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/testfilemanager.h"
  60 #include "testutils/testoptions.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 void SetUpTestCase();
  73
  74         static int               s_debugLevel;
  75
  76         SelectionCollectionTest();
  77         ~SelectionCollectionTest();
  78
  79         void setAtomCount(int natoms)
  80         {
  81             ASSERT_NO_THROW(sc_.setTopology(NULL, natoms));
  82         }
  83         void loadTopology(const char *filename);
  84
  85         gmx::SelectionCollection sc_;
  86         gmx::SelectionList       sel_;
  87         t_topology              *top_;
  88         t_trxframe              *frame_;
  89 };
  90
  91 int SelectionCollectionTest::s_debugLevel = 0;
  92
  93 void SelectionCollectionTest::SetUpTestCase()
  94 {
  95     gmx::Options options(NULL, NULL);
  96     options.addOption(gmx::IntegerOption("seldebug").store(&s_debugLevel));
  97     gmx::test::parseTestOptions(&options);
  98 }
  99
 100
 101 SelectionCollectionTest::SelectionCollectionTest()
 102     : top_(NULL), frame_(NULL)
 103 {
 104     sc_.setDebugLevel(s_debugLevel);
 105     sc_.setReferencePosType("atom");
 106     sc_.setOutputPosType("atom");
 107 }
 108
 109
 110 SelectionCollectionTest::~SelectionCollectionTest()
 111 {
 112     if (top_ != NULL)
 113     {
 114         free_t_atoms(&top_->atoms, TRUE);
 115         done_top(top_);
 116         sfree(top_);
 117     }
 118
 119     if (frame_ != NULL)
 120     {
 121         sfree(frame_->x);
 122         sfree(frame_);
 123     }
 124 }
 125
 126
 127 void
 128 SelectionCollectionTest::loadTopology(const char *filename)
 129 {
 130     char    title[STRLEN];
 131     int     ePBC;
 132     rvec   *xtop;
 133     matrix  box;
 134
 135     snew(top_, 1);
 136     read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
 137                   title, top_, &ePBC, &xtop, NULL, box, FALSE);
 138
 139     snew(frame_, 1);
 140     frame_->flags  = TRX_NEED_X;
 141     frame_->natoms = top_->atoms.nr;
 142     frame_->bX     = TRUE;
 143     snew(frame_->x, frame_->natoms);
 144     memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
 145     frame_->bBox   = TRUE;
 146     copy_mat(box, frame_->box);
 147
 148     sfree(xtop);
 149
 150     ASSERT_NO_THROW(sc_.setTopology(top_, -1));
 151 }
 152
 153
 154 /********************************************************************
 155  * Test fixture for selection testing with reference data
 156  */
 157
 158 class SelectionCollectionDataTest : public SelectionCollectionTest
 159 {
 160     public:
 161         enum TestFlag
 162         {
 163             efTestEvaluation            = 1<<0,
 164             efTestPositionAtoms         = 1<<1,
 165             efTestPositionCoordinates   = 1<<2,
 166             efTestPositionMapping       = 1<<3,
 167             efTestPositionMasses        = 1<<4,
 168             efTestPositionCharges       = 1<<5,
 169             efDontTestCompiledAtoms     = 1<<8
 170         };
 171         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 172
 173         SelectionCollectionDataTest()
 174             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 175         {
 176         }
 177
 178         void setFlags(TestFlags flags) { flags_ = flags; }
 179
 180         template <size_t count>
 181         void runTest(int natoms, const char *const (&selections)[count])
 182         {
 183             runTest(natoms, selections, count);
 184         }
 185         template <size_t count>
 186         void runTest(const char *filename, const char *const (&selections)[count])
 187         {
 188             runTest(filename, selections, count);
 189         }
 190
 191         template <size_t count>
 192         void runParser(const char *const (&selections)[count])
 193         {
 194             runParser(selections, count);
 195         }
 196
 197         void runCompiler();
 198         void runEvaluate();
 199         void runEvaluateFinal();
 200
 201     private:
 202         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 203                                    const gmx::Selection &sel, TestFlags flags);
 204
 205         void runTest(int natoms, const char *const *selections, size_t count);
 206         void runTest(const char *filename, const char *const *selections,
 207                      size_t count);
 208         void runParser(const char *const *selections, size_t count);
 209
 210         void checkCompiled();
 211
 212         gmx::test::TestReferenceData    data_;
