src/gromacs/selection/tests/selectioncollection.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests selection parsing and compilation.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include <gtest/gtest.h>
  43
  44 #include "gromacs/options/basicoptions.h"
  45 #include "gromacs/options/options.h"
  46 #include "gromacs/selection/indexutil.h"
  47 #include "gromacs/selection/selectioncollection.h"
  48 #include "gromacs/selection/selection.h"
  49 #include "gromacs/topology/topology.h"
  50 #include "gromacs/utility/arrayref.h"
  51 #include "gromacs/utility/exceptions.h"
  52 #include "gromacs/utility/flags.h"
  53 #include "gromacs/utility/gmxregex.h"
  54 #include "gromacs/utility/stringutil.h"
  55
  56 #include "testutils/refdata.h"
  57 #include "testutils/testasserts.h"
  58 #include "testutils/testfilemanager.h"
  59 #include "testutils/testoptions.h"
  60
  61 #include "toputils.h"
  62
  63 namespace
  64 {
  65
  66 /********************************************************************
  67  * Test fixture for selection testing
  68  */
  69
  70 class SelectionCollectionTest : public ::testing::Test
  71 {
  72     public:
  73         static int               s_debugLevel;
  74
  75         SelectionCollectionTest();
  76         ~SelectionCollectionTest();
  77
  78         void setAtomCount(int natoms)
  79         {
  80             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  81         }
  82         void loadTopology(const char *filename);
  83         void setTopology();
  84         void loadIndexGroups(const char *filename);
  85
  86         gmx::test::TopologyManager  topManager_;
  87         gmx::SelectionCollection    sc_;
  88         gmx::SelectionList          sel_;
  89         t_topology                 *top_;
  90         t_trxframe                 *frame_;
  91         gmx_ana_indexgrps_t        *grps_;
  92 };
  93
  94 int SelectionCollectionTest::s_debugLevel = 0;
  95
  96 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
  97 #ifndef DOXYGEN
  98 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  99 {
 100     options->addOption(gmx::IntegerOption("seldebug")
 101                            .store(&SelectionCollectionTest::s_debugLevel)
 102                            .description("Set selection debug level"));
 103 }
 104 #endif
 105
 106 SelectionCollectionTest::SelectionCollectionTest()
 107     : top_(NULL), frame_(NULL), grps_(NULL)
 108 {
 109     topManager_.requestFrame();
 110     sc_.setDebugLevel(s_debugLevel);
 111     sc_.setReferencePosType("atom");
 112     sc_.setOutputPosType("atom");
 113 }
 114
 115 SelectionCollectionTest::~SelectionCollectionTest()
 116 {
 117     if (grps_ != NULL)
 118     {
 119         gmx_ana_indexgrps_free(grps_);
 120     }
 121 }
 122
 123 void
 124 SelectionCollectionTest::loadTopology(const char *filename)
 125 {
 126     topManager_.loadTopology(filename);
 127     setTopology();
 128 }
 129
 130 void
 131 SelectionCollectionTest::setTopology()
 132 {
 133     top_   = topManager_.topology();
 134     frame_ = topManager_.frame();
 135
 136     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 137 }
 138
 139 void
 140 SelectionCollectionTest::loadIndexGroups(const char *filename)
 141 {
 142     GMX_RELEASE_ASSERT(grps_ == NULL,
 143                        "External groups can only be loaded once");
 144     std::string fullpath =
 145         gmx::test::TestFileManager::getInputFilePath(filename);
 146     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 147     sc_.setIndexGroups(grps_);
 148 }
 149
 150
 151 /********************************************************************
 152  * Test fixture for selection testing with reference data
 153  */
 154
 155 class SelectionCollectionDataTest : public SelectionCollectionTest
 156 {
 157     public:
 158         enum TestFlag
 159         {
 160             efTestEvaluation            = 1<<0,
 161             efTestPositionAtoms         = 1<<1,
 162             efTestPositionCoordinates   = 1<<2,
 163             efTestPositionMapping       = 1<<3,
 164             efTestPositionMasses        = 1<<4,
 165             efTestPositionCharges       = 1<<5,
 166             efTestSelectionNames        = 1<<6,
 167             efDontTestCompiledAtoms     = 1<<8
 168         };
 169         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 170
 171         SelectionCollectionDataTest()
 172             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 173         {
 174         }
 175
 176         void setFlags(TestFlags flags) { flags_ = flags; }
 177
 178         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 179         void runCompiler();
 180         void runEvaluate();
 181         void runEvaluateFinal();
 182
 183         void runTest(int                                     natoms,
 184                      const gmx::ConstArrayRef<const char *> &selections);
 185         void runTest(const char                             *filename,
 186                      const gmx::ConstArrayRef<const char *> &selections);
 187
 188     private:
 189         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 190                                    const gmx::Selection &sel, TestFlags flags);
 191
 192         void checkCompiled();
 193
 194         gmx::test::TestReferenceData    data_;
 195         gmx::test::TestReferenceChecker checker_;
 196         size_t                          count_;
