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, RecoversFromMissingMoleculeInfo)
 514 {
 515     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 516     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 517     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 518 }
 519
 520 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 521 {
 522     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 523     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 524     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 525 }
 526
 527 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 528 {
 529     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 530     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 531     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 532 }
 533
 534 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 535 {
 536     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 537     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 538     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 539 }
 540
 541 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 542 {
 543     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 544     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 545     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 546 }
 547
 548 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 549 {
 550     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 551     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 552     ASSERT_NO_THROW_GMX(sc_.compile());
 553     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 554 }
 555
 556 // TODO: Tests for evaluation errors
 557
 558
 559 /********************************************************************
 560  * Tests for selection keywords
 561  */
 562
 563 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 564 {
 565     static const char * const selections[] = {
 566         "all",
 567         "none"
 568     };
 569     runTest(10, selections);
 570 }
 571
 572 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 573 {
 574     static const char * const selections[] = {
 575         "atomnr 1 to 3 6 to 8",
 576         "atomnr 4 2 5 to 7",
 577         "atomnr <= 5"
 578     };
 579     runTest(10, selections);
 580 }
 581
 582 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 583 {
 584     static const char * const selections[] = {
 585         "resnr 1 2 5",
 586         "resid 4 to 3"
 587     };
 588     runTest("simple.gro", selections);
 589 }
 590
 591 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 592 {
 593     static const char * const selections[] = {
 594         "resindex 1 4",
 595         "residue 1 3"
 596     };
 597     runTest("simple.pdb", selections);
 598 }
 599
 600 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 601 {
 602     static const char * const selections[] = {
 603         "molindex 1 4",
 604         "molecule 2 3 5"
 605     };
 606     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 607     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 608     topManager_.initUniformMolecules(3);
 609     ASSERT_NO_FATAL_FAILURE(runCompiler());
 610 }
 611
 612 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 613 {
 614     static const char * const selections[] = {
 615         "name CB",
 616         "atomname S1 S2"
 617     };
 618     runTest("simple.gro", selections);
 619 }
 620
 621 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 622 {
 623     static const char * const selections[] = {
 624         "name HG21",
 625         "name 1HG2",
 626         "pdbname HG21 CB",
 627         "pdbatomname 1HG2"
 628     };
 629     runTest("simple.pdb", selections);
 630 }
 631
 632
 633 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 634 {
 635     static const char * const selections[] = {
 636         "atomtype CA"
 637     };
 638     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 639     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 640     const char *const types[] = { "CA", "SA", "SB" };
 641     topManager_.initAtomTypes(types);
 642     ASSERT_NO_FATAL_FAILURE(runCompiler());
 643 }
 644
 645 TEST_F(SelectionCollectionDataTest, HandlesChain)
 646 {
 647     static const char * const selections[] = {
 648         "chain A",
 649         "chain B"
 650     };
 651     runTest("simple.pdb", selections);
 652 }
 653
 654 TEST_F(SelectionCollectionDataTest, HandlesMass)
 655 {
 656     static const char * const selections[] = {
 657         "mass > 5"
 658     };
 659     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 660     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 661     for (int i = 0; i < top_->atoms.nr; ++i)
 662     {
 663         top_->atoms.atom[i].m = 1.0 + i;
 664     }
 665     ASSERT_NO_FATAL_FAILURE(runCompiler());
 666 }
 667
 668 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 669 {
 670     static const char * const selections[] = {
 671         "charge < 0.5"
 672     };
 673     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 674     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 675     for (int i = 0; i < top_->atoms.nr; ++i)
 676     {
 677         top_->atoms.atom[i].q = i / 10.0;
 678     }
 679     ASSERT_NO_FATAL_FAILURE(runCompiler());
 680 }
 681
 682 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 683 {
 684     static const char * const selections[] = {
 685         "altloc \" \"",
 686         "altloc A"
 687     };
 688     runTest("simple.pdb", selections);
 689 }
 690
 691 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 692 {
 693     static const char * const selections[] = {
 694         "insertcode \" \"",
 695         "insertcode A"
 696     };
