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     checkCompiled();
 368 }
 369
 370
 371 void
 372 SelectionCollectionDataTest::runTest(int natoms, const char * const *selections,
 373                                      size_t count)
 374 {
 375     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 376     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 377     ASSERT_NO_FATAL_FAILURE(runCompiler());
 378 }
 379
 380
 381 void
 382 SelectionCollectionDataTest::runTest(const char         *filename,
 383                                      const char * const *selections,
 384                                      size_t              count)
 385 {
 386     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 387     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 388     ASSERT_NO_FATAL_FAILURE(runCompiler());
 389     if (flags_.test(efTestEvaluation))
 390     {
 391         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 392         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 393     }
 394 }
 395
 396
 397 /********************************************************************
 398  * Tests for SelectionCollection functionality without reference data
 399  */
 400
 401 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 402 {
 403     EXPECT_FALSE(sc_.requiresTopology());
 404     EXPECT_NO_THROW_GMX(sc_.compile());
 405 }
 406
 407 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 408 {
 409     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 410     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 411     ASSERT_EQ(2U, sel_.size());
 412     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 413     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 414     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 415     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 416     ASSERT_NO_THROW_GMX(sc_.compile());
 417     EXPECT_TRUE(sel_[0].hasVelocities());
 418     EXPECT_TRUE(sel_[1].hasVelocities());
 419     EXPECT_TRUE(sel_[0].hasForces());
 420     EXPECT_TRUE(sel_[1].hasForces());
 421 }
 422
 423 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 424 {
 425     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 426                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 427     // These should match the contents of selfile.dat
 428     ASSERT_EQ(2U, sel_.size());
 429     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 430     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 431 }
 432
 433 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 434 {
 435     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 436     EXPECT_THROW_GMX({
 437                          sc_.parseFromString("resname ~ \"R[A\"");
 438                          sc_.compile();
 439                      }, gmx::InvalidInputError);
 440 }
 441
 442 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 443 {
 444     if (!gmx::Regex::isSupported())
 445     {
 446         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 447         EXPECT_THROW_GMX({
 448                              sc_.parseFromString("resname \"R[AD]\"");
 449                              sc_.compile();
 450                          }, gmx::InvalidInputError);
 451     }
 452 }
 453
 454 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 455 {
 456     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 457                      gmx::InvalidInputError);
 458 }
 459
 460 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 461 {
 462     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 463                      gmx::InvalidInputError);
 464 }
 465
 466 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 467 {
 468     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 469                      gmx::InvalidInputError);
 470 }
 471
 472 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 473 {
 474     EXPECT_THROW_GMX(sc_.parseFromString("resname help"),
 475                      gmx::InvalidInputError);
 476 }
 477
 478 // TODO: Tests for more parser errors
 479
 480 TEST_F(SelectionCollectionTest, RecoversFromUnknownGroupReference)
 481 {
 482     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 483     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 484     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
 485     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 486 }
 487
 488 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 489 {
 490     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 491     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 492     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 493 }
 494
 495 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 496 {
 497     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 498     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 499     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 500 }
 501
 502 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 503 {
 504     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 505     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 506     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 507 }
 508
 509 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 510 {
 511     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 512     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 513     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 514 }
 515
 516 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 517 {
 518     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 519     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 520     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 521 }
 522
 523 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 524 {
 525     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 526     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 527     ASSERT_NO_THROW_GMX(sc_.compile());
 528     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 529 }
 530
 531 // TODO: Tests for evaluation errors
 532
 533
 534 /********************************************************************
 535  * Tests for selection keywords
 536  */
 537