 197         int                             framenr_;
 198         TestFlags                       flags_;
 199 };
 200
 201
 202 void
 203 SelectionCollectionDataTest::checkSelection(
 204         gmx::test::TestReferenceChecker *checker,
 205         const gmx::Selection &sel, TestFlags flags)
 206 {
 207     using gmx::test::TestReferenceChecker;
 208
 209     {
 210         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 211         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 212     }
 213     if (flags.test(efTestPositionAtoms)
 214         || flags.test(efTestPositionCoordinates)
 215         || flags.test(efTestPositionMapping)
 216         || flags.test(efTestPositionMasses)
 217         || flags.test(efTestPositionCharges))
 218     {
 219         TestReferenceChecker compound(
 220                 checker->checkSequenceCompound("Positions", sel.posCount()));
 221         for (int i = 0; i < sel.posCount(); ++i)
 222         {
 223             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 224             const gmx::SelectionPosition &p = sel.position(i);
 225             if (flags.test(efTestPositionAtoms))
 226             {
 227                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 228                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 229             }
 230             if (flags.test(efTestPositionCoordinates))
 231             {
 232                 poscompound.checkVector(p.x(), "Coordinates");
 233             }
 234             if (flags.test(efTestPositionMapping))
 235             {
 236                 poscompound.checkInteger(p.refId(), "RefId");
 237                 poscompound.checkInteger(p.mappedId(), "MappedId");
 238             }
 239             if (flags.test(efTestPositionMasses))
 240             {
 241                 poscompound.checkReal(p.mass(), "Mass");
 242             }
 243             if (flags.test(efTestPositionCharges))
 244             {
 245                 poscompound.checkReal(p.charge(), "Charge");
 246             }
 247         }
 248     }
 249 }
 250
 251
 252 void
 253 SelectionCollectionDataTest::runParser(
 254         const gmx::ConstArrayRef<const char *> &selections)
 255 {
 256     using gmx::test::TestReferenceChecker;
 257
 258     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 259     size_t               varcount = 0;
 260     count_ = 0;
 261     for (size_t i = 0; i < selections.size(); ++i)
 262     {
 263         SCOPED_TRACE(std::string("Parsing selection \"")
 264                      + selections[i] + "\"");
 265         gmx::SelectionList result;
 266         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 267         sel_.insert(sel_.end(), result.begin(), result.end());
 268         if (sel_.size() == count_)
 269         {
 270             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 271             TestReferenceChecker varcompound(
 272                     compound.checkCompound("ParsedVariable", id.c_str()));
 273             varcompound.checkString(selections[i], "Input");
 274             ++varcount;
 275         }
 276         else
 277         {
 278             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 279             TestReferenceChecker selcompound(
 280                     compound.checkCompound("ParsedSelection", id.c_str()));
 281             selcompound.checkString(selections[i], "Input");
 282             if (flags_.test(efTestSelectionNames))
 283             {
 284                 selcompound.checkString(sel_[count_].name(), "Name");
 285             }
 286             selcompound.checkString(sel_[count_].selectionText(), "Text");
 287             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 288             ++count_;
 289         }
 290     }
 291 }
 292
 293
 294 void
 295 SelectionCollectionDataTest::runCompiler()
 296 {
 297     ASSERT_NO_THROW_GMX(sc_.compile());
 298     ASSERT_EQ(count_, sel_.size());
 299     checkCompiled();
 300 }
 301
 302
 303 void
 304 SelectionCollectionDataTest::checkCompiled()
 305 {
 306     using gmx::test::TestReferenceChecker;
 307     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 308
 309     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 310     for (size_t i = 0; i < count_; ++i)
 311     {
 312         SCOPED_TRACE(std::string("Checking selection \"") +
 313                      sel_[i].selectionText() + "\"");
 314         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 315         TestReferenceChecker selcompound(
 316                 compound.checkCompound("Selection", id.c_str()));
 317         if (flags_.test(efTestSelectionNames))
 318         {
 319             selcompound.checkString(sel_[i].name(), "Name");
 320         }
 321         if (!flags_.test(efDontTestCompiledAtoms))
 322         {
 323             checkSelection(&selcompound, sel_[i], flags_ & mask);
 324         }
 325     }
 326 }
 327
 328
 329 void
 330 SelectionCollectionDataTest::runEvaluate()
 331 {
 332     using gmx::test::TestReferenceChecker;
 333
 334     ++framenr_;
 335     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 336     std::string          frame = gmx::formatString("Frame%d", framenr_);
 337     TestReferenceChecker compound(
 338             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 339     for (size_t i = 0; i < count_; ++i)
 340     {
 341         SCOPED_TRACE(std::string("Checking selection \"") +