 213         gmx::test::TestReferenceChecker checker_;
 214         size_t                          count_;
 215         int                             framenr_;
 216         TestFlags                       flags_;
 217 };
 218
 219
 220 void
 221 SelectionCollectionDataTest::checkSelection(
 222         gmx::test::TestReferenceChecker *checker,
 223         const gmx::Selection &sel, TestFlags flags)
 224 {
 225     using gmx::test::TestReferenceChecker;
 226
 227     {
 228         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 229         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 230     }
 231     if (flags.test(efTestPositionAtoms)
 232         || flags.test(efTestPositionCoordinates)
 233         || flags.test(efTestPositionMapping)
 234         || flags.test(efTestPositionMasses)
 235         || flags.test(efTestPositionCharges))
 236     {
 237         TestReferenceChecker compound(
 238                 checker->checkSequenceCompound("Positions", sel.posCount()));
 239         for (int i = 0; i < sel.posCount(); ++i)
 240         {
 241             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 242             const gmx::SelectionPosition &p = sel.position(i);
 243             if (flags.test(efTestPositionAtoms))
 244             {
 245                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 246                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 247             }
 248             if (flags.test(efTestPositionCoordinates))
 249             {
 250                 poscompound.checkVector(p.x(), "Coordinates");
 251             }
 252             if (flags.test(efTestPositionMapping))
 253             {
 254                 poscompound.checkInteger(p.refId(), "RefId");
 255                 poscompound.checkInteger(p.mappedId(), "MappedId");
 256             }
 257             if (flags.test(efTestPositionMasses))
 258             {
 259                 poscompound.checkReal(p.mass(), "Mass");
 260             }
 261             if (flags.test(efTestPositionCharges))
 262             {
 263                 poscompound.checkReal(p.charge(), "Charge");
 264             }
 265         }
 266     }
 267 }
 268
 269
 270 void
 271 SelectionCollectionDataTest::runParser(const char *const *selections,
 272                                        size_t             count)
 273 {
 274     using gmx::test::TestReferenceChecker;
 275
 276     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 277     size_t               varcount = 0;
 278     count_ = 0;
 279     for (size_t i = 0; i < count; ++i)
 280     {
 281         SCOPED_TRACE(std::string("Parsing selection \"")
 282                      + selections[i] + "\"");
 283         gmx::SelectionList result;
 284         ASSERT_NO_THROW(result = sc_.parseFromString(selections[i]));
 285         sel_.insert(sel_.end(), result.begin(), result.end());
 286         if (sel_.size() == count_)
 287         {
 288             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 289             TestReferenceChecker varcompound(
 290                     compound.checkCompound("ParsedVariable", id.c_str()));
 291             varcompound.checkString(selections[i], "Input");
 292             ++varcount;
 293         }
 294         else
 295         {
 296             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 297             TestReferenceChecker selcompound(
 298                     compound.checkCompound("ParsedSelection", id.c_str()));
 299             selcompound.checkString(selections[i], "Input");
 300             selcompound.checkString(sel_[count_].name(), "Name");
 301             selcompound.checkString(sel_[count_].selectionText(), "Text");
 302             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 303             ++count_;
 304         }
 305     }
 306 }
 307
 308
 309 void
 310 SelectionCollectionDataTest::runCompiler()
 311 {
 312     ASSERT_NO_THROW(sc_.compile());
 313     ASSERT_EQ(count_, sel_.size());
 314     checkCompiled();
 315 }
 316
 317
 318 void
 319 SelectionCollectionDataTest::checkCompiled()
 320 {
 321     using gmx::test::TestReferenceChecker;
 322     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 323
 324     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 325     for (size_t i = 0; i < count_; ++i)
 326     {
 327         SCOPED_TRACE(std::string("Checking selection \"") +
 328                      sel_[i].selectionText() + "\"");
 329         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 330         TestReferenceChecker selcompound(
