src/gromacs/selection/tests/selectioncollection.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests selection parsing and compilation.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include <gtest/gtest.h>
  43
  44 #include "gromacs/options/basicoptions.h"
  45 #include "gromacs/options/options.h"
  46 #include "gromacs/selection/selectioncollection.h"
  47 #include "gromacs/selection/selection.h"
  48 #include "gromacs/utility/exceptions.h"
  49 #include "gromacs/utility/flags.h"
  50 #include "gromacs/utility/gmxregex.h"
  51 #include "gromacs/utility/stringutil.h"
  52
  53 #include "testutils/refdata.h"
  54 #include "testutils/testasserts.h"
  55 #include "testutils/testfilemanager.h"
  56 #include "testutils/testoptions.h"
  57
  58 #include "toputils.h"
  59
  60 namespace
  61 {
  62
  63 /********************************************************************
  64  * Test fixture for selection testing
  65  */
  66
  67 class SelectionCollectionTest : public ::testing::Test
  68 {
  69     public:
  70         static int               s_debugLevel;
  71
  72         SelectionCollectionTest();
  73
  74         void setAtomCount(int natoms)
  75         {
  76             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  77         }
  78         void loadTopology(const char *filename);
  79         void setTopology();
  80
  81         gmx::test::TopologyManager  topManager_;
  82         gmx::SelectionCollection    sc_;
  83         gmx::SelectionList          sel_;
  84         t_topology                 *top_;
  85         t_trxframe                 *frame_;
  86 };
  87
  88 int SelectionCollectionTest::s_debugLevel = 0;
  89
  90 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  91 {
  92     options->addOption(gmx::IntegerOption("seldebug")
  93                            .store(&SelectionCollectionTest::s_debugLevel)
  94                            .description("Set selection debug level"));
  95 }
  96
  97 SelectionCollectionTest::SelectionCollectionTest()
  98     : top_(NULL), frame_(NULL)
  99 {
 100     topManager_.requestFrame();
 101     sc_.setDebugLevel(s_debugLevel);
 102     sc_.setReferencePosType("atom");
 103     sc_.setOutputPosType("atom");
 104 }
 105
 106 void
 107 SelectionCollectionTest::loadTopology(const char *filename)
 108 {
 109     topManager_.loadTopology(filename);
 110     setTopology();
 111 }
 112
 113 void
 114 SelectionCollectionTest::setTopology()
 115 {
 116     top_   = topManager_.topology();
 117     frame_ = topManager_.frame();
 118
 119     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 120 }
 121
 122
 123 /********************************************************************
 124  * Test fixture for selection testing with reference data
 125  */
 126
 127 class SelectionCollectionDataTest : public SelectionCollectionTest
 128 {
 129     public:
 130         enum TestFlag
 131         {
 132             efTestEvaluation            = 1<<0,
 133             efTestPositionAtoms         = 1<<1,
 134             efTestPositionCoordinates   = 1<<2,
 135             efTestPositionMapping       = 1<<3,
 136             efTestPositionMasses        = 1<<4,
 137             efTestPositionCharges       = 1<<5,
 138             efDontTestCompiledAtoms     = 1<<8
 139         };
 140         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 141
 142         SelectionCollectionDataTest()
 143             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 144         {
 145         }
 146
 147         void setFlags(TestFlags flags) { flags_ = flags; }
 148
 149         template <size_t count>
 150         void runTest(int natoms, const char *const (&selections)[count])
 151         {
 152             runTest(natoms, selections, count);
 153         }
 154         template <size_t count>
 155         void runTest(const char *filename, const char *const (&selections)[count])
 156         {
 157             runTest(filename, selections, count);
 158         }
 159
 160         template <size_t count>
 161         void runParser(const char *const (&selections)[count])
 162         {
 163             runParser(selections, count);
 164         }
 165
 166         void runCompiler();
 167         void runEvaluate();
 168         void runEvaluateFinal();
 169
 170     private:
 171         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 172                                    const gmx::Selection &sel, TestFlags flags);
 173
 174         void runTest(int natoms, const char *const *selections, size_t count);
 175         void runTest(const char *filename, const char *const *selections,
 176                      size_t count);
 177         void runParser(const char *const *selections, size_t count);
