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 "gmxpre.h"
  43
  44 #include "gromacs/selection/selectioncollection.h"
  45
  46 #include <gtest/gtest.h>
  47
  48 #include "gromacs/fileio/trx.h"
  49 #include "gromacs/options/basicoptions.h"
  50 #include "gromacs/options/options.h"
  51 #include "gromacs/selection/indexutil.h"
  52 #include "gromacs/selection/selection.h"
  53 #include "gromacs/topology/topology.h"
  54 #include "gromacs/utility/arrayref.h"
  55 #include "gromacs/utility/exceptions.h"
  56 #include "gromacs/utility/flags.h"
  57 #include "gromacs/utility/gmxregex.h"
  58 #include "gromacs/utility/stringutil.h"
  59
  60 #include "testutils/interactivetest.h"
  61 #include "testutils/refdata.h"
  62 #include "testutils/testasserts.h"
  63 #include "testutils/testfilemanager.h"
  64 #include "testutils/testoptions.h"
  65
  66 #include "toputils.h"
  67
  68 namespace
  69 {
  70
  71 /********************************************************************
  72  * Test fixture for selection testing
  73  */
  74
  75 class SelectionCollectionTest : public ::testing::Test
  76 {
  77     public:
  78         static int               s_debugLevel;
  79
  80         SelectionCollectionTest();
  81         ~SelectionCollectionTest();
  82
  83         void setAtomCount(int natoms)
  84         {
  85             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  86         }
  87         void loadTopology(const char *filename);
  88         void setTopology();
  89         void loadIndexGroups(const char *filename);
  90
  91         gmx::test::TopologyManager  topManager_;
  92         gmx::SelectionCollection    sc_;
  93         gmx::SelectionList          sel_;
  94         t_topology                 *top_;
  95         t_trxframe                 *frame_;
  96         gmx_ana_indexgrps_t        *grps_;
  97 };
  98
  99 int SelectionCollectionTest::s_debugLevel = 0;
 100
 101 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
 102 #ifndef DOXYGEN
 103 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
 104 {
 105     options->addOption(gmx::IntegerOption("seldebug")
 106                            .store(&SelectionCollectionTest::s_debugLevel)
 107                            .description("Set selection debug level"));
 108 }
 109 #endif
 110
 111 SelectionCollectionTest::SelectionCollectionTest()
 112     : top_(NULL), frame_(NULL), grps_(NULL)
 113 {
 114     topManager_.requestFrame();
 115     sc_.setDebugLevel(s_debugLevel);
 116     sc_.setReferencePosType("atom");
 117     sc_.setOutputPosType("atom");
 118 }
 119
 120 SelectionCollectionTest::~SelectionCollectionTest()
 121 {
 122     if (grps_ != NULL)
 123     {
 124         gmx_ana_indexgrps_free(grps_);
 125     }
 126 }
 127
 128 void
 129 SelectionCollectionTest::loadTopology(const char *filename)
 130 {
 131     topManager_.loadTopology(filename);
 132     setTopology();
 133 }
 134
 135 void
 136 SelectionCollectionTest::setTopology()
 137 {
 138     top_   = topManager_.topology();
 139     frame_ = topManager_.frame();
 140
 141     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 142 }
 143
 144 void
 145 SelectionCollectionTest::loadIndexGroups(const char *filename)
 146 {
 147     GMX_RELEASE_ASSERT(grps_ == NULL,
 148                        "External groups can only be loaded once");
 149     std::string fullpath =
 150         gmx::test::TestFileManager::getInputFilePath(filename);
 151     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 152     sc_.setIndexGroups(grps_);
 153 }
 154
 155
 156 /********************************************************************
 157  * Test fixture for interactive SelectionCollection tests
 158  */
 159
 160 class SelectionCollectionInteractiveTest : public SelectionCollectionTest
 161 {
 162     public:
 163         SelectionCollectionInteractiveTest()
 164             : helper_(data_.rootChecker())
 165         {
 166         }
 167
 168         void runTest(int count, bool bInteractive,
 169                      const gmx::ConstArrayRef<const char *> &input);
 170
 171         gmx::test::TestReferenceData      data_;
 172         gmx::test::InteractiveTestHelper  helper_;
 173 };
 174
 175 void SelectionCollectionInteractiveTest::runTest(
 176         int count, bool bInteractive,
 177         const gmx::ConstArrayRef<const char *> &inputLines)
 178 {
 179     helper_.setInputLines(inputLines);
 180     // TODO: Check something about the returned selections as well.
