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 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  96 {
  97     options->addOption(gmx::IntegerOption("seldebug")
  98                            .store(&SelectionCollectionTest::s_debugLevel)
  99                            .description("Set selection debug level"));
 100 }
 101
 102 SelectionCollectionTest::SelectionCollectionTest()
 103     : top_(NULL), frame_(NULL), grps_(NULL)
 104 {
 105     topManager_.requestFrame();
 106     sc_.setDebugLevel(s_debugLevel);
 107     sc_.setReferencePosType("atom");
 108     sc_.setOutputPosType("atom");
 109 }
 110
 111 SelectionCollectionTest::~SelectionCollectionTest()
 112 {
 113     if (grps_ != NULL)
 114     {
 115         gmx_ana_indexgrps_free(grps_);
 116     }
 117 }
 118
 119 void
 120 SelectionCollectionTest::loadTopology(const char *filename)
 121 {
 122     topManager_.loadTopology(filename);
 123     setTopology();
 124 }
 125
 126 void
 127 SelectionCollectionTest::setTopology()
 128 {
 129     top_   = topManager_.topology();
 130     frame_ = topManager_.frame();
 131
 132     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 133 }
 134
 135 void
 136 SelectionCollectionTest::loadIndexGroups(const char *filename)
 137 {
 138     GMX_RELEASE_ASSERT(grps_ == NULL,
 139                        "External groups can only be loaded once");
 140     std::string fullpath =
 141         gmx::test::TestFileManager::getInputFilePath(filename);
 142     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 143     sc_.setIndexGroups(grps_);
 144 }
 145
 146
 147 /********************************************************************
 148  * Test fixture for selection testing with reference data
 149  */
 150
 151 class SelectionCollectionDataTest : public SelectionCollectionTest
 152 {
 153     public:
 154         enum TestFlag
 155         {
 156             efTestEvaluation            = 1<<0,
 157             efTestPositionAtoms         = 1<<1,
 158             efTestPositionCoordinates   = 1<<2,
 159             efTestPositionMapping       = 1<<3,
 160             efTestPositionMasses        = 1<<4,
 161             efTestPositionCharges       = 1<<5,
 162             efTestSelectionNames        = 1<<6,
 163             efDontTestCompiledAtoms     = 1<<8
 164         };
 165         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 166
 167         SelectionCollectionDataTest()
 168             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 169         {
 170         }
 171
 172         void setFlags(TestFlags flags) { flags_ = flags; }
 173
 174         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 175         void runCompiler();
 176         void runEvaluate();
 177         void runEvaluateFinal();
 178
 179         void runTest(int                                     natoms,
 180                      const gmx::ConstArrayRef<const char *> &selections);
 181         void runTest(const char                             *filename,
 182                      const gmx::ConstArrayRef<const char *> &selections);
 183
 184     private:
 185         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 186                                    const gmx::Selection &sel, TestFlags flags);
 187
 188         void checkCompiled();
 189
 190         gmx::test::TestReferenceData    data_;
 191         gmx::test::TestReferenceChecker checker_;
 192         size_t                          count_;
 193         int                             framenr_;
 194         TestFlags                       flags_;
 195 };
 196
 197
 198 void
 199 SelectionCollectionDataTest::checkSelection(
 200         gmx::test::TestReferenceChecker *checker,
 201         const gmx::Selection &sel, TestFlags flags)
 202 {
 203     using gmx::test::TestReferenceChecker;
 204
 205     {
 206         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 207         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 208     }
 209     if (flags.test(efTestPositionAtoms)
 210         || flags.test(efTestPositionCoordinates)
 211         || flags.test(efTestPositionMapping)
 212         || flags.test(efTestPositionMasses)
 213         || flags.test(efTestPositionCharges))
 214     {
 215         TestReferenceChecker compound(
 216                 checker->checkSequenceCompound("Positions", sel.posCount()));
 217         for (int i = 0; i < sel.posCount(); ++i)
 218         {
 219             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 220             const gmx::SelectionPosition &p = sel.position(i);
 221             if (flags.test(efTestPositionAtoms))
 222             {
 223                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 224                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 225             }
 226             if (flags.test(efTestPositionCoordinates))
 227             {
 228                 poscompound.checkVector(p.x(), "Coordinates");
 229             }
 230             if (flags.test(efTestPositionMapping))
 231             {
 232                 poscompound.checkInteger(p.refId(), "RefId");
 233                 poscompound.checkInteger(p.mappedId(), "MappedId");
 234             }
 235             if (flags.test(efTestPositionMasses))
 236             {
 237                 poscompound.checkReal(p.mass(), "Mass");
 238             }
 239             if (flags.test(efTestPositionCharges))
 240             {
 241                 poscompound.checkReal(p.charge(), "Charge");
 242             }
 243         }
 244     }
 245 }
 246
 247
 248 void
 249 SelectionCollectionDataTest::runParser(
 250         const gmx::ConstArrayRef<const char *> &selections)
 251 {
 252     using gmx::test::TestReferenceChecker;