 178
 179         void checkCompiled();
 180
 181         gmx::test::TestReferenceData    data_;
 182         gmx::test::TestReferenceChecker checker_;
 183         size_t                          count_;
 184         int                             framenr_;
 185         TestFlags                       flags_;
 186 };
 187
 188
 189 void
 190 SelectionCollectionDataTest::checkSelection(
 191         gmx::test::TestReferenceChecker *checker,
 192         const gmx::Selection &sel, TestFlags flags)
 193 {
 194     using gmx::test::TestReferenceChecker;
 195
 196     {
 197         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 198         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 199     }
 200     if (flags.test(efTestPositionAtoms)
 201         || flags.test(efTestPositionCoordinates)
 202         || flags.test(efTestPositionMapping)
 203         || flags.test(efTestPositionMasses)
 204         || flags.test(efTestPositionCharges))
 205     {
 206         TestReferenceChecker compound(
 207                 checker->checkSequenceCompound("Positions", sel.posCount()));
 208         for (int i = 0; i < sel.posCount(); ++i)
 209         {
 210             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 211             const gmx::SelectionPosition &p = sel.position(i);
 212             if (flags.test(efTestPositionAtoms))
 213             {
 214                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 215                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 216             }
 217             if (flags.test(efTestPositionCoordinates))
 218             {
 219                 poscompound.checkVector(p.x(), "Coordinates");
 220             }
 221             if (flags.test(efTestPositionMapping))
 222             {
 223                 poscompound.checkInteger(p.refId(), "RefId");
 224                 poscompound.checkInteger(p.mappedId(), "MappedId");
 225             }
 226             if (flags.test(efTestPositionMasses))
 227             {
 228                 poscompound.checkReal(p.mass(), "Mass");
 229             }
 230             if (flags.test(efTestPositionCharges))
 231             {
 232                 poscompound.checkReal(p.charge(), "Charge");
 233             }
 234         }
 235     }
 236 }
 237
 238
 239 void
 240 SelectionCollectionDataTest::runParser(const char *const *selections,
 241                                        size_t             count)
 242 {
 243     using gmx::test::TestReferenceChecker;
 244
 245     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 246     size_t               varcount = 0;
 247     count_ = 0;
 248     for (size_t i = 0; i < count; ++i)
 249     {
 250         SCOPED_TRACE(std::string("Parsing selection \"")
 251                      + selections[i] + "\"");
 252         gmx::SelectionList result;
 253         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 254         sel_.insert(sel_.end(), result.begin(), result.end());
 255         if (sel_.size() == count_)
 256         {
 257             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 258             TestReferenceChecker varcompound(
 259                     compound.checkCompound("ParsedVariable", id.c_str()));
 260             varcompound.checkString(selections[i], "Input");
 261             ++varcount;
 262         }
 263         else
 264         {
 265             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 266             TestReferenceChecker selcompound(
 267                     compound.checkCompound("ParsedSelection", id.c_str()));
 268             selcompound.checkString(selections[i], "Input");
 269             selcompound.checkString(sel_[count_].name(), "Name");
 270             selcompound.checkString(sel_[count_].selectionText(), "Text");
 271             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 272             ++count_;
 273         }
 274     }
 275 }
 276
 277
 278 void
 279 SelectionCollectionDataTest::runCompiler()
 280 {
 281     ASSERT_NO_THROW_GMX(sc_.compile());
 282     ASSERT_EQ(count_, sel_.size());
 283     checkCompiled();
 284 }
 285
 286
 287 void
 288 SelectionCollectionDataTest::checkCompiled()
 289 {
 290     using gmx::test::TestReferenceChecker;
 291     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 292
 293     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 294     for (size_t i = 0; i < count_; ++i)
 295     {
 296         SCOPED_TRACE(std::string("Checking selection \"") +
 297                      sel_[i].selectionText() + "\"");
 298         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 299         TestReferenceChecker selcompound(
 300                 compound.checkCompound("Selection", id.c_str()));
