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/utility/arrayref.h"
  50 #include "gromacs/utility/exceptions.h"
  51 #include "gromacs/utility/flags.h"
  52 #include "gromacs/utility/gmxregex.h"
  53 #include "gromacs/utility/stringutil.h"
  54
  55 #include "testutils/refdata.h"
  56 #include "testutils/testasserts.h"
  57 #include "testutils/testfilemanager.h"
  58 #include "testutils/testoptions.h"
  59
  60 #include "toputils.h"
  61
  62 namespace
  63 {
  64
  65 /********************************************************************
  66  * Test fixture for selection testing
  67  */
  68
  69 class SelectionCollectionTest : public ::testing::Test
  70 {
  71     public:
  72         static int               s_debugLevel;
  73
  74         SelectionCollectionTest();
  75         ~SelectionCollectionTest();
  76
  77         void setAtomCount(int natoms)
  78         {
  79             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  80         }
  81         void loadTopology(const char *filename);
  82         void setTopology();
  83         void loadIndexGroups(const char *filename);
  84
  85         gmx::test::TopologyManager  topManager_;
  86         gmx::SelectionCollection    sc_;
  87         gmx::SelectionList          sel_;
  88         t_topology                 *top_;
  89         t_trxframe                 *frame_;
  90         gmx_ana_indexgrps_t        *grps_;
  91 };
  92
  93 int SelectionCollectionTest::s_debugLevel = 0;
  94
  95 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
  96 #ifndef DOXYGEN
  97 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  98 {
  99     options->addOption(gmx::IntegerOption("seldebug")
 100                            .store(&SelectionCollectionTest::s_debugLevel)
 101                            .description("Set selection debug level"));
 102 }
 103 #endif
 104
 105 SelectionCollectionTest::SelectionCollectionTest()
 106     : top_(NULL), frame_(NULL), grps_(NULL)
 107 {
 108     topManager_.requestFrame();
 109     sc_.setDebugLevel(s_debugLevel);
 110     sc_.setReferencePosType("atom");
 111     sc_.setOutputPosType("atom");
 112 }
 113
 114 SelectionCollectionTest::~SelectionCollectionTest()
 115 {
 116     if (grps_ != NULL)
 117     {
 118         gmx_ana_indexgrps_free(grps_);
 119     }
 120 }
 121
 122 void
 123 SelectionCollectionTest::loadTopology(const char *filename)
 124 {
 125     topManager_.loadTopology(filename);
 126     setTopology();
 127 }
 128
 129 void
 130 SelectionCollectionTest::setTopology()
 131 {
 132     top_   = topManager_.topology();
 133     frame_ = topManager_.frame();
 134
 135     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 136 }
 137
 138 void
 139 SelectionCollectionTest::loadIndexGroups(const char *filename)
 140 {
 141     GMX_RELEASE_ASSERT(grps_ == NULL,
 142                        "External groups can only be loaded once");
 143     std::string fullpath =
 144         gmx::test::TestFileManager::getInputFilePath(filename);
 145     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 146     sc_.setIndexGroups(grps_);
 147 }
 148
 149
 150 /********************************************************************
 151  * Test fixture for selection testing with reference data
 152  */
 153
 154 class SelectionCollectionDataTest : public SelectionCollectionTest
 155 {
 156     public:
 157         enum TestFlag
 158         {
 159             efTestEvaluation            = 1<<0,
 160             efTestPositionAtoms         = 1<<1,
 161             efTestPositionCoordinates   = 1<<2,
 162             efTestPositionMapping       = 1<<3,
 163             efTestPositionMasses        = 1<<4,
 164             efTestPositionCharges       = 1<<5,
 165             efTestSelectionNames        = 1<<6,
 166             efDontTestCompiledAtoms     = 1<<8
 167         };
 168         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 169
 170         SelectionCollectionDataTest()
 171             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 172         {
 173         }
 174
 175         void setFlags(TestFlags flags) { flags_ = flags; }
 176
 177         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 178         void runCompiler();
 179         void runEvaluate();
 180         void runEvaluateFinal();
 181
 182         void runTest(int                                     natoms,
 183                      const gmx::ConstArrayRef<const char *> &selections);
 184         void runTest(const char                             *filename,