 342                      sel_[i].selectionText() + "\"");
 343         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 344         TestReferenceChecker selcompound(
 345                 compound.checkCompound("Selection", id.c_str()));
 346         checkSelection(&selcompound, sel_[i], flags_);
 347     }
 348 }
 349
 350
 351 void
 352 SelectionCollectionDataTest::runEvaluateFinal()
 353 {
 354     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 355     checkCompiled();
 356 }
 357
 358
 359 void
 360 SelectionCollectionDataTest::runTest(
 361         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 362 {
 363     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 364     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 365     ASSERT_NO_FATAL_FAILURE(runCompiler());
 366 }
 367
 368
 369 void
 370 SelectionCollectionDataTest::runTest(
 371         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 372 {
 373     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 374     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 375     ASSERT_NO_FATAL_FAILURE(runCompiler());
 376     if (flags_.test(efTestEvaluation))
 377     {
 378         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 379         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 380     }
 381 }
 382
 383
 384 /********************************************************************
 385  * Tests for SelectionCollection functionality without reference data
 386  */
 387
 388 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 389 {
 390     EXPECT_FALSE(sc_.requiresTopology());
 391     EXPECT_NO_THROW_GMX(sc_.compile());
 392 }
 393
 394 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 395 {
 396     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 397     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 398     ASSERT_EQ(2U, sel_.size());
 399     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 400     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 401     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 402     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 403     ASSERT_NO_THROW_GMX(sc_.compile());
 404     EXPECT_TRUE(sel_[0].hasVelocities());
 405     EXPECT_TRUE(sel_[1].hasVelocities());
 406     EXPECT_TRUE(sel_[0].hasForces());
 407     EXPECT_TRUE(sel_[1].hasForces());
 408 }
 409
 410 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 411 {
 412     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 413                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 414     // These should match the contents of selfile.dat
 415     ASSERT_EQ(2U, sel_.size());
 416     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 417     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 418 }
 419
 420 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 421 {
 422     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 423     EXPECT_THROW_GMX({
 424                          sc_.parseFromString("resname ~ \"R[A\"");
 425                          sc_.compile();
 426                      }, gmx::InvalidInputError);
 427 }
 428
 429 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 430 {
 431     if (!gmx::Regex::isSupported())
 432     {
 433         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 434         EXPECT_THROW_GMX({
 435                              sc_.parseFromString("resname \"R[AD]\"");
 436                              sc_.compile();
 437                          }, gmx::InvalidInputError);
 438     }
 439 }
 440
 441 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 442 {
 443     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 444                      gmx::InvalidInputError);
 445 }
 446
 447 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 448 {
 449     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 450                      gmx::InvalidInputError);
 451 }
 452
 453 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 454 {
 455     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 456                      gmx::InvalidInputError);
 457 }
 458
 459 // TODO: Tests for more parser errors
 460
 461 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 462 {
 463     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 464     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 465     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 466 }
 467
 468 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 469 {
 470     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 471     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 472     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 473 }
 474
 475 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 476 {
 477     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 478     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 479     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 480     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 481 }
 482
 483 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 484 {
 485     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 486     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 487     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 488     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 489 }
 490
 491 // TODO: Make the check less eager so that it doesn't break other tests, and
 492 // adapt these tests accordingly.
