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37 * Tests selection parsing and compilation.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
42 #include <gtest/gtest.h>
44 #include "gromacs/options/basicoptions.h"
45 #include "gromacs/options/options.h"
46 #include "gromacs/selection/indexutil.h"
47 #include "gromacs/selection/selectioncollection.h"
48 #include "gromacs/selection/selection.h"
49 #include "gromacs/utility/arrayref.h"
50 #include "gromacs/utility/exceptions.h"
51 #include "gromacs/utility/flags.h"
52 #include "gromacs/utility/gmxregex.h"
53 #include "gromacs/utility/stringutil.h"
55 #include "testutils/refdata.h"
56 #include "testutils/testasserts.h"
57 #include "testutils/testfilemanager.h"
58 #include "testutils/testoptions.h"
65 /********************************************************************
66 * Test fixture for selection testing
69 class SelectionCollectionTest : public ::testing::Test
72 static int s_debugLevel;
74 SelectionCollectionTest();
75 ~SelectionCollectionTest();
77 void setAtomCount(int natoms)
79 ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
81 void loadTopology(const char *filename);
83 void loadIndexGroups(const char *filename);
85 gmx::test::TopologyManager topManager_;
86 gmx::SelectionCollection sc_;
87 gmx::SelectionList sel_;
90 gmx_ana_indexgrps_t *grps_;
93 int SelectionCollectionTest::s_debugLevel = 0;
95 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
97 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
99 options->addOption(gmx::IntegerOption("seldebug")
100 .store(&SelectionCollectionTest::s_debugLevel)
101 .description("Set selection debug level"));
105 SelectionCollectionTest::SelectionCollectionTest()
106 : top_(NULL), frame_(NULL), grps_(NULL)
108 topManager_.requestFrame();
109 sc_.setDebugLevel(s_debugLevel);
110 sc_.setReferencePosType("atom");
111 sc_.setOutputPosType("atom");
114 SelectionCollectionTest::~SelectionCollectionTest()
118 gmx_ana_indexgrps_free(grps_);
123 SelectionCollectionTest::loadTopology(const char *filename)
125 topManager_.loadTopology(filename);
130 SelectionCollectionTest::setTopology()
132 top_ = topManager_.topology();
133 frame_ = topManager_.frame();
135 ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
139 SelectionCollectionTest::loadIndexGroups(const char *filename)
141 GMX_RELEASE_ASSERT(grps_ == NULL,
142 "External groups can only be loaded once");
143 std::string fullpath =
144 gmx::test::TestFileManager::getInputFilePath(filename);
145 gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
146 sc_.setIndexGroups(grps_);
150 /********************************************************************
151 * Test fixture for selection testing with reference data
154 class SelectionCollectionDataTest : public SelectionCollectionTest
159 efTestEvaluation = 1<<0,
160 efTestPositionAtoms = 1<<1,
161 efTestPositionCoordinates = 1<<2,
162 efTestPositionMapping = 1<<3,
163 efTestPositionMasses = 1<<4,
164 efTestPositionCharges = 1<<5,
165 efTestSelectionNames = 1<<6,
166 efDontTestCompiledAtoms = 1<<8
168 typedef gmx::FlagsTemplate<TestFlag> TestFlags;
170 SelectionCollectionDataTest()
171 : checker_(data_.rootChecker()), count_(0), framenr_(0)
175 void setFlags(TestFlags flags) { flags_ = flags; }
177 void runParser(const gmx::ConstArrayRef<const char *> &selections);
180 void runEvaluateFinal();
182 void runTest(int natoms,
183 const gmx::ConstArrayRef<const char *> &selections);
184 void runTest(const char *filename,
185 const gmx::ConstArrayRef<const char *> &selections);
188 static void checkSelection(gmx::test::TestReferenceChecker *checker,
189 const gmx::Selection &sel, TestFlags flags);
191 void checkCompiled();
193 gmx::test::TestReferenceData data_;
194 gmx::test::TestReferenceChecker checker_;
202 SelectionCollectionDataTest::checkSelection(
203 gmx::test::TestReferenceChecker *checker,
204 const gmx::Selection &sel, TestFlags flags)
206 using gmx::test::TestReferenceChecker;
209 gmx::ConstArrayRef<int> atoms = sel.atomIndices();
210 checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
212 if (flags.test(efTestPositionAtoms)
213 || flags.test(efTestPositionCoordinates)
214 || flags.test(efTestPositionMapping)
215 || flags.test(efTestPositionMasses)
216 || flags.test(efTestPositionCharges))
218 TestReferenceChecker compound(
219 checker->checkSequenceCompound("Positions", sel.posCount()));
220 for (int i = 0; i < sel.posCount(); ++i)
222 TestReferenceChecker poscompound(compound.checkCompound("Position", NULL));
223 const gmx::SelectionPosition &p = sel.position(i);
224 if (flags.test(efTestPositionAtoms))
226 gmx::ConstArrayRef<int> atoms = p.atomIndices();
227 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
229 if (flags.test(efTestPositionCoordinates))
231 poscompound.checkVector(p.x(), "Coordinates");
233 if (flags.test(efTestPositionMapping))
235 poscompound.checkInteger(p.refId(), "RefId");
236 poscompound.checkInteger(p.mappedId(), "MappedId");
238 if (flags.test(efTestPositionMasses))
240 poscompound.checkReal(p.mass(), "Mass");
242 if (flags.test(efTestPositionCharges))
244 poscompound.checkReal(p.charge(), "Charge");
252 SelectionCollectionDataTest::runParser(
253 const gmx::ConstArrayRef<const char *> &selections)
255 using gmx::test::TestReferenceChecker;
257 TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
260 for (size_t i = 0; i < selections.size(); ++i)
262 SCOPED_TRACE(std::string("Parsing selection \"")
263 + selections[i] + "\"");
264 gmx::SelectionList result;
265 ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
266 sel_.insert(sel_.end(), result.begin(), result.end());
267 if (sel_.size() == count_)