 185                      const gmx::ConstArrayRef<const char *> &selections);
 186
 187     private:
 188         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 189                                    const gmx::Selection &sel, TestFlags flags);
 190
 191         void checkCompiled();
 192
 193         gmx::test::TestReferenceData    data_;
 194         gmx::test::TestReferenceChecker checker_;
 195         size_t                          count_;
 196         int                             framenr_;
 197         TestFlags                       flags_;
 198 };
 199
 200
 201 void
 202 SelectionCollectionDataTest::checkSelection(
 203         gmx::test::TestReferenceChecker *checker,
 204         const gmx::Selection &sel, TestFlags flags)
 205 {
 206     using gmx::test::TestReferenceChecker;
 207
 208     {
 209         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 210         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 211     }
 212     if (flags.test(efTestPositionAtoms)
 213         || flags.test(efTestPositionCoordinates)
 214         || flags.test(efTestPositionMapping)
 215         || flags.test(efTestPositionMasses)
 216         || flags.test(efTestPositionCharges))
 217     {
 218         TestReferenceChecker compound(
 219                 checker->checkSequenceCompound("Positions", sel.posCount()));
 220         for (int i = 0; i < sel.posCount(); ++i)
 221         {
 222             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 223             const gmx::SelectionPosition &p = sel.position(i);
 224             if (flags.test(efTestPositionAtoms))
 225             {
 226                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 227                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 228             }
 229             if (flags.test(efTestPositionCoordinates))
 230             {
 231                 poscompound.checkVector(p.x(), "Coordinates");
 232             }
 233             if (flags.test(efTestPositionMapping))
 234             {
 235                 poscompound.checkInteger(p.refId(), "RefId");
 236                 poscompound.checkInteger(p.mappedId(), "MappedId");
 237             }
 238             if (flags.test(efTestPositionMasses))
 239             {
 240                 poscompound.checkReal(p.mass(), "Mass");
 241             }
 242             if (flags.test(efTestPositionCharges))
 243             {
 244                 poscompound.checkReal(p.charge(), "Charge");
 245             }
 246         }
 247     }
 248 }
 249
 250
 251 void
 252 SelectionCollectionDataTest::runParser(
 253         const gmx::ConstArrayRef<const char *> &selections)
 254 {
 255     using gmx::test::TestReferenceChecker;
 256
 257     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 258     size_t               varcount = 0;
 259     count_ = 0;
 260     for (size_t i = 0; i < selections.size(); ++i)
 261     {
 262         SCOPED_TRACE(std::string("Parsing selection \"")
 263                      + selections[i] + "\"");
 264         gmx::SelectionList result;
 265         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 266         sel_.insert(sel_.end(), result.begin(), result.end());
 267         if (sel_.size() == count_)
 268         {
 269             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 270             TestReferenceChecker varcompound(
 271                     compound.checkCompound("ParsedVariable", id.c_str()));
 272             varcompound.checkString(selections[i], "Input");
 273             ++varcount;
 274         }
 275         else
 276         {
 277             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 278             TestReferenceChecker selcompound(
 279                     compound.checkCompound("ParsedSelection", id.c_str()));
 280             selcompound.checkString(selections[i], "Input");
 281             if (flags_.test(efTestSelectionNames))
 282             {
 283                 selcompound.checkString(sel_[count_].name(), "Name");
 284             }
 285             selcompound.checkString(sel_[count_].selectionText(), "Text");
 286             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 287             ++count_;
 288         }
 289     }
 290 }
 291
 292
 293 void
 294 SelectionCollectionDataTest::runCompiler()
 295 {
 296     ASSERT_NO_THROW_GMX(sc_.compile());
 297     ASSERT_EQ(count_, sel_.size());
 298     checkCompiled();
 299 }
 300
 301
 302 void
 303 SelectionCollectionDataTest::checkCompiled()