 331                 compound.checkCompound("Selection", id.c_str()));
 332         if (!flags_.test(efDontTestCompiledAtoms))
 333         {
 334             checkSelection(&selcompound, sel_[i], flags_ & mask);
 335         }
 336     }
 337 }
 338
 339
 340 void
 341 SelectionCollectionDataTest::runEvaluate()
 342 {
 343     using gmx::test::TestReferenceChecker;
 344
 345     ++framenr_;
 346     ASSERT_NO_THROW(sc_.evaluate(frame_, NULL));
 347     std::string          frame = gmx::formatString("Frame%d", framenr_);
 348     TestReferenceChecker compound(
 349             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 350     for (size_t i = 0; i < count_; ++i)
 351     {
 352         SCOPED_TRACE(std::string("Checking selection \"") +
 353                      sel_[i].selectionText() + "\"");
 354         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 355         TestReferenceChecker selcompound(
 356                 compound.checkCompound("Selection", id.c_str()));
 357         checkSelection(&selcompound, sel_[i], flags_);
 358     }
 359 }
 360
 361
 362 void
 363 SelectionCollectionDataTest::runEvaluateFinal()
 364 {
 365     ASSERT_NO_THROW(sc_.evaluateFinal(framenr_));
 366     if (!checker_.isWriteMode())
 367     {
 368         checkCompiled();
 369     }
 370 }
 371
 372
 373 void
 374 SelectionCollectionDataTest::runTest(int natoms, const char * const *selections,
 375                                      size_t count)
 376 {
 377     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 378     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 379     ASSERT_NO_FATAL_FAILURE(runCompiler());
 380 }
 381
 382
 383 void
 384 SelectionCollectionDataTest::runTest(const char         *filename,
 385                                      const char * const *selections,
 386                                      size_t              count)
 387 {
 388     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 389     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 390     ASSERT_NO_FATAL_FAILURE(runCompiler());
 391     if (flags_.test(efTestEvaluation))
 392     {
 393         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 394         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 395     }
 396 }
 397
 398
 399 /********************************************************************
 400  * Tests for SelectionCollection functionality without reference data
 401  */
 402
 403 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 404 {
 405     EXPECT_FALSE(sc_.requiresTopology());
 406     EXPECT_NO_THROW(sc_.compile());
 407 }
 408
 409 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 410 {
 411     ASSERT_NO_THROW(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 412     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 413     ASSERT_EQ(2U, sel_.size());
 414     ASSERT_NO_THROW(sel_[0].setEvaluateVelocities(true));
 415     ASSERT_NO_THROW(sel_[1].setEvaluateVelocities(true));
 416     ASSERT_NO_THROW(sel_[0].setEvaluateForces(true));
 417     ASSERT_NO_THROW(sel_[1].setEvaluateForces(true));
 418     ASSERT_NO_THROW(sc_.compile());
 419     EXPECT_TRUE(sel_[0].hasVelocities());
 420     EXPECT_TRUE(sel_[1].hasVelocities());
 421     EXPECT_TRUE(sel_[0].hasForces());
 422     EXPECT_TRUE(sel_[1].hasForces());
 423 }
 424
 425 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 426 {
 427     ASSERT_NO_THROW(sel_ = sc_.parseFromFile(
 428                                 gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 429     // These should match the contents of selfile.dat
 430     ASSERT_EQ(2U, sel_.size());
 431     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 432     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 433 }
 434
 435 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 436 {
 437     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 438     EXPECT_THROW({
 439                      sc_.parseFromString("resname ~ \"R[A\"");
 440                      sc_.compile();
 441                  }, gmx::InvalidInputError);
 442 }
 443
 444 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 445 {
 446     if (!gmx::Regex::isSupported())
 447     {
 448         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 449         EXPECT_THROW({
 450                          sc_.parseFromString("resname \"R[AD]\"");
 451                          sc_.compile();
 452                      }, gmx::InvalidInputError);
 453     }
 454 }
 455
 456 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 457 {