 301         if (!flags_.test(efDontTestCompiledAtoms))
 302         {
 303             checkSelection(&selcompound, sel_[i], flags_ & mask);
 304         }
 305     }
 306 }
 307
 308
 309 void
 310 SelectionCollectionDataTest::runEvaluate()
 311 {
 312     using gmx::test::TestReferenceChecker;
 313
 314     ++framenr_;
 315     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 316     std::string          frame = gmx::formatString("Frame%d", framenr_);
 317     TestReferenceChecker compound(
 318             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 319     for (size_t i = 0; i < count_; ++i)
 320     {
 321         SCOPED_TRACE(std::string("Checking selection \"") +
 322                      sel_[i].selectionText() + "\"");
 323         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 324         TestReferenceChecker selcompound(
 325                 compound.checkCompound("Selection", id.c_str()));
 326         checkSelection(&selcompound, sel_[i], flags_);
 327     }
 328 }
 329
 330
 331 void
 332 SelectionCollectionDataTest::runEvaluateFinal()
 333 {
 334     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 335     checkCompiled();
 336 }
 337
 338
 339 void
 340 SelectionCollectionDataTest::runTest(int natoms, const char * const *selections,
 341                                      size_t count)
 342 {
 343     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 344     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 345     ASSERT_NO_FATAL_FAILURE(runCompiler());
 346 }
 347
 348
 349 void
 350 SelectionCollectionDataTest::runTest(const char         *filename,
 351                                      const char * const *selections,
 352                                      size_t              count)
 353 {
 354     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 355     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 356     ASSERT_NO_FATAL_FAILURE(runCompiler());
 357     if (flags_.test(efTestEvaluation))
 358     {
 359         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 360         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 361     }
 362 }
 363
 364
 365 /********************************************************************
 366  * Tests for SelectionCollection functionality without reference data
 367  */
 368
 369 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 370 {
 371     EXPECT_FALSE(sc_.requiresTopology());
 372     EXPECT_NO_THROW_GMX(sc_.compile());
 373 }
 374
 375 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 376 {
 377     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 378     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 379     ASSERT_EQ(2U, sel_.size());
 380     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 381     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 382     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 383     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 384     ASSERT_NO_THROW_GMX(sc_.compile());
 385     EXPECT_TRUE(sel_[0].hasVelocities());
 386     EXPECT_TRUE(sel_[1].hasVelocities());
 387     EXPECT_TRUE(sel_[0].hasForces());
 388     EXPECT_TRUE(sel_[1].hasForces());
 389 }
 390
 391 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 392 {
 393     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 394                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 395     // These should match the contents of selfile.dat
 396     ASSERT_EQ(2U, sel_.size());
 397     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 398     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 399 }
 400
 401 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 402 {
 403     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 404     EXPECT_THROW_GMX({
 405                          sc_.parseFromString("resname ~ \"R[A\"");
 406                          sc_.compile();
 407                      }, gmx::InvalidInputError);
 408 }
 409
 410 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 411 {
 412     if (!gmx::Regex::isSupported())
 413     {
 414         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 415         EXPECT_THROW_GMX({
 416                              sc_.parseFromString("resname \"R[AD]\"");
 417                              sc_.compile();
 418                          }, gmx::InvalidInputError);
 419     }
 420 }
 421
 422 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 423 {
 424     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 425                      gmx::InvalidInputError);
 426 }
 427
 428 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 429 {
 430     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 431                      gmx::InvalidInputError);
