src/gromacs/selection/tests/selectioncollection.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests selection parsing and compilation.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include <gtest/gtest.h>
  43
  44 #include "gromacs/options/basicoptions.h"
  45 #include "gromacs/options/options.h"
  46 #include "gromacs/selection/indexutil.h"
  47 #include "gromacs/selection/selectioncollection.h"
  48 #include "gromacs/selection/selection.h"
  49 #include "gromacs/topology/topology.h"
  50 #include "gromacs/utility/arrayref.h"
  51 #include "gromacs/utility/exceptions.h"
  52 #include "gromacs/utility/flags.h"
  53 #include "gromacs/utility/gmxregex.h"
  54 #include "gromacs/utility/stringutil.h"
  55
  56 #include "testutils/refdata.h"
  57 #include "testutils/testasserts.h"
  58 #include "testutils/testfilemanager.h"
  59 #include "testutils/testoptions.h"
  60
  61 #include "toputils.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 int               s_debugLevel;
  74
  75         SelectionCollectionTest();
  76         ~SelectionCollectionTest();
  77
  78         void setAtomCount(int natoms)
  79         {
  80             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  81         }
  82         void loadTopology(const char *filename);
  83         void setTopology();
  84         void loadIndexGroups(const char *filename);
  85
  86         gmx::test::TopologyManager  topManager_;
  87         gmx::SelectionCollection    sc_;
  88         gmx::SelectionList          sel_;
  89         t_topology                 *top_;
  90         t_trxframe                 *frame_;
  91         gmx_ana_indexgrps_t        *grps_;
  92 };
  93
  94 int SelectionCollectionTest::s_debugLevel = 0;
  95
  96 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
  97 #ifndef DOXYGEN
  98 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  99 {
 100     options->addOption(gmx::IntegerOption("seldebug")
 101                            .store(&SelectionCollectionTest::s_debugLevel)
 102                            .description("Set selection debug level"));
 103 }
 104 #endif
 105
 106 SelectionCollectionTest::SelectionCollectionTest()
 107     : top_(NULL), frame_(NULL), grps_(NULL)
 108 {
 109     topManager_.requestFrame();
 110     sc_.setDebugLevel(s_debugLevel);
 111     sc_.setReferencePosType("atom");
 112     sc_.setOutputPosType("atom");
 113 }
 114
 115 SelectionCollectionTest::~SelectionCollectionTest()
 116 {
 117     if (grps_ != NULL)
 118     {
 119         gmx_ana_indexgrps_free(grps_);
 120     }
 121 }
 122
 123 void
 124 SelectionCollectionTest::loadTopology(const char *filename)
 125 {
 126     topManager_.loadTopology(filename);
 127     setTopology();
 128 }
 129
 130 void
 131 SelectionCollectionTest::setTopology()
 132 {
 133     top_   = topManager_.topology();
 134     frame_ = topManager_.frame();
 135
 136     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 137 }
 138
 139 void
 140 SelectionCollectionTest::loadIndexGroups(const char *filename)
 141 {
 142     GMX_RELEASE_ASSERT(grps_ == NULL,
 143                        "External groups can only be loaded once");
 144     std::string fullpath =
 145         gmx::test::TestFileManager::getInputFilePath(filename);
 146     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 147     sc_.setIndexGroups(grps_);
 148 }
 149
 150
 151 /********************************************************************
 152  * Test fixture for selection testing with reference data
 153  */
 154
 155 class SelectionCollectionDataTest : public SelectionCollectionTest
 156 {
 157     public:
 158         enum TestFlag
 159         {
 160             efTestEvaluation            = 1<<0,
 161             efTestPositionAtoms         = 1<<1,
 162             efTestPositionCoordinates   = 1<<2,
 163             efTestPositionMapping       = 1<<3,
 164             efTestPositionMasses        = 1<<4,
 165             efTestPositionCharges       = 1<<5,
 166             efTestSelectionNames        = 1<<6,
 167             efDontTestCompiledAtoms     = 1<<8
 168         };
 169         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 170
 171         SelectionCollectionDataTest()
 172             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 173         {
 174         }
 175
 176         void setFlags(TestFlags flags) { flags_ = flags; }
 177
 178         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 179         void runCompiler();
 180         void runEvaluate();
 181         void runEvaluateFinal();
 182
 183         void runTest(int                                     natoms,
 184                      const gmx::ConstArrayRef<const char *> &selections);
 185         void runTest(const char                             *filename,
 186                      const gmx::ConstArrayRef<const char *> &selections);
 187
 188     private:
 189         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 190                                    const gmx::Selection &sel, TestFlags flags);
 191
 192         void checkCompiled();
 193
 194         gmx::test::TestReferenceData    data_;
 195         gmx::test::TestReferenceChecker checker_;
 196         size_t                          count_;
 197         int                             framenr_;
 198         TestFlags                       flags_;
 199 };