 181     ASSERT_NO_THROW_GMX(sc_.parseInteractive(
 182                                 count, &helper_.inputStream(),
 183                                 bInteractive ? &helper_.outputStream() : NULL,
 184                                 "for test context"));
 185     helper_.checkSession();
 186 }
 187
 188
 189 /********************************************************************
 190  * Test fixture for selection testing with reference data
 191  */
 192
 193 class SelectionCollectionDataTest : public SelectionCollectionTest
 194 {
 195     public:
 196         enum TestFlag
 197         {
 198             efTestEvaluation            = 1<<0,
 199             efTestPositionAtoms         = 1<<1,
 200             efTestPositionCoordinates   = 1<<2,
 201             efTestPositionMapping       = 1<<3,
 202             efTestPositionMasses        = 1<<4,
 203             efTestPositionCharges       = 1<<5,
 204             efTestSelectionNames        = 1<<6,
 205             efDontTestCompiledAtoms     = 1<<8
 206         };
 207         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 208
 209         SelectionCollectionDataTest()
 210             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 211         {
 212         }
 213
 214         void setFlags(TestFlags flags) { flags_ = flags; }
 215
 216         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 217         void runCompiler();
 218         void runEvaluate();
 219         void runEvaluateFinal();
 220
 221         void runTest(int                                     natoms,
 222                      const gmx::ConstArrayRef<const char *> &selections);
 223         void runTest(const char                             *filename,
 224                      const gmx::ConstArrayRef<const char *> &selections);
 225
 226     private:
 227         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 228                                    const gmx::Selection &sel, TestFlags flags);
 229
 230         void checkCompiled();
 231
 232         gmx::test::TestReferenceData    data_;
 233         gmx::test::TestReferenceChecker checker_;
 234         size_t                          count_;
 235         int                             framenr_;
 236         TestFlags                       flags_;
 237 };
 238
 239
 240 void
 241 SelectionCollectionDataTest::checkSelection(
 242         gmx::test::TestReferenceChecker *checker,
 243         const gmx::Selection &sel, TestFlags flags)
 244 {
 245     using gmx::test::TestReferenceChecker;
 246
 247     {
 248         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 249         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 250     }
 251     if (flags.test(efTestPositionAtoms)
 252         || flags.test(efTestPositionCoordinates)
 253         || flags.test(efTestPositionMapping)
 254         || flags.test(efTestPositionMasses)
 255         || flags.test(efTestPositionCharges))
 256     {
 257         TestReferenceChecker compound(
 258                 checker->checkSequenceCompound("Positions", sel.posCount()));
 259         for (int i = 0; i < sel.posCount(); ++i)
 260         {
 261             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 262             const gmx::SelectionPosition &p = sel.position(i);
 263             if (flags.test(efTestPositionAtoms))
 264             {
 265                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 266                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 267             }
 268             if (flags.test(efTestPositionCoordinates))
 269             {
 270                 poscompound.checkVector(p.x(), "Coordinates");
 271             }
 272             if (flags.test(efTestPositionMapping))
 273             {
 274                 poscompound.checkInteger(p.refId(), "RefId");
 275                 poscompound.checkInteger(p.mappedId(), "MappedId");
 276             }
 277             if (flags.test(efTestPositionMasses))
 278             {
 279                 poscompound.checkReal(p.mass(), "Mass");
 280             }
 281             if (flags.test(efTestPositionCharges))
 282             {
 283                 poscompound.checkReal(p.charge(), "Charge");
 284             }
 285         }
 286     }
 287 }
 288
 289
 290 void
 291 SelectionCollectionDataTest::runParser(
 292         const gmx::ConstArrayRef<const char *> &selections)
 293 {
 294     using gmx::test::TestReferenceChecker;
 295
 296     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 297     size_t               varcount = 0;
 298     count_ = 0;
 299     for (size_t i = 0; i < selections.size(); ++i)
 300     {
 301         SCOPED_TRACE(std::string("Parsing selection \"")
 302                      + selections[i] + "\"");
 303         gmx::SelectionList result;
 304         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 305         sel_.insert(sel_.end(), result.begin(), result.end());
 306         if (sel_.size() == count_)
 307         {
 308             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 309             TestReferenceChecker varcompound(
 310                     compound.checkCompound("ParsedVariable", id.c_str()));
 311             varcompound.checkString(selections[i], "Input");
 312             ++varcount;
 313         }
 314         else
 315         {
 316             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 317             TestReferenceChecker selcompound(
 318                     compound.checkCompound("ParsedSelection", id.c_str()));
 319             selcompound.checkString(selections[i], "Input");
 320             if (flags_.test(efTestSelectionNames))
 321             {
 322                 selcompound.checkString(sel_[count_].name(), "Name");
 323             }
 324             selcompound.checkString(sel_[count_].selectionText(), "Text");
 325             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 326             ++count_;
 327         }
 328     }
 329 }
 330
 331
 332 void
 333 SelectionCollectionDataTest::runCompiler()
 334 {
 335     ASSERT_NO_THROW_GMX(sc_.compile());
 336     ASSERT_EQ(count_, sel_.size());
 337     checkCompiled();
 338 }
 339
 340
 341 void
 342 SelectionCollectionDataTest::checkCompiled()
 343 {
 344     using gmx::test::TestReferenceChecker;
 345     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 346
 347     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 348     for (size_t i = 0; i < count_; ++i)
 349     {
 350         SCOPED_TRACE(std::string("Checking selection \"") +
 351                      sel_[i].selectionText() + "\"");
 352         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 353         TestReferenceChecker selcompound(
 354                 compound.checkCompound("Selection", id.c_str()));
 355         if (flags_.test(efTestSelectionNames))
 356         {
 357             selcompound.checkString(sel_[i].name(), "Name");
 358         }
 359         if (!flags_.test(efDontTestCompiledAtoms))
 360         {
 361             checkSelection(&selcompound, sel_[i], flags_ & mask);
 362         }
 363     }
 364 }
 365
 366
 367 void
 368 SelectionCollectionDataTest::runEvaluate()
 369 {
 370     using gmx::test::TestReferenceChecker;
 371
 372     ++framenr_;
 373     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 374     std::string          frame = gmx::formatString("Frame%d", framenr_);
 375     TestReferenceChecker compound(
 376             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 377     for (size_t i = 0; i < count_; ++i)
 378     {
 379         SCOPED_TRACE(std::string("Checking selection \"") +
 380                      sel_[i].selectionText() + "\"");
 381         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 382         TestReferenceChecker selcompound(
 383                 compound.checkCompound("Selection", id.c_str()));
 384         checkSelection(&selcompound, sel_[i], flags_);
 385     }
 386 }
 387
 388
 389 void
 390 SelectionCollectionDataTest::runEvaluateFinal()
 391 {
 392     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 393     checkCompiled();
 394 }
 395
 396
 397 void
 398 SelectionCollectionDataTest::runTest(
 399         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 400 {
 401     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 402     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 403     ASSERT_NO_FATAL_FAILURE(runCompiler());
 404 }
 405
 406
 407 void
 408 SelectionCollectionDataTest::runTest(
 409         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 410 {
 411     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 412     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 413     ASSERT_NO_FATAL_FAILURE(runCompiler());