 253
 254     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 255     size_t               varcount = 0;
 256     count_ = 0;
 257     for (size_t i = 0; i < selections.size(); ++i)
 258     {
 259         SCOPED_TRACE(std::string("Parsing selection \"")
 260                      + selections[i] + "\"");
 261         gmx::SelectionList result;
 262         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 263         sel_.insert(sel_.end(), result.begin(), result.end());
 264         if (sel_.size() == count_)
 265         {
 266             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 267             TestReferenceChecker varcompound(
 268                     compound.checkCompound("ParsedVariable", id.c_str()));
 269             varcompound.checkString(selections[i], "Input");
 270             ++varcount;
 271         }
 272         else
 273         {
 274             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 275             TestReferenceChecker selcompound(
 276                     compound.checkCompound("ParsedSelection", id.c_str()));
 277             selcompound.checkString(selections[i], "Input");
 278             if (flags_.test(efTestSelectionNames))
 279             {
 280                 selcompound.checkString(sel_[count_].name(), "Name");
 281             }
 282             selcompound.checkString(sel_[count_].selectionText(), "Text");
 283             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 284             ++count_;
 285         }
 286     }
 287 }
 288
 289
 290 void
 291 SelectionCollectionDataTest::runCompiler()
 292 {
 293     ASSERT_NO_THROW_GMX(sc_.compile());
 294     ASSERT_EQ(count_, sel_.size());
 295     checkCompiled();
 296 }
 297
 298
 299 void
 300 SelectionCollectionDataTest::checkCompiled()
 301 {
 302     using gmx::test::TestReferenceChecker;
 303     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 304
 305     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 306     for (size_t i = 0; i < count_; ++i)
 307     {
 308         SCOPED_TRACE(std::string("Checking selection \"") +
 309                      sel_[i].selectionText() + "\"");
 310         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 311         TestReferenceChecker selcompound(
 312                 compound.checkCompound("Selection", id.c_str()));
 313         if (flags_.test(efTestSelectionNames))
 314         {
 315             selcompound.checkString(sel_[i].name(), "Name");
 316         }
 317         if (!flags_.test(efDontTestCompiledAtoms))
 318         {
 319             checkSelection(&selcompound, sel_[i], flags_ & mask);
 320         }
 321     }
 322 }
 323
 324
 325 void
 326 SelectionCollectionDataTest::runEvaluate()
 327 {
 328     using gmx::test::TestReferenceChecker;
 329
 330     ++framenr_;
 331     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 332     std::string          frame = gmx::formatString("Frame%d", framenr_);
 333     TestReferenceChecker compound(
 334             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 335     for (size_t i = 0; i < count_; ++i)
 336     {
 337         SCOPED_TRACE(std::string("Checking selection \"") +
 338                      sel_[i].selectionText() + "\"");
 339         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 340         TestReferenceChecker selcompound(
 341                 compound.checkCompound("Selection", id.c_str()));
 342         checkSelection(&selcompound, sel_[i], flags_);
 343     }
 344 }
 345
 346
 347 void
 348 SelectionCollectionDataTest::runEvaluateFinal()
 349 {
 350     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 351     checkCompiled();
 352 }
 353
 354
 355 void
 356 SelectionCollectionDataTest::runTest(
 357         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 358 {
 359     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 360     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 361     ASSERT_NO_FATAL_FAILURE(runCompiler());
 362 }
 363
 364
 365 void
 366 SelectionCollectionDataTest::runTest(
 367         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 368 {
 369     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 370     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 371     ASSERT_NO_FATAL_FAILURE(runCompiler());
 372     if (flags_.test(efTestEvaluation))
 373     {
 374         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 375         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 376     }
 377 }
 378
 379
 380 /********************************************************************
 381  * Tests for SelectionCollection functionality without reference data
 382  */
 383
 384 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 385 {
 386     EXPECT_FALSE(sc_.requiresTopology());
 387     EXPECT_NO_THROW_GMX(sc_.compile());
 388 }
 389
 390 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 391 {
 392     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 393     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 394     ASSERT_EQ(2U, sel_.size());
 395     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 396     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 397     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 398     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 399     ASSERT_NO_THROW_GMX(sc_.compile());
 400     EXPECT_TRUE(sel_[0].hasVelocities());
 401     EXPECT_TRUE(sel_[1].hasVelocities());
 402     EXPECT_TRUE(sel_[0].hasForces());
 403     EXPECT_TRUE(sel_[1].hasForces());
 404 }
 405
 406 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 407 {
 408     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 409                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 410     // These should match the contents of selfile.dat
