src/gromacs/selection/tests/selectioncollection.cpp

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  31 /*! \internal \file
  32  * \brief
  33  * Tests selection parsing and compilation.
  34  *
  35  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  36  * \ingroup module_selection
  37  */
  38 #include <gtest/gtest.h>
  39
  40 #include "gromacs/legacyheaders/smalloc.h"
  41 #include "gromacs/legacyheaders/statutil.h"
  42 #include "gromacs/legacyheaders/tpxio.h"
  43 #include "gromacs/legacyheaders/vec.h"
  44
  45 #include "gromacs/options/basicoptions.h"
  46 #include "gromacs/options/options.h"
  47 #include "gromacs/selection/selectioncollection.h"
  48 #include "gromacs/selection/selection.h"
  49 #include "gromacs/utility/exceptions.h"
  50 #include "gromacs/utility/flags.h"
  51 #include "gromacs/utility/gmxregex.h"
  52 #include "gromacs/utility/stringutil.h"
  53
  54 #include "testutils/refdata.h"
  55 #include "testutils/testfilemanager.h"
  56 #include "testutils/testoptions.h"
  57
  58 namespace
  59 {
  60
  61 /********************************************************************
  62  * Test fixture for selection testing
  63  */
  64
  65 class SelectionCollectionTest : public ::testing::Test
  66 {
  67     public:
  68         static void SetUpTestCase();
  69
  70         static int               s_debugLevel;
  71
  72         SelectionCollectionTest();
  73         ~SelectionCollectionTest();
  74
  75         void setAtomCount(int natoms)
  76         {
  77             ASSERT_NO_THROW(sc_.setTopology(NULL, natoms));
  78         }
  79         void loadTopology(const char *filename);
  80
  81         gmx::SelectionCollection sc_;
  82         gmx::SelectionList       sel_;
  83         t_topology              *top_;
  84         t_trxframe              *frame_;
  85 };
  86
  87 int SelectionCollectionTest::s_debugLevel = 0;
  88
  89 void SelectionCollectionTest::SetUpTestCase()
  90 {
  91     gmx::Options options(NULL, NULL);
  92     options.addOption(gmx::IntegerOption("seldebug").store(&s_debugLevel));
  93     gmx::test::parseTestOptions(&options);
  94 }
  95
  96
  97 SelectionCollectionTest::SelectionCollectionTest()
  98     : top_(NULL), frame_(NULL)
  99 {
 100     sc_.setDebugLevel(s_debugLevel);
 101     sc_.setReferencePosType("atom");
 102     sc_.setOutputPosType("atom");
 103 }
 104
 105
 106 SelectionCollectionTest::~SelectionCollectionTest()
 107 {
 108     if (top_ != NULL)
 109     {
 110         free_t_atoms(&top_->atoms, TRUE);
 111         done_top(top_);
 112         sfree(top_);
 113     }
 114
 115     if (frame_ != NULL)
 116     {
 117         sfree(frame_->x);
 118         sfree(frame_);
 119     }
 120 }
 121
 122
 123 void
 124 SelectionCollectionTest::loadTopology(const char *filename)
 125 {
 126     char    title[STRLEN];
 127     int     ePBC;
 128     rvec   *xtop;
 129     matrix  box;
 130
 131     snew(top_, 1);
 132     read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
 133                   title, top_, &ePBC, &xtop, NULL, box, FALSE);
 134
 135     snew(frame_, 1);
 136     frame_->flags  = TRX_NEED_X;
 137     frame_->natoms = top_->atoms.nr;
 138     frame_->bX     = TRUE;
 139     snew(frame_->x, frame_->natoms);
 140     memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
 141     frame_->bBox   = TRUE;
 142     copy_mat(box, frame_->box);
 143
 144     sfree(xtop);
 145
 146     ASSERT_NO_THROW(sc_.setTopology(top_, -1));
 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             efDontTestCompiledAtoms     = 1<<8
 166         };
 167         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 168
 169         SelectionCollectionDataTest()
 170             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 171         {
 172         }
 173
 174         void setFlags(TestFlags flags) { flags_ = flags; }
 175
 176         template <size_t count>
 177         void runTest(int natoms, const char *const (&selections)[count])
 178         {
 179             runTest(natoms, selections, count);
 180         }
 181         template <size_t count>
 182         void runTest(const char *filename, const char *const (&selections)[count])
 183         {
 184             runTest(filename, selections, count);
 185         }
 186
 187         template <size_t count>
 188         void runParser(const char *const (&selections)[count])
 189         {
 190             runParser(selections, count);
 191         }
 192
 193         void runCompiler();
 194         void runEvaluate();
 195         void runEvaluateFinal();
 196
 197     private:
 198         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 199                                    const gmx::Selection &sel, TestFlags flags);