 200
 201
 202 void
 203 SelectionCollectionDataTest::checkSelection(
 204         gmx::test::TestReferenceChecker *checker,
 205         const gmx::Selection &sel, TestFlags flags)
 206 {
 207     using gmx::test::TestReferenceChecker;
 208
 209     {
 210         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 211         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 212     }
 213     if (flags.test(efTestPositionAtoms)
 214         || flags.test(efTestPositionCoordinates)
 215         || flags.test(efTestPositionMapping)
 216         || flags.test(efTestPositionMasses)
 217         || flags.test(efTestPositionCharges))
 218     {
 219         TestReferenceChecker compound(
 220                 checker->checkSequenceCompound("Positions", sel.posCount()));
 221         for (int i = 0; i < sel.posCount(); ++i)
 222         {
 223             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 224             const gmx::SelectionPosition &p = sel.position(i);
 225             if (flags.test(efTestPositionAtoms))
 226             {
 227                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 228                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 229             }
 230             if (flags.test(efTestPositionCoordinates))
 231             {
 232                 poscompound.checkVector(p.x(), "Coordinates");
 233             }
 234             if (flags.test(efTestPositionMapping))
 235             {
 236                 poscompound.checkInteger(p.refId(), "RefId");
 237                 poscompound.checkInteger(p.mappedId(), "MappedId");
 238             }
 239             if (flags.test(efTestPositionMasses))
 240             {
 241                 poscompound.checkReal(p.mass(), "Mass");
 242             }
 243             if (flags.test(efTestPositionCharges))
 244             {
 245                 poscompound.checkReal(p.charge(), "Charge");
 246             }
 247         }
 248     }
 249 }
 250
 251
 252 void
 253 SelectionCollectionDataTest::runParser(
 254         const gmx::ConstArrayRef<const char *> &selections)
 255 {
 256     using gmx::test::TestReferenceChecker;
 257
 258     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 259     size_t               varcount = 0;
 260     count_ = 0;
 261     for (size_t i = 0; i < selections.size(); ++i)
 262     {
 263         SCOPED_TRACE(std::string("Parsing selection \"")
 264                      + selections[i] + "\"");
 265         gmx::SelectionList result;
 266         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 267         sel_.insert(sel_.end(), result.begin(), result.end());
 268         if (sel_.size() == count_)
 269         {
 270             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 271             TestReferenceChecker varcompound(
 272                     compound.checkCompound("ParsedVariable", id.c_str()));
 273             varcompound.checkString(selections[i], "Input");
 274             ++varcount;
 275         }
 276         else
 277         {
 278             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 279             TestReferenceChecker selcompound(
 280                     compound.checkCompound("ParsedSelection", id.c_str()));
 281             selcompound.checkString(selections[i], "Input");
 282             if (flags_.test(efTestSelectionNames))
 283             {
 284                 selcompound.checkString(sel_[count_].name(), "Name");
 285             }
 286             selcompound.checkString(sel_[count_].selectionText(), "Text");
 287             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 288             ++count_;
 289         }
 290     }
 291 }
 292
 293
 294 void
 295 SelectionCollectionDataTest::runCompiler()
 296 {
 297     ASSERT_NO_THROW_GMX(sc_.compile());
 298     ASSERT_EQ(count_, sel_.size());
 299     checkCompiled();
 300 }
 301
 302
 303 void
 304 SelectionCollectionDataTest::checkCompiled()
 305 {
 306     using gmx::test::TestReferenceChecker;
 307     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 308
 309     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 310     for (size_t i = 0; i < count_; ++i)
 311     {
 312         SCOPED_TRACE(std::string("Checking selection \"") +
 313                      sel_[i].selectionText() + "\"");
 314         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 315         TestReferenceChecker selcompound(
 316                 compound.checkCompound("Selection", id.c_str()));
 317         if (flags_.test(efTestSelectionNames))
 318         {
 319             selcompound.checkString(sel_[i].name(), "Name");
 320         }
 321         if (!flags_.test(efDontTestCompiledAtoms))
 322         {
 323             checkSelection(&selcompound, sel_[i], flags_ & mask);
 324         }
 325     }
 326 }
 327
 328
 329 void
 330 SelectionCollectionDataTest::runEvaluate()
 331 {
 332     using gmx::test::TestReferenceChecker;
 333
 334     ++framenr_;
 335     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 336     std::string          frame = gmx::formatString("Frame%d", framenr_);
 337     TestReferenceChecker compound(
 338             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 339     for (size_t i = 0; i < count_; ++i)
 340     {
 341         SCOPED_TRACE(std::string("Checking selection \"") +