 411     ASSERT_EQ(2U, sel_.size());
 412     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 413     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 414 }
 415
 416 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 417 {
 418     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 419     EXPECT_THROW_GMX({
 420                          sc_.parseFromString("resname ~ \"R[A\"");
 421                          sc_.compile();
 422                      }, gmx::InvalidInputError);
 423 }
 424
 425 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 426 {
 427     if (!gmx::Regex::isSupported())
 428     {
 429         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 430         EXPECT_THROW_GMX({
 431                              sc_.parseFromString("resname \"R[AD]\"");
 432                              sc_.compile();
 433                          }, gmx::InvalidInputError);
 434     }
 435 }
 436
 437 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 438 {
 439     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 440                      gmx::InvalidInputError);
 441 }
 442
 443 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 444 {
 445     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 446                      gmx::InvalidInputError);
 447 }
 448
 449 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 450 {
 451     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 452                      gmx::InvalidInputError);
 453 }
 454
 455 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 456 {
 457     EXPECT_THROW_GMX(sc_.parseFromString("resname help"),
 458                      gmx::InvalidInputError);
 459 }
 460
 461 // TODO: Tests for more parser errors
 462
 463 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 464 {
 465     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 466     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 467     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 468 }
 469
 470 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 471 {
 472     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 473     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 474     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 475 }
 476
 477 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 478 {
 479     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 480     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 481     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 482     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 483 }
 484
 485 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 486 {
 487     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 488     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 489     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 490     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 491 }
 492
 493 TEST_F(SelectionCollectionTest, 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, 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, HandlesConstantPositions)
 931 {
 932     static const char * const selections[] = {
 933         "[1, -2, 3.5]"
 934     };
 935     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 936     runTest("simple.gro", selections);
 937 }
 938
 939
 940 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 941 {
 942     static const char * const selections[] = {
 943         "within 1 of [2, 1, 0]"
 944     };
 945     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 946     runTest("simple.gro", selections);
 947 }
 948
 949
 950 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 951 {
 952     static const char * const selections[] = {
 953         "name = S1 \"C?\"",
 954         "name ? S1 \"C?\""
 955     };
 956     runTest("simple.gro", selections);
 957 }
 958
 959
 960 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 961 {
 962     static const char * const selections[] = {
 963         "name \"S?\"",
 964         "name ? \"S?\""
 965     };
 966     runTest("simple.gro", selections);
 967 }
 968
 969
 970 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 971 {
 972     static const char * const selections[] = {
 973         "resname \"R[BD]\"",
 974         "resname ~ \"R[BD]\""
 975     };
 976     if (gmx::Regex::isSupported())
 977     {
 978         runTest("simple.gro", selections);
 979     }
 980 }
 981
 982
 983 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 984 {
 985     static const char * const selections[] = {
 986         "atomnr 1 to 5 and atomnr 2 to 7",
 987         "atomnr 1 to 5 or not atomnr 3 to 8",
 988         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 989         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 990         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 991     };
 992     runTest(10, selections);
 993 }
 994
 995
 996 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
 997 {
 998     static const char * const selections[] = {
 999         "same residue as (atomnr 3 5 13 or y > 5)",
1000         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1001     };
1002     setFlags(TestFlags() | efTestEvaluation);
1003     runTest("simple.gro", selections);
1004 }
1005
1006
1007 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1008 {
1009     static const char * const selections[] = {
1010         "none and x > 2",
1011         "none and same resname as resnr 2"
1012     };
1013     runTest("simple.gro", selections);
1014 }
1015
1016
1017 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1018 {
1019     static const char * const selections[] = {