 200
 201         void runTest(int natoms, const char *const *selections, size_t count);
 202         void runTest(const char *filename, const char *const *selections,
 203                      size_t count);
 204         void runParser(const char *const *selections, size_t count);
 205
 206         void checkCompiled();
 207
 208         gmx::test::TestReferenceData    data_;
 209         gmx::test::TestReferenceChecker checker_;
 210         size_t                          count_;
 211         int                             framenr_;
 212         TestFlags                       flags_;
 213 };
 214
 215
 216 void
 217 SelectionCollectionDataTest::checkSelection(
 218         gmx::test::TestReferenceChecker *checker,
 219         const gmx::Selection &sel, TestFlags flags)
 220 {
 221     using gmx::test::TestReferenceChecker;
 222
 223     {
 224         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 225         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 226     }
 227     if (flags.test(efTestPositionAtoms)
 228         || flags.test(efTestPositionCoordinates)
 229         || flags.test(efTestPositionMapping)
 230         || flags.test(efTestPositionMasses)
 231         || flags.test(efTestPositionCharges))
 232     {
 233         TestReferenceChecker compound(
 234                 checker->checkSequenceCompound("Positions", sel.posCount()));
 235         for (int i = 0; i < sel.posCount(); ++i)
 236         {
 237             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 238             const gmx::SelectionPosition &p = sel.position(i);
 239             if (flags.test(efTestPositionAtoms))
 240             {
 241                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 242                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 243             }
 244             if (flags.test(efTestPositionCoordinates))
 245             {
 246                 poscompound.checkVector(p.x(), "Coordinates");
 247             }
 248             if (flags.test(efTestPositionMapping))
 249             {
 250                 poscompound.checkInteger(p.refId(), "RefId");
 251                 poscompound.checkInteger(p.mappedId(), "MappedId");
 252             }
 253             if (flags.test(efTestPositionMasses))
 254             {
 255                 poscompound.checkReal(p.mass(), "Mass");
 256             }
 257             if (flags.test(efTestPositionCharges))
 258             {
 259                 poscompound.checkReal(p.charge(), "Charge");
 260             }
 261         }
 262     }
 263 }
 264
 265
 266 void
 267 SelectionCollectionDataTest::runParser(const char *const *selections,
 268                                        size_t             count)
 269 {
 270     using gmx::test::TestReferenceChecker;
 271
 272     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 273     size_t               varcount = 0;
 274     count_ = 0;
 275     for (size_t i = 0; i < count; ++i)
 276     {
 277         SCOPED_TRACE(std::string("Parsing selection \"")
 278                      + selections[i] + "\"");
 279         gmx::SelectionList result;
 280         ASSERT_NO_THROW(result = sc_.parseFromString(selections[i]));
 281         sel_.insert(sel_.end(), result.begin(), result.end());
 282         if (sel_.size() == count_)
 283         {
 284             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 285             TestReferenceChecker varcompound(
 286                     compound.checkCompound("ParsedVariable", id.c_str()));
 287             varcompound.checkString(selections[i], "Input");
 288             ++varcount;
 289         }
 290         else
 291         {
 292             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 293             TestReferenceChecker selcompound(
 294                     compound.checkCompound("ParsedSelection", id.c_str()));
 295             selcompound.checkString(selections[i], "Input");
 296             selcompound.checkString(sel_[count_].name(), "Name");
 297             selcompound.checkString(sel_[count_].selectionText(), "Text");
 298             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 299             ++count_;
 300         }
 301     }
 302 }
 303
 304
 305 void
 306 SelectionCollectionDataTest::runCompiler()
 307 {
 308     ASSERT_NO_THROW(sc_.compile());
 309     ASSERT_EQ(count_, sel_.size());
 310     checkCompiled();
 311 }
 312
 313
 314 void
 315 SelectionCollectionDataTest::checkCompiled()
 316 {
 317     using gmx::test::TestReferenceChecker;
 318     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 319