 414     if (flags_.test(efTestEvaluation))
 415     {
 416         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 417         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 418     }
 419 }
 420
 421
 422 /********************************************************************
 423  * Tests for SelectionCollection functionality without reference data
 424  */
 425
 426 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 427 {
 428     EXPECT_FALSE(sc_.requiresTopology());
 429     EXPECT_NO_THROW_GMX(sc_.compile());
 430 }
 431
 432 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 433 {
 434     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 435     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 436     ASSERT_EQ(2U, sel_.size());
 437     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 438     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 439     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 440     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 441     ASSERT_NO_THROW_GMX(sc_.compile());
 442     EXPECT_TRUE(sel_[0].hasVelocities());
 443     EXPECT_TRUE(sel_[1].hasVelocities());
 444     EXPECT_TRUE(sel_[0].hasForces());
 445     EXPECT_TRUE(sel_[1].hasForces());
 446 }
 447
 448 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 449 {
 450     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 451                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 452     // These should match the contents of selfile.dat
 453     ASSERT_EQ(2U, sel_.size());
 454     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 455     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 456 }
 457
 458 TEST_F(SelectionCollectionTest, HandlesAtypicalWhitespace)
 459 {
 460     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr\n1\r\nto\t10;\vatomnr 3\f to 14\r"));
 461     ASSERT_EQ(2U, sel_.size());
 462     EXPECT_STREQ("atomnr 1 to 10", sel_[0].selectionText());
 463     // TODO: Get rid of the trailing whitespace.
 464     EXPECT_STREQ("atomnr 3 to 14 ", sel_[1].selectionText());
 465 }
 466
 467 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 468 {
 469     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 470     EXPECT_THROW_GMX({
 471                          sc_.parseFromString("resname ~ \"R[A\"");
 472                          sc_.compile();
 473                      }, gmx::InvalidInputError);
 474 }
 475
 476 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 477 {
 478     if (!gmx::Regex::isSupported())
 479     {
 480         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 481         EXPECT_THROW_GMX({
 482                              sc_.parseFromString("resname \"R[AD]\"");
 483                              sc_.compile();
 484                          }, gmx::InvalidInputError);
 485     }
 486 }
 487
 488 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 489 {
 490     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 491                      gmx::InvalidInputError);
 492 }
 493
 494 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 495 {
 496     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 497                      gmx::InvalidInputError);
 498 }
 499
 500 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 501 {
 502     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 503                      gmx::InvalidInputError);
 504 }
 505
 506 // TODO: Tests for more parser errors
 507
 508 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 509 {
 510     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 511     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 512     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 513 }
 514
 515 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 516 {
 517     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 518     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 519     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 520 }
 521
 522 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 523 {
 524     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 525     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 526     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 527     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 528 }
 529
 530 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 531 {
 532     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 533     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 534     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 535     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 536 }
 537
 538 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 539 {
 540     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 541     EXPECT_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""),
 542                      gmx::InconsistentInputError);
 543     EXPECT_THROW_GMX(sc_.parseFromString("group 2 or atomnr 2 to 5"),
 544                      gmx::InconsistentInputError);
 545     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of group 2"),
 546                      gmx::InconsistentInputError);
 547 }
 548
 549 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 550 {
 551     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""));
 552     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group 2"));
 553     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 554     // TODO: Add a separate check in the selection compiler for a safer API
 555     // (makes sense in the future if the compiler needs the information for
 556     // other purposes as well).
 557     // EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 558 }
 559
 560 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroup)
 561 {
 562     ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
 563     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 564     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpB\""), gmx::InconsistentInputError);
 565 }
 566
 567 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed)
 568 {
 569     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 570     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
 571     EXPECT_THROW_GMX(sc_.setTopology(NULL, 5), gmx::InconsistentInputError);
 572 }
 573
 574 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed2)
 575 {
 576     ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
 577     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
 578     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 579 }
 580
 581 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 582 {
 583     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 584     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 585     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 586 }
 587
 588 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 589 {
 590     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 591     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 592     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 593 }
 594
 595 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 596 {
 597     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 598     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 599     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 600 }
 601
 602 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 603 {
 604     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 605     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 606     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 607 }
 608
 609 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 610 {
 611     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 612     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 613     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 614 }
 615
 616 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 617 {
 618     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 619     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 620     ASSERT_NO_THROW_GMX(sc_.compile());
 621     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 622 }
 623
 624 TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets)
 625 {
 626     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 3 to 10"));
 627     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 628     ASSERT_NO_THROW_GMX(sc_.compile());
 629     frame_->natoms = 8;
 630     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 631 }
 632
 633 TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets2)
 634 {
 635     // Evaluating the positions will require atoms 1-9.