 458     EXPECT_THROW(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 459                  gmx::InvalidInputError);
 460 }
 461
 462 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 463 {
 464     EXPECT_THROW(sc_.parseFromString("within 1 of"),
 465                  gmx::InvalidInputError);
 466 }
 467
 468 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 469 {
 470     EXPECT_THROW(sc_.parseFromString("within of atomnr 1"),
 471                  gmx::InvalidInputError);
 472 }
 473
 474 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 475 {
 476     EXPECT_THROW(sc_.parseFromString("resname help"),
 477                  gmx::InvalidInputError);
 478 }
 479
 480 // TODO: Tests for more parser errors
 481
 482 TEST_F(SelectionCollectionTest, RecoversFromUnknownGroupReference)
 483 {
 484     ASSERT_NO_THROW(sc_.parseFromString("group \"foo\""));
 485     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 486     EXPECT_THROW(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
 487     EXPECT_THROW(sc_.compile(), gmx::APIError);
 488 }
 489
 490 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 491 {
 492     ASSERT_NO_THROW(sc_.parseFromString("molindex 1 to 5"));
 493     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 494     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 495 }
 496
 497 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 498 {
 499     ASSERT_NO_THROW(sc_.parseFromString("type CA"));
 500     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 501     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 502 }
 503
 504 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 505 {
 506     ASSERT_NO_THROW(sc_.parseFromString("altloc A"));
 507     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 508     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 509 }
 510
 511 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 512 {
 513     ASSERT_NO_THROW(sc_.parseFromString("all permute 1 1"));
 514     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 515     EXPECT_THROW(sc_.compile(), gmx::InvalidInputError);
 516 }
 517
 518 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 519 {
 520     ASSERT_NO_THROW(sc_.parseFromString("all permute 3 2 1"));
 521     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 522     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 523 }
 524
 525 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 526 {
 527     ASSERT_NO_THROW(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 528     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 529     ASSERT_NO_THROW(sc_.compile());
 530     EXPECT_THROW(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 531 }
 532
 533 // TODO: Tests for evaluation errors
 534
 535
 536 /********************************************************************
 537  * Tests for selection keywords
 538  */
 539
 540 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 541 {
 542     static const char * const selections[] = {
 543         "all",
 544         "none"
 545     };
 546     runTest(10, selections);
 547 }
 548
 549 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 550 {
 551     static const char * const selections[] = {
 552         "atomnr 1 to 3 6 to 8",
 553         "atomnr 4 2 5 to 7",
 554         "atomnr <= 5"
 555     };
 556     runTest(10, selections);
 557 }
 558
 559 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 560 {
 561     static const char * const selections[] = {
 562         "resnr 1 2 5",
 563         "resid 4 to 3"
 564     };
 565     runTest("simple.gro", selections);
 566 }
 567
 568 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 569 {
 570     static const char * const selections[] = {
 571         "resindex 1 4",
 572         "residue 1 3"
 573     };
 574     runTest("simple.pdb", selections);
 575 }
 576
 577 // TODO: Add test for "molindex"
 578
 579 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 580 {
 581     static const char * const selections[] = {
 582         "name CB",
 583         "atomname S1 S2"
 584     };
 585     runTest("simple.gro", selections);
 586 }
 587
 588 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 589 {
 590     static const char * const selections[] = {
 591         "name HG21",
 592         "name 1HG2",
 593         "pdbname HG21 CB",
 594         "pdbatomname 1HG2"
 595     };
 596     runTest("simple.pdb", selections);
 597 }
 598
 599 // TODO: Add test for atomtype
 600
 601 TEST_F(SelectionCollectionDataTest, HandlesChain)
 602 {