 320     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 321     for (size_t i = 0; i < count_; ++i)
 322     {
 323         SCOPED_TRACE(std::string("Checking selection \"") +
 324                      sel_[i].selectionText() + "\"");
 325         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 326         TestReferenceChecker selcompound(
 327                 compound.checkCompound("Selection", id.c_str()));
 328         if (!flags_.test(efDontTestCompiledAtoms))
 329         {
 330             checkSelection(&selcompound, sel_[i], flags_ & mask);
 331         }
 332     }
 333 }
 334
 335
 336 void
 337 SelectionCollectionDataTest::runEvaluate()
 338 {
 339     using gmx::test::TestReferenceChecker;
 340
 341     ++framenr_;
 342     ASSERT_NO_THROW(sc_.evaluate(frame_, NULL));
 343     std::string          frame = gmx::formatString("Frame%d", framenr_);
 344     TestReferenceChecker compound(
 345             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 346     for (size_t i = 0; i < count_; ++i)
 347     {
 348         SCOPED_TRACE(std::string("Checking selection \"") +
 349                      sel_[i].selectionText() + "\"");
 350         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 351         TestReferenceChecker selcompound(
 352                 compound.checkCompound("Selection", id.c_str()));
 353         checkSelection(&selcompound, sel_[i], flags_);
 354     }
 355 }
 356
 357
 358 void
 359 SelectionCollectionDataTest::runEvaluateFinal()
 360 {
 361     ASSERT_NO_THROW(sc_.evaluateFinal(framenr_));
 362     if (!checker_.isWriteMode())
 363     {
 364         checkCompiled();
 365     }
 366 }
 367
 368
 369 void
 370 SelectionCollectionDataTest::runTest(int natoms, const char * const *selections,
 371                                      size_t count)
 372 {
 373     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 374     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 375     ASSERT_NO_FATAL_FAILURE(runCompiler());
 376 }
 377
 378
 379 void
 380 SelectionCollectionDataTest::runTest(const char         *filename,
 381                                      const char * const *selections,
 382                                      size_t              count)
 383 {
 384     ASSERT_NO_FATAL_FAILURE(runParser(selections, count));
 385     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 386     ASSERT_NO_FATAL_FAILURE(runCompiler());
 387     if (flags_.test(efTestEvaluation))
 388     {
 389         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 390         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 391     }
 392 }
 393
 394
 395 /********************************************************************
 396  * Tests for SelectionCollection functionality without reference data
 397  */
 398
 399 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 400 {
 401     EXPECT_FALSE(sc_.requiresTopology());
 402     EXPECT_NO_THROW(sc_.compile());
 403 }
 404
 405 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 406 {
 407     ASSERT_NO_THROW(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 408     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 409     ASSERT_EQ(2U, sel_.size());
 410     ASSERT_NO_THROW(sel_[0].setEvaluateVelocities(true));
 411     ASSERT_NO_THROW(sel_[1].setEvaluateVelocities(true));
 412     ASSERT_NO_THROW(sel_[0].setEvaluateForces(true));
 413     ASSERT_NO_THROW(sel_[1].setEvaluateForces(true));
 414     ASSERT_NO_THROW(sc_.compile());
 415     EXPECT_TRUE(sel_[0].hasVelocities());
 416     EXPECT_TRUE(sel_[1].hasVelocities());
 417     EXPECT_TRUE(sel_[0].hasForces());
 418     EXPECT_TRUE(sel_[1].hasForces());
 419 }
 420
 421 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 422 {
 423     ASSERT_NO_THROW(sel_ = sc_.parseFromFile(
 424                                 gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 425     // These should match the contents of selfile.dat
 426     ASSERT_EQ(2U, sel_.size());
 427     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 428     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 429 }
 430
 431 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 432 {
 433     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 434     EXPECT_THROW({
 435                      sc_.parseFromString("resname ~ \"R[A\"");
 436                      sc_.compile();
 437                  }, gmx::InvalidInputError);
 438 }
 439
 440 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 441 {
 442     if (!gmx::Regex::isSupported())
 443     {
 444         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 445         EXPECT_THROW({
 446                          sc_.parseFromString("resname \"R[AD]\"");