 304 {
 305     using gmx::test::TestReferenceChecker;
 306     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 307
 308     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 309     for (size_t i = 0; i < count_; ++i)
 310     {
 311         SCOPED_TRACE(std::string("Checking selection \"") +
 312                      sel_[i].selectionText() + "\"");
 313         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 314         TestReferenceChecker selcompound(
 315                 compound.checkCompound("Selection", id.c_str()));
 316         if (flags_.test(efTestSelectionNames))
 317         {
 318             selcompound.checkString(sel_[i].name(), "Name");
 319         }
 320         if (!flags_.test(efDontTestCompiledAtoms))
 321         {
 322             checkSelection(&selcompound, sel_[i], flags_ & mask);
 323         }
 324     }
 325 }
 326
 327
 328 void
 329 SelectionCollectionDataTest::runEvaluate()
 330 {
 331     using gmx::test::TestReferenceChecker;
 332
 333     ++framenr_;
 334     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 335     std::string          frame = gmx::formatString("Frame%d", framenr_);
 336     TestReferenceChecker compound(
 337             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 338     for (size_t i = 0; i < count_; ++i)
 339     {
 340         SCOPED_TRACE(std::string("Checking selection \"") +
 341                      sel_[i].selectionText() + "\"");
 342         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 343         TestReferenceChecker selcompound(
 344                 compound.checkCompound("Selection", id.c_str()));
 345         checkSelection(&selcompound, sel_[i], flags_);
 346     }
 347 }
 348
 349
 350 void
 351 SelectionCollectionDataTest::runEvaluateFinal()
 352 {
 353     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 354     checkCompiled();
 355 }
 356
 357
 358 void
 359 SelectionCollectionDataTest::runTest(
 360         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 361 {
 362     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 363     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 364     ASSERT_NO_FATAL_FAILURE(runCompiler());
 365 }
 366
 367
 368 void
 369 SelectionCollectionDataTest::runTest(
 370         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 371 {
 372     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 373     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 374     ASSERT_NO_FATAL_FAILURE(runCompiler());
 375     if (flags_.test(efTestEvaluation))
 376     {
 377         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 378         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 379     }
 380 }
 381
 382
 383 /********************************************************************
 384  * Tests for SelectionCollection functionality without reference data
 385  */
 386
 387 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 388 {
 389     EXPECT_FALSE(sc_.requiresTopology());
 390     EXPECT_NO_THROW_GMX(sc_.compile());
 391 }
 392
 393 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 394 {
 395     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 396     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 397     ASSERT_EQ(2U, sel_.size());
 398     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 399     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 400     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 401     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 402     ASSERT_NO_THROW_GMX(sc_.compile());
 403     EXPECT_TRUE(sel_[0].hasVelocities());
 404     EXPECT_TRUE(sel_[1].hasVelocities());
 405     EXPECT_TRUE(sel_[0].hasForces());
 406     EXPECT_TRUE(sel_[1].hasForces());
 407 }
 408
 409 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 410 {
 411     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 412                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 413     // These should match the contents of selfile.dat
 414     ASSERT_EQ(2U, sel_.size());
 415     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 416     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 417 }
 418
 419 TEST_F(SelectionCollectionTest, HandlesAtypicalWhitespace)
 420 {
 421     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr\n1\r\nto\t10;\vatomnr 3\f to 14\r"));
 422     ASSERT_EQ(2U, sel_.size());
 423     EXPECT_STREQ("atomnr 1 to 10", sel_[0].selectionText());
 424     // TODO: Get rid of the trailing whitespace.