 432 }
 433
 434 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 435 {
 436     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 437                      gmx::InvalidInputError);
 438 }
 439
 440 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 441 {
 442     EXPECT_THROW_GMX(sc_.parseFromString("resname help"),
 443                      gmx::InvalidInputError);
 444 }
 445
 446 // TODO: Tests for more parser errors
 447
 448 TEST_F(SelectionCollectionTest, RecoversFromUnknownGroupReference)
 449 {
 450     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 451     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 452     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
 453     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 454 }
 455
 456 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 457 {
 458     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 459     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 460     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 461 }
 462
 463 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 464 {
 465     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 466     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 467     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 468 }
 469
 470 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 471 {
 472     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 473     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 474     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 475 }
 476
 477 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 478 {
 479     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 480     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 481     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 482 }
 483
 484 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 485 {
 486     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 487     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 488     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 489 }
 490
 491 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 492 {
 493     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 494     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 495     ASSERT_NO_THROW_GMX(sc_.compile());
 496     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 497 }
 498
 499 // TODO: Tests for evaluation errors
 500
 501
 502 /********************************************************************
 503  * Tests for selection keywords
 504  */
 505
 506 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 507 {
 508     static const char * const selections[] = {
 509         "all",
 510         "none"
 511     };
 512     runTest(10, selections);
 513 }
 514
 515 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 516 {
 517     static const char * const selections[] = {
 518         "atomnr 1 to 3 6 to 8",
 519         "atomnr 4 2 5 to 7",
 520         "atomnr <= 5"
 521     };
 522     runTest(10, selections);
 523 }
 524
 525 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 526 {
 527     static const char * const selections[] = {
 528         "resnr 1 2 5",
 529         "resid 4 to 3"
 530     };
 531     runTest("simple.gro", selections);
 532 }
 533
 534 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 535 {
 536     static const char * const selections[] = {
 537         "resindex 1 4",
 538         "residue 1 3"
 539     };
 540     runTest("simple.pdb", selections);
 541 }
 542
 543 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 544 {
 545     static const char * const selections[] = {
 546         "molindex 1 4",
 547         "molecule 2 3 5"
 548     };
 549     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 550     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 551     topManager_.initUniformMolecules(3);
 552     ASSERT_NO_FATAL_FAILURE(runCompiler());
 553 }
 554
 555 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 556 {
 557     static const char * const selections[] = {
 558         "name CB",
 559         "atomname S1 S2"
 560     };
 561     runTest("simple.gro", selections);
 562 }
 563
 564 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 565 {
 566     static const char * const selections[] = {
 567         "name HG21",
 568         "name 1HG2",
 569         "pdbname HG21 CB",
 570         "pdbatomname 1HG2"
 571     };
 572     runTest("simple.pdb", selections);
 573 }
 574
 575
 576 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 577 {
 578     static const char * const selections[] = {
 579         "atomtype CA"
 580     };