 603     static const char * const selections[] = {
 604         "chain A",
 605         "chain B"
 606     };
 607     runTest("simple.pdb", selections);
 608 }
 609
 610 TEST_F(SelectionCollectionDataTest, HandlesMass)
 611 {
 612     static const char * const selections[] = {
 613         "mass > 5"
 614     };
 615     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 616     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 617     for (int i = 0; i < top_->atoms.nr; ++i)
 618     {
 619         top_->atoms.atom[i].m = 1.0 + i;
 620     }
 621     ASSERT_NO_FATAL_FAILURE(runCompiler());
 622 }
 623
 624 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 625 {
 626     static const char * const selections[] = {
 627         "charge < 0.5"
 628     };
 629     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 630     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 631     for (int i = 0; i < top_->atoms.nr; ++i)
 632     {
 633         top_->atoms.atom[i].q = i / 10.0;
 634     }
 635     ASSERT_NO_FATAL_FAILURE(runCompiler());
 636 }
 637
 638 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 639 {
 640     static const char * const selections[] = {
 641         "altloc \" \"",
 642         "altloc A"
 643     };
 644     runTest("simple.pdb", selections);
 645 }
 646
 647 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 648 {
 649     static const char * const selections[] = {
 650         "insertcode \" \"",
 651         "insertcode A"
 652     };
 653     runTest("simple.pdb", selections);
 654 }
 655
 656 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 657 {
 658     static const char * const selections[] = {
 659         "occupancy 1",
 660         "occupancy < .5"
 661     };
 662     runTest("simple.pdb", selections);
 663 }
 664
 665 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 666 {
 667     static const char * const selections[] = {
 668         "beta 0",
 669         "beta >= 0.3"
 670     };
 671     runTest("simple.pdb", selections);
 672 }
 673
 674 TEST_F(SelectionCollectionDataTest, HandlesResname)
 675 {
 676     static const char * const selections[] = {
 677         "resname RA",
 678         "resname RB RC"
 679     };
 680     runTest("simple.gro", selections);
 681 }
 682
 683 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 684 {
 685     static const char * const selections[] = {
 686         "x < 3",
 687         "y >= 3",
 688         "x {-1 to 2}"
 689     };
 690     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 691     runTest("simple.gro", selections);
 692 }
 693
 694
 695 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 696 {
 697     static const char * const selections[] = {
 698         "same residue as atomnr 1 4 12"
 699     };
 700     runTest("simple.gro", selections);
 701 }
 702
 703
 704 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 705 {
 706     static const char * const selections[] = {
 707         "same resname as atomnr 1 14"
 708     };
 709     runTest("simple.gro", selections);
 710 }
 711
 712
 713 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 714 {
 715     static const char * const selections[] = {
 716         "cog of resnr 1 3",
 717         "res_cog of name CB and resnr 1 3",
 718         "whole_res_cog of name CB and resnr 1 3",
 719         "part_res_cog of x < 3",
 720         "dyn_res_cog of x < 3"
 721     };
 722     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 723              | efTestPositionAtoms);
 724     runTest("simple.gro", selections);
 725 }
 726
 727
 728 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 729 {
 730     static const char * const selections[] = {
 731         "distance from cog of resnr 1 < 2"
 732     };
 733     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 734     runTest("simple.gro", selections);
 735 }
 736
 737
 738 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 739 {
 740     static const char * const selections[] = {
 741         "mindistance from resnr 1 < 2"
 742     };
 743     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 744     runTest("simple.gro", selections);
 745 }
 746
 747
 748 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 749 {
 750     static const char * const selections[] = {
 751         "within 1 of resnr 2"
 752     };
 753     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 754     runTest("simple.gro", selections);
 755 }
 756
 757
 758 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 759 {
 760     // Both of these should evaluate to empty on a correct implementation.