269 std::string id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
270 TestReferenceChecker varcompound(
271 compound.checkCompound("ParsedVariable", id.c_str()));
272 varcompound.checkString(selections[i], "Input");
277 std::string id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
278 TestReferenceChecker selcompound(
279 compound.checkCompound("ParsedSelection", id.c_str()));
280 selcompound.checkString(selections[i], "Input");
281 if (flags_.test(efTestSelectionNames))
283 selcompound.checkString(sel_[count_].name(), "Name");
285 selcompound.checkString(sel_[count_].selectionText(), "Text");
286 selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
294 SelectionCollectionDataTest::runCompiler()
296 ASSERT_NO_THROW_GMX(sc_.compile());
297 ASSERT_EQ(count_, sel_.size());
303 SelectionCollectionDataTest::checkCompiled()
305 using gmx::test::TestReferenceChecker;
306 const TestFlags mask = ~TestFlags(efTestPositionCoordinates);
308 TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
309 for (size_t i = 0; i < count_; ++i)
311 SCOPED_TRACE(std::string("Checking selection \"") +
312 sel_[i].selectionText() + "\"");
313 std::string id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
314 TestReferenceChecker selcompound(
315 compound.checkCompound("Selection", id.c_str()));
316 if (flags_.test(efTestSelectionNames))
318 selcompound.checkString(sel_[i].name(), "Name");
320 if (!flags_.test(efDontTestCompiledAtoms))
322 checkSelection(&selcompound, sel_[i], flags_ & mask);
329 SelectionCollectionDataTest::runEvaluate()
331 using gmx::test::TestReferenceChecker;
334 ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
335 std::string frame = gmx::formatString("Frame%d", framenr_);
336 TestReferenceChecker compound(
337 checker_.checkCompound("EvaluatedSelections", frame.c_str()));
338 for (size_t i = 0; i < count_; ++i)
340 SCOPED_TRACE(std::string("Checking selection \"") +
341 sel_[i].selectionText() + "\"");
342 std::string id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
343 TestReferenceChecker selcompound(
344 compound.checkCompound("Selection", id.c_str()));
345 checkSelection(&selcompound, sel_[i], flags_);
351 SelectionCollectionDataTest::runEvaluateFinal()
353 ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
359 SelectionCollectionDataTest::runTest(
360 int natoms, const gmx::ConstArrayRef<const char *> &selections)
362 ASSERT_NO_FATAL_FAILURE(runParser(selections));
363 ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
364 ASSERT_NO_FATAL_FAILURE(runCompiler());
369 SelectionCollectionDataTest::runTest(
370 const char *filename, const gmx::ConstArrayRef<const char *> &selections)
372 ASSERT_NO_FATAL_FAILURE(runParser(selections));
373 ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
374 ASSERT_NO_FATAL_FAILURE(runCompiler());
375 if (flags_.test(efTestEvaluation))
377 ASSERT_NO_FATAL_FAILURE(runEvaluate());
378 ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
383 /********************************************************************
384 * Tests for SelectionCollection functionality without reference data
387 TEST_F(SelectionCollectionTest, HandlesNoSelections)
389 EXPECT_FALSE(sc_.requiresTopology());
390 EXPECT_NO_THROW_GMX(sc_.compile());
393 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
395 ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
396 ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
397 ASSERT_EQ(2U, sel_.size());
398 ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
399 ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
400 ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
401 ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
402 ASSERT_NO_THROW_GMX(sc_.compile());
403 EXPECT_TRUE(sel_[0].hasVelocities());
404 EXPECT_TRUE(sel_[1].hasVelocities());
405 EXPECT_TRUE(sel_[0].hasForces());
406 EXPECT_TRUE(sel_[1].hasForces());
409 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
411 ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
412 gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
413 // These should match the contents of selfile.dat
414 ASSERT_EQ(2U, sel_.size());
415 EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
416 EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
419 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
421 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
423 sc_.parseFromString("resname ~ \"R[A\"");
425 }, gmx::InvalidInputError);
428 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
430 if (!gmx::Regex::isSupported())
432 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
434 sc_.parseFromString("resname \"R[AD]\"");
436 }, gmx::InvalidInputError);
440 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
442 EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
443 gmx::InvalidInputError);
446 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
448 EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
449 gmx::InvalidInputError);
452 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
454 EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
455 gmx::InvalidInputError);
458 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
460 EXPECT_THROW_GMX(sc_.parseFromString("resname help"),
461 gmx::InvalidInputError);
464 // TODO: Tests for more parser errors
466 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
468 ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
469 EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
470 EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
473 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
475 ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