 581     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 582     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 583     const char *const types[] = { "CA", "SA", "SB" };
 584     topManager_.initAtomTypes(types);
 585     ASSERT_NO_FATAL_FAILURE(runCompiler());
 586 }
 587
 588 TEST_F(SelectionCollectionDataTest, HandlesChain)
 589 {
 590     static const char * const selections[] = {
 591         "chain A",
 592         "chain B"
 593     };
 594     runTest("simple.pdb", selections);
 595 }
 596
 597 TEST_F(SelectionCollectionDataTest, HandlesMass)
 598 {
 599     static const char * const selections[] = {
 600         "mass > 5"
 601     };
 602     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 603     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 604     for (int i = 0; i < top_->atoms.nr; ++i)
 605     {
 606         top_->atoms.atom[i].m = 1.0 + i;
 607     }
 608     ASSERT_NO_FATAL_FAILURE(runCompiler());
 609 }
 610
 611 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 612 {
 613     static const char * const selections[] = {
 614         "charge < 0.5"
 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].q = i / 10.0;
 621     }
 622     ASSERT_NO_FATAL_FAILURE(runCompiler());
 623 }
 624
 625 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 626 {
 627     static const char * const selections[] = {
 628         "altloc \" \"",
 629         "altloc A"
 630     };
 631     runTest("simple.pdb", selections);
 632 }
 633
 634 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 635 {
 636     static const char * const selections[] = {
 637         "insertcode \" \"",
 638         "insertcode A"
 639     };
 640     runTest("simple.pdb", selections);
 641 }
 642
 643 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 644 {
 645     static const char * const selections[] = {
 646         "occupancy 1",
 647         "occupancy < .5"
 648     };
 649     runTest("simple.pdb", selections);
 650 }
 651
 652 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 653 {
 654     static const char * const selections[] = {
 655         "beta 0",
 656         "beta >= 0.3"
 657     };
 658     runTest("simple.pdb", selections);
 659 }
 660
 661 TEST_F(SelectionCollectionDataTest, HandlesResname)
 662 {
 663     static const char * const selections[] = {
 664         "resname RA",
 665         "resname RB RC"
 666     };
 667     runTest("simple.gro", selections);
 668 }
 669
 670 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 671 {
 672     static const char * const selections[] = {
 673         "x < 3",
 674         "y >= 3",
 675         "x {-1 to 2}"
 676     };
 677     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 678     runTest("simple.gro", selections);
 679 }
 680
 681
 682 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 683 {
 684     static const char * const selections[] = {
 685         "same residue as atomnr 1 4 12"
 686     };
 687     runTest("simple.gro", selections);
 688 }
 689
 690
 691 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 692 {
 693     static const char * const selections[] = {
 694         "same resname as atomnr 1 14"
 695     };
 696     runTest("simple.gro", selections);
 697 }
 698
 699
 700 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 701 {
 702     static const char * const selections[] = {
 703         "cog of resnr 1 3",
 704         "res_cog of name CB and resnr 1 3",
 705         "whole_res_cog of name CB and resnr 1 3",
 706         "part_res_cog of x < 3",
 707         "dyn_res_cog of x < 3"
 708     };
 709     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 710              | efTestPositionAtoms);
 711     runTest("simple.gro", selections);
 712 }
 713
 714
 715 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 716 {
 717     static const char * const selections[] = {
 718         "distance from cog of resnr 1 < 2"
 719     };
 720     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 721     runTest("simple.gro", selections);
 722 }
 723
 724
 725 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 726 {
 727     static const char * const selections[] = {
 728         "mindistance from resnr 1 < 2"
 729     };
 730     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 731     runTest("simple.gro", selections);
 732 }
 733
 734
 735 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 736 {
 737     static const char * const selections[] = {
 738         "within 1 of resnr 2"
 739     };
 740     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 741     runTest("simple.gro", selections);
 742 }
 743
 744
 745 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 746 {
 747     // Both of these should evaluate to empty on a correct implementation.