 342                      sel_[i].selectionText() + "\"");
 343         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 344         TestReferenceChecker selcompound(
 345                 compound.checkCompound("Selection", id.c_str()));
 346         checkSelection(&selcompound, sel_[i], flags_);
 347     }
 348 }
 349
 350
 351 void
 352 SelectionCollectionDataTest::runEvaluateFinal()
 353 {
 354     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 355     checkCompiled();
 356 }
 357
 358
 359 void
 360 SelectionCollectionDataTest::runTest(
 361         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 362 {
 363     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 364     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 365     ASSERT_NO_FATAL_FAILURE(runCompiler());
 366 }
 367
 368
 369 void
 370 SelectionCollectionDataTest::runTest(
 371         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 372 {
 373     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 374     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 375     ASSERT_NO_FATAL_FAILURE(runCompiler());
 376     if (flags_.test(efTestEvaluation))
 377     {
 378         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 379         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 380     }
 381 }
 382
 383
 384 /********************************************************************
 385  * Tests for SelectionCollection functionality without reference data
 386  */
 387
 388 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 389 {
 390     EXPECT_FALSE(sc_.requiresTopology());
 391     EXPECT_NO_THROW_GMX(sc_.compile());
 392 }
 393
 394 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 395 {
 396     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 397     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 398     ASSERT_EQ(2U, sel_.size());
 399     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 400     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 401     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 402     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 403     ASSERT_NO_THROW_GMX(sc_.compile());
 404     EXPECT_TRUE(sel_[0].hasVelocities());
 405     EXPECT_TRUE(sel_[1].hasVelocities());
 406     EXPECT_TRUE(sel_[0].hasForces());
 407     EXPECT_TRUE(sel_[1].hasForces());
 408 }
 409
 410 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 411 {
 412     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 413                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 414     // These should match the contents of selfile.dat
 415     ASSERT_EQ(2U, sel_.size());
 416     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 417     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 418 }
 419
 420 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 421 {
 422     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 423     EXPECT_THROW_GMX({
 424                          sc_.parseFromString("resname ~ \"R[A\"");
 425                          sc_.compile();
 426                      }, gmx::InvalidInputError);
 427 }
 428
 429 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 430 {
 431     if (!gmx::Regex::isSupported())
 432     {
 433         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 434         EXPECT_THROW_GMX({
 435                              sc_.parseFromString("resname \"R[AD]\"");
 436                              sc_.compile();
 437                          }, gmx::InvalidInputError);
 438     }
 439 }
 440
 441 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 442 {
 443     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 444                      gmx::InvalidInputError);
 445 }
 446
 447 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 448 {
 449     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 450                      gmx::InvalidInputError);
 451 }
 452
 453 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 454 {
 455     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 456                      gmx::InvalidInputError);
 457 }
 458
 459 // TODO: Tests for more parser errors
 460
 461 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 462 {
 463     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 464     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 465     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 466 }
 467
 468 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 469 {
 470     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 471     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 472     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 473 }
 474
 475 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 476 {
 477     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 478     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 479     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 480     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 481 }
 482
 483 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 484 {
 485     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 486     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 487     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 488     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 489 }
 490
 491 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 492 {