 425     EXPECT_STREQ("atomnr 3 to 14 ", sel_[1].selectionText());
 426 }
 427
 428 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 429 {
 430     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 431     EXPECT_THROW_GMX({
 432                          sc_.parseFromString("resname ~ \"R[A\"");
 433                          sc_.compile();
 434                      }, gmx::InvalidInputError);
 435 }
 436
 437 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 438 {
 439     if (!gmx::Regex::isSupported())
 440     {
 441         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 442         EXPECT_THROW_GMX({
 443                              sc_.parseFromString("resname \"R[AD]\"");
 444                              sc_.compile();
 445                          }, gmx::InvalidInputError);
 446     }
 447 }
 448
 449 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 450 {
 451     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 452                      gmx::InvalidInputError);
 453 }
 454
 455 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 456 {
 457     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 458                      gmx::InvalidInputError);
 459 }
 460
 461 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 462 {
 463     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 464                      gmx::InvalidInputError);
 465 }
 466
 467 // TODO: Tests for more parser errors
 468
 469 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 470 {
 471     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 472     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 473     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 474 }
 475
 476 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 477 {
 478     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 479     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 480     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 481 }
 482
 483 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 484 {
 485     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 486     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 487     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 488     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 489 }
 490
 491 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 492 {
 493     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 494     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 495     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 496     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 497 }
 498
 499 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 500 {
 501     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 502     EXPECT_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""),
 503                      gmx::InconsistentInputError);
 504     EXPECT_THROW_GMX(sc_.parseFromString("group 2 or atomnr 2 to 5"),
 505                      gmx::InconsistentInputError);
 506     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of group 2"),
 507                      gmx::InconsistentInputError);
 508 }
 509
 510 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 511 {
 512     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""));
 513     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group 2"));
 514     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 515     // TODO: Add a separate check in the selection compiler for a safer API
 516     // (makes sense in the future if the compiler needs the information for
 517     // other purposes as well).
 518     // EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 519 }
 520
 521 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 522 {
 523     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 524     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 525     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 526 }
 527
 528 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 529 {
 530     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 531     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 532     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 533 }
 534
 535 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 536 {
 537     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 538     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 539     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 540 }
 541
 542 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 543 {
 544     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 545     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 546     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 547 }
 548
 549 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 550 {
 551     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 552     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 553     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 554 }
 555
 556 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 557 {
 558     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 559     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 560     ASSERT_NO_THROW_GMX(sc_.compile());
 561     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 562 }
 563
 564 // TODO: Tests for evaluation errors
 565
 566
 567 /********************************************************************
 568  * Tests for selection keywords
 569  */
 570
 571 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 572 {
 573     static const char * const selections[] = {
 574         "all",
 575         "none"
 576     };
 577     runTest(10, selections);
 578 }
 579
 580 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 581 {
 582     static const char * const selections[] = {
 583         "atomnr 1 to 3 6 to 8",
 584         "atomnr 4 2 5 to 7",
 585         "atomnr <= 5"
 586     };
 587     runTest(10, selections);
 588 }
 589
 590 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 591 {
 592     static const char * const selections[] = {
 593         "resnr 1 2 5",
 594         "resid 4 to 3"
 595     };
 596     runTest("simple.gro", selections);
 597 }
 598
 599 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 600 {