 636     ASSERT_NO_THROW_GMX(sc_.parseFromString("whole_res_com of atomnr 2 5 7"));
 637     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 638     ASSERT_NO_THROW_GMX(sc_.compile());
 639     frame_->natoms = 8;
 640     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 641 }
 642
 643 TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets3)
 644 {
 645     ASSERT_NO_THROW_GMX(sc_.parseFromString("mindistance from atomnr 1 to 5 < 2"));
 646     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 647     ASSERT_NO_THROW_GMX(sc_.compile());
 648     frame_->natoms = 10;
 649     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 650 }
 651
 652 // TODO: Tests for more evaluation errors
 653
 654 /********************************************************************
 655  * Tests for interactive selection input
 656  */
 657
 658 TEST_F(SelectionCollectionInteractiveTest, HandlesBasicInput)
 659 {
 660     const char *const input[] = {
 661         "foo = resname RA",
 662         "resname RB",
 663         "\"Name\" resname RC"
 664     };
 665     runTest(-1, true, input);
 666 }
 667
 668 TEST_F(SelectionCollectionInteractiveTest, HandlesContinuation)
 669 {
 670     const char *const input[] = {
 671         "resname RB and \\",
 672         "resname RC"
 673     };
 674     runTest(-1, true, input);
 675 }
 676
 677 TEST_F(SelectionCollectionInteractiveTest, HandlesSingleSelectionInput)
 678 {
 679     const char *const input[] = {
 680         "foo = resname RA",
 681         "resname RA"
 682     };
 683     runTest(1, true, input);
 684 }
 685
 686 TEST_F(SelectionCollectionInteractiveTest, HandlesTwoSelectionInput)
 687 {
 688     const char *const input[] = {
 689         "resname RA",
 690         "resname RB"
 691     };
 692     runTest(2, true, input);
 693 }
 694
 695 TEST_F(SelectionCollectionInteractiveTest, HandlesStatusWithGroups)
 696 {
 697     const char *const input[] = {
 698         "resname RA",
 699         ""
 700     };
 701     loadIndexGroups("simple.ndx");
 702     runTest(-1, true, input);
 703 }
 704
 705 TEST_F(SelectionCollectionInteractiveTest, HandlesStatusWithExistingSelections)
 706 {
 707     const char *const input[] = {
 708         "",
 709         "bar = resname RC",
 710         "resname RA",
 711         ""
 712     };
 713     ASSERT_NO_THROW_GMX(sc_.parseFromString("foo = resname RA"));
 714     ASSERT_NO_THROW_GMX(sc_.parseFromString("resname RB"));
 715     runTest(-1, true, input);
 716 }
 717
 718 TEST_F(SelectionCollectionInteractiveTest, HandlesSingleSelectionInputStatus)
 719 {
 720     const char *const input[] = {
 721         "foo = resname RA",
 722         "",
 723         "resname RB"
 724     };
 725     runTest(1, true, input);
 726 }
 727
 728 TEST_F(SelectionCollectionInteractiveTest, HandlesTwoSelectionInputStatus)
 729 {
 730     const char *const input[] = {
 731         "\"Sel\" resname RA",
 732         "",
 733         "resname RB"
 734     };
 735     runTest(2, true, input);
 736 }
 737
 738 TEST_F(SelectionCollectionInteractiveTest, HandlesMultiSelectionInputStatus)
 739 {
 740     const char *const input[] = {
 741         "\"Sel\" resname RA",
 742         "\"Sel2\" resname RB",
 743         ""
 744     };
 745     runTest(-1, true, input);
 746 }
 747
 748 TEST_F(SelectionCollectionInteractiveTest, HandlesNoFinalNewline)
 749 {
 750     // TODO: There is an extra prompt printed after the input is finished; it
 751     // would be cleaner not to have it, but it's only a cosmetic issue.