 748     static const char * const selections[] = {
 749         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 750         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 751     };
 752     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 753     runTest("sphere.gro", selections);
 754 }
 755
 756
 757 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 758 {
 759     static const char * const selections[] = {
 760         "all permute 3 1 2",
 761         "res_cog of resnr 1 to 4 permute 2 1",
 762         "name CB S1 and res_cog x < 3 permute 2 1"
 763     };
 764     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 765              | efTestPositionAtoms | efTestPositionMapping);
 766     runTest("simple.gro", selections);
 767 }
 768
 769
 770 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 771 {
 772     static const char * const selections[] = {
 773         "name S2 plus name S1",
 774         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 775         "name S1 and y < 3 plus res_cog of x < 2.5"
 776     };
 777     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 778              | efTestPositionAtoms | efTestPositionMapping);
 779     runTest("simple.gro", selections);
 780 }
 781
 782
 783 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 784 {
 785     static const char * const selections[] = {
 786         "name S2 merge name S1",
 787         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 788         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 789     };
 790     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 791              | efTestPositionAtoms | efTestPositionMapping);
 792     runTest("simple.gro", selections);
 793 }
 794
 795
 796 /********************************************************************
 797  * Tests for generic selection evaluation
 798  */
 799
 800 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 801 {
 802     static const char * const selections[] = {
 803         "name CB",
 804         "y > 2",
 805         "res_cog of y > 2"
 806     };
 807     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 808              | efTestPositionMasses | efTestPositionCharges);
 809     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 810     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 811     for (int i = 0; i < top_->atoms.nr; ++i)
 812     {
 813         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 814         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 815     }
 816     ASSERT_NO_FATAL_FAILURE(runCompiler());
 817     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 818     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 819 }
 820
 821 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 822 {
 823     static const char * const selections[] = {
 824         "atomnr 1 to 3 8 to 9",
 825         "y > 2",
 826         "cog of (y > 2)"
 827     };
 828     setFlags(TestFlags() | efTestPositionAtoms
 829              | efTestPositionMasses | efTestPositionCharges);
 830     runTest(10, selections);
 831 }
 832
 833
 834 /********************************************************************
 835  * Tests for selection syntactic constructs
 836  */
 837
 838 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 839 {
 840     static const char * const selections[] = {
 841         "[1, -2, 3.5]"
 842     };
 843     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 844     runTest("simple.gro", selections);
 845 }
 846
 847
 848 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 849 {
 850     static const char * const selections[] = {
 851         "within 1 of [2, 1, 0]"
 852     };
 853     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 854     runTest("simple.gro", selections);
 855 }
 856
 857
 858 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 859 {
 860     static const char * const selections[] = {
 861         "name = S1 \"C?\"",
 862         "name ? S1 \"C?\""
 863     };
 864     runTest("simple.gro", selections);
 865 }
 866
 867
 868 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 869 {
 870     static const char * const selections[] = {
 871         "name \"S?\"",
 872         "name ? \"S?\""
 873     };
 874     runTest("simple.gro", selections);
 875 }
 876
 877
 878 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 879 {
 880     static const char * const selections[] = {
 881         "resname \"R[BD]\"",
 882         "resname ~ \"R[BD]\""
 883     };
 884     if (gmx::Regex::isSupported())
 885     {
 886         runTest("simple.gro", selections);
 887     }
 888 }
 889
 890
 891 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 892 {
 893     static const char * const selections[] = {
 894         "atomnr 1 to 5 and atomnr 2 to 7",
 895         "atomnr 1 to 5 or not atomnr 3 to 8",
 896         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 897         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 898         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 899     };
 900     runTest(10, selections);
 901 }
 902
 903
 904 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
 905 {
 906     static const char * const selections[] = {
 907         "same residue as (atomnr 3 5 13 or y > 5)",
 908         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
 909     };
 910     setFlags(TestFlags() | efTestEvaluation);
 911     runTest("simple.gro", selections);
 912 }
 913
 914
 915 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
 916 {
 917     static const char * const selections[] = {
 918         "x > 2",
 919         "2 < x",
 920         "y > resnr",