 493     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 494     EXPECT_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""),
 495                      gmx::InconsistentInputError);
 496     EXPECT_THROW_GMX(sc_.parseFromString("group 2 or atomnr 2 to 5"),
 497                      gmx::InconsistentInputError);
 498     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of group 2"),
 499                      gmx::InconsistentInputError);
 500 }
 501
 502 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 503 {
 504     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""));
 505     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group 2"));
 506     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 507     // TODO: Add a separate check in the selection compiler for a safer API
 508     // (makes sense in the future if the compiler needs the information for
 509     // other purposes as well).
 510     // EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 511 }
 512
 513 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroup)
 514 {
 515     ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
 516     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 517     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpB\""), gmx::InconsistentInputError);
 518 }
 519
 520 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed)
 521 {
 522     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 523     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
 524     EXPECT_THROW_GMX(sc_.setTopology(NULL, 5), gmx::InconsistentInputError);
 525 }
 526
 527 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed2)
 528 {
 529     ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
 530     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
 531     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 532 }
 533
 534 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 535 {
 536     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 537     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 538     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 539 }
 540
 541 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 542 {
 543     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 544     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 545     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 546 }
 547
 548 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 549 {
 550     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 551     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 552     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 553 }
 554
 555 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 556 {
 557     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 558     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 559     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 560 }
 561
 562 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 563 {
 564     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 565     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 566     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 567 }
 568
 569 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 570 {
 571     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 572     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 573     ASSERT_NO_THROW_GMX(sc_.compile());
 574     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 575 }
 576
 577 // TODO: Tests for evaluation errors
 578
 579
 580 /********************************************************************
 581  * Tests for selection keywords
 582  */
 583
 584 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 585 {
 586     static const char * const selections[] = {
 587         "all",
 588         "none"
 589     };
 590     runTest(10, selections);
 591 }
 592
 593 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 594 {
 595     static const char * const selections[] = {
 596         "atomnr 1 to 3 6 to 8",
 597         "atomnr 4 2 5 to 7",
 598         "atomnr <= 5"
 599     };
 600     runTest(10, selections);
 601 }
 602
 603 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 604 {
 605     static const char * const selections[] = {
 606         "resnr 1 2 5",
 607         "resid 4 to 3"
 608     };
 609     runTest("simple.gro", selections);
 610 }
 611
 612 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 613 {
 614     static const char * const selections[] = {
 615         "resindex 1 4",
 616         "residue 1 3"
 617     };
 618     runTest("simple.pdb", selections);
 619 }
 620
 621 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 622 {
 623     static const char * const selections[] = {
 624         "molindex 1 4",
 625         "molecule 2 3 5"
 626     };
 627     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 628     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 629     topManager_.initUniformMolecules(3);
 630     ASSERT_NO_FATAL_FAILURE(runCompiler());
 631 }
 632
 633 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 634 {
 635     static const char * const selections[] = {
 636         "name CB",
 637         "atomname S1 S2"
 638     };
 639     runTest("simple.gro", selections);
 640 }
 641
 642 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 643 {
