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, ParsesSelectionsFromFile)
 406 {
 407     ASSERT_NO_THROW(sel_ = sc_.parseFromFile(
 408                                 gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 409     // These should match the contents of selfile.dat
 410     ASSERT_EQ(2U, sel_.size());
 411     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 412     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 413 }
 414
 415 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 416 {
 417     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 418     EXPECT_THROW({
 419                      sc_.parseFromString("resname ~ \"R[A\"");
 420                      sc_.compile();
 421                  }, gmx::InvalidInputError);
 422 }
 423
 424 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 425 {
 426     if (!gmx::Regex::isSupported())
 427     {
 428         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 429         EXPECT_THROW({
 430                          sc_.parseFromString("resname \"R[AD]\"");
 431                          sc_.compile();
 432                      }, gmx::InvalidInputError);
 433     }
 434 }
 435
 436 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 437 {
 438     EXPECT_THROW(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 439                  gmx::InvalidInputError);
 440 }
 441
 442 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 443 {
 444     EXPECT_THROW(sc_.parseFromString("within 1 of"),
 445                  gmx::InvalidInputError);
 446 }
 447
 448 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 449 {
 450     EXPECT_THROW(sc_.parseFromString("within of atomnr 1"),
 451                  gmx::InvalidInputError);
 452 }
 453
 454 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 455 {
 456     EXPECT_THROW(sc_.parseFromString("resname help"),
 457                  gmx::InvalidInputError);
 458 }
 459
 460 // TODO: Tests for more parser errors
 461
 462 TEST_F(SelectionCollectionTest, RecoversFromUnknownGroupReference)
 463 {
 464     ASSERT_NO_THROW(sc_.parseFromString("group \"foo\""));
 465     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 466     EXPECT_THROW(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
 467     EXPECT_THROW(sc_.compile(), gmx::APIError);
 468 }
 469
 470 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 471 {
 472     ASSERT_NO_THROW(sc_.parseFromString("molindex 1 to 5"));
 473     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 474     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 475 }
 476
 477 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 478 {
 479     ASSERT_NO_THROW(sc_.parseFromString("type CA"));
 480     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 481     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 482 }
 483
 484 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 485 {
 486     ASSERT_NO_THROW(sc_.parseFromString("altloc A"));
 487     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 488     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 489 }
 490
 491 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 492 {
 493     ASSERT_NO_THROW(sc_.parseFromString("all permute 1 1"));
 494     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 495     EXPECT_THROW(sc_.compile(), gmx::InvalidInputError);
 496 }
 497
 498 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 499 {
 500     ASSERT_NO_THROW(sc_.parseFromString("all permute 3 2 1"));
 501     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 502     EXPECT_THROW(sc_.compile(), gmx::InconsistentInputError);
 503 }
 504
 505 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 506 {
 507     ASSERT_NO_THROW(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 508     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 509     ASSERT_NO_THROW(sc_.compile());
 510     EXPECT_THROW(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 511 }
 512
 513 // TODO: Tests for evaluation errors
 514
 515
 516 /********************************************************************
 517  * Tests for selection keywords
 518  */
 519
 520 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 521 {
 522     static const char * const selections[] = {
 523         "all",
 524         "none"
 525     };
 526     runTest(10, selections);
 527 }
 528
 529 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 530 {
 531     static const char * const selections[] = {
 532         "atomnr 1 to 3 6 to 8",
 533         "atomnr 4 2 5 to 7",
 534         "atomnr <= 5"
 535     };
 536     runTest(10, selections);
 537 }
 538
 539 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 540 {
 541     static const char * const selections[] = {
 542         "resnr 1 2 5",
 543         "resid 4 to 3"
 544     };
 545     runTest("simple.gro", selections);
 546 }
 547
 548 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 549 {
 550     static const char * const selections[] = {
 551         "resindex 1 4",
 552         "residue 1 3"
 553     };
 554     runTest("simple.pdb", selections);
 555 }
 556
 557 // TODO: Add test for "molindex"
 558