 752     const char *const input[] = {
 753         "resname RA"
 754     };
 755     helper_.setLastNewline(false);
 756     runTest(-1, true, input);
 757 }
 758
 759 TEST_F(SelectionCollectionInteractiveTest, HandlesEmptySelections)
 760 {
 761     const char *const input[] = {
 762         "resname RA;",
 763         "; resname RB;;",
 764         " ",
 765         ";"
 766     };
 767     runTest(-1, true, input);
 768 }
 769
 770 TEST_F(SelectionCollectionInteractiveTest, HandlesMultipleSelectionsOnLine)
 771 {
 772     const char *const input[] = {
 773         "resname RA; resname RB and \\",
 774         "resname RC"
 775     };
 776     runTest(2, true, input);
 777 }
 778
 779 TEST_F(SelectionCollectionInteractiveTest, HandlesNoninteractiveInput)
 780 {
 781     const char *const input[] = {
 782         "foo = resname RA",
 783         "resname RB",
 784         "\"Name\" resname RC"
 785     };
 786     runTest(-1, false, input);
 787 }
 788
 789 TEST_F(SelectionCollectionInteractiveTest, HandlesSingleSelectionInputNoninteractively)
 790 {
 791     const char *const input[] = {
 792         "foo = resname RA",
 793         "resname RA"
 794     };
 795     runTest(1, false, input);
 796 }
 797
 798
 799 /********************************************************************
 800  * Tests for selection keywords
 801  */
 802
 803 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 804 {
 805     static const char * const selections[] = {
 806         "all",
 807         "none"
 808     };
 809     runTest(10, selections);
 810 }
 811
 812 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 813 {
 814     static const char * const selections[] = {
 815         "atomnr 1 to 3 6 to 8",
 816         "atomnr 4 2 5 to 7",
 817         "atomnr <= 5"
 818     };
 819     runTest(10, selections);
 820 }
 821
 822 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 823 {
 824     static const char * const selections[] = {
 825         "resnr 1 2 5",
 826         "resid 4 to 3"
 827     };
 828     runTest("simple.gro", selections);
 829 }
 830
 831 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 832 {
 833     static const char * const selections[] = {
 834         "resindex 1 4",
 835         "residue 1 3"
 836     };
 837     runTest("simple.pdb", selections);
 838 }
 839
 840 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 841 {
 842     static const char * const selections[] = {
 843         "molindex 1 4",
 844         "molecule 2 3 5"
 845     };
 846     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 847     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 848     topManager_.initUniformMolecules(3);
 849     ASSERT_NO_FATAL_FAILURE(runCompiler());
 850 }
 851
 852 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 853 {
 854     static const char * const selections[] = {
 855         "name CB",
 856         "atomname S1 S2"
 857     };
 858     runTest("simple.gro", selections);
 859 }
 860
 861 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 862 {
 863     static const char * const selections[] = {
 864         "name HG21",
 865         "name 1HG2",
 866         "pdbname HG21 CB",
 867         "pdbatomname 1HG2"
 868     };
 869     runTest("simple.pdb", selections);
 870 }
 871
 872
 873 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 874 {
 875     static const char * const selections[] = {
 876         "atomtype CA"
 877     };
 878     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 879     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 880     const char *const types[] = { "CA", "SA", "SB" };
 881     topManager_.initAtomTypes(types);
 882     ASSERT_NO_FATAL_FAILURE(runCompiler());
 883 }
 884
 885 TEST_F(SelectionCollectionDataTest, HandlesChain)
 886 {
 887     static const char * const selections[] = {
 888         "chain A",
 889         "chain B"
 890     };
 891     runTest("simple.pdb", selections);
 892 }
 893
 894 TEST_F(SelectionCollectionDataTest, HandlesMass)
 895 {
 896     static const char * const selections[] = {
 897         "mass > 5"
 898     };
 899     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 900     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 901     for (int i = 0; i < top_->atoms.nr; ++i)
 902     {
 903         top_->atoms.atom[i].m = 1.0 + i;
 904     }
 905     ASSERT_NO_FATAL_FAILURE(runCompiler());
 906 }
 907
 908 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 909 {
 910     static const char * const selections[] = {
 911         "charge < 0.5"
 912     };
 913     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 914     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 915     for (int i = 0; i < top_->atoms.nr; ++i)
 916     {
 917         top_->atoms.atom[i].q = i / 10.0;
 918     }
 919     ASSERT_NO_FATAL_FAILURE(runCompiler());
 920 }
 921
 922 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 923 {
 924     static const char * const selections[] = {
 925         "altloc \" \"",
 926         "altloc A"
 927     };
 928     runTest("simple.pdb", selections);
 929 }
 930
 931 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 932 {
 933     static const char * const selections[] = {
 934         "insertcode \" \"",
 935         "insertcode A"
 936     };
 937     runTest("simple.pdb", selections);
 938 }
 939
 940 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 941 {
 942     static const char * const selections[] = {
 943         "occupancy 1",
 944         "occupancy < .5"
 945     };
 946     runTest("simple.pdb", selections);
 947 }
 948
 949 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 950 {
 951     static const char * const selections[] = {
 952         "beta 0",
 953         "beta >= 0.3"
 954     };
 955     runTest("simple.pdb", selections);
 956 }
 957
 958 TEST_F(SelectionCollectionDataTest, HandlesResname)
 959 {
 960     static const char * const selections[] = {
 961         "resname RA",
 962         "resname RB RC"
 963     };
 964     runTest("simple.gro", selections);
 965 }
 966
 967 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 968 {
 969     static const char * const selections[] = {
 970         "x < 3",
 971         "y >= 3",
 972         "x {-1 to 2}"
 973     };
 974     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 975     runTest("simple.gro", selections);
 976 }
 977
 978
 979 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 980 {
 981     static const char * const selections[] = {
 982         "same residue as atomnr 1 4 12"
 983     };
 984     runTest("simple.gro", selections);
 985 }
 986
 987
 988 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 989 {
 990     static const char * const selections[] = {
 991         "same resname as atomnr 1 14"
 992     };
 993     runTest("simple.gro", selections);
 994 }
 995
 996
 997 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 998 {
 999     static const char * const selections[] = {
1000         "cog of resnr 1 3",
1001         "res_cog of name CB and resnr 1 3",
1002         "whole_res_cog of name CB and resnr 1 3",
1003         "part_res_cog of x < 3",
1004         "dyn_res_cog of x < 3"
1005     };
1006     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1007              | efTestPositionAtoms);
1008     runTest("simple.gro", selections);
1009 }
1010
1011
1012 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
1013 {
1014     static const char * const selections[] = {
1015         "distance from cog of resnr 1 < 2"
1016     };
1017     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1018     runTest("simple.gro", selections);
1019 }
1020
1021
1022 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
1023 {
1024     static const char * const selections[] = {
1025         "mindistance from resnr 1 < 2"
1026     };
1027     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1028     runTest("simple.gro", selections);
1029 }
1030
1031
1032 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
1033 {
1034     static const char * const selections[] = {
1035         "within 1 of resnr 2"
1036     };
1037     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1038     runTest("simple.gro", selections);
1039 }
1040
1041
1042 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
1043 {
1044     // Both of these should evaluate to empty on a correct implementation.
