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/legacyheaders/smalloc.h"
  45 #include "gromacs/legacyheaders/statutil.h"
  46 #include "gromacs/legacyheaders/tpxio.h"
  47 #include "gromacs/legacyheaders/vec.h"
  48
  49 #include "gromacs/options/basicoptions.h"
  50 #include "gromacs/options/options.h"
  51 #include "gromacs/selection/selectioncollection.h"
  52 #include "gromacs/selection/selection.h"
  53 #include "gromacs/utility/exceptions.h"
  54 #include "gromacs/utility/flags.h"
  55 #include "gromacs/utility/gmxregex.h"
  56 #include "gromacs/utility/stringutil.h"
  57
  58 #include "testutils/refdata.h"
  59 #include "testutils/testasserts.h"
  60 #include "testutils/testfilemanager.h"
  61 #include "testutils/testoptions.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 void SetUpTestCase();
  74
  75         static int               s_debugLevel;
  76
  77         SelectionCollectionTest();
  78         ~SelectionCollectionTest();
  79
  80         void setAtomCount(int natoms)
  81         {
  82             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  83         }
  84         void loadTopology(const char *filename);
  85
  86         gmx::SelectionCollection sc_;
  87         gmx::SelectionList       sel_;
  88         t_topology              *top_;
  89         t_trxframe              *frame_;
  90 };
  91
  92 int SelectionCollectionTest::s_debugLevel = 0;
  93
  94 void SelectionCollectionTest::SetUpTestCase()
  95 {
  96     gmx::Options options(NULL, NULL);
  97     options.addOption(gmx::IntegerOption("seldebug").store(&s_debugLevel));
  98     gmx::test::parseTestOptions(&options);
  99 }
 100
 101
 102 SelectionCollectionTest::SelectionCollectionTest()
 103     : top_(NULL), frame_(NULL)
 104 {
 105     sc_.setDebugLevel(s_debugLevel);
 106     sc_.setReferencePosType("atom");
 107     sc_.setOutputPosType("atom");
 108 }
 109
 110
 111 SelectionCollectionTest::~SelectionCollectionTest()
 112 {
 113     if (top_ != NULL)
 114     {
 115         free_t_atoms(&top_->atoms, TRUE);
 116         done_top(top_);
 117         sfree(top_);
 118     }
 119
 120     if (frame_ != NULL)
 121     {
 122         sfree(frame_->x);
 123         sfree(frame_);
 124     }
 125 }
 126
 127
 128 void
 129 SelectionCollectionTest::loadTopology(const char *filename)
 130 {
 131     char    title[STRLEN];
 132     int     ePBC;
 133     rvec   *xtop;
 134     matrix  box;
 135
 136     snew(top_, 1);
 137     read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
 138                   title, top_, &ePBC, &xtop, NULL, box, FALSE);
 139
 140     snew(frame_, 1);
 141     frame_->flags  = TRX_NEED_X;
 142     frame_->natoms = top_->atoms.nr;
 143     frame_->bX     = TRUE;
 144     snew(frame_->x, frame_->natoms);
 145     memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
 146     frame_->bBox   = TRUE;
 147     copy_mat(box, frame_->box);
 148
 149     sfree(xtop);
 150
 151     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 152 }
 153
 154
 155 /********************************************************************
 156  * Test fixture for selection testing with reference data
 157  */
 158
 159 class SelectionCollectionDataTest : public SelectionCollectionTest
 160 {
 161     public:
 162         enum TestFlag
 163         {
 164             efTestEvaluation            = 1<<0,
 165             efTestPositionAtoms         = 1<<1,
 166             efTestPositionCoordinates   = 1<<2,
 167             efTestPositionMapping       = 1<<3,
 168             efTestPositionMasses        = 1<<4,
 169             efTestPositionCharges       = 1<<5,
 170             efDontTestCompiledAtoms     = 1<<8
 171         };
 172         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 173
 174         SelectionCollectionDataTest()
 175             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 176         {
 177         }
 178
 179         void setFlags(TestFlags flags) { flags_ = flags; }
 180
 181         template <size_t count>
 182         void runTest(int natoms, const char *const (&selections)[count])
 183         {
 184             runTest(natoms, selections, count);
 185         }
 186         template <size_t count>
 187         void runTest(const char *filename, const char *const (&selections)[count])
 188         {
 189             runTest(filename, selections, count);
 190         }
 191
 192         template <size_t count>
 193         void runParser(const char *const (&selections)[count])
 194         {
 195             runParser(selections, count);
 196         }
 197
 198         void runCompiler();
 199         void runEvaluate();
 200         void runEvaluateFinal();
 201
 202     private:
 203         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 204                                    const gmx::Selection &sel, TestFlags flags);
 205
 206         void runTest(int natoms, const char *const *selections, size_t count);
 207         void runTest(const char *filename, const char *const *selections,
 208                      size_t count);
 209         void runParser(const char *const *selections, size_t count);
 210
 211         void checkCompiled();
 212
 213         gmx::test::TestReferenceData    data_;
 214         gmx::test::TestReferenceChecker checker_;
 215         size_t                          count_;
 216         int                             framenr_;
 217         TestFlags                       flags_;
 218 };
 219
 220
 221 void
 222 SelectionCollectionDataTest::checkSelection(
 223         gmx::test::TestReferenceChecker *checker,
 224         const gmx::Selection &sel, TestFlags flags)
 225 {
 226     using gmx::test::TestReferenceChecker;
 227
 228     {
 229         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 230         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 231     }
 232     if (flags.test(efTestPositionAtoms)
 233         || flags.test(efTestPositionCoordinates)
 234         || flags.test(efTestPositionMapping)
 235         || flags.test(efTestPositionMasses)
 236         || flags.test(efTestPositionCharges))
 237     {
 238         TestReferenceChecker compound(
 239                 checker->checkSequenceCompound("Positions", sel.posCount()));
 240         for (int i = 0; i < sel.posCount(); ++i)
 241         {
 242             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 243             const gmx::SelectionPosition &p = sel.position(i);
 244             if (flags.test(efTestPositionAtoms))
 245             {
 246                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 247                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 248             }
 249             if (flags.test(efTestPositionCoordinates))
 250             {
 251                 poscompound.checkVector(p.x(), "Coordinates");
 252             }
 253             if (flags.test(efTestPositionMapping))
 254             {
 255                 poscompound.checkInteger(p.refId(), "RefId");
 256                 poscompound.checkInteger(p.mappedId(), "MappedId");
 257             }
 258             if (flags.test(efTestPositionMasses))
 259             {
 260                 poscompound.checkReal(p.mass(), "Mass");
 261             }
 262             if (flags.test(efTestPositionCharges))
 263             {
 264                 poscompound.checkReal(p.charge(), "Charge");
 265             }
 266         }
 267     }
 268 }
 269
 270
 271 void
 272 SelectionCollectionDataTest::runParser(const char *const *selections,
 273                                        size_t             count)
 274 {
 275     using gmx::test::TestReferenceChecker;
 276
 277     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 278     size_t               varcount = 0;
 279     count_ = 0;
 280     for (size_t i = 0; i < count; ++i)
 281     {
 282         SCOPED_TRACE(std::string("Parsing selection \"")
 283                      + selections[i] + "\"");
 284         gmx::SelectionList result;
 285         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 286         sel_.insert(sel_.end(), result.begin(), result.end());
 287         if (sel_.size() == count_)
 288         {
 289             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 290             TestReferenceChecker varcompound(
 291                     compound.checkCompound("ParsedVariable", id.c_str()));
 292             varcompound.checkString(selections[i], "Input");
 293             ++varcount;
 294         }
 295         else
 296         {
 297             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 298             TestReferenceChecker selcompound(
 299                     compound.checkCompound("ParsedSelection", id.c_str()));
 300             selcompound.checkString(selections[i], "Input");
 301             selcompound.checkString(sel_[count_].name(), "Name");
 302             selcompound.checkString(sel_[count_].selectionText(), "Text");
 303             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 304             ++count_;
 305         }
 306     }
 307 }
 308
 309
 310 void
 311 SelectionCollectionDataTest::runCompiler()
 312 {
 313     ASSERT_NO_THROW_GMX(sc_.compile());
 314     ASSERT_EQ(count_, sel_.size());
 315     checkCompiled();
 316 }
 317
 318
 319 void
 320 SelectionCollectionDataTest::checkCompiled()
 321 {
 322     using gmx::test::TestReferenceChecker;