 493 TEST_F(SelectionCollectionTest, DISABLED_HandlesUnsortedGroupReference)
 494 {
 495     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 496     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
 497                      gmx::InconsistentInputError);
 498     EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
 499 }
 500
 501 TEST_F(SelectionCollectionTest, DISABLED_HandlesUnsortedGroupReferenceDelayed)
 502 {
 503     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
 504     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 505     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 506 }
 507
 508 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 509 {
 510     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 511     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 512     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 513 }
 514
 515 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 516 {
 517     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 518     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 519     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 520 }
 521
 522 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 523 {
 524     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 525     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 526     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 527 }
 528
 529 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 530 {
 531     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 532     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 533     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 534 }
 535
 536 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 537 {
 538     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 539     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 540     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 541 }
 542
 543 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 544 {
 545     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 546     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 547     ASSERT_NO_THROW_GMX(sc_.compile());
 548     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 549 }
 550
 551 // TODO: Tests for evaluation errors
 552
 553
 554 /********************************************************************
 555  * Tests for selection keywords
 556  */
 557
 558 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 559 {
 560     static const char * const selections[] = {
 561         "all",
 562         "none"
 563     };
 564     runTest(10, selections);
 565 }
 566
 567 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 568 {
 569     static const char * const selections[] = {
 570         "atomnr 1 to 3 6 to 8",
 571         "atomnr 4 2 5 to 7",
 572         "atomnr <= 5"
 573     };
 574     runTest(10, selections);
 575 }
 576
 577 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 578 {
 579     static const char * const selections[] = {
 580         "resnr 1 2 5",
 581         "resid 4 to 3"
 582     };
 583     runTest("simple.gro", selections);
 584 }
 585
 586 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 587 {
 588     static const char * const selections[] = {
 589         "resindex 1 4",
 590         "residue 1 3"
 591     };
 592     runTest("simple.pdb", selections);
 593 }
 594
 595 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 596 {
 597     static const char * const selections[] = {
 598         "molindex 1 4",
 599         "molecule 2 3 5"
 600     };
 601     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 602     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 603     topManager_.initUniformMolecules(3);
 604     ASSERT_NO_FATAL_FAILURE(runCompiler());
 605 }
 606
 607 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 608 {
 609     static const char * const selections[] = {
 610         "name CB",
 611         "atomname S1 S2"
 612     };
 613     runTest("simple.gro", selections);
 614 }
 615
 616 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 617 {
 618     static const char * const selections[] = {
 619         "name HG21",
 620         "name 1HG2",
 621         "pdbname HG21 CB",
 622         "pdbatomname 1HG2"
 623     };
 624     runTest("simple.pdb", selections);
 625 }
 626
 627
 628 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 629 {
 630     static const char * const selections[] = {
 631         "atomtype CA"
 632     };
 633     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 634     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 635     const char *const types[] = { "CA", "SA", "SB" };
 636     topManager_.initAtomTypes(types);
 637     ASSERT_NO_FATAL_FAILURE(runCompiler());
 638 }
 639
 640 TEST_F(SelectionCollectionDataTest, HandlesChain)
 641 {
 642     static const char * const selections[] = {
 643         "chain A",
 644         "chain B"
 645     };
 646     runTest("simple.pdb", selections);
 647 }
 648
 649 TEST_F(SelectionCollectionDataTest, HandlesMass)
 650 {
 651     static const char * const selections[] = {
 652         "mass > 5"
 653     };
 654     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 655     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 656     for (int i = 0; i < top_->atoms.nr; ++i)
 657     {
 658         top_->atoms.atom[i].m = 1.0 + i;
 659     }
 660     ASSERT_NO_FATAL_FAILURE(runCompiler());
 661 }
 662
 663 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 664 {
 665     static const char * const selections[] = {
 666         "charge < 0.5"
 667     };