 538 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 539 {
 540     static const char * const selections[] = {
 541         "all",
 542         "none"
 543     };
 544     runTest(10, selections);
 545 }
 546
 547 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 548 {
 549     static const char * const selections[] = {
 550         "atomnr 1 to 3 6 to 8",
 551         "atomnr 4 2 5 to 7",
 552         "atomnr <= 5"
 553     };
 554     runTest(10, selections);
 555 }
 556
 557 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 558 {
 559     static const char * const selections[] = {
 560         "resnr 1 2 5",
 561         "resid 4 to 3"
 562     };
 563     runTest("simple.gro", selections);
 564 }
 565
 566 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 567 {
 568     static const char * const selections[] = {
 569         "resindex 1 4",
 570         "residue 1 3"
 571     };
 572     runTest("simple.pdb", selections);
 573 }
 574
 575 // TODO: Add test for "molindex"
 576
 577 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 578 {
 579     static const char * const selections[] = {
 580         "name CB",
 581         "atomname S1 S2"
 582     };
 583     runTest("simple.gro", selections);
 584 }
 585
 586 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 587 {
 588     static const char * const selections[] = {
 589         "name HG21",
 590         "name 1HG2",
 591         "pdbname HG21 CB",
 592         "pdbatomname 1HG2"
 593     };
 594     runTest("simple.pdb", selections);
 595 }
 596
 597 // TODO: Add test for atomtype
 598
 599 TEST_F(SelectionCollectionDataTest, HandlesChain)
 600 {
 601     static const char * const selections[] = {
 602         "chain A",
 603         "chain B"
 604     };
 605     runTest("simple.pdb", selections);
 606 }
 607
 608 TEST_F(SelectionCollectionDataTest, HandlesMass)
 609 {
 610     static const char * const selections[] = {
 611         "mass > 5"
 612     };
 613     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 614     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 615     for (int i = 0; i < top_->atoms.nr; ++i)
 616     {
 617         top_->atoms.atom[i].m = 1.0 + i;
 618     }
 619     ASSERT_NO_FATAL_FAILURE(runCompiler());
 620 }
 621
 622 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 623 {
 624     static const char * const selections[] = {
 625         "charge < 0.5"
 626     };
 627     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 628     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 629     for (int i = 0; i < top_->atoms.nr; ++i)
 630     {
 631         top_->atoms.atom[i].q = i / 10.0;
 632     }
 633     ASSERT_NO_FATAL_FAILURE(runCompiler());
 634 }
 635
 636 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 637 {
 638     static const char * const selections[] = {
 639         "altloc \" \"",
 640         "altloc A"
 641     };
 642     runTest("simple.pdb", selections);
 643 }
 644
 645 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 646 {
 647     static const char * const selections[] = {
 648         "insertcode \" \"",
 649         "insertcode A"
 650     };
 651     runTest("simple.pdb", selections);
 652 }
 653
 654 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 655 {
 656     static const char * const selections[] = {
 657         "occupancy 1",
 658         "occupancy < .5"
 659     };
 660     runTest("simple.pdb", selections);
 661 }
 662
 663 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 664 {
 665     static const char * const selections[] = {
 666         "beta 0",
 667         "beta >= 0.3"
 668     };
 669     runTest("simple.pdb", selections);
 670 }
 671
 672 TEST_F(SelectionCollectionDataTest, HandlesResname)
 673 {
 674     static const char * const selections[] = {
 675         "resname RA",
 676         "resname RB RC"
 677     };
 678     runTest("simple.gro", selections);
 679 }
 680
 681 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 682 {
 683     static const char * const selections[] = {
 684         "x < 3",
 685         "y >= 3",
 686         "x {-1 to 2}"
 687     };
 688     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 689     runTest("simple.gro", selections);
 690 }
 691
 692
 693 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 694 {
 695     static const char * const selections[] = {
 696         "same residue as atomnr 1 4 12"
 697     };
 698     runTest("simple.gro", selections);
 699 }
 700
 701
 702 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 703 {
 704     static const char * const selections[] = {
 705         "same resname as atomnr 1 14"
 706     };
 707     runTest("simple.gro", selections);
 708 }
 709
 710
 711 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 712 {
 713     static const char * const selections[] = {
 714         "cog of resnr 1 3",
 715         "res_cog of name CB and resnr 1 3",
 716         "whole_res_cog of name CB and resnr 1 3",
 717         "part_res_cog of x < 3",
 718         "dyn_res_cog of x < 3"
 719     };
 720     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 721              | efTestPositionAtoms);
 722     runTest("simple.gro", selections);
 723 }
 724
 725
 726 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 727 {
 728     static const char * const selections[] = {
 729         "distance from cog of resnr 1 < 2"
 730     };
 731     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 732     runTest("simple.gro", selections);
 733 }
 734
 735
 736 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 737 {
 738     static const char * const selections[] = {
 739         "mindistance from resnr 1 < 2"
 740     };
 741     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 742     runTest("simple.gro", selections);
 743 }
 744
 745
 746 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 747 {
 748     static const char * const selections[] = {
 749         "within 1 of resnr 2"
 750     };
 751     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 752     runTest("simple.gro", selections);
 753 }
 754
 755
 756 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 757 {
 758     // Both of these should evaluate to empty on a correct implementation.