 323     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 324
 325     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 326     for (size_t i = 0; i < count_; ++i)
 327     {
 328         SCOPED_TRACE(std::string("Checking selection \"") +
 329                      sel_[i].selectionText() + "\"");
 330         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 331         TestReferenceChecker selcompound(
 332                 compound.checkCompound("Selection", id.c_str()));
 333         if (!flags_.test(efDontTestCompiledAtoms))
 334         {
 335             checkSelection(&selcompound, sel_[i], flags_ & mask);
 336         }
 337     }
 338 }
 339
 340
 341 void
 342 SelectionCollectionDataTest::runEvaluate()
 343 {
 344     using gmx::test::TestReferenceChecker;
 345
 346     ++framenr_;
 347     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 348     std::string          frame = gmx::formatString("Frame%d", framenr_);
 349     TestReferenceChecker compound(
 350             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 351     for (size_t i = 0; i < count_; ++i)
 352     {
 353         SCOPED_TRACE(std::string("Checking selection \"") +
 354                      sel_[i].selectionText() + "\"");
 355         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 356         TestReferenceChecker selcompound(
 357                 compound.checkCompound("Selection", id.c_str()));
 358         checkSelection(&selcompound, sel_[i], flags_);
 359     }
 360 }
 361
 362
 363 void
 364 SelectionCollectionDataTest::runEvaluateFinal()
 365 {
 366     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 367     if (!checker_.isWriteMode())
 368     {
 369         checkCompiled();
 370     }
 371 }
 372
 373
 374 void
 375 SelectionCollectionDataTest::runTest(int natoms, const char * const *selections,
 376                                      size_t count)
 377 {
 378     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 379     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 380     ASSERT_NO_FATAL_FAILURE(runCompiler());
 381 }
 382
 383
 384 void
 385 SelectionCollectionDataTest::runTest(const char         *filename,
 386                                      const char * const *selections,
 387                                      size_t              count)
 388 {
 389     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 390     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 391     ASSERT_NO_FATAL_FAILURE(runCompiler());
 392     if (flags_.test(efTestEvaluation))
 393     {
 394         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 395         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 396     }
 397 }
 398
 399
 400 /********************************************************************
 401  * Tests for SelectionCollection functionality without reference data
 402  */
 403
 404 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 405 {
 406     EXPECT_FALSE(sc_.requiresTopology());
 407     EXPECT_NO_THROW_GMX(sc_.compile());
 408 }
 409
 410 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 411 {
 412     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 413     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 414     ASSERT_EQ(2U, sel_.size());
 415     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 416     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 417     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 418     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 419     ASSERT_NO_THROW_GMX(sc_.compile());
 420     EXPECT_TRUE(sel_[0].hasVelocities());
 421     EXPECT_TRUE(sel_[1].hasVelocities());
 422     EXPECT_TRUE(sel_[0].hasForces());
 423     EXPECT_TRUE(sel_[1].hasForces());
 424 }
 425
 426 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 427 {
 428     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 429                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 430     // These should match the contents of selfile.dat
 431     ASSERT_EQ(2U, sel_.size());
 432     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 433     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 434 }
 435
 436 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 437 {
 438     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 439     EXPECT_THROW_GMX({
 440                          sc_.parseFromString("resname ~ \"R[A\"");
 441                          sc_.compile();
 442                      }, gmx::InvalidInputError);
 443 }
 444
 445 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 446 {
 447     if (!gmx::Regex::isSupported())
 448     {
 449         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 450         EXPECT_THROW_GMX({