 559 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 560 {
 561     static const char * const selections[] = {
 562         "name CB",
 563         "atomname S1 S2"
 564     };
 565     runTest("simple.gro", selections);
 566 }
 567
 568 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 569 {
 570     static const char * const selections[] = {
 571         "name HG21",
 572         "name 1HG2",
 573         "pdbname HG21 CB",
 574         "pdbatomname 1HG2"
 575     };
 576     runTest("simple.pdb", selections);
 577 }
 578
 579 // TODO: Add test for atomtype
 580
 581 TEST_F(SelectionCollectionDataTest, HandlesChain)
 582 {
 583     static const char * const selections[] = {
 584         "chain A",
 585         "chain B"
 586     };
 587     runTest("simple.pdb", selections);
 588 }
 589
 590 TEST_F(SelectionCollectionDataTest, HandlesMass)
 591 {
 592     static const char * const selections[] = {
 593         "mass > 5"
 594     };
 595     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 596     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 597     for (int i = 0; i < top_->atoms.nr; ++i)
 598     {
 599         top_->atoms.atom[i].m = 1.0 + i;
 600     }
 601     ASSERT_NO_FATAL_FAILURE(runCompiler());
 602 }
 603
 604 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 605 {
 606     static const char * const selections[] = {
 607         "charge < 0.5"
 608     };
 609     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 610     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 611     for (int i = 0; i < top_->atoms.nr; ++i)
 612     {
 613         top_->atoms.atom[i].q = i / 10.0;
 614     }
 615     ASSERT_NO_FATAL_FAILURE(runCompiler());
 616 }
 617
 618 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 619 {
 620     static const char * const selections[] = {
 621         "altloc \" \"",
 622         "altloc A"
 623     };
 624     runTest("simple.pdb", selections);
 625 }
 626
 627 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 628 {
 629     static const char * const selections[] = {
 630         "insertcode \" \"",
 631         "insertcode A"
 632     };
 633     runTest("simple.pdb", selections);
 634 }
 635
 636 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 637 {
 638     static const char * const selections[] = {
 639         "occupancy 1",
 640         "occupancy < .5"
 641     };
 642     runTest("simple.pdb", selections);
 643 }
 644
 645 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 646 {
 647     static const char * const selections[] = {
 648         "beta 0",
 649         "beta >= 0.3"
 650     };
 651     runTest("simple.pdb", selections);
 652 }
 653
 654 TEST_F(SelectionCollectionDataTest, HandlesResname)
 655 {
 656     static const char * const selections[] = {
 657         "resname RA",
 658         "resname RB RC"
 659     };
 660     runTest("simple.gro", selections);
 661 }
 662
 663 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 664 {
 665     static const char * const selections[] = {
 666         "x < 3",
 667         "y >= 3",
 668         "x {-1 to 2}"
 669     };
 670     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 671     runTest("simple.gro", selections);
 672 }
 673
 674
 675 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 676 {
 677     static const char * const selections[] = {
 678         "same residue as atomnr 1 4 12"
 679     };
 680     runTest("simple.gro", selections);
 681 }
 682
 683
 684 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 685 {
 686     static const char * const selections[] = {
 687         "same resname as atomnr 1 14"
 688     };
 689     runTest("simple.gro", selections);
 690 }
 691
 692
 693 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 694 {
 695     static const char * const selections[] = {
 696         "cog of resnr 1 3",
 697         "res_cog of name CB and resnr 1 3",
 698         "whole_res_cog of name CB and resnr 1 3",
 699         "part_res_cog of x < 3",
 700         "dyn_res_cog of x < 3"
 701     };
 702     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 703              | efTestPositionAtoms);
 704     runTest("simple.gro", selections);
 705 }
 706
 707
 708 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 709 {
 710     static const char * const selections[] = {
 711         "distance from cog of resnr 1 < 2"
 712     };
 713     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 714     runTest("simple.gro", selections);
 715 }
 716
 717
 718 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 719 {
 720     static const char * const selections[] = {
 721         "mindistance from resnr 1 < 2"
 722     };
 723     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 724     runTest("simple.gro", selections);
 725 }
 726
 727
 728 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 729 {
 730     static const char * const selections[] = {
 731         "within 1 of resnr 2"
 732     };
 733     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 734     runTest("simple.gro", selections);
 735 }
 736
 737
 738 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 739 {
 740     // Both of these should evaluate to empty on a correct implementation.