476 EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
477 EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
480 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
482 ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
483 ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
484 EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
485 EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
488 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
490 ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
491 ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
492 EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
493 EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
496 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
498 ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
499 EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
500 gmx::InconsistentInputError);
501 EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
504 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
506 ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
507 EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
508 EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
511 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
513 ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
514 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
515 EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
518 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
520 ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
521 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
522 EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
525 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
527 ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
528 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
529 EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
532 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
534 ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
535 ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
536 EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
539 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
541 ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
542 ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
543 EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
546 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
548 ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
549 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
550 ASSERT_NO_THROW_GMX(sc_.compile());
551 EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
554 // TODO: Tests for evaluation errors
557 /********************************************************************
558 * Tests for selection keywords
561 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
563 static const char * const selections[] = {
567 runTest(10, selections);
570 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
572 static const char * const selections[] = {
573 "atomnr 1 to 3 6 to 8",
577 runTest(10, selections);
580 TEST_F(SelectionCollectionDataTest, HandlesResnr)
582 static const char * const selections[] = {
586 runTest("simple.gro", selections);
589 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
591 static const char * const selections[] = {
595 runTest("simple.pdb", selections);
598 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
600 static const char * const selections[] = {
604 ASSERT_NO_FATAL_FAILURE(runParser(selections));
605 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
606 topManager_.initUniformMolecules(3);
607 ASSERT_NO_FATAL_FAILURE(runCompiler());
610 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
612 static const char * const selections[] = {
616 runTest("simple.gro", selections);
619 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
621 static const char * const selections[] = {
627 runTest("simple.pdb", selections);
631 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
633 static const char * const selections[] = {
636 ASSERT_NO_FATAL_FAILURE(runParser(selections));
637 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
638 const char *const types[] = { "CA", "SA", "SB" };
639 topManager_.initAtomTypes(types);
640 ASSERT_NO_FATAL_FAILURE(runCompiler());
643 TEST_F(SelectionCollectionDataTest, HandlesChain)
645 static const char * const selections[] = {
649 runTest("simple.pdb", selections);
652 TEST_F(SelectionCollectionDataTest, HandlesMass)
654 static const char * const selections[] = {
657 ASSERT_NO_FATAL_FAILURE(runParser(selections));
658 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
659 for (int i = 0; i < top_->atoms.nr; ++i)
661 top_->atoms.atom[i].m = 1.0 + i;
663 ASSERT_NO_FATAL_FAILURE(runCompiler());
666 TEST_F(SelectionCollectionDataTest, HandlesCharge)
668 static const char * const selections[] = {
671 ASSERT_NO_FATAL_FAILURE(runParser(selections));
672 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
673 for (int i = 0; i < top_->atoms.nr; ++i)
675 top_->atoms.atom[i].q = i / 10.0;
677 ASSERT_NO_FATAL_FAILURE(runCompiler());
680 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
682 static const char * const selections[] = {
686 runTest("simple.pdb", selections);
689 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
691 static const char * const selections[] = {
695 runTest("simple.pdb", selections);
698 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
700 static const char * const selections[] = {
704 runTest("simple.pdb", selections);
707 TEST_F(SelectionCollectionDataTest, HandlesBeta)
709 static const char * const selections[] = {
713 runTest("simple.pdb", selections);