 451                              sc_.parseFromString("resname \"R[AD]\"");
 452                              sc_.compile();
 453                          }, gmx::InvalidInputError);
 454     }
 455 }
 456
 457 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 458 {
 459     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 460                      gmx::InvalidInputError);
 461 }
 462
 463 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 464 {
 465     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 466                      gmx::InvalidInputError);
 467 }
 468
 469 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 470 {
 471     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 472                      gmx::InvalidInputError);
 473 }
 474
 475 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 476 {
 477     EXPECT_THROW_GMX(sc_.parseFromString("resname help"),
 478                      gmx::InvalidInputError);
 479 }
 480
 481 // TODO: Tests for more parser errors
 482
 483 TEST_F(SelectionCollectionTest, RecoversFromUnknownGroupReference)
 484 {
 485     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 486     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 487     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
 488     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 489 }
 490
 491 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 492 {
 493     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 494     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 495     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 496 }
 497
 498 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 499 {
 500     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 501     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 502     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 503 }
 504
 505 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 506 {
 507     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 508     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 509     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 510 }
 511
 512 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 513 {
 514     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 515     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 516     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 517 }
 518
 519 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 520 {
 521     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 522     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 523     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 524 }
 525
 526 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 527 {
 528     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 529     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 530     ASSERT_NO_THROW_GMX(sc_.compile());
 531     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 532 }
 533
 534 // TODO: Tests for evaluation errors
 535
 536
 537 /********************************************************************
 538  * Tests for selection keywords
 539  */
 540
 541 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 542 {
 543     static const char * const selections[] = {
 544         "all",
 545         "none"
 546     };
 547     runTest(10, selections);
 548 }
 549
 550 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 551 {
 552     static const char * const selections[] = {
 553         "atomnr 1 to 3 6 to 8",
 554         "atomnr 4 2 5 to 7",
 555         "atomnr <= 5"
 556     };
 557     runTest(10, selections);
 558 }
 559
 560 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 561 {
 562     static const char * const selections[] = {
 563         "resnr 1 2 5",
 564         "resid 4 to 3"
 565     };
 566     runTest("simple.gro", selections);
 567 }
 568
 569 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 570 {
 571     static const char * const selections[] = {
 572         "resindex 1 4",
 573         "residue 1 3"
 574     };
 575     runTest("simple.pdb", selections);
 576 }
 577
 578 // TODO: Add test for "molindex"
 579
 580 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 581 {
 582     static const char * const selections[] = {
 583         "name CB",
 584         "atomname S1 S2"
 585     };
 586     runTest("simple.gro", selections);
 587 }
 588
 589 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 590 {
 591     static const char * const selections[] = {
 592         "name HG21",
 593         "name 1HG2",
 594         "pdbname HG21 CB",
 595         "pdbatomname 1HG2"
 596     };
 597     runTest("simple.pdb", selections);
 598 }
