, 1, 0]"
 941     };
 942     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 943     runTest("simple.gro", selections);
 944 }
 945
 946
 947 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 948 {
 949     static const char * const selections[] = {
 950         "name = S1 \"C?\"",
 951         "name ? S1 \"C?\""
 952     };
 953     runTest("simple.gro", selections);
 954 }
 955
 956
 957 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 958 {
 959     static const char * const selections[] = {
 960         "name \"S?\"",
 961         "name ? \"S?\""
 962     };
 963     runTest("simple.gro", selections);
 964 }
 965
 966
 967 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 968 {
 969     static const char * const selections[] = {
 970         "resname \"R[BD]\"",
 971         "resname ~ \"R[BD]\""
 972     };
 973     if (gmx::Regex::isSupported())
 974     {
 975         runTest("simple.gro", selections);
 976     }
 977 }
 978
 979
 980 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 981 {
 982     static const char * const selections[] = {
 983         "atomnr 1 to 5 and atomnr 2 to 7",
 984         "atomnr 1 to 5 or not atomnr 3 to 8",
 985         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 986         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 987         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 988     };
 989     runTest(10, selections);
 990 }
 991
 992
 993 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
 994 {
 995     static const char * const selections[] = {
 996         "same residue as (atomnr 3 5 13 or y > 5)",
 997         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
 998     };
 999     setFlags(TestFlags() | efTestEvaluation);
1000     runTest("simple.gro", selections);
1001 }
1002
1003
1004 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1005 {
1006     static const char * const selections[] = {
1007         "none and x > 2",
1008         "none and same resname as resnr 2"
1009     };
1010     runTest("simple.gro", selections);
1011 }
1012
1013
1014 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1015 {
1016     static const char * const selections[] = {
1017         "x > 2",
1018         "2 < x",
1019         "y > resnr",
1020         "resnr < 2.5",
1021         "2.5 > resnr"
1022     };
1023     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1024     runTest("simple.gro", selections);
1025 }
1026
1027
1028 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1029 {
1030     static const char * const selections[] = {
1031         "x+1 > 3",
1032         "(y-1)^2 <= 1",
1033         "x+--1 > 3",
1034         "-x+-1 < -3"
1035     };
1036     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1037     runTest("simple.gro", selections);
1038 }
1039
1040
1041 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1042 {
1043     static const char * const selections[] = {
1044         "value = x + y",
1045         "value <= 4",
1046         "index = resnr",
1047         "index < 3"
1048     };
1049     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1050     runTest("simple.gro", selections);
1051 }
1052
1053
1054 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1055 {
1056     static const char * const selections[] = {
1057         "value = x + y",
1058         "resname RA and value <= 4",
1059         "resname RA RB and x < 3 and value <= 4",
1060         "index = atomnr",
1061         "resname RA and index < 3",
1062         "resname RB and y < 3 and index < 6"
1063     };
1064     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1065     runTest("simple.gro", selections);
1066 }
1067
1068
1069 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1070 {
1071     static const char * const selections[] = {
1072         "foo = res_cog of resname RA",
1073         "foo",
1074         "within 1 of foo",
1075         "bar = cog of resname RA",
1076         "bar",
1077         "within 1 of bar"
1078     };
1079     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1080     runTest("simple.gro", selections);
1081 }
1082
1083
1084 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1085 {
1086     static const char * const selections[] = {
1087         "constpos = [1.0, 2.5, 0.5]",
1088         "constpos",
1089         "within 2 of constpos"
1090     };
1091     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1092              | efTestPositionAtoms);
1093     runTest("simple.gro", selections);
1094 }
1095
1096
1097 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1098 {
1099     static const char * const selections[] = {
1100         "constint = 4",
1101         "constreal1 = 0.5",
1102         "constreal2 = 2.7",
1103         "resnr < constint",
1104         "x + constreal1 < constreal2"
1105     };
1106     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1107     runTest("simple.gro", selections);
1108 }
1109
1110
1111 /********************************************************************
1112  * Tests for complex boolean syntax
1113  */
1114
1115 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1116 {
1117     static const char * const selections[] = {
1118         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1119         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1120         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1121         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1122         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1123     };
1124     runTest(10, selections);
1125 }
1126
1127
1128 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1129 {
1130     static const char * const selections[] = {
1131         "foo = atomnr 4 to 7 or x < 2",
1132         "atomnr 1 to 4 and foo",
1133         "atomnr 2 to 6 and y < 3 and foo",
1134         "atomnr 6 to 10 and not foo"
1135     };
1136     runTest(10, selections);
1137 }
1138
1139
1140 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1141 {
1142     static const char * const selections[] = {
1143         "foo = atomnr 4 to 7",
1144         "bar = foo and x < 2",
1145         "bar2 = foo and y < 2",
1146         "atomnr 1 to 4 and bar",
1147         "atomnr 2 to 6 and y < 3 and bar2",
1148         "atomnr 6 to 10 and not foo"
1149     };
1150     runTest(10, selections);
1151 }
1152
1153
1154 /********************************************************************
1155  * Tests for complex subexpression cases
1156  *
1157  * These tests use some knowledge of the implementation to trigger different
1158  * paths in the code.
1159  */
1160
1161 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1162 {
1163     static const char * const selections[] = {
1164         "unused1 = atomnr 1 to 3",
1165         "foo = atomnr 4 to 7",
1166         "atomnr 1 to 6 and foo",
1167         "unused2 = atomnr 3 to 5"
1168     };
1169     runTest(10, selections);
1170 }
1171
1172
1173 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1174 {
1175     static const char * const selections[] = {
1176         "foo = atomnr 4 to 7 and x < 2",
1177         "atomnr 1 to 5 and foo",
1178         "atomnr 3 to 7 and foo"
1179     };
1180     runTest(10, selections);
1181 }
1182
1183
1184 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1185 {
1186     static const char * const selections[] = {
1187         "foo = atomnr 4 to 7 and x < 2",
1188         "atomnr 1 to 6 and foo",
1189         "within 1 of foo",
1190         "foo"
1191     };
1192     runTest(10, selections);
1193 }
1194
1195
1196 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1197 {
1198     static const char * const selections[] = {
1199         "foo = atomnr 1 to 8 and x < 10",
1200         "atomnr 1 to 5 and y < 10 and foo",
1201         "foo"
1202     };
1203     setFlags(TestFlags() | efTestEvaluation);
1204     runTest("simple.gro", selections);
1205 }
1206
1207
1208 } // namespace