 761     static const char * const selections[] = {
 762         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 763         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 764     };
 765     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 766     runTest("sphere.gro", selections);
 767 }
 768
 769
 770 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 771 {
 772     static const char * const selections[] = {
 773         "all permute 3 1 2",
 774         "res_cog of resnr 1 to 4 permute 2 1",
 775         "name CB S1 and res_cog x < 3 permute 2 1"
 776     };
 777     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 778              | efTestPositionAtoms | efTestPositionMapping);
 779     runTest("simple.gro", selections);
 780 }
 781
 782
 783 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 784 {
 785     static const char * const selections[] = {
 786         "name S2 plus name S1",
 787         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 788         "name S1 and y < 3 plus res_cog of x < 2.5"
 789     };
 790     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 791              | efTestPositionAtoms | efTestPositionMapping);
 792     runTest("simple.gro", selections);
 793 }
 794
 795
 796 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 797 {
 798     static const char * const selections[] = {
 799         "name S2 merge name S1",
 800         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 801         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 802     };
 803     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 804              | efTestPositionAtoms | efTestPositionMapping);
 805     runTest("simple.gro", selections);
 806 }
 807
 808
 809 /********************************************************************
 810  * Tests for generic selection evaluation
 811  */
 812
 813 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 814 {
 815     static const char * const selections[] = {
 816         "name CB",
 817         "y > 2",
 818         "res_cog of y > 2"
 819     };
 820     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 821              | efTestPositionMasses | efTestPositionCharges);
 822     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 823     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 824     for (int i = 0; i < top_->atoms.nr; ++i)
 825     {
 826         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 827         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 828     }
 829     ASSERT_NO_FATAL_FAILURE(runCompiler());
 830     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 831     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 832 }
 833
 834 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 835 {
 836     static const char * const selections[] = {
 837         "atomnr 1 to 3 8 to 9",
 838         "y > 2",
 839         "cog of (y > 2)"
 840     };
 841     setFlags(TestFlags() | efTestPositionAtoms
 842              | efTestPositionMasses | efTestPositionCharges);
 843     runTest(10, selections);
 844 }
 845
 846
 847 /********************************************************************
 848  * Tests for selection syntactic constructs
 849  */
 850
 851 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 852 {
 853     static const char * const selections[] = {
 854         "[1, -2, 3.5]"
 855     };
 856     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 857     runTest("simple.gro", selections);
 858 }
 859
 860
 861 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 862 {
 863     static const char * const selections[] = {
 864         "within 1 of [2, 1, 0]"
 865     };
 866     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 867     runTest("simple.gro", selections);
 868 }
 869
 870
 871 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 872 {
 873     static const char * const selections[] = {
 874         "name = S1 \"C?\"",
 875         "name ? S1 \"C?\""
 876     };
 877     runTest("simple.gro", selections);
 878 }
 879
 880
 881 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 882 {
 883     static const char * const selections[] = {
 884         "name \"S?\"",
 885         "name ? \"S?\""
 886     };
 887     runTest("simple.gro", selections);
 888 }
 889
 890
 891 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 892 {
 893     static const char * const selections[] = {
 894         "resname \"R[BD]\"",
 895         "resname ~ \"R[BD]\""
 896     };
 897     if (gmx::Regex::isSupported())
 898     {
 899         runTest("simple.gro", selections);
 900     }
 901 }
 902
 903
 904 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 905 {
 906     static const char * const selections[] = {
 907         "atomnr 1 to 5 and atomnr 2 to 7",
 908         "atomnr 1 to 5 or not atomnr 3 to 8",
 909         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 910         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 911         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 912     };
 913     runTest(10, selections);
 914 }
 915
 916
 917 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
 918 {
 919     static const char * const selections[] = {
 920         "x > 2",
 921         "2 < x",
 922         "y > resnr",