 644     static const char * const selections[] = {
 645         "name HG21",
 646         "name 1HG2",
 647         "pdbname HG21 CB",
 648         "pdbatomname 1HG2"
 649     };
 650     runTest("simple.pdb", selections);
 651 }
 652
 653
 654 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 655 {
 656     static const char * const selections[] = {
 657         "atomtype CA"
 658     };
 659     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 660     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 661     const char *const types[] = { "CA", "SA", "SB" };
 662     topManager_.initAtomTypes(types);
 663     ASSERT_NO_FATAL_FAILURE(runCompiler());
 664 }
 665
 666 TEST_F(SelectionCollectionDataTest, HandlesChain)
 667 {
 668     static const char * const selections[] = {
 669         "chain A",
 670         "chain B"
 671     };
 672     runTest("simple.pdb", selections);
 673 }
 674
 675 TEST_F(SelectionCollectionDataTest, HandlesMass)
 676 {
 677     static const char * const selections[] = {
 678         "mass > 5"
 679     };
 680     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 681     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 682     for (int i = 0; i < top_->atoms.nr; ++i)
 683     {
 684         top_->atoms.atom[i].m = 1.0 + i;
 685     }
 686     ASSERT_NO_FATAL_FAILURE(runCompiler());
 687 }
 688
 689 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 690 {
 691     static const char * const selections[] = {
 692         "charge < 0.5"
 693     };
 694     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 695     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 696     for (int i = 0; i < top_->atoms.nr; ++i)
 697     {
 698         top_->atoms.atom[i].q = i / 10.0;
 699     }
 700     ASSERT_NO_FATAL_FAILURE(runCompiler());
 701 }
 702
 703 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 704 {
 705     static const char * const selections[] = {
 706         "altloc \" \"",
 707         "altloc A"
 708     };
 709     runTest("simple.pdb", selections);
 710 }
 711
 712 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 713 {
 714     static const char * const selections[] = {
 715         "insertcode \" \"",
 716         "insertcode A"
 717     };
 718     runTest("simple.pdb", selections);
 719 }
 720
 721 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 722 {
 723     static const char * const selections[] = {
 724         "occupancy 1",
 725         "occupancy < .5"
 726     };
 727     runTest("simple.pdb", selections);
 728 }
 729
 730 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 731 {
 732     static const char * const selections[] = {
 733         "beta 0",
 734         "beta >= 0.3"
 735     };
 736     runTest("simple.pdb", selections);
 737 }
 738
 739 TEST_F(SelectionCollectionDataTest, HandlesResname)
 740 {
 741     static const char * const selections[] = {
 742         "resname RA",
 743         "resname RB RC"
 744     };
 745     runTest("simple.gro", selections);
 746 }
 747
 748 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 749 {
 750     static const char * const selections[] = {
 751         "x < 3",
 752         "y >= 3",
 753         "x {-1 to 2}"
 754     };
 755     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 756     runTest("simple.gro", selections);
 757 }
 758
 759
 760 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 761 {
 762     static const char * const selections[] = {
 763         "same residue as atomnr 1 4 12"
 764     };
 765     runTest("simple.gro", selections);
 766 }
 767
 768
 769 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 770 {
 771     static const char * const selections[] = {
 772         "same resname as atomnr 1 14"
 773     };
 774     runTest("simple.gro", selections);
 775 }
 776
 777
 778 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 779 {
 780     static const char * const selections[] = {
 781         "cog of resnr 1 3",
 782         "res_cog of name CB and resnr 1 3",
 783         "whole_res_cog of name CB and resnr 1 3",
 784         "part_res_cog of x < 3",
 785         "dyn_res_cog of x < 3"
 786     };
 787     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 788              | efTestPositionAtoms);
 789     runTest("simple.gro", selections);
 790 }
 791
 792
 793 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 794 {
 795     static const char * const selections[] = {
 796         "distance from cog of resnr 1 < 2"
 797     };
 798     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 799     runTest("simple.gro", selections);
 800 }
 801
 802
 803 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 804 {
 805     static const char * const selections[] = {
 806         "mindistance from resnr 1 < 2"
 807     };
 808     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 809     runTest("simple.gro", selections);
 810 }
 811
 812
 813 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 814 {
 815     static const char * const selections[] = {
 816         "within 1 of resnr 2"
 817     };
 818     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 819     runTest("simple.gro", selections);
 820 }
 821
 822
 823 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 824 {
 825     // Both of these should evaluate to empty on a correct implementation.