 601     static const char * const selections[] = {
 602         "resindex 1 4",
 603         "residue 1 3"
 604     };
 605     runTest("simple.pdb", selections);
 606 }
 607
 608 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 609 {
 610     static const char * const selections[] = {
 611         "molindex 1 4",
 612         "molecule 2 3 5"
 613     };
 614     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 615     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 616     topManager_.initUniformMolecules(3);
 617     ASSERT_NO_FATAL_FAILURE(runCompiler());
 618 }
 619
 620 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 621 {
 622     static const char * const selections[] = {
 623         "name CB",
 624         "atomname S1 S2"
 625     };
 626     runTest("simple.gro", selections);
 627 }
 628
 629 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 630 {
 631     static const char * const selections[] = {
 632         "name HG21",
 633         "name 1HG2",
 634         "pdbname HG21 CB",
 635         "pdbatomname 1HG2"
 636     };
 637     runTest("simple.pdb", selections);
 638 }
 639
 640
 641 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 642 {
 643     static const char * const selections[] = {
 644         "atomtype CA"
 645     };
 646     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 647     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 648     const char *const types[] = { "CA", "SA", "SB" };
 649     topManager_.initAtomTypes(types);
 650     ASSERT_NO_FATAL_FAILURE(runCompiler());
 651 }
 652
 653 TEST_F(SelectionCollectionDataTest, HandlesChain)
 654 {
 655     static const char * const selections[] = {
 656         "chain A",
 657         "chain B"
 658     };
 659     runTest("simple.pdb", selections);
 660 }
 661
 662 TEST_F(SelectionCollectionDataTest, HandlesMass)
 663 {
 664     static const char * const selections[] = {
 665         "mass > 5"
 666     };
 667     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 668     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 669     for (int i = 0; i < top_->atoms.nr; ++i)
 670     {
 671         top_->atoms.atom[i].m = 1.0 + i;
 672     }
 673     ASSERT_NO_FATAL_FAILURE(runCompiler());
 674 }
 675
 676 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 677 {
 678     static const char * const selections[] = {
 679         "charge < 0.5"
 680     };
 681     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 682     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 683     for (int i = 0; i < top_->atoms.nr; ++i)
 684     {
 685         top_->atoms.atom[i].q = i / 10.0;
 686     }
 687     ASSERT_NO_FATAL_FAILURE(runCompiler());
 688 }
 689
 690 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 691 {
 692     static const char * const selections[] = {
 693         "altloc \" \"",
 694         "altloc A"
 695     };
 696     runTest("simple.pdb", selections);
 697 }
 698
 699 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 700 {
 701     static const char * const selections[] = {
 702         "insertcode \" \"",
 703         "insertcode A"
 704     };
 705     runTest("simple.pdb", selections);
 706 }
 707
 708 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 709 {
 710     static const char * const selections[] = {
 711         "occupancy 1",
 712         "occupancy < .5"
 713     };
 714     runTest("simple.pdb", selections);
 715 }
 716
 717 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 718 {
 719     static const char * const selections[] = {
 720         "beta 0",
 721         "beta >= 0.3"
 722     };
 723     runTest("simple.pdb", selections);
 724 }
 725
 726 TEST_F(SelectionCollectionDataTest, HandlesResname)
 727 {
 728     static const char * const selections[] = {
 729         "resname RA",
 730         "resname RB RC"
 731     };
 732     runTest("simple.gro", selections);
 733 }
 734
 735 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 736 {
 737     static const char * const selections[] = {
 738         "x < 3",
 739         "y >= 3",
 740         "x {-1 to 2}"
 741     };
 742     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 743     runTest("simple.gro", selections);
 744 }
 745
 746
 747 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 748 {
 749     static const char * const selections[] = {
 750         "same residue as atomnr 1 4 12"
 751     };
 752     runTest("simple.gro", selections);
 753 }
 754
 755
 756 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 757 {
 758     static const char * const selections[] = {
 759         "same resname as atomnr 1 14"
 760     };
 761     runTest("simple.gro", selections);
 762 }
 763
 764
 765 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 766 {
 767     static const char * const selections[] = {
 768         "cog of resnr 1 3",
 769         "res_cog of name CB and resnr 1 3",
 770         "whole_res_cog of name CB and resnr 1 3",
 771         "part_res_cog of x < 3",
 772         "dyn_res_cog of x < 3"
 773     };
 774     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 775              | efTestPositionAtoms);
 776     runTest("simple.gro", selections);
 777 }
 778
 779
 780 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 781 {
 782     static const char * const selections[] = {
 783         "distance from cog of resnr 1 < 2"
 784     };
 785     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 786     runTest("simple.gro", selections);
 787 }
 788
 789
 790 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 791 {
 792     static const char * const selections[] = {
 793         "mindistance from resnr 1 < 2"
 794     };
 795     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 796     runTest("simple.gro", selections);
 797 }
 798
 799
 800 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 801 {
 802     static const char * const selections[] = {
 803         "within 1 of resnr 2"
 804     };
 805     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 806     runTest("simple.gro", selections);
 807 }
 808
 809
 810 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 811 {
 812     // Both of these should evaluate to empty on a correct implementation.