 447                          sc_.compile();
 448                      }, gmx::InvalidInputError);
 449     }
 450 }
 451
 452 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 453 {
 454     EXPECT_THROW(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 455                  gmx::InvalidInputError);
 456 }
 457
 458 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 459 {
 460     EXPECT_THROW(sc_.parseFromString("within 1 of"),
 461                  gmx::InvalidInputError);
 462 }
 463
 464 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 465 {
 466     EXPECT_THROW(sc_.parseFromString("within of atomnr 1"),
 467                  gmx::InvalidInputError);
 468 }
 469
 470 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 471 {
 472     EXPECT_THROW(sc_.parseFromString("resname help"),
 473                  gmx::InvalidInputError);
 474 }
 475
 476 // TODO: Tests for more parser errors
 477
 478 TEST_F(SelectionCollectionTest, RecoversFromUnknownGroupReference)
 479 {
 480     ASSERT_NO_THROW(sc_.parseFromString("group \"foo\""));
 481     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 482     EXPECT_THROW(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
 483     EXPECT_THROW(sc_.compile(), gmx::APIError);
 484 }
 485
 486 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 487 {
 488     ASSERT_NO_THROW(sc_.parseFromString("molindex 1 to 5"));
 489     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 490     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 491 }
 492
 493 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 494 {
 495     ASSERT_NO_THROW(sc_.parseFromString("type CA"));
 496     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 497     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 498 }
 499
 500 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 501 {
 502     ASSERT_NO_THROW(sc_.parseFromString("altloc A"));
 503     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 504     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 505 }
 506
 507 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 508 {
 509     ASSERT_NO_THROW(sc_.parseFromString("all permute 1 1"));
 510     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 511     EXPECT_THROW(sc_.compile(), gmx::InvalidInputError);
 512 }
 513
 514 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 515 {
 516     ASSERT_NO_THROW(sc_.parseFromString("all permute 3 2 1"));
 517     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 518     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 519 }
 520
 521 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 522 {
 523     ASSERT_NO_THROW(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 524     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 525     ASSERT_NO_THROW(sc_.compile());
 526     EXPECT_THROW(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 527 }
 528
 529 // TODO: Tests for evaluation errors
 530
 531
 532 /********************************************************************
 533  * Tests for selection keywords
 534  */
 535
 536 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 537 {
 538     static const char * const selections[] = {
 539         "all",
 540         "none"
 541     };
 542     runTest(10, selections);
 543 }
 544
 545 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 546 {
 547     static const char * const selections[] = {
 548         "atomnr 1 to 3 6 to 8",
 549         "atomnr 4 2 5 to 7",
 550         "atomnr <= 5"
 551     };
 552     runTest(10, selections);
 553 }
 554
 555 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 556 {
 557     static const char * const selections[] = {
 558         "resnr 1 2 5",
 559         "resid 4 to 3"
 560     };
 561     runTest("simple.gro", selections);
 562 }
 563
 564 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 565 {
 566     static const char * const selections[] = {
 567         "resindex 1 4",
 568         "residue 1 3"
 569     };
 570     runTest("simple.pdb", selections);
 571 }
 572
 573 // TODO: Add test for "molindex"
 574
 575 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 576 {
 577     static const char * const selections[] = {
 578         "name CB",
 579         "atomname S1 S2"
 580     };
 581     runTest("simple.gro", selections);
 582 }
 583
 584 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 585 {
 586     static const char * const selections[] = {
 587         "name HG21",
 588         "name 1HG2",
 589         "pdbname HG21 CB",
 590         "pdbatomname 1HG2"
 591     };
 592     runTest("simple.pdb", selections);
 593 }
 594