 599
 600 // TODO: Add test for atomtype
 601
 602 TEST_F(SelectionCollectionDataTest, HandlesChain)
 603 {
 604     static const char * const selections[] = {
 605         "chain A",
 606         "chain B"
 607     };
 608     runTest("simple.pdb", selections);
 609 }
 610
 611 TEST_F(SelectionCollectionDataTest, HandlesMass)
 612 {
 613     static const char * const selections[] = {
 614         "mass > 5"
 615     };
 616     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 617     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 618     for (int i = 0; i < top_->atoms.nr; ++i)
 619     {
 620         top_->atoms.atom[i].m = 1.0 + i;
 621     }
 622     ASSERT_NO_FATAL_FAILURE(runCompiler());
 623 }
 624
 625 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 626 {
 627     static const char * const selections[] = {
 628         "charge < 0.5"
 629     };
 630     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 631     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 632     for (int i = 0; i < top_->atoms.nr; ++i)
 633     {
 634         top_->atoms.atom[i].q = i / 10.0;
 635     }
 636     ASSERT_NO_FATAL_FAILURE(runCompiler());
 637 }
 638
 639 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 640 {
 641     static const char * const selections[] = {
 642         "altloc \" \"",
 643         "altloc A"
 644     };
 645     runTest("simple.pdb", selections);
 646 }
 647
 648 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 649 {
 650     static const char * const selections[] = {
 651         "insertcode \" \"",
 652         "insertcode A"
 653     };
 654     runTest("simple.pdb", selections);
 655 }
 656
 657 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 658 {
 659     static const char * const selections[] = {
 660         "occupancy 1",
 661         "occupancy < .5"
 662     };
 663     runTest("simple.pdb", selections);
 664 }
 665
 666 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 667 {
 668     static const char * const selections[] = {
 669         "beta 0",
 670         "beta >= 0.3"
 671     };
 672     runTest("simple.pdb", selections);
 673 }
 674
 675 TEST_F(SelectionCollectionDataTest, HandlesResname)
 676 {
 677     static const char * const selections[] = {
 678         "resname RA",
 679         "resname RB RC"
 680     };
 681     runTest("simple.gro", selections);
 682 }
 683
 684 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 685 {
 686     static const char * const selections[] = {
 687         "x < 3",
 688         "y >= 3",
 689         "x {-1 to 2}"
 690     };
 691     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 692     runTest("simple.gro", selections);
 693 }
 694
 695
 696 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 697 {
 698     static const char * const selections[] = {
 699         "same residue as atomnr 1 4 12"
 700     };
 701     runTest("simple.gro", selections);
 702 }
 703
 704
 705 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 706 {
 707     static const char * const selections[] = {
 708         "same resname as atomnr 1 14"
 709     };
 710     runTest("simple.gro", selections);
 711 }
 712
 713
 714 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 715 {
 716     static const char * const selections[] = {
 717         "cog of resnr 1 3",
 718         "res_cog of name CB and resnr 1 3",
 719         "whole_res_cog of name CB and resnr 1 3",
 720         "part_res_cog of x < 3",
 721         "dyn_res_cog of x < 3"
 722     };
 723     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 724              | efTestPositionAtoms);
 725     runTest("simple.gro", selections);
 726 }
 727
 728
 729 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 730 {
 731     static const char * const selections[] = {
 732         "distance from cog of resnr 1 < 2"
 733     };
 734     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 735     runTest("simple.gro", selections);
 736 }
 737
 738
 739 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 740 {
 741     static const char * const selections[] = {
 742         "mindistance from resnr 1 < 2"
 743     };
 744     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 745     runTest("simple.gro", selections);
 746 }
 747
 748
 749 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 750 {
 751     static const char * const selections[] = {
 752         "within 1 of resnr 2"
 753     };
 754     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 755     runTest("simple.gro", selections);
 756 }
 757
 758
 759 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 760 {
 761     // Both of these should evaluate to empty on a correct implementation.