 813     static const char * const selections[] = {
 814         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 815         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 816     };
 817     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 818     runTest("sphere.gro", selections);
 819 }
 820
 821
 822 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 823 {
 824     static const char * const selections[] = {
 825         "all permute 3 1 2",
 826         "res_cog of resnr 1 to 4 permute 2 1",
 827         "name CB S1 and res_cog x < 3 permute 2 1"
 828     };
 829     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 830              | efTestPositionAtoms | efTestPositionMapping);
 831     runTest("simple.gro", selections);
 832 }
 833
 834
 835 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 836 {
 837     static const char * const selections[] = {
 838         "name S2 plus name S1",
 839         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 840         "name S1 and y < 3 plus res_cog of x < 2.5"
 841     };
 842     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 843              | efTestPositionAtoms | efTestPositionMapping);
 844     runTest("simple.gro", selections);
 845 }
 846
 847
 848 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 849 {
 850     static const char * const selections[] = {
 851         "name S2 merge name S1",
 852         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 853         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 854     };
 855     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 856              | efTestPositionAtoms | efTestPositionMapping);
 857     runTest("simple.gro", selections);
 858 }
 859
 860
 861 /********************************************************************
 862  * Tests for generic selection evaluation
 863  */
 864
 865 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 866 {
 867     static const char * const selections[] = {
 868         "name CB",
 869         "y > 2",
 870         "res_cog of y > 2"
 871     };
 872     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 873              | efTestPositionMasses | efTestPositionCharges);
 874     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 875     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 876     for (int i = 0; i < top_->atoms.nr; ++i)
 877     {
 878         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 879         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 880     }
 881     ASSERT_NO_FATAL_FAILURE(runCompiler());
 882     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 883     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 884 }
 885
 886 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 887 {
 888     static const char * const selections[] = {
 889         "atomnr 1 to 3 8 to 9",
 890         "y > 2",
 891         "cog of (y > 2)"
 892     };
 893     setFlags(TestFlags() | efTestPositionAtoms
 894              | efTestPositionMasses | efTestPositionCharges);
 895     runTest(10, selections);
 896 }
 897
 898
 899 /********************************************************************
 900  * Tests for selection syntactic constructs
 901  */
 902
 903 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 904 {
 905     static const char * const selections[] = {
 906         "\"GroupSelection\" group \"GrpA\"",
 907         "\"DynamicSelection\" x < 5",
 908         "y < 3"
 909     };
 910     setFlags(TestFlags() | efTestSelectionNames);
 911     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 912     runTest(10, selections);
 913 }
 914
 915 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 916 {
 917     static const char * const selections[] = {
 918         "group \"GrpA\"",
 919         "GrpB",
 920         "1",
 921         "group \"GrpB\" and resname RB"
 922     };
 923     setFlags(TestFlags() | efTestSelectionNames);
 924     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 925     runTest("simple.gro", selections);
 926 }
 927
 928 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 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_FATAL_FAILURE(runParser(selections));
 938     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 939     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 940     ASSERT_NO_FATAL_FAILURE(runCompiler());
 941 }
 942
 943 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
 944 {
 945     static const char * const selections[] = {
 946         "foo = group \"GrpUnsorted\"",
 947         "group \"GrpUnsorted\"",
 948         "GrpUnsorted",
 949         "2",
 950         "res_cog of group \"GrpUnsorted\"",
 951         "group \"GrpUnsorted\" permute 2 1",
 952         "foo"
 953     };
 954     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
 955              | efTestSelectionNames);
 956     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 957     runTest("simple.gro", selections);
 958 }
 959