1045     static const char * const selections[] = {
1046         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
1047         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
1048     };
1049     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
1050     runTest("sphere.gro", selections);
1051 }
1052
1053
1054 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
1055 {
1056     static const char * const selections[] = {
1057         "all permute 3 1 2",
1058         "res_cog of resnr 1 to 4 permute 2 1",
1059         "name CB S1 and res_cog x < 3 permute 2 1"
1060     };
1061     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1062              | efTestPositionAtoms | efTestPositionMapping);
1063     runTest("simple.gro", selections);
1064 }
1065
1066
1067 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
1068 {
1069     static const char * const selections[] = {
1070         "name S2 plus name S1",
1071         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
1072         "name S1 and y < 3 plus res_cog of x < 2.5"
1073     };
1074     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1075              | efTestPositionAtoms | efTestPositionMapping);
1076     runTest("simple.gro", selections);
1077 }
1078
1079
1080 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
1081 {
1082     static const char * const selections[] = {
1083         "name S2 merge name S1",
1084         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
1085         "name S1 and x < 2.5 merge res_cog of x < 2.5"
1086     };
1087     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1088              | efTestPositionAtoms | efTestPositionMapping);
1089     runTest("simple.gro", selections);
1090 }
1091
1092
1093 /********************************************************************
1094  * Tests for generic selection evaluation
1095  */
1096
1097 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
1098 {
1099     static const char * const selections[] = {
1100         "name CB",
1101         "y > 2",
1102         "res_cog of y > 2"
1103     };
1104     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
1105              | efTestPositionMasses | efTestPositionCharges);
1106     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1107     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1108     for (int i = 0; i < top_->atoms.nr; ++i)
1109     {
1110         top_->atoms.atom[i].m =   1.0 + i / 100.0;
1111         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
1112     }
1113     ASSERT_NO_FATAL_FAILURE(runCompiler());
1114     ASSERT_NO_FATAL_FAILURE(runEvaluate());
1115     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
1116 }
1117
1118 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
1119 {
1120     static const char * const selections[] = {
1121         "atomnr 1 to 3 8 to 9",
1122         "y > 2",
1123         "cog of (y > 2)"
1124     };
1125     setFlags(TestFlags() | efTestPositionAtoms
1126              | efTestPositionMasses | efTestPositionCharges);
1127     runTest(10, selections);
1128 }
1129
1130
1131 /********************************************************************
1132  * Tests for selection syntactic constructs
1133  */
1134
1135 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
1136 {
1137     static const char * const selections[] = {
1138         "\"GroupSelection\" group \"GrpA\"",
1139         "\"DynamicSelection\" x < 5",
1140         "y < 3"
1141     };
1142     setFlags(TestFlags() | efTestSelectionNames);
1143     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1144     runTest(10, selections);
1145 }
1146
1147 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
1148 {
1149     static const char * const selections[] = {
1150         "group \"GrpA\"",
1151         "GrpB",
1152         "1",
1153         // These test that the name of the group is not too eagerly promoted to
1154         // the name of the selection.