 668     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 669     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 670     for (int i = 0; i < top_->atoms.nr; ++i)
 671     {
 672         top_->atoms.atom[i].q = i / 10.0;
 673     }
 674     ASSERT_NO_FATAL_FAILURE(runCompiler());
 675 }
 676
 677 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 678 {
 679     static const char * const selections[] = {
 680         "altloc \" \"",
 681         "altloc A"
 682     };
 683     runTest("simple.pdb", selections);
 684 }
 685
 686 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 687 {
 688     static const char * const selections[] = {
 689         "insertcode \" \"",
 690         "insertcode A"
 691     };
 692     runTest("simple.pdb", selections);
 693 }
 694
 695 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 696 {
 697     static const char * const selections[] = {
 698         "occupancy 1",
 699         "occupancy < .5"
 700     };
 701     runTest("simple.pdb", selections);
 702 }
 703
 704 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 705 {
 706     static const char * const selections[] = {
 707         "beta 0",
 708         "beta >= 0.3"
 709     };
 710     runTest("simple.pdb", selections);
 711 }
 712
 713 TEST_F(SelectionCollectionDataTest, HandlesResname)
 714 {
 715     static const char * const selections[] = {
 716         "resname RA",
 717         "resname RB RC"
 718     };
 719     runTest("simple.gro", selections);
 720 }
 721
 722 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 723 {
 724     static const char * const selections[] = {
 725         "x < 3",
 726         "y >= 3",
 727         "x {-1 to 2}"
 728     };
 729     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 730     runTest("simple.gro", selections);
 731 }
 732
 733
 734 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 735 {
 736     static const char * const selections[] = {
 737         "same residue as atomnr 1 4 12"
 738     };
 739     runTest("simple.gro", selections);
 740 }
 741
 742
 743 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 744 {
 745     static const char * const selections[] = {
 746         "same resname as atomnr 1 14"
 747     };
 748     runTest("simple.gro", selections);
 749 }
 750
 751
 752 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 753 {
 754     static const char * const selections[] = {
 755         "cog of resnr 1 3",
 756         "res_cog of name CB and resnr 1 3",
 757         "whole_res_cog of name CB and resnr 1 3",
 758         "part_res_cog of x < 3",
 759         "dyn_res_cog of x < 3"
 760     };
 761     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 762              | efTestPositionAtoms);
 763     runTest("simple.gro", selections);
 764 }
 765
 766
 767 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 768 {
 769     static const char * const selections[] = {
 770         "distance from cog of resnr 1 < 2"
 771     };
 772     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 773     runTest("simple.gro", selections);
 774 }
 775
 776
 777 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 778 {
 779     static const char * const selections[] = {
 780         "mindistance from resnr 1 < 2"
 781     };
 782     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 783     runTest("simple.gro", selections);
 784 }
 785
 786
 787 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 788 {
 789     static const char * const selections[] = {
 790         "within 1 of resnr 2"
 791     };
 792     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 793     runTest("simple.gro", selections);
 794 }
 795
 796
 797 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 798 {
 799     // Both of these should evaluate to empty on a correct implementation.
 800     static const char * const selections[] = {
 801         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 802         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 803     };
 804     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 805     runTest("sphere.gro", selections);
 806 }
 807
 808
 809 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 810 {
 811     static const char * const selections[] = {
 812         "all permute 3 1 2",
 813         "res_cog of resnr 1 to 4 permute 2 1",
 814         "name CB S1 and res_cog x < 3 permute 2 1"
 815     };
 816     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 817              | efTestPositionAtoms | efTestPositionMapping);
 818     runTest("simple.gro", selections);
 819 }
 820
 821
 822 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 823 {
 824     static const char * const selections[] = {
 825         "name S2 plus name S1",
 826         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 827         "name S1 and y < 3 plus res_cog of x < 2.5"
 828     };
 829     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 830              | efTestPositionAtoms | efTestPositionMapping);
 831     runTest("simple.gro", selections);
 832 }
 833
 834
 835 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 836 {
 837     static const char * const selections[] = {
 838         "name S2 merge name S1",
 839         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 840         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 841     };
 842     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 843              | efTestPositionAtoms | efTestPositionMapping);
 844     runTest("simple.gro", selections);
 845 }
 846
 847
 848 /********************************************************************
 849  * Tests for generic selection evaluation
 850  */
 851