716 TEST_F(SelectionCollectionDataTest, HandlesResname)
718 static const char * const selections[] = {
722 runTest("simple.gro", selections);
725 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
727 static const char * const selections[] = {
732 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
733 runTest("simple.gro", selections);
737 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
739 static const char * const selections[] = {
740 "same residue as atomnr 1 4 12"
742 runTest("simple.gro", selections);
746 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
748 static const char * const selections[] = {
749 "same resname as atomnr 1 14"
751 runTest("simple.gro", selections);
755 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
757 static const char * const selections[] = {
759 "res_cog of name CB and resnr 1 3",
760 "whole_res_cog of name CB and resnr 1 3",
761 "part_res_cog of x < 3",
762 "dyn_res_cog of x < 3"
764 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
765 | efTestPositionAtoms);
766 runTest("simple.gro", selections);
770 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
772 static const char * const selections[] = {
773 "distance from cog of resnr 1 < 2"
775 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
776 runTest("simple.gro", selections);
780 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
782 static const char * const selections[] = {
783 "mindistance from resnr 1 < 2"
785 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
786 runTest("simple.gro", selections);
790 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
792 static const char * const selections[] = {
793 "within 1 of resnr 2"
795 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
796 runTest("simple.gro", selections);
800 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
802 // Both of these should evaluate to empty on a correct implementation.
803 static const char * const selections[] = {
804 "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
805 "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
807 setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
808 runTest("sphere.gro", selections);
812 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
814 static const char * const selections[] = {
816 "res_cog of resnr 1 to 4 permute 2 1",
817 "name CB S1 and res_cog x < 3 permute 2 1"
819 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
820 | efTestPositionAtoms | efTestPositionMapping);
821 runTest("simple.gro", selections);
825 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
827 static const char * const selections[] = {
828 "name S2 plus name S1",
829 "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
830 "name S1 and y < 3 plus res_cog of x < 2.5"
832 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
833 | efTestPositionAtoms | efTestPositionMapping);
834 runTest("simple.gro", selections);
838 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
840 static const char * const selections[] = {
841 "name S2 merge name S1",
842 "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
843 "name S1 and x < 2.5 merge res_cog of x < 2.5"
845 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
846 | efTestPositionAtoms | efTestPositionMapping);
847 runTest("simple.gro", selections);
851 /********************************************************************
852 * Tests for generic selection evaluation
855 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
857 static const char * const selections[] = {
862 setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
863 | efTestPositionMasses | efTestPositionCharges);
864 ASSERT_NO_FATAL_FAILURE(runParser(selections));
865 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
866 for (int i = 0; i < top_->atoms.nr; ++i)
868 top_->atoms.atom[i].m = 1.0 + i / 100.0;
869 top_->atoms.atom[i].q = -(1.0 + i / 100.0);
871 ASSERT_NO_FATAL_FAILURE(runCompiler());
872 ASSERT_NO_FATAL_FAILURE(runEvaluate());
873 ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
876 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
878 static const char * const selections[] = {
879 "atomnr 1 to 3 8 to 9",
883 setFlags(TestFlags() | efTestPositionAtoms
884 | efTestPositionMasses | efTestPositionCharges);
885 runTest(10, selections);
889 /********************************************************************
890 * Tests for selection syntactic constructs
893 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
895 static const char * const selections[] = {
896 "\"GroupSelection\" group \"GrpA\"",
897 "\"DynamicSelection\" x < 5",
900 setFlags(TestFlags() | efTestSelectionNames);
901 ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
902 runTest(10, selections);
905 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
907 static const char * const selections[] = {
911 "group \"GrpB\" and resname RB"
913 setFlags(TestFlags() | efTestSelectionNames);
914 ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
915 runTest("simple.gro", selections);
918 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
920 static const char * const selections[] = {
924 "group \"GrpB\" and resname RB"
926 setFlags(TestFlags() | efTestSelectionNames);
927 ASSERT_NO_FATAL_FAILURE(runParser(selections));
928 ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
929 ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
930 ASSERT_NO_FATAL_FAILURE(runCompiler());
933 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
935 static const char * const selections[] = {
938 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
939 runTest("simple.gro", selections);
943 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
