Changeset 842aac


Ignore:
Timestamp:
Nov 16, 2012, 11:10:27 AM (12 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
d893672
Parents:
060c7d
git-author:
Michael Ankele <ankele@…> (10/01/12 14:05:07)
git-committer:
Frederik Heber <heber@…> (11/16/12 11:10:27)
Message:

Refactoring: FillSurfaceAction uses ShapeRegistry

Files:
3 deleted
19 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FillAction/FillSurfaceAction.cpp

    r060c7d r842aac  
    4848#include "molecule.hpp"
    4949#include "Shapes/BaseShapes.hpp"
    50 #include "Shapes/ShapeFactory.hpp"
     50#include "Shapes/ShapeRegistry.hpp"
    5151#include "World.hpp"
    5252
    … …  
    109109        );
    110110
    111     Shape s = ShapeFactory::getInstance().produce();
     111
     112    std::vector<Shape*> selectedShapes = ShapeRegistry::getInstance().getSelectedShapes();
     113    if (selectedShapes.size() != 1){
     114      ELOG(1, "FillSurfaceAction::performCall(): there has to be exactly 1 selected shape.");
     115      return Action::failure;
     116    }
    112117
    113118    boost::function<const NodeSet ()> func =
    114         boost::bind(&Shape::getHomogeneousPointsOnSurface, boost::ref(s), params.N.get());
     119        boost::bind(&Shape::getHomogeneousPointsOnSurface, boost::ref(*selectedShapes[0]), params.N.get());
    115120    Mesh *mesh = new MeshAdaptor(func);
    116121    Inserter *inserter = new Inserter(
    117         Inserter::impl_ptr(new SurfaceInserter(s, params.AlignedAxis.get())));
     122        Inserter::impl_ptr(new SurfaceInserter(*selectedShapes[0], params.AlignedAxis.get())));
    118123
    119124    // fill

  • src/Actions/GlobalListOfActions.hpp

    r060c7d r842aac  
    121121  (FillSurface) \
    122122  (ShapeCombineShapes) \
    123   (ShapeCreateShape) \
    124   (ShapeSetShape)
     123  (ShapeCreateShape)
    125124
    126125// we need to append the automation action in case we have the JobMarket

  • src/Actions/Makefile.am

    r060c7d r842aac  
    417417SHAPEACTIONSOURCE = \
    418418  Actions/ShapeAction/CombineShapesAction.cpp \
    419   Actions/ShapeAction/CreateShapeAction.cpp \
    420   Actions/ShapeAction/SetShapeAction.cpp
     419  Actions/ShapeAction/CreateShapeAction.cpp
    421420SHAPEACTIONHEADER = \
    422421  Actions/ShapeAction/CombineShapesAction.hpp \
    423   Actions/ShapeAction/CreateShapeAction.hpp \
    424   Actions/ShapeAction/SetShapeAction.hpp
     422  Actions/ShapeAction/CreateShapeAction.hpp
    425423SHAPEACTIONDEFS = \
    426424  Actions/ShapeAction/CombineShapesAction.def \
    427   Actions/ShapeAction/CreateShapeAction.def \
    428   Actions/ShapeAction/SetShapeAction.def
     425  Actions/ShapeAction/CreateShapeAction.def
    429426       
    430427TESSELATIONACTIONSOURCE = \

  • src/Actions/ShapeAction/CreateShapeAction.cpp

    r060c7d r842aac  
    5454  LOG(1, "Adding shape into ShapeRegistry.");
    5555
    56   Shape s = ShapeFactory::getInstance().produce();
     56  Shape s = ShapeFactory::getInstance().produce(ShapeFactory::getInstance().getShapeByName(params.shape_type.get()),
     57      params.translation.get(), params.stretch.get(),
     58      params.angle_x.get(), params.angle_y.get(), params.angle_z.get());
    5759  if (params.shape_name.get() != "")
    5860    s.setName(params.shape_name.get());
    … …  
    8082  ShapeCreateShapeState *state = assert_cast<ShapeCreateShapeState*>(_state.get());
    8183
    82   Shape s = ShapeFactory::getInstance().produce();
     84  /*Shape s = ShapeFactory::getInstance().produce();
    8385  s.setName(state->old_name);
    84   ShapeRegistry::getInstance().addShape(s);
     86  ShapeRegistry::getInstance().addShape(s);*/
    8587
    8688  return Action::state_ptr(_state);