 759     static const char * const selections[] = {
 760         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 761         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 762     };
 763     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 764     runTest("sphere.gro", selections);
 765 }
 766
 767
 768 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 769 {
 770     static const char * const selections[] = {
 771         "all permute 3 1 2",
 772         "res_cog of resnr 1 to 4 permute 2 1",
 773         "name CB S1 and res_cog x < 3 permute 2 1"
 774     };
 775     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 776              | efTestPositionAtoms | efTestPositionMapping);
 777     runTest("simple.gro", selections);
 778 }
 779
 780
 781 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 782 {
 783     static const char * const selections[] = {
 784         "name S2 plus name S1",
 785         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 786         "name S1 and y < 3 plus res_cog of x < 2.5"
 787     };
 788     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 789              | efTestPositionAtoms | efTestPositionMapping);
 790     runTest("simple.gro", selections);
 791 }
 792
 793
 794 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 795 {
 796     static const char * const selections[] = {
 797         "name S2 merge name S1",
 798         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 799         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 800     };
 801     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 802              | efTestPositionAtoms | efTestPositionMapping);
 803     runTest("simple.gro", selections);
 804 }
 805
 806
 807 /********************************************************************
 808  * Tests for generic selection evaluation
 809  */
 810
 811 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 812 {
 813     static const char * const selections[] = {
 814         "name CB",
 815         "y > 2",
 816         "res_cog of y > 2"
 817     };
 818     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 819              | efTestPositionMasses | efTestPositionCharges);
 820     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 821     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 822     for (int i = 0; i < top_->atoms.nr; ++i)
 823     {
 824         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 825         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 826     }
 827     ASSERT_NO_FATAL_FAILURE(runCompiler());
 828     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 829     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 830 }
 831
 832 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 833 {
 834     static const char * const selections[] = {
 835         "atomnr 1 to 3 8 to 9",
 836         "y > 2",
 837         "cog of (y > 2)"
 838     };
 839     setFlags(TestFlags() | efTestPositionAtoms
 840              | efTestPositionMasses | efTestPositionCharges);
 841     runTest(10, selections);
 842 }
 843
 844
 845 /********************************************************************
 846  * Tests for selection syntactic constructs
 847  */
 848
 849 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 850 {
 851     static const char * const selections[] = {
 852         "[1, -2, 3.5]"
 853     };
 854     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 855     runTest("simple.gro", selections);
 856 }
 857
 858
 859 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 860 {
 861     static const char * const selections[] = {
 862         "within 1 of [2, 1, 0]"
 863     };
 864     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 865     runTest("simple.gro", selections);
 866 }
 867
 868
 869 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 870 {
 871     static const char * const selections[] = {
 872         "name = S1 \"C?\"",
 873         "name ? S1 \"C?\""
 874     };
 875     runTest("simple.gro", selections);
 876 }
 877
 878
 879 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 880 {
 881     static const char * const selections[] = {
 882         "name \"S?\"",
 883         "name ? \"S?\""
 884     };
 885     runTest("simple.gro", selections);
 886 }
 887
 888
 889 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 890 {
 891     static const char * const selections[] = {
 892         "resname \"R[BD]\"",
 893         "resname ~ \"R[BD]\""
 894     };
 895     if (gmx::Regex::isSupported())
 896     {
 897         runTest("simple.gro", selections);
 898     }
 899 }
 900
 901
 902 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 903 {
 904     static const char * const selections[] = {
 905         "atomnr 1 to 5 and atomnr 2 to 7",
 906         "atomnr 1 to 5 or not atomnr 3 to 8",
 907         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 908         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 909         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 910     };
 911     runTest(10, selections);
 912 }
 913
 914
 915 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
 916 {
 917     static const char * const selections[] = {
 918         "same residue as (atomnr 3 5 13 or y > 5)",
 919         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or y > 5)"
 920     };
 921     setFlags(TestFlags() | efTestEvaluation);
 922     runTest("simple.gro", selections);
 923 }
 924
 925
 926 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
 927 {
 928     static const char * const selections[] = {
 929         "x > 2",
 930         "2 < x",