1155         "group \"GrpB\" and resname RB",
1156         "group \"GrpA\" permute 5 3 2 1 4",
1157         "group \"GrpA\" plus group \"GrpB\"",
1158         "res_cog of group \"GrpA\""
1159     };
1160     setFlags(TestFlags() | efTestSelectionNames);
1161     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1162     runTest("simple.gro", selections);
1163 }
1164
1165 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
1166 {
1167     static const char * const selections[] = {
1168         "group \"GrpA\"",
1169         "GrpB",
1170         "1",
1171         "group \"GrpB\" and resname RB"
1172     };
1173     setFlags(TestFlags() | efTestSelectionNames);
1174     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1175     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1176     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1177     ASSERT_NO_FATAL_FAILURE(runCompiler());
1178 }
1179
1180 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
1181 {
1182     static const char * const selections[] = {
1183         "foo = group \"GrpUnsorted\"",
1184         "group \"GrpUnsorted\"",
1185         "GrpUnsorted",
1186         "2",
1187         "res_cog of group \"GrpUnsorted\"",
1188         "group \"GrpUnsorted\" permute 2 1",
1189         "foo"
1190     };
1191     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
1192              | efTestSelectionNames);
1193     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1194     runTest("simple.gro", selections);
1195 }
1196
1197 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelectionsDelayed)
1198 {
1199     static const char * const selections[] = {
1200         "foo = group \"GrpUnsorted\"",
1201         "group \"GrpUnsorted\"",
1202         "GrpUnsorted",
1203         "2",
1204         "res_cog of group \"GrpUnsorted\"",
1205         "group \"GrpUnsorted\" permute 2 1",
1206         "foo"
1207     };
1208     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1209     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1210     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1211     ASSERT_NO_FATAL_FAILURE(runCompiler());
1212 }
1213
1214
1215 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
1216 {
1217     static const char * const selections[] = {
1218         "[1, -2, 3.5]"
1219     };
1220     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1221              | efTestPositionMapping);
1222     runTest("simple.gro", selections);
1223 }
1224
1225
1226 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionsWithModifiers)
1227 {
1228     static const char * const selections[] = {
1229         "[0, 0, 0] plus [0, 1, 0]"
1230     };
1231     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1232              | efTestPositionMapping);
1233     runTest("simple.gro", selections);
1234 }
1235
1236
1237 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
1238 {
1239     static const char * const selections[] = {
1240         "within 1 of [2, 1, 0]"
1241     };
1242     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1243     runTest("simple.gro", selections);
1244 }
1245
1246
1247 TEST_F(SelectionCollectionDataTest, HandlesOverlappingIntegerRanges)
1248 {
1249     static const char * const selections[] = {
1250         "atomnr 2 to 4 5 to 8",
1251         "atomnr 2 to 5 4 to 7"
1252     };
1253     ASSERT_NO_FATAL_FAILURE(runTest(10, selections));
1254 }
1255
1256
1257 TEST_F(SelectionCollectionDataTest, HandlesOverlappingRealRanges)
1258 {
1259     static const char * const selections[] = {
1260         "charge {-0.35 to -0.05 0.25 to 0.75}",
1261         "charge {0.05 to -0.3 -0.05 to 0.55}"
1262     };
1263     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1264     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1265     for (int i = 0; i < top_->atoms.nr; ++i)
1266     {
1267         top_->atoms.atom[i].q = i / 10.0 - 0.5;
1268     }
1269     ASSERT_NO_FATAL_FAILURE(runCompiler());
1270 }
1271
1272
1273 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
1274 {
1275     static const char * const selections[] = {
1276         "name = S1 \"C?\"",
1277         "name ? S1 \"C?\""
1278     };
1279     runTest("simple.gro", selections);
1280 }
1281
1282
1283 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
1284 {
1285     static const char * const selections[] = {
1286         "name \"S?\"",
1287         "name ? \"S?\""
1288     };
1289     runTest("simple.gro", selections);
1290 }
1291
1292
1293 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
1294 {
1295     static const char * const selections[] = {
1296         "resname \"R[BD]\"",
1297         "resname ~ \"R[BD]\""
1298     };
1299     if (gmx::Regex::isSupported())
1300     {
1301         runTest("simple.gro", selections);
1302     }
1303 }
1304
1305
1306 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
1307 {
1308     static const char * const selections[] = {
1309         "atomnr 1 to 5 and atomnr 2 to 7",
1310         "atomnr 1 to 5 or not atomnr 3 to 8",
1311         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1312         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1313         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1314     };
1315     runTest(10, selections);
1316 }
1317
1318
1319 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1320 {
1321     static const char * const selections[] = {
1322         "same residue as (atomnr 3 5 13 or y > 5)",
1323         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1324     };
1325     setFlags(TestFlags() | efTestEvaluation);
1326     runTest("simple.gro", selections);
1327 }
1328
1329
1330 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1331 {
1332     static const char * const selections[] = {
1333         "none and x > 2",
1334         "none and same resname as resnr 2"
1335     };
1336     runTest("simple.gro", selections);
1337 }
1338
1339
1340 TEST_F(SelectionCollectionDataTest, HandlesEmptyReferenceForSame)
1341 {
1342     static const char * const selections[] = {
1343         "same residue as none",
1344         "same resname as none"
1345     };
1346     runTest("simple.gro", selections);
1347 }
1348
1349
1350 TEST_F(SelectionCollectionDataTest, HandlesPositionModifiersForKeywords)
1351 {
1352     static const char * const selections[] = {
1353         "res_cog x > 2",
1354         "name CB and res_cog y > 2.5"
1355     };
1356     setFlags(TestFlags() | efTestEvaluation);
1357     runTest("simple.gro", selections);
1358 }
1359
1360
1361 TEST_F(SelectionCollectionDataTest, HandlesPositionModifiersForMethods)
1362 {
1363     static const char * const selections[] = {