 923         "resnr < 2.5",
 924         "2.5 > resnr"
 925     };
 926     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 927     runTest("simple.gro", selections);
 928 }
 929
 930
 931 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
 932 {
 933     static const char * const selections[] = {
 934         "x+1 > 3",
 935         "(y-1)^2 <= 1",
 936         "x+--1 > 3",
 937         "-x+-1 < -3"
 938     };
 939     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 940     runTest("simple.gro", selections);
 941 }
 942
 943
 944 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
 945 {
 946     static const char * const selections[] = {
 947         "value = x + y",
 948         "value <= 4",
 949         "index = resnr",
 950         "index < 3"
 951     };
 952     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 953     runTest("simple.gro", selections);
 954 }
 955
 956
 957 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
 958 {
 959     static const char * const selections[] = {
 960         "value = x + y",
 961         "resname RA and value <= 4",
 962         "resname RA RB and x < 3 and value <= 4",
 963         "index = atomnr",
 964         "resname RA and index < 3",
 965         "resname RB and y < 3 and index < 6"
 966     };
 967     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 968     runTest("simple.gro", selections);
 969 }
 970
 971
 972 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
 973 {
 974     static const char * const selections[] = {
 975         "foo = res_cog of resname RA",
 976         "foo",
 977         "within 1 of foo",
 978         "bar = cog of resname RA",
 979         "bar",
 980         "within 1 of bar"
 981     };
 982     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 983     runTest("simple.gro", selections);
 984 }
 985
 986
 987 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
 988 {
 989     static const char * const selections[] = {
 990         "constpos = [1.0, 2.5, 0.5]",
 991         "constpos",
 992         "within 2 of constpos"
 993     };
 994     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 995              | efTestPositionAtoms);
 996     runTest("simple.gro", selections);
 997 }
 998
 999
1000 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1001 {
1002     static const char * const selections[] = {
1003         "constint = 4",
1004         "constreal1 = 0.5",
1005         "constreal2 = 2.7",
1006         "resnr < constint",
1007         "x + constreal1 < constreal2"
1008     };
1009     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1010     runTest("simple.gro", selections);
1011 }
1012
1013
1014 /********************************************************************
1015  * Tests for complex boolean syntax
1016  */
1017
1018 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1019 {
1020     static const char * const selections[] = {
1021         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1022         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1023         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1024         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1025         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1026     };
1027     runTest(10, selections);
1028 }
1029
1030
1031 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1032 {
1033     static const char * const selections[] = {
1034         "foo = atomnr 4 to 7 or x < 2",
1035         "atomnr 1 to 4 and foo",
1036         "atomnr 2 to 6 and y < 3 and foo",
1037         "atomnr 6 to 10 and not foo"
1038     };
1039     runTest(10, selections);
1040 }
1041
1042
1043 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1044 {
1045     static const char * const selections[] = {
1046         "foo = atomnr 4 to 7",
1047         "bar = foo and x < 2",
1048         "bar2 = foo and y < 2",
1049         "atomnr 1 to 4 and bar",
1050         "atomnr 2 to 6 and y < 3 and bar2",
1051         "atomnr 6 to 10 and not foo"
1052     };
1053     runTest(10, selections);
1054 }
1055
1056
1057 /********************************************************************
1058  * Tests for complex subexpression cases
1059  *
1060  * These tests use some knowledge of the implementation to trigger different
1061  * paths in the code.
1062  */
1063
1064 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1065 {
1066     static const char * const selections[] = {
1067         "unused1 = atomnr 1 to 3",
1068         "foo = atomnr 4 to 7",
1069         "atomnr 1 to 6 and foo",
1070         "unused2 = atomnr 3 to 5"
1071     };
1072     runTest(10, selections);
1073 }
1074
1075
1076 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1077 {
1078     static const char * const selections[] = {
1079         "foo = atomnr 4 to 7 and x < 2",
1080         "atomnr 1 to 5 and foo",
1081         "atomnr 3 to 7 and foo"
1082     };
1083     runTest(10, selections);
1084 }
1085
1086
1087 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1088 {
1089     static const char * const selections[] = {
1090         "foo = atomnr 4 to 7 and x < 2",
1091         "atomnr 1 to 6 and foo",
1092         "within 1 of foo",
1093         "foo"
1094     };
1095     runTest(10, selections);
1096 }
1097
1098
1099 } // namespace