 931         "y > resnr",
 932         "resnr < 2.5",
 933         "2.5 > resnr"
 934     };
 935     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 936     runTest("simple.gro", selections);
 937 }
 938
 939
 940 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
 941 {
 942     static const char * const selections[] = {
 943         "x+1 > 3",
 944         "(y-1)^2 <= 1",
 945         "x+--1 > 3",
 946         "-x+-1 < -3"
 947     };
 948     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 949     runTest("simple.gro", selections);
 950 }
 951
 952
 953 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
 954 {
 955     static const char * const selections[] = {
 956         "value = x + y",
 957         "value <= 4",
 958         "index = resnr",
 959         "index < 3"
 960     };
 961     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 962     runTest("simple.gro", selections);
 963 }
 964
 965
 966 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
 967 {
 968     static const char * const selections[] = {
 969         "value = x + y",
 970         "resname RA and value <= 4",
 971         "resname RA RB and x < 3 and value <= 4",
 972         "index = atomnr",
 973         "resname RA and index < 3",
 974         "resname RB and y < 3 and index < 6"
 975     };
 976     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 977     runTest("simple.gro", selections);
 978 }
 979
 980
 981 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
 982 {
 983     static const char * const selections[] = {
 984         "foo = res_cog of resname RA",
 985         "foo",
 986         "within 1 of foo",
 987         "bar = cog of resname RA",
 988         "bar",
 989         "within 1 of bar"
 990     };
 991     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 992     runTest("simple.gro", selections);
 993 }
 994
 995
 996 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
 997 {
 998     static const char * const selections[] = {
 999         "constpos = [1.0, 2.5, 0.5]",
1000         "constpos",
1001         "within 2 of constpos"
1002     };
1003     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1004              | efTestPositionAtoms);
1005     runTest("simple.gro", selections);
1006 }
1007
1008
1009 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1010 {
1011     static const char * const selections[] = {
1012         "constint = 4",
1013         "constreal1 = 0.5",
1014         "constreal2 = 2.7",
1015         "resnr < constint",
1016         "x + constreal1 < constreal2"
1017     };
1018     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1019     runTest("simple.gro", selections);
1020 }
1021
1022
1023 /********************************************************************
1024  * Tests for complex boolean syntax
1025  */
1026
1027 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1028 {
1029     static const char * const selections[] = {
1030         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1031         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1032         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1033         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1034         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1035     };
1036     runTest(10, selections);
1037 }
1038
1039
1040 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1041 {
1042     static const char * const selections[] = {
1043         "foo = atomnr 4 to 7 or x < 2",
1044         "atomnr 1 to 4 and foo",
1045         "atomnr 2 to 6 and y < 3 and foo",
1046         "atomnr 6 to 10 and not foo"
1047     };
1048     runTest(10, selections);
1049 }
1050
1051
1052 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1053 {
1054     static const char * const selections[] = {
1055         "foo = atomnr 4 to 7",
1056         "bar = foo and x < 2",
1057         "bar2 = foo and y < 2",
1058         "atomnr 1 to 4 and bar",
1059         "atomnr 2 to 6 and y < 3 and bar2",
1060         "atomnr 6 to 10 and not foo"
1061     };
1062     runTest(10, selections);
1063 }
1064
1065
1066 /********************************************************************
1067  * Tests for complex subexpression cases
1068  *
1069  * These tests use some knowledge of the implementation to trigger different
1070  * paths in the code.
1071  */
1072
1073 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1074 {
1075     static const char * const selections[] = {
1076         "unused1 = atomnr 1 to 3",
1077         "foo = atomnr 4 to 7",
1078         "atomnr 1 to 6 and foo",
1079         "unused2 = atomnr 3 to 5"
1080     };
1081     runTest(10, selections);
1082 }
1083
1084
1085 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1086 {
1087     static const char * const selections[] = {
1088         "foo = atomnr 4 to 7 and x < 2",
1089         "atomnr 1 to 5 and foo",
1090         "atomnr 3 to 7 and foo"
1091     };
1092     runTest(10, selections);
1093 }
1094
1095
1096 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1097 {
1098     static const char * const selections[] = {
1099         "foo = atomnr 4 to 7 and x < 2",
1100         "atomnr 1 to 6 and foo",
1101         "within 1 of foo",
1102         "foo"
1103     };
1104     runTest(10, selections);
1105 }
1106
1107
1108 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1109 {
1110     static const char * const selections[] = {
1111         "foo = atomnr 1 to 8 and x < 10",
1112         "atomnr 1 to 5 and y < 10 and foo",
1113         "foo"
1114     };
1115     setFlags(TestFlags() | efTestEvaluation);
1116     runTest("simple.gro", selections);
1117 }
1118
1119
1120 } // namespace