 960 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelectionsDelayed)
 961 {
 962     static const char * const selections[] = {
 963         "foo = group \"GrpUnsorted\"",
 964         "group \"GrpUnsorted\"",
 965         "GrpUnsorted",
 966         "2",
 967         "res_cog of group \"GrpUnsorted\"",
 968         "group \"GrpUnsorted\" permute 2 1",
 969         "foo"
 970     };
 971     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 972     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 973     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 974     ASSERT_NO_FATAL_FAILURE(runCompiler());
 975 }
 976
 977 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 978 {
 979     static const char * const selections[] = {
 980         "[1, -2, 3.5]"
 981     };
 982     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 983     runTest("simple.gro", selections);
 984 }
 985
 986
 987 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 988 {
 989     static const char * const selections[] = {
 990         "within 1 of [2, 1, 0]"
 991     };
 992     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 993     runTest("simple.gro", selections);
 994 }
 995
 996
 997 TEST_F(SelectionCollectionDataTest, HandlesOverlappingIntegerRanges)
 998 {
 999     static const char * const selections[] = {
1000         "atomnr 2 to 4 5 to 8",
1001         "atomnr 2 to 5 4 to 7"
1002     };
1003     ASSERT_NO_FATAL_FAILURE(runTest(10, selections));
1004 }
1005
1006
1007 TEST_F(SelectionCollectionDataTest, HandlesOverlappingRealRanges)
1008 {
1009     static const char * const selections[] = {
1010         "charge {-0.35 to -0.05 0.25 to 0.75}",
1011         "charge {0.05 to -0.3 -0.05 to 0.55}"
1012     };
1013     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1014     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1015     for (int i = 0; i < top_->atoms.nr; ++i)
1016     {
1017         top_->atoms.atom[i].q = i / 10.0 - 0.5;
1018     }
1019     ASSERT_NO_FATAL_FAILURE(runCompiler());
1020 }
1021
1022
1023 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
1024 {
1025     static const char * const selections[] = {
1026         "name = S1 \"C?\"",
1027         "name ? S1 \"C?\""
1028     };
1029     runTest("simple.gro", selections);
1030 }
1031
1032
1033 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
1034 {
1035     static const char * const selections[] = {
1036         "name \"S?\"",
1037         "name ? \"S?\""
1038     };
1039     runTest("simple.gro", selections);
1040 }
1041
1042
1043 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
1044 {
1045     static const char * const selections[] = {
1046         "resname \"R[BD]\"",
1047         "resname ~ \"R[BD]\""
1048     };
1049     if (gmx::Regex::isSupported())
1050     {
1051         runTest("simple.gro", selections);
1052     }
1053 }
1054
1055
1056 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
1057 {
1058     static const char * const selections[] = {
1059         "atomnr 1 to 5 and atomnr 2 to 7",
1060         "atomnr 1 to 5 or not atomnr 3 to 8",
1061         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1062         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1063         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1064     };
1065     runTest(10, selections);
1066 }
1067
1068
1069 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1070 {
1071     static const char * const selections[] = {
1072         "same residue as (atomnr 3 5 13 or y > 5)",
1073         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1074     };
1075     setFlags(TestFlags() | efTestEvaluation);
1076     runTest("simple.gro", selections);
1077 }
1078
1079
1080 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1081 {
1082     static const char * const selections[] = {
1083         "none and x > 2",
1084         "none and same resname as resnr 2"
1085     };
1086     runTest("simple.gro", selections);
1087 }
1088
1089
1090 TEST_F(SelectionCollectionDataTest, HandlesEmptyReferenceForSame)
1091 {
1092     static const char * const selections[] = {
1093         "same residue as none",
1094         "same resname as none"
1095     };
1096     runTest("simple.gro", selections);
1097 }
1098
1099
1100 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1101 {
1102     static const char * const selections[] = {
1103         "x > 2",
1104         "2 < x",
1105         "y > resnr",
1106         "resnr < 2.5",
1107         "2.5 > resnr"
1108     };
1109     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1110     runTest("simple.gro", selections);
1111 }
1112
1113
1114 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1115 {
1116     static const char * const selections[] = {
1117         "x+1 > 3",
1118         "(y-1)^2 <= 1",
1119         "x+--1 > 3",
1120         "-x+-1 < -3"
1121     };
1122     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1123     runTest("simple.gro", selections);
1124 }
1125
1126
1127 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1128 {