 762     static const char * const selections[] = {
 763         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 764         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 765     };
 766     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 767     runTest("sphere.gro", selections);
 768 }
 769
 770
 771 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 772 {
 773     static const char * const selections[] = {
 774         "all permute 3 1 2",
 775         "res_cog of resnr 1 to 4 permute 2 1",
 776         "name CB S1 and res_cog x < 3 permute 2 1"
 777     };
 778     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 779              | efTestPositionAtoms | efTestPositionMapping);
 780     runTest("simple.gro", selections);
 781 }
 782
 783
 784 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 785 {
 786     static const char * const selections[] = {
 787         "name S2 plus name S1",
 788         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 789         "name S1 and y < 3 plus res_cog of x < 2.5"
 790     };
 791     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 792              | efTestPositionAtoms | efTestPositionMapping);
 793     runTest("simple.gro", selections);
 794 }
 795
 796
 797 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 798 {
 799     static const char * const selections[] = {
 800         "name S2 merge name S1",
 801         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 802         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 803     };
 804     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 805              | efTestPositionAtoms | efTestPositionMapping);
 806     runTest("simple.gro", selections);
 807 }
 808
 809
 810 /********************************************************************
 811  * Tests for generic selection evaluation
 812  */
 813
 814 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 815 {
 816     static const char * const selections[] = {
 817         "name CB",
 818         "y > 2",
 819         "res_cog of y > 2"
 820     };
 821     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 822              | efTestPositionMasses | efTestPositionCharges);
 823     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 824     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 825     for (int i = 0; i < top_->atoms.nr; ++i)
 826     {
 827         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 828         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 829     }
 830     ASSERT_NO_FATAL_FAILURE(runCompiler());
 831     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 832     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 833 }
 834
 835 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 836 {
 837     static const char * const selections[] = {
 838         "atomnr 1 to 3 8 to 9",
 839         "y > 2",
 840         "cog of (y > 2)"
 841     };
 842     setFlags(TestFlags() | efTestPositionAtoms
 843              | efTestPositionMasses | efTestPositionCharges);
 844     runTest(10, selections);
 845 }
 846
 847
 848 /********************************************************************
 849  * Tests for selection syntactic constructs
 850  */
 851
 852 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 853 {
 854     static const char * const selections[] = {
 855         "[1, -2, 3.5]"
 856     };
 857     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 858     runTest("simple.gro", selections);
 859 }
 860
 861
 862 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 863 {
 864     static const char * const selections[] = {
 865         "within 1 of [2, 1, 0]"
 866     };
 867     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 868     runTest("simple.gro", selections);
 869 }
 870
 871
 872 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 873 {
 874     static const char * const selections[] = {
 875         "name = S1 \"C?\"",
 876         "name ? S1 \"C?\""
 877     };
 878     runTest("simple.gro", selections);
 879 }
 880
 881
 882 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 883 {
 884     static const char * const selections[] = {
 885         "name \"S?\"",
 886         "name ? \"S?\""
 887     };
 888     runTest("simple.gro", selections);
 889 }
 890
 891
 892 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 893 {
 894     static const char * const selections[] = {
 895         "resname \"R[BD]\"",
 896         "resname ~ \"R[BD]\""
 897     };
 898     if (gmx::Regex::isSupported())
 899     {
 900         runTest("simple.gro", selections);
 901     }
 902 }
 903
 904
 905 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 906 {
 907     static const char * const selections[] = {
 908         "atomnr 1 to 5 and atomnr 2 to 7",
 909         "atomnr 1 to 5 or not atomnr 3 to 8",
 910         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 911         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 912         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 913     };
 914     runTest(10, selections);
 915 }
 916
 917
 918 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
 919 {
 920     static const char * const selections[] = {
 921         "same residue as (atomnr 3 5 13 or y > 5)",
 922         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or y > 5)"
 923     };
 924     setFlags(TestFlags() | efTestEvaluation);
 925     runTest("simple.gro", selections);
 926 }
 927
 928
 929 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
 930 {
 931     static const char * const selections[] = {
 932         "x > 2",
 933         "2 < x",