 595 // TODO: Add test for atomtype
 596
 597 TEST_F(SelectionCollectionDataTest, HandlesChain)
 598 {
 599     static const char * const selections[] = {
 600         "chain A",
 601         "chain B"
 602     };
 603     runTest("simple.pdb", selections);
 604 }
 605
 606 TEST_F(SelectionCollectionDataTest, HandlesMass)
 607 {
 608     static const char * const selections[] = {
 609         "mass > 5"
 610     };
 611     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 612     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 613     for (int i = 0; i < top_->atoms.nr; ++i)
 614     {
 615         top_->atoms.atom[i].m = 1.0 + i;
 616     }
 617     ASSERT_NO_FATAL_FAILURE(runCompiler());
 618 }
 619
 620 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 621 {
 622     static const char * const selections[] = {
 623         "charge < 0.5"
 624     };
 625     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 626     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 627     for (int i = 0; i < top_->atoms.nr; ++i)
 628     {
 629         top_->atoms.atom[i].q = i / 10.0;
 630     }
 631     ASSERT_NO_FATAL_FAILURE(runCompiler());
 632 }
 633
 634 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 635 {
 636     static const char * const selections[] = {
 637         "altloc \" \"",
 638         "altloc A"
 639     };
 640     runTest("simple.pdb", selections);
 641 }
 642
 643 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 644 {
 645     static const char * const selections[] = {
 646         "insertcode \" \"",
 647         "insertcode A"
 648     };
 649     runTest("simple.pdb", selections);
 650 }
 651
 652 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 653 {
 654     static const char * const selections[] = {
 655         "occupancy 1",
 656         "occupancy < .5"
 657     };
 658     runTest("simple.pdb", selections);
 659 }
 660
 661 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 662 {
 663     static const char * const selections[] = {
 664         "beta 0",
 665         "beta >= 0.3"
 666     };
 667     runTest("simple.pdb", selections);
 668 }
 669
 670 TEST_F(SelectionCollectionDataTest, HandlesResname)
 671 {
 672     static const char * const selections[] = {
 673         "resname RA",
 674         "resname RB RC"
 675     };
 676     runTest("simple.gro", selections);
 677 }
 678
 679 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 680 {
 681     static const char * const selections[] = {
 682         "x < 3",
 683         "y >= 3",
 684         "x {-1 to 2}"
 685     };
 686     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 687     runTest("simple.gro", selections);
 688 }
 689
 690
 691 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 692 {
 693     static const char * const selections[] = {
 694         "same residue as atomnr 1 4 12"
 695     };
 696     runTest("simple.gro", selections);
 697 }
 698
 699
 700 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 701 {
 702     static const char * const selections[] = {
 703         "same resname as atomnr 1 14"
 704     };
 705     runTest("simple.gro", selections);
 706 }
 707
 708
 709 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 710 {
 711     static const char * const selections[] = {
 712         "cog of resnr 1 3",
 713         "res_cog of name CB and resnr 1 3",
 714         "whole_res_cog of name CB and resnr 1 3",
 715         "part_res_cog of x < 3",
 716         "dyn_res_cog of x < 3"
 717     };
 718     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 719              | efTestPositionAtoms);
 720     runTest("simple.gro", selections);
 721 }
 722
 723
 724 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 725 {
 726     static const char * const selections[] = {
 727         "distance from cog of resnr 1 < 2"
 728     };
 729     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 730     runTest("simple.gro", selections);
 731 }
 732
 733
 734 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 735 {
 736     static const char * const selections[] = {
 737         "mindistance from resnr 1 < 2"
 738     };
 739     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 740     runTest("simple.gro", selections);
 741 }
 742
 743
 744 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 745 {
 746     static const char * const selections[] = {
 747         "within 1 of resnr 2"
 748     };
 749     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 750     runTest("simple.gro", selections);
 751 }
 752
 753
 754 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 755 {
 756     // Both of these should evaluate to empty on a correct implementation.