 826     static const char * const selections[] = {
 827         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 828         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 829     };
 830     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 831     runTest("sphere.gro", selections);
 832 }
 833
 834
 835 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 836 {
 837     static const char * const selections[] = {
 838         "all permute 3 1 2",
 839         "res_cog of resnr 1 to 4 permute 2 1",
 840         "name CB S1 and res_cog x < 3 permute 2 1"
 841     };
 842     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 843              | efTestPositionAtoms | efTestPositionMapping);
 844     runTest("simple.gro", selections);
 845 }
 846
 847
 848 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 849 {
 850     static const char * const selections[] = {
 851         "name S2 plus name S1",
 852         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 853         "name S1 and y < 3 plus res_cog of x < 2.5"
 854     };
 855     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 856              | efTestPositionAtoms | efTestPositionMapping);
 857     runTest("simple.gro", selections);
 858 }
 859
 860
 861 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 862 {
 863     static const char * const selections[] = {
 864         "name S2 merge name S1",
 865         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 866         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 867     };
 868     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 869              | efTestPositionAtoms | efTestPositionMapping);
 870     runTest("simple.gro", selections);
 871 }
 872
 873
 874 /********************************************************************
 875  * Tests for generic selection evaluation
 876  */
 877
 878 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 879 {
 880     static const char * const selections[] = {
 881         "name CB",
 882         "y > 2",
 883         "res_cog of y > 2"
 884     };
 885     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 886              | efTestPositionMasses | efTestPositionCharges);
 887     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 888     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 889     for (int i = 0; i < top_->atoms.nr; ++i)
 890     {
 891         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 892         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 893     }
 894     ASSERT_NO_FATAL_FAILURE(runCompiler());
 895     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 896     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 897 }
 898
 899 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 900 {
 901     static const char * const selections[] = {
 902         "atomnr 1 to 3 8 to 9",
 903         "y > 2",
 904         "cog of (y > 2)"
 905     };
 906     setFlags(TestFlags() | efTestPositionAtoms
 907              | efTestPositionMasses | efTestPositionCharges);
 908     runTest(10, selections);
 909 }
 910
 911
 912 /********************************************************************
 913  * Tests for selection syntactic constructs
 914  */
 915
 916 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 917 {
 918     static const char * const selections[] = {
 919         "\"GroupSelection\" group \"GrpA\"",
 920         "\"DynamicSelection\" x < 5",
 921         "y < 3"
 922     };
 923     setFlags(TestFlags() | efTestSelectionNames);
 924     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 925     runTest(10, selections);
 926 }
 927
 928 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 929 {
 930     static const char * const selections[] = {
 931         "group \"GrpA\"",
 932         "GrpB",
 933         "1",
 934         "group \"GrpB\" and resname RB"
 935     };
 936     setFlags(TestFlags() | efTestSelectionNames);
 937     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 938     runTest("simple.gro", selections);
 939 }
 940
 941 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 942 {
 943     static const char * const selections[] = {
 944         "group \"GrpA\"",
 945         "GrpB",
 946         "1",
 947         "group \"GrpB\" and resname RB"
 948     };
 949     setFlags(TestFlags() | efTestSelectionNames);
 950     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 951     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 952     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 953     ASSERT_NO_FATAL_FAILURE(runCompiler());
 954 }
 955
 956 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
 957 {
 958     static const char * const selections[] = {