 697     runTest("simple.pdb", selections);
 698 }
 699
 700 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 701 {
 702     static const char * const selections[] = {
 703         "occupancy 1",
 704         "occupancy < .5"
 705     };
 706     runTest("simple.pdb", selections);
 707 }
 708
 709 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 710 {
 711     static const char * const selections[] = {
 712         "beta 0",
 713         "beta >= 0.3"
 714     };
 715     runTest("simple.pdb", selections);
 716 }
 717
 718 TEST_F(SelectionCollectionDataTest, HandlesResname)
 719 {
 720     static const char * const selections[] = {
 721         "resname RA",
 722         "resname RB RC"
 723     };
 724     runTest("simple.gro", selections);
 725 }
 726
 727 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 728 {
 729     static const char * const selections[] = {
 730         "x < 3",
 731         "y >= 3",
 732         "x {-1 to 2}"
 733     };
 734     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 735     runTest("simple.gro", selections);
 736 }
 737
 738
 739 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 740 {
 741     static const char * const selections[] = {
 742         "same residue as atomnr 1 4 12"
 743     };
 744     runTest("simple.gro", selections);
 745 }
 746
 747
 748 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 749 {
 750     static const char * const selections[] = {
 751         "same resname as atomnr 1 14"
 752     };
 753     runTest("simple.gro", selections);
 754 }
 755
 756
 757 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 758 {
 759     static const char * const selections[] = {
 760         "cog of resnr 1 3",
 761         "res_cog of name CB and resnr 1 3",
 762         "whole_res_cog of name CB and resnr 1 3",
 763         "part_res_cog of x < 3",
 764         "dyn_res_cog of x < 3"
 765     };
 766     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 767              | efTestPositionAtoms);
 768     runTest("simple.gro", selections);
 769 }
 770
 771
 772 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 773 {
 774     static const char * const selections[] = {
 775         "distance from cog of resnr 1 < 2"
 776     };
 777     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 778     runTest("simple.gro", selections);
 779 }
 780
 781
 782 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 783 {
 784     static const char * const selections[] = {
 785         "mindistance from resnr 1 < 2"
 786     };
 787     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 788     runTest("simple.gro", selections);
 789 }
 790
 791
 792 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 793 {
 794     static const char * const selections[] = {
 795         "within 1 of resnr 2"
 796     };
 797     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 798     runTest("simple.gro", selections);
 799 }
 800
 801
 802 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 803 {
 804     // Both of these should evaluate to empty on a correct implementation.
 805     static const char * const selections[] = {
 806         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 807         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 808     };
 809     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 810     runTest("sphere.gro", selections);
 811 }
 812
 813
 814 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 815 {
 816     static const char * const selections[] = {
 817         "all permute 3 1 2",
 818         "res_cog of resnr 1 to 4 permute 2 1",
 819         "name CB S1 and res_cog x < 3 permute 2 1"
 820     };
 821     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 822              | efTestPositionAtoms | efTestPositionMapping);
 823     runTest("simple.gro", selections);
 824 }
 825
 826
 827 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 828 {
 829     static const char * const selections[] = {
 830         "name S2 plus name S1",
 831         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 832         "name S1 and y < 3 plus res_cog of x < 2.5"
 833     };
 834     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 835              | efTestPositionAtoms | efTestPositionMapping);
 836     runTest("simple.gro", selections);
 837 }
 838
 839
 840 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 841 {
 842     static const char * const selections[] = {
 843         "name S2 merge name S1",
 844         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 845         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 846     };
 847     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 848              | efTestPositionAtoms | efTestPositionMapping);
 849     runTest("simple.gro", selections);
 850 }
 851
 852
 853 /********************************************************************
 854  * Tests for generic selection evaluation
 855  */
 856
 857 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 858 {
 859     static const char * const selections[] = {
 860         "name CB",
 861         "y > 2",
 862         "res_cog of y > 2"
 863     };
 864     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 865              | efTestPositionMasses | efTestPositionCharges);
 866     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 867     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 868     for (int i = 0; i < top_->atoms.nr; ++i)
 869     {
 870         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 871         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 872     }
 873     ASSERT_NO_FATAL_FAILURE(runCompiler());
 874     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 875     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 876 }