1129     static const char * const selections[] = {
1130         "value = x + y",
1131         "value <= 4",
1132         "index = resnr",
1133         "index < 3"
1134     };
1135     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1136     runTest("simple.gro", selections);
1137 }
1138
1139
1140 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1141 {
1142     static const char * const selections[] = {
1143         "value = x + y",
1144         "resname RA and value <= 4",
1145         "resname RA RB and x < 3 and value <= 4",
1146         "index = atomnr",
1147         "resname RA and index < 3",
1148         "resname RB and y < 3 and index < 6"
1149     };
1150     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1151     runTest("simple.gro", selections);
1152 }
1153
1154
1155 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1156 {
1157     static const char * const selections[] = {
1158         "foo = res_cog of resname RA",
1159         "foo",
1160         "within 1 of foo",
1161         "bar = cog of resname RA",
1162         "bar",
1163         "within 1 of bar"
1164     };
1165     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1166     runTest("simple.gro", selections);
1167 }
1168
1169
1170 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1171 {
1172     static const char * const selections[] = {
1173         "constpos = [1.0, 2.5, 0.5]",
1174         "constpos",
1175         "within 2 of constpos"
1176     };
1177     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1178              | efTestPositionAtoms);
1179     runTest("simple.gro", selections);
1180 }
1181
1182
1183 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1184 {
1185     static const char * const selections[] = {
1186         "constint = 4",
1187         "constreal1 = 0.5",
1188         "constreal2 = 2.7",
1189         "resnr < constint",
1190         "x + constreal1 < constreal2"
1191     };
1192     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1193     runTest("simple.gro", selections);
1194 }
1195
1196
1197 /********************************************************************
1198  * Tests for complex boolean syntax
1199  */
1200
1201 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1202 {
1203     static const char * const selections[] = {
1204         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1205         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1206         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1207         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1208         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1209     };
1210     runTest(10, selections);
1211 }
1212
1213
1214 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1215 {
1216     static const char * const selections[] = {
1217         "foo = atomnr 4 to 7 or x < 2",
1218         "atomnr 1 to 4 and foo",
1219         "atomnr 2 to 6 and y < 3 and foo",
1220         "atomnr 6 to 10 and not foo"
1221     };
1222     runTest(10, selections);
1223 }
1224
1225
1226 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1227 {
1228     static const char * const selections[] = {
1229         "foo = atomnr 4 to 7",
1230         "bar = foo and x < 2",
1231         "bar2 = foo and y < 2",
1232         "atomnr 1 to 4 and bar",
1233         "atomnr 2 to 6 and y < 3 and bar2",
1234         "atomnr 6 to 10 and not foo"
1235     };
1236     runTest(10, selections);
1237 }
1238
1239
1240 /********************************************************************
1241  * Tests for complex subexpression cases
1242  *
1243  * These tests use some knowledge of the implementation to trigger different
1244  * paths in the code.
1245  */
1246
1247 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1248 {
1249     static const char * const selections[] = {
1250         "unused1 = atomnr 1 to 3",
1251         "foo = atomnr 4 to 7",
1252         "atomnr 1 to 6 and foo",
1253         "unused2 = atomnr 3 to 5"
1254     };
1255     runTest(10, selections);
1256 }
1257
1258
1259 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1260 {
1261     static const char * const selections[] = {
1262         "foo = atomnr 4 to 7 and x < 2",
1263         "atomnr 1 to 5 and foo",
1264         "atomnr 3 to 7 and foo"
1265     };
1266     runTest(10, selections);
1267 }
1268
1269
1270 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1271 {
1272     static const char * const selections[] = {
1273         "foo = atomnr 4 to 7 and x < 2",
1274         "atomnr 1 to 6 and foo",
1275         "within 1 of foo",
1276         "foo"
1277     };
1278     runTest(10, selections);
1279 }
1280
1281
1282 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1283 {
1284     static const char * const selections[] = {
1285         "foo = atomnr 1 to 8 and x < 10",
1286         "atomnr 1 to 5 and y < 10 and foo",
1287         "foo"
1288     };
1289     setFlags(TestFlags() | efTestEvaluation);
1290     runTest("simple.gro", selections);
1291 }
1292
1293
1294 } // namespace