 757     static const char * const selections[] = {
 758         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 759         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 760     };
 761     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 762     runTest("sphere.gro", selections);
 763 }
 764
 765
 766 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 767 {
 768     static const char * const selections[] = {
 769         "all permute 3 1 2",
 770         "res_cog of resnr 1 to 4 permute 2 1",
 771         "name CB S1 and res_cog x < 3 permute 2 1"
 772     };
 773     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 774              | efTestPositionAtoms | efTestPositionMapping);
 775     runTest("simple.gro", selections);
 776 }
 777
 778
 779 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 780 {
 781     static const char * const selections[] = {
 782         "name S2 plus name S1",
 783         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 784         "name S1 and y < 3 plus res_cog of x < 2.5"
 785     };
 786     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 787              | efTestPositionAtoms | efTestPositionMapping);
 788     runTest("simple.gro", selections);
 789 }
 790
 791
 792 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 793 {
 794     static const char * const selections[] = {
 795         "name S2 merge name S1",
 796         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 797         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 798     };
 799     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 800              | efTestPositionAtoms | efTestPositionMapping);
 801     runTest("simple.gro", selections);
 802 }
 803
 804
 805 /********************************************************************
 806  * Tests for generic selection evaluation
 807  */
 808
 809 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 810 {
 811     static const char * const selections[] = {
 812         "name CB",
 813         "y > 2",
 814         "res_cog of y > 2"
 815     };
 816     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 817              | efTestPositionMasses | efTestPositionCharges);
 818     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 819     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 820     for (int i = 0; i < top_->atoms.nr; ++i)
 821     {
 822         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 823         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 824     }
 825     ASSERT_NO_FATAL_FAILURE(runCompiler());
 826     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 827     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 828 }
 829
 830 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 831 {
 832     static const char * const selections[] = {
 833         "atomnr 1 to 3 8 to 9",
 834         "y > 2",
 835         "cog of (y > 2)"
 836     };
 837     setFlags(TestFlags() | efTestPositionAtoms
 838              | efTestPositionMasses | efTestPositionCharges);
 839     runTest(10, selections);
 840 }
 841
 842
 843 /********************************************************************
 844  * Tests for selection syntactic constructs
 845  */
 846
 847 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 848 {
 849     static const char * const selections[] = {
 850         "[1, -2, 3.5]"
 851     };
 852     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 853     runTest("simple.gro", selections);
 854 }
 855
 856
 857 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 858 {
 859     static const char * const selections[] = {
 860         "within 1 of [2, 1, 0]"
 861     };
 862     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 863     runTest("simple.gro", selections);
 864 }
 865
 866
 867 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 868 {
 869     static const char * const selections[] = {
 870         "name = S1 \"C?\"",
 871         "name ? S1 \"C?\""
 872     };
 873     runTest("simple.gro", selections);
 874 }
 875
 876
 877 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 878 {
 879     static const char * const selections[] = {
 880         "name \"S?\"",
 881         "name ? \"S?\""
 882     };
 883     runTest("simple.gro", selections);
 884 }
 885
 886
 887 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 888 {
 889     static const char * const selections[] = {
 890         "resname \"R[BD]\"",
 891         "resname ~ \"R[BD]\""
 892     };
 893     if (gmx::Regex::isSupported())
 894     {
 895         runTest("simple.gro", selections);
 896     }
 897 }
 898
 899
 900 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 901 {
 902     static const char * const selections[] = {
 903         "atomnr 1 to 5 and atomnr 2 to 7",
 904         "atomnr 1 to 5 or not atomnr 3 to 8",
 905         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 906         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 907         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 908     };
 909     runTest(10, selections);
 910 }
 911
 912
 913 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
 914 {
 915     static const char * const selections[] = {
 916         "x > 2",
 917         "2 < x",
 918         "y > resnr",