 877
 878 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 879 {
 880     static const char * const selections[] = {
 881         "atomnr 1 to 3 8 to 9",
 882         "y > 2",
 883         "cog of (y > 2)"
 884     };
 885     setFlags(TestFlags() | efTestPositionAtoms
 886              | efTestPositionMasses | efTestPositionCharges);
 887     runTest(10, selections);
 888 }
 889
 890
 891 /********************************************************************
 892  * Tests for selection syntactic constructs
 893  */
 894
 895 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 896 {
 897     static const char * const selections[] = {
 898         "\"GroupSelection\" group \"GrpA\"",
 899         "\"DynamicSelection\" x < 5",
 900         "y < 3"
 901     };
 902     setFlags(TestFlags() | efTestSelectionNames);
 903     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 904     runTest(10, selections);
 905 }
 906
 907 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 908 {
 909     static const char * const selections[] = {
 910         "group \"GrpA\"",
 911         "GrpB",
 912         "1",
 913         "group \"GrpB\" and resname RB"
 914     };
 915     setFlags(TestFlags() | efTestSelectionNames);
 916     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 917     runTest("simple.gro", selections);
 918 }
 919
 920 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 921 {
 922     static const char * const selections[] = {
 923         "group \"GrpA\"",
 924         "GrpB",
 925         "1",
 926         "group \"GrpB\" and resname RB"
 927     };
 928     setFlags(TestFlags() | efTestSelectionNames);
 929     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 930     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 931     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 932     ASSERT_NO_FATAL_FAILURE(runCompiler());
 933 }
 934
 935 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
 936 {
 937     static const char * const selections[] = {
 938         "foo = group \"GrpUnsorted\"",
 939         "group \"GrpUnsorted\"",
 940         "GrpUnsorted",
 941         "2",
 942         "res_cog of group \"GrpUnsorted\"",
 943         "group \"GrpUnsorted\" permute 2 1",
 944         "foo"
 945     };
 946     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
 947              | efTestSelectionNames);
 948     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 949     runTest("simple.gro", selections);
 950 }
 951
 952 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelectionsDelayed)
 953 {
 954     static const char * const selections[] = {
 955         "foo = group \"GrpUnsorted\"",
 956         "group \"GrpUnsorted\"",
 957         "GrpUnsorted",
 958         "2",
 959         "res_cog of group \"GrpUnsorted\"",
 960         "group \"GrpUnsorted\" permute 2 1",
 961         "foo"
 962     };
 963     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 964     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 965     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 966     ASSERT_NO_FATAL_FAILURE(runCompiler());
 967 }
 968
 969 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 970 {
 971     static const char * const selections[] = {
 972         "[1, -2, 3.5]"
 973     };
 974     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 975     runTest("simple.gro", selections);
 976 }
 977
 978
 979 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 980 {
 981     static const char * const selections[] = {
 982         "within 1 of [2, 1, 0]"
 983     };
 984     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 985     runTest("simple.gro", selections);
 986 }
 987
 988
 989 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 990 {
 991     static const char * const selections[] = {
 992         "name = S1 \"C?\"",
 993         "name ? S1 \"C?\""
 994     };
 995     runTest("simple.gro", selections);
 996 }
 997
 998
 999 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
1000 {
1001     static const char * const selections[] = {
1002         "name \"S?\"",
1003         "name ? \"S?\""
1004     };
1005     runTest("simple.gro", selections);
1006 }
1007
1008
1009 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
1010 {
1011     static const char * const selections[] = {
1012         "resname \"R[BD]\"",
1013         "resname ~ \"R[BD]\""
1014     };
1015     if (gmx::Regex::isSupported())
1016     {
1017         runTest("simple.gro", selections);
1018     }
1019 }
1020
1021
1022 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
1023 {
1024     static const char * const selections[] = {
1025         "atomnr 1 to 5 and atomnr 2 to 7",
1026         "atomnr 1 to 5 or not atomnr 3 to 8",
1027         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1028         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1029         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1030     };
1031     runTest(10, selections);
1032 }
1033
1034
1035 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1036 {
1037     static const char * const selections[] = {
1038         "same residue as (atomnr 3 5 13 or y > 5)",
1039         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1040     };
1041     setFlags(TestFlags() | efTestEvaluation);
1042     runTest("simple.gro", selections);
1043 }
1044
1045
1046 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1047 {
1048     static const char * const selections[] = {
1049         "none and x > 2",
1050         "none and same resname as resnr 2"
1051     };
1052     runTest("simple.gro", selections);
1053 }
1054
1055
1056 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1057 {