 959         "foo = group \"GrpUnsorted\"",
 960         "group \"GrpUnsorted\"",
 961         "GrpUnsorted",
 962         "2",
 963         "res_cog of group \"GrpUnsorted\"",
 964         "group \"GrpUnsorted\" permute 2 1",
 965         "foo"
 966     };
 967     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
 968              | efTestSelectionNames);
 969     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 970     runTest("simple.gro", selections);
 971 }
 972
 973 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelectionsDelayed)
 974 {
 975     static const char * const selections[] = {
 976         "foo = group \"GrpUnsorted\"",
 977         "group \"GrpUnsorted\"",
 978         "GrpUnsorted",
 979         "2",
 980         "res_cog of group \"GrpUnsorted\"",
 981         "group \"GrpUnsorted\" permute 2 1",
 982         "foo"
 983     };
 984     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 985     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 986     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 987     ASSERT_NO_FATAL_FAILURE(runCompiler());
 988 }
 989
 990 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 991 {
 992     static const char * const selections[] = {
 993         "[1, -2, 3.5]"
 994     };
 995     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 996     runTest("simple.gro", selections);
 997 }
 998
 999
1000 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
1001 {
1002     static const char * const selections[] = {
1003         "within 1 of [2, 1, 0]"
1004     };
1005     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1006     runTest("simple.gro", selections);
1007 }
1008
1009
1010 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
1011 {
1012     static const char * const selections[] = {
1013         "name = S1 \"C?\"",
1014         "name ? S1 \"C?\""
1015     };
1016     runTest("simple.gro", selections);
1017 }
1018
1019
1020 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
1021 {
1022     static const char * const selections[] = {
1023         "name \"S?\"",
1024         "name ? \"S?\""
1025     };
1026     runTest("simple.gro", selections);
1027 }
1028
1029
1030 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
1031 {
1032     static const char * const selections[] = {
1033         "resname \"R[BD]\"",
1034         "resname ~ \"R[BD]\""
1035     };
1036     if (gmx::Regex::isSupported())
1037     {
1038         runTest("simple.gro", selections);
1039     }
1040 }
1041
1042
1043 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
1044 {
1045     static const char * const selections[] = {
1046         "atomnr 1 to 5 and atomnr 2 to 7",
1047         "atomnr 1 to 5 or not atomnr 3 to 8",
1048         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1049         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1050         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1051     };
1052     runTest(10, selections);
1053 }
1054
1055
1056 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1057 {
1058     static const char * const selections[] = {
1059         "same residue as (atomnr 3 5 13 or y > 5)",
1060         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1061     };
1062     setFlags(TestFlags() | efTestEvaluation);
1063     runTest("simple.gro", selections);
1064 }
1065
1066
1067 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1068 {
1069     static const char * const selections[] = {
1070         "none and x > 2",
1071         "none and same resname as resnr 2"
1072     };
1073     runTest("simple.gro", selections);
1074 }
1075
1076
1077 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1078 {
1079     static const char * const selections[] = {
1080         "x > 2",
1081         "2 < x",
1082         "y > resnr",
1083         "resnr < 2.5",
1084         "2.5 > resnr"
1085     };
1086     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1087     runTest("simple.gro", selections);
1088 }
1089
1090
1091 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1092 {
1093     static const char * const selections[] = {
1094         "x+1 > 3",
1095         "(y-1)^2 <= 1",
1096         "x+--1 > 3",
1097         "-x+-1 < -3"
1098     };
1099     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1100     runTest("simple.gro", selections);
1101 }
1102
1103
1104 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1105 {
1106     static const char * const selections[] = {
1107         "value = x + y",
1108         "value <= 4",
1109         "index = resnr",
1110         "index < 3"
1111     };
1112     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1113     runTest("simple.gro", selections);
1114 }
1115
1116