 741     static const char * const selections[] = {
 742         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 743         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 744     };
 745     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 746     runTest("sphere.gro", selections);
 747 }
 748
 749
 750 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 751 {
 752     static const char * const selections[] = {
 753         "all permute 3 1 2",
 754         "res_cog of resnr 1 to 4 permute 2 1",
 755         "name CB S1 and res_cog x < 3 permute 2 1"
 756     };
 757     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 758              | efTestPositionAtoms | efTestPositionMapping);
 759     runTest("simple.gro", selections);
 760 }
 761
 762
 763 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 764 {
 765     static const char * const selections[] = {
 766         "name S2 plus name S1",
 767         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 768         "name S1 and y < 3 plus res_cog of x < 2.5"
 769     };
 770     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 771              | efTestPositionAtoms | efTestPositionMapping);
 772     runTest("simple.gro", selections);
 773 }
 774
 775
 776 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 777 {
 778     static const char * const selections[] = {
 779         "name S2 merge name S1",
 780         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 781         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 782     };
 783     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 784              | efTestPositionAtoms | efTestPositionMapping);
 785     runTest("simple.gro", selections);
 786 }
 787
 788
 789 /********************************************************************
 790  * Tests for generic selection evaluation
 791  */
 792
 793 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 794 {
 795     static const char * const selections[] = {
 796         "name CB",
 797         "y > 2",
 798         "res_cog of y > 2"
 799     };
 800     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 801              | efTestPositionMasses | efTestPositionCharges);
 802     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 803     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 804     for (int i = 0; i < top_->atoms.nr; ++i)
 805     {
 806         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 807         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 808     }
 809     ASSERT_NO_FATAL_FAILURE(runCompiler());
 810     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 811     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 812 }
 813
 814 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 815 {
 816     static const char * const selections[] = {
 817         "atomnr 1 to 3 8 to 9",
 818         "y > 2",
 819         "cog of (y > 2)"
 820     };
 821     setFlags(TestFlags() | efTestPositionAtoms
 822              | efTestPositionMasses | efTestPositionCharges);
 823     runTest(10, selections);
 824 }
 825
 826
 827 /********************************************************************
 828  * Tests for selection syntactic constructs
 829  */
 830
 831 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 832 {
 833     static const char * const selections[] = {
 834         "[1, -2, 3.5]"
 835     };
 836     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 837     runTest("simple.gro", selections);
 838 }
 839
 840
 841 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 842 {
 843     static const char * const selections[] = {
 844         "within 1 of [2, 1, 0]"
 845     };
 846     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 847     runTest("simple.gro", selections);
 848 }
 849
 850
 851 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 852 {
 853     static const char * const selections[] = {
 854         "name = S1 \"C?\"",
 855         "name ? S1 \"C?\""
 856     };
 857     runTest("simple.gro", selections);
 858 }
 859
 860
 861 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 862 {
 863     static const char * const selections[] = {
 864         "name \"S?\"",
 865         "name ? \"S?\""
 866     };
 867     runTest("simple.gro", selections);
 868 }
 869
 870
 871 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 872 {
 873     static const char * const selections[] = {
 874         "resname \"R[BD]\"",
 875         "resname ~ \"R[BD]\""
 876     };
 877     if (gmx::Regex::isSupported())
 878     {
 879         runTest("simple.gro", selections);
 880     }
 881 }
 882
 883
 884 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 885 {
 886     static const char * const selections[] = {
 887         "atomnr 1 to 5 and atomnr 2 to 7",
 888         "atomnr 1 to 5 or not atomnr 3 to 8",
 889         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 890         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 891         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 892     };
 893     runTest(10, selections);
 894 }
 895
 896
 897 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
 898 {
 899     static const char * const selections[] = {
 900         "x > 2",
 901         "2 < x",
 902         "y > resnr",