1058     static const char * const selections[] = {
1059         "x > 2",
1060         "2 < x",
1061         "y > resnr",
1062         "resnr < 2.5",
1063         "2.5 > resnr"
1064     };
1065     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1066     runTest("simple.gro", selections);
1067 }
1068
1069
1070 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1071 {
1072     static const char * const selections[] = {
1073         "x+1 > 3",
1074         "(y-1)^2 <= 1",
1075         "x+--1 > 3",
1076         "-x+-1 < -3"
1077     };
1078     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1079     runTest("simple.gro", selections);
1080 }
1081
1082
1083 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1084 {
1085     static const char * const selections[] = {
1086         "value = x + y",
1087         "value <= 4",
1088         "index = resnr",
1089         "index < 3"
1090     };
1091     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1092     runTest("simple.gro", selections);
1093 }
1094
1095
1096 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1097 {
1098     static const char * const selections[] = {
1099         "value = x + y",
1100         "resname RA and value <= 4",
1101         "resname RA RB and x < 3 and value <= 4",
1102         "index = atomnr",
1103         "resname RA and index < 3",
1104         "resname RB and y < 3 and index < 6"
1105     };
1106     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1107     runTest("simple.gro", selections);
1108 }
1109
1110
1111 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1112 {
1113     static const char * const selections[] = {
1114         "foo = res_cog of resname RA",
1115         "foo",
1116         "within 1 of foo",
1117         "bar = cog of resname RA",
1118         "bar",
1119         "within 1 of bar"
1120     };
1121     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1122     runTest("simple.gro", selections);
1123 }
1124
1125
1126 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1127 {
1128     static const char * const selections[] = {
1129         "constpos = [1.0, 2.5, 0.5]",
1130         "constpos",
1131         "within 2 of constpos"
1132     };
1133     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1134              | efTestPositionAtoms);
1135     runTest("simple.gro", selections);
1136 }
1137
1138
1139 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1140 {
1141     static const char * const selections[] = {
1142         "constint = 4",
1143         "constreal1 = 0.5",
1144         "constreal2 = 2.7",
1145         "resnr < constint",
1146         "x + constreal1 < constreal2"
1147     };
1148     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1149     runTest("simple.gro", selections);
1150 }
1151
1152
1153 /********************************************************************
1154  * Tests for complex boolean syntax
1155  */
1156
1157 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1158 {
1159     static const char * const selections[] = {
1160         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1161         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1162         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1163         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1164         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1165     };
1166     runTest(10, selections);
1167 }
1168
1169
1170 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1171 {
1172     static const char * const selections[] = {
1173         "foo = atomnr 4 to 7 or x < 2",
1174         "atomnr 1 to 4 and foo",
1175         "atomnr 2 to 6 and y < 3 and foo",
1176         "atomnr 6 to 10 and not foo"
1177     };
1178     runTest(10, selections);
1179 }
1180
1181
1182 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1183 {
1184     static const char * const selections[] = {
1185         "foo = atomnr 4 to 7",
1186         "bar = foo and x < 2",
1187         "bar2 = foo and y < 2",
1188         "atomnr 1 to 4 and bar",
1189         "atomnr 2 to 6 and y < 3 and bar2",
1190         "atomnr 6 to 10 and not foo"
1191     };
1192     runTest(10, selections);
1193 }
1194
1195
1196 /********************************************************************
1197  * Tests for complex subexpression cases
1198  *
1199  * These tests use some knowledge of the implementation to trigger different
1200  * paths in the code.
1201  */
1202
1203 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1204 {
1205     static const char * const selections[] = {
1206         "unused1 = atomnr 1 to 3",
1207         "foo = atomnr 4 to 7",
1208         "atomnr 1 to 6 and foo",
1209         "unused2 = atomnr 3 to 5"
1210     };
1211     runTest(10, selections);
1212 }
1213
1214
1215 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1216 {
1217     static const char * const selections[] = {
1218         "foo = atomnr 4 to 7 and x < 2",
1219         "atomnr 1 to 5 and foo",
1220         "atomnr 3 to 7 and foo"
1221     };
1222     runTest(10, selections);
1223 }
1224
1225
1226 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1227 {
1228     static const char * const selections[] = {
1229         "foo = atomnr 4 to 7 and x < 2",
1230         "atomnr 1 to 6 and foo",
1231         "within 1 of foo",
1232         "foo"
1233     };
1234     runTest(10, selections);
1235 }
1236
1237
1238 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1239 {
1240     static const char * const selections[] = {
1241         "foo = atomnr 1 to 8 and x < 10",
1242         "atomnr 1 to 5 and y < 10 and foo",
1243         "foo"
1244     };
1245     setFlags(TestFlags() | efTestEvaluation);
1246     runTest("simple.gro", selections);
1247 }
1248
1249
1250 } // namespace