1020         "x > 2",
1021         "2 < x",
1022         "y > resnr",
1023         "resnr < 2.5",
1024         "2.5 > resnr"
1025     };
1026     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1027     runTest("simple.gro", selections);
1028 }
1029
1030
1031 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1032 {
1033     static const char * const selections[] = {
1034         "x+1 > 3",
1035         "(y-1)^2 <= 1",
1036         "x+--1 > 3",
1037         "-x+-1 < -3"
1038     };
1039     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1040     runTest("simple.gro", selections);
1041 }
1042
1043
1044 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1045 {
1046     static const char * const selections[] = {
1047         "value = x + y",
1048         "value <= 4",
1049         "index = resnr",
1050         "index < 3"
1051     };
1052     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1053     runTest("simple.gro", selections);
1054 }
1055
1056
1057 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1058 {
1059     static const char * const selections[] = {
1060         "value = x + y",
1061         "resname RA and value <= 4",
1062         "resname RA RB and x < 3 and value <= 4",
1063         "index = atomnr",
1064         "resname RA and index < 3",
1065         "resname RB and y < 3 and index < 6"
1066     };
1067     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1068     runTest("simple.gro", selections);
1069 }
1070
1071
1072 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1073 {
1074     static const char * const selections[] = {
1075         "foo = res_cog of resname RA",
1076         "foo",
1077         "within 1 of foo",
1078         "bar = cog of resname RA",
1079         "bar",
1080         "within 1 of bar"
1081     };
1082     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1083     runTest("simple.gro", selections);
1084 }
1085
1086
1087 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1088 {
1089     static const char * const selections[] = {
1090         "constpos = [1.0, 2.5, 0.5]",
1091         "constpos",
1092         "within 2 of constpos"
1093     };
1094     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1095              | efTestPositionAtoms);
1096     runTest("simple.gro", selections);
1097 }
1098
1099
1100 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1101 {
1102     static const char * const selections[] = {
1103         "constint = 4",
1104         "constreal1 = 0.5",
1105         "constreal2 = 2.7",
1106         "resnr < constint",
1107         "x + constreal1 < constreal2"
1108     };
1109     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1110     runTest("simple.gro", selections);
1111 }
1112
1113
1114 /********************************************************************
1115  * Tests for complex boolean syntax
1116  */
1117
1118 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1119 {
1120     static const char * const selections[] = {
1121         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1122         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1123         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1124         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1125         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1126     };
1127     runTest(10, selections);
1128 }
1129
1130
1131 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1132 {
1133     static const char * const selections[] = {
1134         "foo = atomnr 4 to 7 or x < 2",
1135         "atomnr 1 to 4 and foo",
1136         "atomnr 2 to 6 and y < 3 and foo",
1137         "atomnr 6 to 10 and not foo"
1138     };
1139     runTest(10, selections);
1140 }
1141
1142
1143 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1144 {
1145     static const char * const selections[] = {
1146         "foo = atomnr 4 to 7",
1147         "bar = foo and x < 2",
1148         "bar2 = foo and y < 2",
1149         "atomnr 1 to 4 and bar",
1150         "atomnr 2 to 6 and y < 3 and bar2",
1151         "atomnr 6 to 10 and not foo"
1152     };
1153     runTest(10, selections);
1154 }
1155
1156
1157 /********************************************************************
1158  * Tests for complex subexpression cases
1159  *
1160  * These tests use some knowledge of the implementation to trigger different
1161  * paths in the code.
1162  */
1163
1164 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1165 {
1166     static const char * const selections[] = {
1167         "unused1 = atomnr 1 to 3",
1168         "foo = atomnr 4 to 7",
1169         "atomnr 1 to 6 and foo",
1170         "unused2 = atomnr 3 to 5"
1171     };
1172     runTest(10, selections);
1173 }
1174
1175
1176 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1177 {
1178     static const char * const selections[] = {
1179         "foo = atomnr 4 to 7 and x < 2",
1180         "atomnr 1 to 5 and foo",
1181         "atomnr 3 to 7 and foo"
1182     };
1183     runTest(10, selections);
1184 }
1185
1186
1187 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1188 {
1189     static const char * const selections[] = {
1190         "foo = atomnr 4 to 7 and x < 2",
1191         "atomnr 1 to 6 and foo",
1192         "within 1 of foo",
1193         "foo"
1194     };
1195     runTest(10, selections);
1196 }
1197
1198
1199 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1200 {
1201     static const char * const selections[] = {
1202         "foo = atomnr 1 to 8 and x < 10",
1203         "atomnr 1 to 5 and y < 10 and foo",
1204         "foo"
1205     };
1206     setFlags(TestFlags() | efTestEvaluation);
1207     runTest("simple.gro", selections);
1208 }
1209
1210
1211 } // namespace