  • src/Actions/ShapeAction/CreateShapeAction.def

    r060c7d r842aac  
    1010
    1111#include "Parameters/Validators/DummyValidator.hpp"
     12#include "Parameters/Validators/Specific/ShapeTypeValidator.hpp"
     13#include "Parameters/Validators/Specific/VectorPositiveComponentsValidator.hpp"
    1214
    1315// i.e. there is an integer with variable name Z that can be found in
    1416// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    1517// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
    16 #define paramtypes (std::string)
    17 #define paramtokens ("shape-name")
    18 #define paramdescriptions ("name shape to create")
    19 #define paramdefaults (PARAM_DEFAULT(std::string("")))
    20 #define paramreferences (shape_name)
     18#define paramtypes (std::string)(std::string)(Vector)(Vector)(double)(double)(double)
     19#define paramtokens ("shape-name")("shape-type")("translation")("stretch")("angle-x")("angle-y")("angle-z")
     20#define paramdescriptions ("name shape to create")("type of shape to create")("translation distance")("scaling factors")("rotation x")("rotation y")("rotation z")
     21#define paramdefaults (PARAM_DEFAULT(std::string("")))(NOPARAM_DEFAULT)(PARAM_DEFAULT(Vector(0.,0.,0.)))(PARAM_DEFAULT(Vector(1.,1.,1.)))(PARAM_DEFAULT(0.))(PARAM_DEFAULT(0.))(PARAM_DEFAULT(0.))
     22#define paramreferences (shape_name)(shape_type)(translation)(stretch)(angle_x)(angle_y)(angle_z)
    2123#define paramvalids \
    22 (DummyValidator<std::string>())
     24(DummyValidator<std::string>()) \
     25(ShapeTypeValidator()) \
     26(DummyValidator<Vector>()) \
     27(VectorPositiveComponentsValidator()) \
     28(DummyValidator<double>()) \
     29(DummyValidator<double>()) \
     30(DummyValidator<double>())
    2331
    2432#define statetypes (std::string)
    … …  
    3543
    3644// finally the information stored in the ActionTrait specialization
    37 #define DESCRIPTION "sets the properties for the next shape to be created by the shape factory"
     45#define DESCRIPTION "creates a new shape and puts it into the ShapeRegistry"
    3846#undef SHORTFORM

  • src/Shapes/ShapeFactory.cpp

    r060c7d r842aac  
    5555  for (int i=0; i<MAX_ShapeType; i++)
    5656    nameShapeMap.insert(std::pair<std::string, ShapeType>(shapeNames[i], (ShapeType)i));
    57 
    58   // Init state.
    59   type = SphereType;
    60   translation.Zero();
    61   stretch = Vector(1.,1.,1.);
    62   for (int i=0; i<NDIM; i++)
    63     angle[i] = 0;
    6457}
    6558
    … …  
    9083}
    9184
    92 
    93 void ShapeFactory::setType(ShapeType type)
    94 {
    95   ShapeNameMap::iterator iter = shapeNameMap.find(type);
    96   ASSERT(iter != shapeNameMap.end(),
    97       "ShapeFactory::setType() - unknown type: "+toString(type)+".");
    98   this->type = type;
    99 }
    100 
    101 void ShapeFactory::setStretch(const Vector &stretch)
     85Shape ShapeFactory::produce(ShapeType type, const Vector &translation, const Vector &stretch, double angleX, double angleY, double angleZ) const
    10286{
    10387  for (int i=0; i<NDIM; i++){
    10488    ASSERT(stretch[i] > 0,
    105       "ShapeFactory::setStretch() - non positive component.");
     89        "ShapeFactory::setStretch() - non positive component.");
    10690  }
    107   this->stretch = stretch;
    108 }
    10991
    110 Shape ShapeFactory::produce() const
    111 {
    11292  // Create the basic shape.
    11393  Shape s = Nowhere();
    … …  
    130110  if (stretch != Vector(1., 1., 1.))
    131111    s = ::stretch(s, stretch);
    132   for (int i=0; i<NDIM; i++)
    133     if (angle[i] != 0){
    134       RealSpaceMatrix rotation;
    135       rotation.setRotation(angle);
    136       s = transform(s, rotation);
    137       break;
    138     }
     112  if ((angleX != 0) && (angleY != 0) && (angleZ != 0)){
     113    RealSpaceMatrix rotation;
     114    rotation.setRotation(angleX, angleY, angleZ);
     115    s = transform(s, rotation);
     116  }
    139117  if (!translation.IsZero())
    140118    s = translate(s, translation);