 934         "y > resnr",
 935         "resnr < 2.5",
 936         "2.5 > resnr"
 937     };
 938     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 939     runTest("simple.gro", selections);
 940 }
 941
 942
 943 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
 944 {
 945     static const char * const selections[] = {
 946         "x+1 > 3",
 947         "(y-1)^2 <= 1",
 948         "x+--1 > 3",
 949         "-x+-1 < -3"
 950     };
 951     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 952     runTest("simple.gro", selections);
 953 }
 954
 955
 956 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
 957 {
 958     static const char * const selections[] = {
 959         "value = x + y",
 960         "value <= 4",
 961         "index = resnr",
 962         "index < 3"
 963     };
 964     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 965     runTest("simple.gro", selections);
 966 }
 967
 968
 969 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
 970 {
 971     static const char * const selections[] = {
 972         "value = x + y",
 973         "resname RA and value <= 4",
 974         "resname RA RB and x < 3 and value <= 4",
 975         "index = atomnr",
 976         "resname RA and index < 3",
 977         "resname RB and y < 3 and index < 6"
 978     };
 979     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 980     runTest("simple.gro", selections);
 981 }
 982
 983
 984 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
 985 {
 986     static const char * const selections[] = {
 987         "foo = res_cog of resname RA",
 988         "foo",
 989         "within 1 of foo",
 990         "bar = cog of resname RA",
 991         "bar",
 992         "within 1 of bar"
 993     };
 994     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 995     runTest("simple.gro", selections);
 996 }
 997
 998
 999 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1000 {
1001     static const char * const selections[] = {
1002         "constpos = [1.0, 2.5, 0.5]",
1003         "constpos",
1004         "within 2 of constpos"
1005     };
1006     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1007              | efTestPositionAtoms);
1008     runTest("simple.gro", selections);
1009 }
1010
1011
1012 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1013 {
1014     static const char * const selections[] = {
1015         "constint = 4",
1016         "constreal1 = 0.5",
1017         "constreal2 = 2.7",
1018         "resnr < constint",
1019         "x + constreal1 < constreal2"
1020     };
1021     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1022     runTest("simple.gro", selections);
1023 }
1024
1025
1026 /********************************************************************
1027  * Tests for complex boolean syntax
1028  */
1029
1030 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1031 {
1032     static const char * const selections[] = {
1033         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1034         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1035         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1036         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1037         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1038     };
1039     runTest(10, selections);
1040 }
1041
1042
1043 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1044 {
1045     static const char * const selections[] = {
1046         "foo = atomnr 4 to 7 or x < 2",
1047         "atomnr 1 to 4 and foo",
1048         "atomnr 2 to 6 and y < 3 and foo",
1049         "atomnr 6 to 10 and not foo"
1050     };
1051     runTest(10, selections);
1052 }
1053
1054
1055 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1056 {
1057     static const char * const selections[] = {
1058         "foo = atomnr 4 to 7",
1059         "bar = foo and x < 2",
1060         "bar2 = foo and y < 2",
1061         "atomnr 1 to 4 and bar",
1062         "atomnr 2 to 6 and y < 3 and bar2",
1063         "atomnr 6 to 10 and not foo"
1064     };
1065     runTest(10, selections);
1066 }
1067
1068
1069 /********************************************************************
1070  * Tests for complex subexpression cases
1071  *
1072  * These tests use some knowledge of the implementation to trigger different
1073  * paths in the code.
1074  */
1075
1076 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1077 {
1078     static const char * const selections[] = {
1079         "unused1 = atomnr 1 to 3",
1080         "foo = atomnr 4 to 7",
1081         "atomnr 1 to 6 and foo",
1082         "unused2 = atomnr 3 to 5"
1083     };
1084     runTest(10, selections);
1085 }
1086
1087
1088 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1089 {
1090     static const char * const selections[] = {
1091         "foo = atomnr 4 to 7 and x < 2",
1092         "atomnr 1 to 5 and foo",
1093         "atomnr 3 to 7 and foo"
1094     };
1095     runTest(10, selections);
1096 }
1097
1098
1099 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1100 {
1101     static const char * const selections[] = {
1102         "foo = atomnr 4 to 7 and x < 2",
1103         "atomnr 1 to 6 and foo",
1104         "within 1 of foo",
1105         "foo"
1106     };
1107     runTest(10, selections);
1108 }
1109
1110
1111 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1112 {
1113     static const char * const selections[] = {
1114         "foo = atomnr 1 to 8 and x < 10",
1115         "atomnr 1 to 5 and y < 10 and foo",
1116         "foo"
1117     };
1118     setFlags(TestFlags() | efTestEvaluation);
1119     runTest("simple.gro", selections);
1120 }
1121
1122
1123 } // namespace