 903         "resnr < 2.5",
 904         "2.5 > resnr"
 905     };
 906     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 907     runTest("simple.gro", selections);
 908 }
 909
 910
 911 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
 912 {
 913     static const char * const selections[] = {
 914         "x+1 > 3",
 915         "(y-1)^2 <= 1",
 916         "x+--1 > 3",
 917         "-x+-1 < -3"
 918     };
 919     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 920     runTest("simple.gro", selections);
 921 }
 922
 923
 924 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
 925 {
 926     static const char * const selections[] = {
 927         "value = x + y",
 928         "value <= 4",
 929         "index = resnr",
 930         "index < 3"
 931     };
 932     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 933     runTest("simple.gro", selections);
 934 }
 935
 936
 937 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
 938 {
 939     static const char * const selections[] = {
 940         "value = x + y",
 941         "resname RA and value <= 4",
 942         "resname RA RB and x < 3 and value <= 4",
 943         "index = atomnr",
 944         "resname RA and index < 3",
 945         "resname RB and y < 3 and index < 6"
 946     };
 947     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 948     runTest("simple.gro", selections);
 949 }
 950
 951
 952 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
 953 {
 954     static const char * const selections[] = {
 955         "foo = res_cog of resname RA",
 956         "foo",
 957         "within 1 of foo",
 958         "bar = cog of resname RA",
 959         "bar",
 960         "within 1 of bar"
 961     };
 962     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 963     runTest("simple.gro", selections);
 964 }
 965
 966
 967 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
 968 {
 969     static const char * const selections[] = {
 970         "constpos = [1.0, 2.5, 0.5]",
 971         "constpos",
 972         "within 2 of constpos"
 973     };
 974     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 975              | efTestPositionAtoms);
 976     runTest("simple.gro", selections);
 977 }
 978
 979
 980 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
 981 {
 982     static const char * const selections[] = {
 983         "constint = 4",
 984         "constreal1 = 0.5",
 985         "constreal2 = 2.7",
 986         "resnr < constint",
 987         "x + constreal1 < constreal2"
 988     };
 989     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 990     runTest("simple.gro", selections);
 991 }
 992
 993
 994 /********************************************************************
 995  * Tests for complex boolean syntax
 996  */
 997
 998 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
 999 {
1000     static const char * const selections[] = {
1001         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1002         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1003         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1004         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1005         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1006     };
1007     runTest(10, selections);
1008 }
1009
1010
1011 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1012 {
1013     static const char * const selections[] = {
1014         "foo = atomnr 4 to 7 or x < 2",
1015         "atomnr 1 to 4 and foo",
1016         "atomnr 2 to 6 and y < 3 and foo",
1017         "atomnr 6 to 10 and not foo"
1018     };
1019     runTest(10, selections);
1020 }
1021
1022
1023 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1024 {
1025     static const char * const selections[] = {
1026         "foo = atomnr 4 to 7",
1027         "bar = foo and x < 2",
1028         "bar2 = foo and y < 2",
1029         "atomnr 1 to 4 and bar",
1030         "atomnr 2 to 6 and y < 3 and bar2",
1031         "atomnr 6 to 10 and not foo"
1032     };
1033     runTest(10, selections);
1034 }
1035
1036
1037 /********************************************************************
1038  * Tests for complex subexpression cases
1039  *
1040  * These tests use some knowledge of the implementation to trigger different
1041  * paths in the code.
1042  */
1043
1044 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1045 {
1046     static const char * const selections[] = {
1047         "unused1 = atomnr 1 to 3",
1048         "foo = atomnr 4 to 7",
1049         "atomnr 1 to 6 and foo",
1050         "unused2 = atomnr 3 to 5"
1051     };
1052     runTest(10, selections);
1053 }
1054
1055
1056 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1057 {
1058     static const char * const selections[] = {
1059         "foo = atomnr 4 to 7 and x < 2",
1060         "atomnr 1 to 5 and foo",
1061         "atomnr 3 to 7 and foo"
1062     };
1063     runTest(10, selections);
1064 }
1065
1066
1067 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1068 {
1069     static const char * const selections[] = {
1070         "foo = atomnr 4 to 7 and x < 2",
1071         "atomnr 1 to 6 and foo",
1072         "within 1 of foo",
1073         "foo"
1074     };
1075     runTest(10, selections);
1076 }
1077
1078
1079 } // namespace