  • src/Shapes/ShapeFactory.hpp

    r060c7d r842aac  
    3030  bool isValidShapeName(const std::string &name);
    3131
    32 
    33   // setters/getters for the current state
    34   const double* getAngle() const { return angle; }
    35   void setAngle(double angleX, double angleY, double angleZ) { angle[0] = angleX; angle[1] = angleY; angle[2] = angleZ; }
    36 
    37   Vector getStretch() const { return stretch; }
    38   void setStretch(const Vector &stretch);
    39 
    40   Vector getTranslation() const { return translation; }
    41   void setTranslation(const Vector &translation) { this->translation = translation; }
    42 
    43   ShapeType getType() const { return type; }
    44   void setType(ShapeType type);
    45 
    4632  // create a shape
    47   Shape produce() const;
     33  Shape produce(ShapeType type, const Vector &translation = Vector(0., 0., 0.), const Vector &stretch = Vector(1., 1., 1.), double angleX = 0, double angleY = 0, double angleZ = 0) const;
    4834
    4935private:
    … …  
    5844  typedef std::map<std::string,ShapeType> NameShapeMap;
    5945  NameShapeMap nameShapeMap;
    60 
    61   // current state
    62   ShapeType type;
    63   Vector translation;
    64   Vector stretch;
    65   double angle[NDIM];
    6646};
    6747