 852 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 853 {
 854     static const char * const selections[] = {
 855         "name CB",
 856         "y > 2",
 857         "res_cog of y > 2"
 858     };
 859     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 860              | efTestPositionMasses | efTestPositionCharges);
 861     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 862     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 863     for (int i = 0; i < top_->atoms.nr; ++i)
 864     {
 865         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 866         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 867     }
 868     ASSERT_NO_FATAL_FAILURE(runCompiler());
 869     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 870     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 871 }
 872
 873 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 874 {
 875     static const char * const selections[] = {
 876         "atomnr 1 to 3 8 to 9",
 877         "y > 2",
 878         "cog of (y > 2)"
 879     };
 880     setFlags(TestFlags() | efTestPositionAtoms
 881              | efTestPositionMasses | efTestPositionCharges);
 882     runTest(10, selections);
 883 }
 884
 885
 886 /********************************************************************
 887  * Tests for selection syntactic constructs
 888  */
 889
 890 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 891 {
 892     static const char * const selections[] = {
 893         "\"GroupSelection\" group \"GrpA\"",
 894         "\"DynamicSelection\" x < 5",
 895         "y < 3"
 896     };
 897     setFlags(TestFlags() | efTestSelectionNames);
 898     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 899     runTest(10, selections);
 900 }
 901
 902 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 903 {
 904     static const char * const selections[] = {
 905         "group \"GrpA\"",
 906         "GrpB",
 907         "1",
 908         "group \"GrpB\" and resname RB"
 909     };
 910     setFlags(TestFlags() | efTestSelectionNames);
 911     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 912     runTest("simple.gro", selections);
 913 }
 914
 915 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 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_FATAL_FAILURE(runParser(selections));
 925     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 926     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 927     ASSERT_NO_FATAL_FAILURE(runCompiler());
 928 }
 929
 930 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
 931 {
 932     static const char * const selections[] = {
 933         "group \"GrpUnsorted\"",
 934         "GrpUnsorted",
 935         "2",
 936         "res_cog of group \"GrpUnsorted\"",
 937         "group \"GrpUnsorted\" permute 2 1"
 938     };
 939     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
 940              | efTestSelectionNames);
 941     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 942     runTest("simple.gro", selections);
 943 }
 944
 945 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 946 {
 947     static const char * const selections[] = {
 948         "[1, -2, 3.5]"
 949     };
 950     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 951     runTest("simple.gro", selections);
 952 }
 953
 954
 955 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 956 {
 957     static const char * const selections[] = {
 958         "within 1 of [2, 1, 0]"
 959     };
 960     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 961     runTest("simple.gro", selections);
 962 }
 963
 964
 965 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 966 {
 967     static const char * const selections[] = {
 968         "name = S1 \"C?\"",
 969         "name ? S1 \"C?\""
 970     };
 971     runTest("simple.gro", selections);
 972 }
 973
 974
 975 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 976 {
 977     static const char * const selections[] = {
 978         "name \"S?\"",
 979         "name ? \"S?\""
 980     };
 981     runTest("simple.gro", selections);
 982 }
 983
 984
 985 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 986 {
 987     static const char * const selections[] = {
 988         "resname \"R[BD]\"",
 989         "resname ~ \"R[BD]\""
 990     };
 991     if (gmx::Regex::isSupported())
 992     {
 993         runTest("simple.gro", selections);
 994     }
 995 }
 996
 997
 998 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 999 {
1000     static const char * const selections[] = {
1001         "atomnr 1 to 5 and atomnr 2 to 7",
1002         "atomnr 1 to 5 or not atomnr 3 to 8",
1003         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1004         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1005         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1006     };
1007     runTest(10, selections);
1008 }
1009
1010
1011 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1012 {
1013     static const char * const selections[] = {
1014         "same residue as (atomnr 3 5 13 or y > 5)",
1015         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1016     };
1017     setFlags(TestFlags() | efTestEvaluation);
1018     runTest("simple.gro", selections);
1019 }
1020
1021
1022 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1023 {
1024     static const char * const selections[] = {
1025         "none and x > 2",
1026         "none and same resname as resnr 2"
1027     };
1028     runTest("simple.gro", selections);
1029 }
1030
1031
1032 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1033 {
1034     static const char * const selections[] = {
1035         "x > 2",
1036         "2 < x",