 921         "resnr < 2.5",
 922         "2.5 > resnr"
 923     };
 924     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 925     runTest("simple.gro", selections);
 926 }
 927
 928
 929 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
 930 {
 931     static const char * const selections[] = {
 932         "x+1 > 3",
 933         "(y-1)^2 <= 1",
 934         "x+--1 > 3",
 935         "-x+-1 < -3"
 936     };
 937     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 938     runTest("simple.gro", selections);
 939 }
 940
 941
 942 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
 943 {
 944     static const char * const selections[] = {
 945         "value = x + y",
 946         "value <= 4",
 947         "index = resnr",
 948         "index < 3"
 949     };
 950     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 951     runTest("simple.gro", selections);
 952 }
 953
 954
 955 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
 956 {
 957     static const char * const selections[] = {
 958         "value = x + y",
 959         "resname RA and value <= 4",
 960         "resname RA RB and x < 3 and value <= 4",
 961         "index = atomnr",
 962         "resname RA and index < 3",
 963         "resname RB and y < 3 and index < 6"
 964     };
 965     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 966     runTest("simple.gro", selections);
 967 }
 968
 969
 970 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
 971 {
 972     static const char * const selections[] = {
 973         "foo = res_cog of resname RA",
 974         "foo",
 975         "within 1 of foo",
 976         "bar = cog of resname RA",
 977         "bar",
 978         "within 1 of bar"
 979     };
 980     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 981     runTest("simple.gro", selections);
 982 }
 983
 984
 985 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
 986 {
 987     static const char * const selections[] = {
 988         "constpos = [1.0, 2.5, 0.5]",
 989         "constpos",
 990         "within 2 of constpos"
 991     };
 992     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 993              | efTestPositionAtoms);
 994     runTest("simple.gro", selections);
 995 }
 996
 997
 998 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
 999 {
1000     static const char * const selections[] = {
1001         "constint = 4",
1002         "constreal1 = 0.5",
1003         "constreal2 = 2.7",
1004         "resnr < constint",
1005         "x + constreal1 < constreal2"
1006     };
1007     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1008     runTest("simple.gro", selections);
1009 }
1010
1011
1012 /********************************************************************
1013  * Tests for complex boolean syntax
1014  */
1015
1016 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1017 {
1018     static const char * const selections[] = {
1019         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1020         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1021         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1022         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1023         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1024     };
1025     runTest(10, selections);
1026 }
1027
1028
1029 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1030 {
1031     static const char * const selections[] = {
1032         "foo = atomnr 4 to 7 or x < 2",
1033         "atomnr 1 to 4 and foo",
1034         "atomnr 2 to 6 and y < 3 and foo",
1035         "atomnr 6 to 10 and not foo"
1036     };
1037     runTest(10, selections);
1038 }
1039
1040
1041 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1042 {
1043     static const char * const selections[] = {
1044         "foo = atomnr 4 to 7",
1045         "bar = foo and x < 2",
1046         "bar2 = foo and y < 2",
1047         "atomnr 1 to 4 and bar",
1048         "atomnr 2 to 6 and y < 3 and bar2",
1049         "atomnr 6 to 10 and not foo"
1050     };
1051     runTest(10, selections);
1052 }
1053
1054
1055 /********************************************************************
1056  * Tests for complex subexpression cases
1057  *
1058  * These tests use some knowledge of the implementation to trigger different
1059  * paths in the code.
1060  */
1061
1062 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1063 {
1064     static const char * const selections[] = {
1065         "unused1 = atomnr 1 to 3",
1066         "foo = atomnr 4 to 7",
1067         "atomnr 1 to 6 and foo",
1068         "unused2 = atomnr 3 to 5"
1069     };
1070     runTest(10, selections);
1071 }
1072
1073
1074 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1075 {
1076     static const char * const selections[] = {
1077         "foo = atomnr 4 to 7 and x < 2",
1078         "atomnr 1 to 5 and foo",
1079         "atomnr 3 to 7 and foo"
1080     };
1081     runTest(10, selections);
1082 }
1083
1084
1085 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1086 {
1087     static const char * const selections[] = {
1088         "foo = atomnr 4 to 7 and x < 2",
1089         "atomnr 1 to 6 and foo",
1090         "within 1 of foo",
1091         "foo"
1092     };
1093     runTest(10, selections);
1094 }
1095
1096
1097 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1098 {
1099     static const char * const selections[] = {
1100         "foo = atomnr 1 to 8 and x < 10",
1101         "atomnr 1 to 5 and y < 10 and foo",
1102         "foo"
1103     };
1104     setFlags(TestFlags() | efTestEvaluation);
1105     runTest("simple.gro", selections);
1106 }
1107
1108
1109 } // namespace