1364         "res_cog distance from cog of resnr 1 < 2",
1365         "res_cog within 2 of cog of resnr 1"
1366     };
1367     setFlags(TestFlags() | efTestEvaluation);
1368     runTest("simple.gro", selections);
1369 }
1370
1371
1372 TEST_F(SelectionCollectionDataTest, HandlesKeywordOfPositions)
1373 {
1374     static const char * const selections[] = {
1375         "x < y of cog of resnr 2"
1376     };
1377     setFlags(TestFlags() | efTestEvaluation);
1378     runTest("simple.gro", selections);
1379 }
1380
1381 TEST_F(SelectionCollectionDataTest, HandlesKeywordOfPositionsInArithmetic)
1382 {
1383     static const char * const selections[] = {
1384         "x - y of cog of resnr 2 < 0"
1385     };
1386     setFlags(TestFlags() | efTestEvaluation);
1387     runTest("simple.gro", selections);
1388 }
1389
1390
1391 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1392 {
1393     static const char * const selections[] = {
1394         "x > 2",
1395         "2 < x",
1396         "y > resnr",
1397         "resnr < 2.5",
1398         "2.5 > resnr"
1399     };
1400     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1401     runTest("simple.gro", selections);
1402 }
1403
1404
1405 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1406 {
1407     static const char * const selections[] = {
1408         "x+1 > 3",
1409         "(y-1)^2 <= 1",
1410         "x+--1 > 3",
1411         "-x+-1 < -3"
1412     };
1413     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1414     runTest("simple.gro", selections);
1415 }
1416
1417
1418 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1419 {
1420     static const char * const selections[] = {
1421         "value = x + y",
1422         "value <= 4",
1423         "index = resnr",
1424         "index < 3"
1425     };
1426     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1427     runTest("simple.gro", selections);
1428 }
1429
1430
1431 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1432 {
1433     static const char * const selections[] = {
1434         "value = x + y",
1435         "resname RA and value <= 4",
1436         "resname RA RB and x < 3 and value <= 4",
1437         "index = atomnr",
1438         "resname RA and index < 3",
1439         "resname RB and y < 3 and index < 6"
1440     };
1441     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1442     runTest("simple.gro", selections);
1443 }
1444
1445
1446 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1447 {
1448     static const char * const selections[] = {
1449         "foo = res_cog of resname RA",
1450         "foo",
1451         "within 1 of foo",
1452         "bar = cog of resname RA",
1453         "bar",
1454         "within 1 of bar"
1455     };
1456     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1457     runTest("simple.gro", selections);
1458 }
1459
1460
1461 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1462 {
1463     static const char * const selections[] = {
1464         "constpos = [1.0, 2.5, 0.5]",
1465         "constpos",
1466         "within 2 of constpos"
1467     };
1468     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1469              | efTestPositionAtoms);
1470     runTest("simple.gro", selections);
1471 }
1472
1473
1474 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1475 {
1476     static const char * const selections[] = {
1477         "constint = 4",
1478         "constreal1 = 0.5",
1479         "constreal2 = 2.7",
1480         "resnr < constint",
1481         "x + constreal1 < constreal2"
1482     };
1483     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1484     runTest("simple.gro", selections);
1485 }
1486
1487
1488 /********************************************************************
1489  * Tests for complex boolean syntax
1490  */
1491
1492 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1493 {
1494     static const char * const selections[] = {
1495         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1496         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1497         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1498         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1499         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1500     };
1501     runTest(10, selections);
1502 }
1503
1504
1505 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1506 {
1507     static const char * const selections[] = {
1508         "foo = atomnr 4 to 7 or x < 2",
1509         "atomnr 1 to 4 and foo",
1510         "atomnr 2 to 6 and y < 3 and foo",
1511         "atomnr 6 to 10 and not foo"
1512     };
1513     runTest(10, selections);
1514 }
1515
1516
1517 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1518 {
1519     static const char * const selections[] = {
1520         "foo = atomnr 4 to 7",
1521         "bar = foo and x < 2",
1522         "bar2 = foo and y < 2",
1523         "atomnr 1 to 4 and bar",
1524         "atomnr 2 to 6 and y < 3 and bar2",
1525         "atomnr 6 to 10 and not foo"
1526     };
1527     runTest(10, selections);
1528 }
1529
1530
1531 /********************************************************************
1532  * Tests for complex subexpression cases
1533  *
1534  * These tests use some knowledge of the implementation to trigger different
1535  * paths in the code.
1536  */
1537
1538 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1539 {
1540     static const char * const selections[] = {
1541         "unused1 = atomnr 1 to 3",
1542         "foo = atomnr 4 to 7",
1543         "atomnr 1 to 6 and foo",
1544         "unused2 = atomnr 3 to 5"
1545     };
1546     runTest(10, selections);
1547 }
1548
1549
1550 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1551 {
1552     static const char * const selections[] = {
1553         "foo = atomnr 4 to 7 and x < 2",
1554         "atomnr 1 to 5 and foo",
1555         "atomnr 3 to 7 and foo"
1556     };
1557     runTest(10, selections);
1558 }
1559
1560
1561 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1562 {
1563     static const char * const selections[] = {
1564         "foo = atomnr 4 to 7 and x < 2",
1565         "atomnr 1 to 6 and foo",
1566         "within 1 of foo",
1567         "foo"
1568     };
1569     runTest(10, selections);
1570 }
1571
1572
1573 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1574 {
1575     static const char * const selections[] = {
1576         "foo = atomnr 1 to 8 and x < 10",
1577         "atomnr 1 to 5 and y < 10 and foo",
1578         "foo"
1579     };
1580     setFlags(TestFlags() | efTestEvaluation);
1581     runTest("simple.gro", selections);
1582 }
1583
1584
1585 } // namespace