 919         "resnr < 2.5",
 920         "2.5 > resnr"
 921     };
 922     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 923     runTest("simple.gro", selections);
 924 }
 925
 926
 927 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
 928 {
 929     static const char * const selections[] = {
 930         "x+1 > 3",
 931         "(y-1)^2 <= 1",
 932         "x+--1 > 3",
 933         "-x+-1 < -3"
 934     };
 935     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 936     runTest("simple.gro", selections);
 937 }
 938
 939
 940 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
 941 {
 942     static const char * const selections[] = {
 943         "value = x + y",
 944         "value <= 4",
 945         "index = resnr",
 946         "index < 3"
 947     };
 948     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 949     runTest("simple.gro", selections);
 950 }
 951
 952
 953 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
 954 {
 955     static const char * const selections[] = {
 956         "value = x + y",
 957         "resname RA and value <= 4",
 958         "resname RA RB and x < 3 and value <= 4",
 959         "index = atomnr",
 960         "resname RA and index < 3",
 961         "resname RB and y < 3 and index < 6"
 962     };
 963     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 964     runTest("simple.gro", selections);
 965 }
 966
 967
 968 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
 969 {
 970     static const char * const selections[] = {
 971         "foo = res_cog of resname RA",
 972         "foo",
 973         "within 1 of foo",
 974         "bar = cog of resname RA",
 975         "bar",
 976         "within 1 of bar"
 977     };
 978     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 979     runTest("simple.gro", selections);
 980 }
 981
 982
 983 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
 984 {
 985     static const char * const selections[] = {
 986         "constpos = [1.0, 2.5, 0.5]",
 987         "constpos",
 988         "within 2 of constpos"
 989     };
 990     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 991              | efTestPositionAtoms);
 992     runTest("simple.gro", selections);
 993 }
 994
 995
 996 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
 997 {
 998     static const char * const selections[] = {
 999         "constint = 4",
1000         "constreal1 = 0.5",
1001         "constreal2 = 2.7",
1002         "resnr < constint",
1003         "x + constreal1 < constreal2"
1004     };
1005     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1006     runTest("simple.gro", selections);
1007 }
1008
1009
1010 /********************************************************************
1011  * Tests for complex boolean syntax
1012  */
1013
1014 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1015 {
1016     static const char * const selections[] = {
1017         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1018         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1019         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1020         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1021         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1022     };
1023     runTest(10, selections);
1024 }
1025
1026
1027 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1028 {
1029     static const char * const selections[] = {
1030         "foo = atomnr 4 to 7 or x < 2",
1031         "atomnr 1 to 4 and foo",
1032         "atomnr 2 to 6 and y < 3 and foo",
1033         "atomnr 6 to 10 and not foo"
1034     };
1035     runTest(10, selections);
1036 }
1037
1038
1039 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1040 {
1041     static const char * const selections[] = {
1042         "foo = atomnr 4 to 7",
1043         "bar = foo and x < 2",
1044         "bar2 = foo and y < 2",
1045         "atomnr 1 to 4 and bar",
1046         "atomnr 2 to 6 and y < 3 and bar2",
1047         "atomnr 6 to 10 and not foo"
1048     };
1049     runTest(10, selections);
1050 }
1051
1052
1053 /********************************************************************
1054  * Tests for complex subexpression cases
1055  *
1056  * These tests use some knowledge of the implementation to trigger different
1057  * paths in the code.
1058  */
1059
1060 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1061 {
1062     static const char * const selections[] = {
1063         "unused1 = atomnr 1 to 3",
1064         "foo = atomnr 4 to 7",
1065         "atomnr 1 to 6 and foo",
1066         "unused2 = atomnr 3 to 5"
1067     };
1068     runTest(10, selections);
1069 }
1070
1071
1072 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1073 {
1074     static const char * const selections[] = {
1075         "foo = atomnr 4 to 7 and x < 2",
1076         "atomnr 1 to 5 and foo",
1077         "atomnr 3 to 7 and foo"
1078     };
1079     runTest(10, selections);
1080 }
1081
1082
1083 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1084 {
1085     static const char * const selections[] = {
1086         "foo = atomnr 4 to 7 and x < 2",
1087         "atomnr 1 to 6 and foo",
1088         "within 1 of foo",
1089         "foo"
1090     };
1091     runTest(10, selections);
1092 }
1093
1094
1095 } // namespace