945 static const char * const selections[] = {
946 "within 1 of [2, 1, 0]"
948 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
949 runTest("simple.gro", selections);
953 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
955 static const char * const selections[] = {
959 runTest("simple.gro", selections);
963 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
965 static const char * const selections[] = {
969 runTest("simple.gro", selections);
973 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
975 static const char * const selections[] = {
977 "resname ~ \"R[BD]\""
979 if (gmx::Regex::isSupported())
981 runTest("simple.gro", selections);
986 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
988 static const char * const selections[] = {
989 "atomnr 1 to 5 and atomnr 2 to 7",
990 "atomnr 1 to 5 or not atomnr 3 to 8",
991 "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
992 "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
993 "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
995 runTest(10, selections);
999 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1001 static const char * const selections[] = {
1002 "same residue as (atomnr 3 5 13 or y > 5)",
1003 "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1005 setFlags(TestFlags() | efTestEvaluation);
1006 runTest("simple.gro", selections);
1010 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1012 static const char * const selections[] = {
1014 "none and same resname as resnr 2"
1016 runTest("simple.gro", selections);
1020 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1022 static const char * const selections[] = {
1029 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1030 runTest("simple.gro", selections);
1034 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1036 static const char * const selections[] = {
1042 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1043 runTest("simple.gro", selections);
1047 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1049 static const char * const selections[] = {
1055 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1056 runTest("simple.gro", selections);
1060 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1062 static const char * const selections[] = {
1064 "resname RA and value <= 4",
1065 "resname RA RB and x < 3 and value <= 4",
1067 "resname RA and index < 3",
1068 "resname RB and y < 3 and index < 6"
1070 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1071 runTest("simple.gro", selections);
1075 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1077 static const char * const selections[] = {
1078 "foo = res_cog of resname RA",
1081 "bar = cog of resname RA",
1085 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1086 runTest("simple.gro", selections);
1090 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1092 static const char * const selections[] = {
1093 "constpos = [1.0, 2.5, 0.5]",
1095 "within 2 of constpos"
1097 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1098 | efTestPositionAtoms);
1099 runTest("simple.gro", selections);
1103 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1105 static const char * const selections[] = {
1110 "x + constreal1 < constreal2"
1112 setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1113 runTest("simple.gro", selections);
1117 /********************************************************************
1118 * Tests for complex boolean syntax
1121 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1123 static const char * const selections[] = {
1124 "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1125 "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1126 "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1127 "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1128 "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1130 runTest(10, selections);
1134 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1136 static const char * const selections[] = {
1137 "foo = atomnr 4 to 7 or x < 2",
1138 "atomnr 1 to 4 and foo",
1139 "atomnr 2 to 6 and y < 3 and foo",
1140 "atomnr 6 to 10 and not foo"
1142 runTest(10, selections);
1146 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1148 static const char * const selections[] = {
1149 "foo = atomnr 4 to 7",
1150 "bar = foo and x < 2",
1151 "bar2 = foo and y < 2",
1152 "atomnr 1 to 4 and bar",
1153 "atomnr 2 to 6 and y < 3 and bar2",
1154 "atomnr 6 to 10 and not foo"
1156 runTest(10, selections);
1160 /********************************************************************
1161 * Tests for complex subexpression cases
1163 * These tests use some knowledge of the implementation to trigger different
1164 * paths in the code.
1167 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1169 static const char * const selections[] = {
1170 "unused1 = atomnr 1 to 3",
1171 "foo = atomnr 4 to 7",
1172 "atomnr 1 to 6 and foo",
1173 "unused2 = atomnr 3 to 5"
1175 runTest(10, selections);
1179 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1181 static const char * const selections[] = {
1182 "foo = atomnr 4 to 7 and x < 2",
1183 "atomnr 1 to 5 and foo",
1184 "atomnr 3 to 7 and foo"
1186 runTest(10, selections);
1190 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1192 static const char * const selections[] = {
1193 "foo = atomnr 4 to 7 and x < 2",
1194 "atomnr 1 to 6 and foo",
1198 runTest(10, selections);
1202 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1204 static const char * const selections[] = {
1205 "foo = atomnr 1 to 8 and x < 10",
1206 "atomnr 1 to 5 and y < 10 and foo",
1209 setFlags(TestFlags() | efTestEvaluation);
1210 runTest("simple.gro", selections);