1037         "y > resnr",
1038         "resnr < 2.5",
1039         "2.5 > resnr"
1040     };
1041     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1042     runTest("simple.gro", selections);
1043 }
1044
1045
1046 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1047 {
1048     static const char * const selections[] = {
1049         "x+1 > 3",
1050         "(y-1)^2 <= 1",
1051         "x+--1 > 3",
1052         "-x+-1 < -3"
1053     };
1054     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1055     runTest("simple.gro", selections);
1056 }
1057
1058
1059 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1060 {
1061     static const char * const selections[] = {
1062         "value = x + y",
1063         "value <= 4",
1064         "index = resnr",
1065         "index < 3"
1066     };
1067     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1068     runTest("simple.gro", selections);
1069 }
1070
1071
1072 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1073 {
1074     static const char * const selections[] = {
1075         "value = x + y",
1076         "resname RA and value <= 4",
1077         "resname RA RB and x < 3 and value <= 4",
1078         "index = atomnr",
1079         "resname RA and index < 3",
1080         "resname RB and y < 3 and index < 6"
1081     };
1082     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1083     runTest("simple.gro", selections);
1084 }
1085
1086
1087 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1088 {
1089     static const char * const selections[] = {
1090         "foo = res_cog of resname RA",
1091         "foo",
1092         "within 1 of foo",
1093         "bar = cog of resname RA",
1094         "bar",
1095         "within 1 of bar"
1096     };
1097     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1098     runTest("simple.gro", selections);
1099 }
1100
1101
1102 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1103 {
1104     static const char * const selections[] = {
1105         "constpos = [1.0, 2.5, 0.5]",
1106         "constpos",
1107         "within 2 of constpos"
1108     };
1109     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1110              | efTestPositionAtoms);
1111     runTest("simple.gro", selections);
1112 }
1113
1114
1115 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1116 {
1117     static const char * const selections[] = {
1118         "constint = 4",
1119         "constreal1 = 0.5",
1120         "constreal2 = 2.7",
1121         "resnr < constint",
1122         "x + constreal1 < constreal2"
1123     };
1124     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1125     runTest("simple.gro", selections);
1126 }
1127
1128
1129 /********************************************************************
1130  * Tests for complex boolean syntax
1131  */
1132
1133 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1134 {
1135     static const char * const selections[] = {
1136         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1137         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1138         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1139         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1140         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1141     };
1142     runTest(10, selections);
1143 }
1144
1145
1146 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1147 {
1148     static const char * const selections[] = {
1149         "foo = atomnr 4 to 7 or x < 2",
1150         "atomnr 1 to 4 and foo",
1151         "atomnr 2 to 6 and y < 3 and foo",
1152         "atomnr 6 to 10 and not foo"
1153     };
1154     runTest(10, selections);
1155 }
1156
1157
1158 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1159 {
1160     static const char * const selections[] = {
1161         "foo = atomnr 4 to 7",
1162         "bar = foo and x < 2",
1163         "bar2 = foo and y < 2",
1164         "atomnr 1 to 4 and bar",
1165         "atomnr 2 to 6 and y < 3 and bar2",
1166         "atomnr 6 to 10 and not foo"
1167     };
1168     runTest(10, selections);
1169 }
1170
1171
1172 /********************************************************************
1173  * Tests for complex subexpression cases
1174  *
1175  * These tests use some knowledge of the implementation to trigger different
1176  * paths in the code.
1177  */
1178
1179 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1180 {
1181     static const char * const selections[] = {
1182         "unused1 = atomnr 1 to 3",
1183         "foo = atomnr 4 to 7",
1184         "atomnr 1 to 6 and foo",
1185         "unused2 = atomnr 3 to 5"
1186     };
1187     runTest(10, selections);
1188 }
1189
1190
1191 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1192 {
1193     static const char * const selections[] = {
1194         "foo = atomnr 4 to 7 and x < 2",
1195         "atomnr 1 to 5 and foo",
1196         "atomnr 3 to 7 and foo"
1197     };
1198     runTest(10, selections);
1199 }
1200
1201
1202 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1203 {
1204     static const char * const selections[] = {
1205         "foo = atomnr 4 to 7 and x < 2",
1206         "atomnr 1 to 6 and foo",
1207         "within 1 of foo",
1208         "foo"
1209     };
1210     runTest(10, selections);
1211 }
1212
1213
1214 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1215 {
1216     static const char * const selections[] = {
1217         "foo = atomnr 1 to 8 and x < 10",
1218         "atomnr 1 to 5 and y < 10 and foo",
1219         "foo"
1220     };
1221     setFlags(TestFlags() | efTestEvaluation);
1222     runTest("simple.gro", selections);
1223 }
1224
1225
1226 } // namespace