1117 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1118 {
1119     static const char * const selections[] = {
1120         "value = x + y",
1121         "resname RA and value <= 4",
1122         "resname RA RB and x < 3 and value <= 4",
1123         "index = atomnr",
1124         "resname RA and index < 3",
1125         "resname RB and y < 3 and index < 6"
1126     };
1127     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1128     runTest("simple.gro", selections);
1129 }
1130
1131
1132 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1133 {
1134     static const char * const selections[] = {
1135         "foo = res_cog of resname RA",
1136         "foo",
1137         "within 1 of foo",
1138         "bar = cog of resname RA",
1139         "bar",
1140         "within 1 of bar"
1141     };
1142     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1143     runTest("simple.gro", selections);
1144 }
1145
1146
1147 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1148 {
1149     static const char * const selections[] = {
1150         "constpos = [1.0, 2.5, 0.5]",
1151         "constpos",
1152         "within 2 of constpos"
1153     };
1154     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1155              | efTestPositionAtoms);
1156     runTest("simple.gro", selections);
1157 }
1158
1159
1160 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1161 {
1162     static const char * const selections[] = {
1163         "constint = 4",
1164         "constreal1 = 0.5",
1165         "constreal2 = 2.7",
1166         "resnr < constint",
1167         "x + constreal1 < constreal2"
1168     };
1169     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1170     runTest("simple.gro", selections);
1171 }
1172
1173
1174 /********************************************************************
1175  * Tests for complex boolean syntax
1176  */
1177
1178 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1179 {
1180     static const char * const selections[] = {
1181         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1182         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1183         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1184         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1185         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1186     };
1187     runTest(10, selections);
1188 }
1189
1190
1191 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1192 {
1193     static const char * const selections[] = {
1194         "foo = atomnr 4 to 7 or x < 2",
1195         "atomnr 1 to 4 and foo",
1196         "atomnr 2 to 6 and y < 3 and foo",
1197         "atomnr 6 to 10 and not foo"
1198     };
1199     runTest(10, selections);
1200 }
1201
1202
1203 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1204 {
1205     static const char * const selections[] = {
1206         "foo = atomnr 4 to 7",
1207         "bar = foo and x < 2",
1208         "bar2 = foo and y < 2",
1209         "atomnr 1 to 4 and bar",
1210         "atomnr 2 to 6 and y < 3 and bar2",
1211         "atomnr 6 to 10 and not foo"
1212     };
1213     runTest(10, selections);
1214 }
1215
1216
1217 /********************************************************************
1218  * Tests for complex subexpression cases
1219  *
1220  * These tests use some knowledge of the implementation to trigger different
1221  * paths in the code.
1222  */
1223
1224 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1225 {
1226     static const char * const selections[] = {
1227         "unused1 = atomnr 1 to 3",
1228         "foo = atomnr 4 to 7",
1229         "atomnr 1 to 6 and foo",
1230         "unused2 = atomnr 3 to 5"
1231     };
1232     runTest(10, selections);
1233 }
1234
1235
1236 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1237 {
1238     static const char * const selections[] = {
1239         "foo = atomnr 4 to 7 and x < 2",
1240         "atomnr 1 to 5 and foo",
1241         "atomnr 3 to 7 and foo"
1242     };
1243     runTest(10, selections);
1244 }
1245
1246
1247 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1248 {
1249     static const char * const selections[] = {
1250         "foo = atomnr 4 to 7 and x < 2",
1251         "atomnr 1 to 6 and foo",
1252         "within 1 of foo",
1253         "foo"
1254     };
1255     runTest(10, selections);
1256 }
1257
1258
1259 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1260 {
1261     static const char * const selections[] = {
1262         "foo = atomnr 1 to 8 and x < 10",
1263         "atomnr 1 to 5 and y < 10 and foo",
1264         "foo"
1265     };
1266     setFlags(TestFlags() | efTestEvaluation);
1267     runTest("simple.gro", selections);
1268 }
1269
1270
1271 } // namespace