  • src/Shapes/unittests/ShapeFactoryUnitTest.cpp

    r060c7d r842aac  
    7171void ShapeFactoryTest::typeTest()
    7272{
    73   ShapeFactory::getInstance().setAngle(0., 0., 0.);
    74   ShapeFactory::getInstance().setStretch(Vector(1., 1., 1.));
    75   ShapeFactory::getInstance().setTranslation(Vector(0., 0., 0.));
     73  CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce(NowhereType).getType(), NowhereType );
    7674
    77   ShapeFactory::getInstance().setType(NowhereType);
    78   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce().getType(), NowhereType );
     75  CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce(EverywhereType).getType(), EverywhereType );
    7976
    80   ShapeFactory::getInstance().setType(EverywhereType);
    81   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce().getType(), EverywhereType );
     77  CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce(SphereType).getType(), SphereType );
    8278
    83   ShapeFactory::getInstance().setType(SphereType);
    84   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce().getType(), SphereType );
     79  CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce(CuboidType).getType(), CuboidType );
    8580
    86   ShapeFactory::getInstance().setType(CuboidType);
    87   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce().getType(), CuboidType );
    88 
    89   ShapeFactory::getInstance().setType(CylinderType);
    90   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce().getType(), CylinderType );
     81  CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().produce(CylinderType).getType(), CylinderType );
    9182}
    9283
    9384void ShapeFactoryTest::resizeTest()
    9485{
    95   ShapeFactory::getInstance().setType(SphereType);
    96   ShapeFactory::getInstance().setAngle(0., 0., 0.);
    97   ShapeFactory::getInstance().setStretch(Vector(2., 2., 2.));
    98   ShapeFactory::getInstance().setTranslation(Vector(0., 0., 0.));
    99   Shape s = ShapeFactory::getInstance().produce();
     86  Shape s = ShapeFactory::getInstance().produce(SphereType, Vector(0., 0., 0.), Vector(2., 2., 2.));
    10087
    10188  CPPUNIT_ASSERT( s.isInside( Vector(1.5,0.,0.) ) );
    … …  
    10996void ShapeFactoryTest::translateTest()
    11097{
    111   ShapeFactory::getInstance().setType(SphereType);
    112   ShapeFactory::getInstance().setAngle(0., 0., 0.);
    113   ShapeFactory::getInstance().setStretch(Vector(1., 1., 1.));
    114   ShapeFactory::getInstance().setTranslation(Vector(1., 0., 0.));
    115   Shape s = ShapeFactory::getInstance().produce();
     98  Shape s = ShapeFactory::getInstance().produce(SphereType, Vector(1., 0., 0.));
    11699
    117100  CPPUNIT_ASSERT( s.isInside( Vector(1.5,0.,0.) ) );
    … …  
    128111void ShapeFactoryTest::stretchTest()
    129112{
    130   ShapeFactory::getInstance().setType(SphereType);
    131   ShapeFactory::getInstance().setAngle(0., 0., 0.);
    132   ShapeFactory::getInstance().setStretch(Vector(2., 1., 1.));
    133   ShapeFactory::getInstance().setTranslation(Vector(0., 0., 0.));
    134   Shape s = ShapeFactory::getInstance().produce();
     113  Shape s = ShapeFactory::getInstance().produce(SphereType, Vector(0., 0., 0.), Vector(2., 1., 1.));
    135114
    136115  CPPUNIT_ASSERT( s.isInside( Vector(1.5,0.,0.) ) );
    … …  
    144123void ShapeFactoryTest::transformTest()
    145124{
    146   ShapeFactory::getInstance().setType(SphereType);
    147   ShapeFactory::getInstance().setAngle(45., 0., 0.);
    148   ShapeFactory::getInstance().setStretch(Vector(1., 1., 1.));
    149   ShapeFactory::getInstance().setTranslation(Vector(0., 0., 0.));
    150   Shape s = ShapeFactory::getInstance().produce();
     125  Shape s = ShapeFactory::getInstance().produce(SphereType, Vector(0., 0., 0.), Vector(1., 1., 1.), 45., 0., 0.);
    151126
    152127  CPPUNIT_ASSERT( s.isInside( Vector(.5,0.,0.) ) );
    … …  
    160135void ShapeFactoryTest::getterSetterTest()
    161136{
    162   ShapeFactory::getInstance().setType(SphereType);
    163   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().getType(), SphereType );
    164   ShapeFactory::getInstance().setType(CuboidType);
    165   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().getType(), CuboidType );
    166137#ifndef NDEBUG
    167   CPPUNIT_ASSERT_THROW( ShapeFactory::getInstance().setType((ShapeType)-1), Assert::AssertionFailure );
     138  CPPUNIT_ASSERT_THROW( ShapeFactory::getInstance().produce((ShapeType)-1), Assert::AssertionFailure );
    168139#endif
    169140
    170141
    171   ShapeFactory::getInstance().setAngle(45., 60., 90.);
    172   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().getAngle()[0], 45. );
    173   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().getAngle()[1], 60. );
    174   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().getAngle()[2], 90. );
    175 
    176 
    177   ShapeFactory::getInstance().setStretch(Vector(2., 3., 4.));
    178   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().getStretch(), Vector(2., 3., 4.) );
    179142#ifndef NDEBUG
    180   CPPUNIT_ASSERT_THROW( ShapeFactory::getInstance().setStretch(Vector(0., 0., 0.)), Assert::AssertionFailure );
     143  CPPUNIT_ASSERT_THROW( ShapeFactory::getInstance().produce(SphereType, Vector(0., 0., 0.), Vector(0., 0., 0.)), Assert::AssertionFailure );
    181144#endif
    182145#ifndef NDEBUG
    183   CPPUNIT_ASSERT_THROW( ShapeFactory::getInstance().setStretch(Vector(1., 1., 0.)), Assert::AssertionFailure );
     146  CPPUNIT_ASSERT_THROW( ShapeFactory::getInstance().produce(SphereType, Vector(0., 0., 0.), Vector(1., 1., 0.)), Assert::AssertionFailure );
    184147#endif
    185 
    186   ShapeFactory::getInstance().setTranslation(Vector(1., 2., 3.));
    187   CPPUNIT_ASSERT_EQUAL( ShapeFactory::getInstance().getTranslation(), Vector(1., 2., 3.) );
    188148}
    189149

  • tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at

    r060c7d r842aac  
    5151AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/pre/water.xyz .], 0)
    5252AT_CHECK([../../molecuilder -i waterbox-mirrored.xyz -o xyz --fill-void water.xyz --distances "3.1,3.1,3.1" --distance-to-boundary "1." --DoRotate 0], 0, [stdout], [stderr])
    53 AT_CHECK([../../molecuilder -i waterbox-mirrored.xyz -I -v 3  --set-shape --shape-type "sphere" --translation "5.63,5.71,5.71" --stretch "0.2,0.2,0.2" --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --select-atoms-molecules --rotate-around-self 180 --axis "0,1,0"], 0, [stdout], [stderr])
     53AT_CHECK([../../molecuilder -i waterbox-mirrored.xyz -I -v 3  --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "5.63,5.71,5.71" --stretch "0.2,0.2,0.2" --select-shape-by-name "sphere1" --select-atoms-inside-volume --select-atoms-molecules --rotate-around-self 180 --axis "0,1,0"], 0, [stdout], [stderr])
    5454AT_CHECK([../../molecuilder -i waterbox-mirrored.xyz -o xyz -I --select-all-molecules --dipole-correlation --bin-start -0.5 --bin-width 1. --bin-end 359.5 --output-file waterbox-mirrored_values.dat --bin-output-file waterbox-mirrored_histogram.dat], 0, [stdout], [stderr])
    5555AT_CHECK([file=waterbox-mirrored_histogram.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox-mirrored_histogram.dat], 0, [ignore], [ignore])

  • tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at

    r060c7d r842aac  
    4141AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
    4242AT_CHECK([chmod u+w $file], 0)
    43 AT_CHECK([../../molecuilder -i $file --set-shape --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $file --create-shape --shape-name "cube1" --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
    4444AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
    4545AT_CHECK([file=test-withoutcuboid.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/post/test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
    … …  
    4848AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
    4949AT_CHECK([chmod u+w $file], 0)
    50 AT_CHECK([../../molecuilder -i $file --select-all-atoms --set-shape --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
     50AT_CHECK([../../molecuilder -i $file --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
    5151AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-cuboid.xyz-sorted], 0, [ignore], [ignore])
    5252AT_CHECK([file=test-cuboid.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/post/test-cuboid.xyz-sorted], 0, [ignore], [ignore])
    … …  
    6363AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
    6464AT_CHECK([chmod u+w $file], 0)
    65 AT_CHECK([../../molecuilder -i $file --select-all-atoms --set-shape --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
     65AT_CHECK([../../molecuilder -i $file --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
    6666AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/$file], 0, [ignore], [ignore])
    6767
    … …  
    6969AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
    7070AT_CHECK([chmod u+w $file], 0)
    71 AT_CHECK([../../molecuilder -i $file --set-shape --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
     71AT_CHECK([../../molecuilder -i $file --create-shape --shape-name "cube1" --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
    7272AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/$file], 0, [ignore], [ignore])
    7373
    … …  
    8181AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
    8282AT_CHECK([chmod u+w $file], 0)
    83 AT_CHECK([../../molecuilder -i $file --set-shape --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
     83AT_CHECK([../../molecuilder -i $file --create-shape --shape-name "cube1" --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
    8484AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
    8585AT_CHECK([file=test-withoutcuboid.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/post/test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
    … …  
    8888AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
    8989AT_CHECK([chmod u+w $file], 0)
    90 AT_CHECK([../../molecuilder -i $file --select-all-atoms --set-shape --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
     90AT_CHECK([../../molecuilder -i $file --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "9.78,2.64,2.64" --stretch "2,2,2" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
    9191AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-cuboid.xyz-sorted], 0, [ignore], [ignore])
    9292AT_CHECK([file=test-cuboid.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/post/test-cuboid.xyz-sorted], 0, [ignore], [ignore])

  • tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at

    r060c7d r842aac  
    4141AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
    4242AT_CHECK([chmod u+w $file], 0)
    43 AT_CHECK([../../molecuilder -i $file --set-shape --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $file --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
    4444AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
    4545AT_CHECK([file=test-withoutsphere.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/post/test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
    … …  
    4848AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
    4949AT_CHECK([chmod u+w $file], 0)
    50 AT_CHECK([../../molecuilder -i $file --select-all-atoms --set-shape --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
     50AT_CHECK([../../molecuilder -i $file --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
    5151AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-sphere.xyz-sorted], 0, [ignore], [ignore])
    5252AT_CHECK([file=test-sphere.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/post/test-sphere.xyz-sorted], 0, [ignore], [ignore])
    … …  
    6363AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
    6464AT_CHECK([chmod u+w $file], 0)
    65 AT_CHECK([../../molecuilder -i $file --set-shape --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
     65AT_CHECK([../../molecuilder -i $file --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
    6666AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/$file], 0, [ignore], [ignore])
    6767
    … …  
    6969AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
    7070AT_CHECK([chmod u+w $file], 0)
    71 AT_CHECK([../../molecuilder -i $file --select-all-atoms --set-shape --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
     71AT_CHECK([../../molecuilder -i $file --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
    7272AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/$file], 0, [ignore], [ignore])
    7373
    … …  
    8181AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
    8282AT_CHECK([chmod u+w $file], 0)
    83 AT_CHECK([../../molecuilder -i $file --set-shape --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
     83AT_CHECK([../../molecuilder -i $file --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
    8484AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
    8585AT_CHECK([file=test-withoutsphere.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/post/test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
    … …  
    8888AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
    8989AT_CHECK([chmod u+w $file], 0)
    90 AT_CHECK([../../molecuilder -i $file --select-all-atoms --set-shape --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
     90AT_CHECK([../../molecuilder -i $file --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "7.283585982, 3.275186040, 3.535886037" --stretch "7., 7., 7." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
    9191AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-sphere.xyz-sorted], 0, [ignore], [ignore])
    9292AT_CHECK([file=test-sphere.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/post/test-sphere.xyz-sorted], 0, [ignore], [ignore])

  • tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at

    r060c7d r842aac  
    4242AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SphericalSurface/pre/tensid.potentials .], 0)
    4343AT_CHECK([chmod u+w $file], 0)
    44 AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i $file --select-all-molecules --rotate-to-principal-axis-system "0,0,-1" --set-shape --shape-type "sphere" --translation "0,0,0" --stretch "20.,20.,20." --fill-surface --count 200 --min-distance 3.1 --Alignment-Axis "0,0,1"], 0, [stdout], [stderr])
     44AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i $file --select-all-molecules --rotate-to-principal-axis-system "0,0,-1" --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "0,0,0" --stretch "20.,20.,20." --select-shape-by-name "sphere1" --fill-surface --count 200 --min-distance 3.1 --Alignment-Axis "0,0,1"], 0, [stdout], [stderr])
    4545AT_CHECK([grep "200 out of 200 returned true from predicate" stdout], 0, [ignore], [ignore])
    4646AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/SphericalSurface/post/tensid.data], 0, [ignore], [ignore])
    … …  
    5656AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SphericalSurface/pre/tensid.potentials .], 0)
    5757AT_CHECK([chmod u+w $file], 0)
    58 AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i $file --select-all-molecules --rotate-to-principal-axis-system "0,0,-1" --set-shape --shape-type "sphere" --translation "0,0,0" --stretch "20.,20.,20." --fill-surface --count 200 --min-distance 3.1 --Alignment-Axis "0,0,1" --undo], 0, [stdout], [stderr])
     58AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i $file --select-all-molecules --rotate-to-principal-axis-system "0,0,-1" --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "0,0,0" --stretch "20.,20.,20." --select-shape-by-name "sphere1" --fill-surface --count 200 --min-distance 3.1 --Alignment-Axis "0,0,1" --undo], 0, [stdout], [stderr])
    5959AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/SphericalSurface/post/$file], 0, [ignore], [ignore])
    6060
    … …  
    6969AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SphericalSurface/pre/tensid.potentials .], 0)
    7070AT_CHECK([chmod u+w $file], 0)
    71 AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i $file --select-all-molecules --rotate-to-principal-axis-system "0,0,-1" --set-shape --shape-type "sphere" --translation "0,0,0" --stretch "20.,20.,20." --fill-surface --count 200 --min-distance 3.1 --Alignment-Axis "0,0,1" --undo --redo], 0, [stdout], [stderr])
     71AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i $file --select-all-molecules --rotate-to-principal-axis-system "0,0,-1" --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "0,0,0" --stretch "20.,20.,20." --select-shape-by-name "sphere1" --fill-surface --count 200 --min-distance 3.1 --Alignment-Axis "0,0,1" --undo --redo], 0, [stdout], [stderr])
    7272AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/SphericalSurface/post/tensid.data], 0, [ignore], [ignore])
    7373

  • tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at

    r060c7d r842aac  
    4242AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    4343AT_CHECK([chmod u+w $file], 0)
    44 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
     44AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
    4545AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
    4646
    … …  
    6363AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    6464AT_CHECK([chmod u+w $file], 0)
    65 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
     65AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
    6666AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
    6767
    … …  
    7575AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    7676AT_CHECK([chmod u+w $file], 0)
    77 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
     77AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
    7878AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
    7979

  • tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at

    r060c7d r842aac  
    4141AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    4242AT_CHECK([chmod u+w $file], 0)
    43 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
    4444AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
    4545
    … …  
    6262AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    6363AT_CHECK([chmod u+w $file], 0)
    64 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
     64AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
    6565AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
    6666
    … …  
    7474AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    7575AT_CHECK([chmod u+w $file], 0)
    76 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
     76AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
    7777AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
    7878

  • tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at

    r060c7d r842aac  
    4242AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    4343AT_CHECK([chmod u+w $file], 0)
    44 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume 0 -r], 0, [stdout], [stderr])
     44AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume 0 -r], 0, [stdout], [stderr])
    4545AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
    4646
    … …  
    6363AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    6464AT_CHECK([chmod u+w $file], 0)
    65 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
     65AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
    6666AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/empty.xyz], 0, [ignore], [ignore])
    6767
    … …  
    7575AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
    7676AT_CHECK([chmod u+w $file], 0)
    77 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
     77AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
    7878AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
    7979

  • tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at

    r060c7d r842aac  
    4141AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    4242AT_CHECK([chmod u+w $file], 0)
    43 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
    4444AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
    4545
    … …  
    6262AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    6363AT_CHECK([chmod u+w $file], 0)
    64 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
     64AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
    6565AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
    6666
    … …  
    7474AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    7575AT_CHECK([chmod u+w $file], 0)
    76 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
     76AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
    7777AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
    7878

  • tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at

    r060c7d r842aac  
    4141AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    4242AT_CHECK([chmod u+w $file], 0)
    43 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
    4444AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
    4545
    … …  
    6262AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    6363AT_CHECK([chmod u+w $file], 0)
    64 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
     64AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
    6565AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
    6666
    … …  
    7474AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    7575AT_CHECK([chmod u+w $file], 0)
    76 AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
     76AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
    7777AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
    7878

  • tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at

    r060c7d r842aac  
    4242AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    4343AT_CHECK([chmod u+w $file], 0)
    44 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume  -r], 0, [stdout], [stderr])
     44AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume  -r], 0, [stdout], [stderr])
    4545AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
    4646
    … …  
    6363AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    6464AT_CHECK([chmod u+w $file], 0)
    65 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
     65AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
    6666AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
    6767
    … …  
    7575AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    7676AT_CHECK([chmod u+w $file], 0)
    77 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
     77AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
    7878AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
    7979

  • tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at

    r060c7d r842aac  
    4141AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    4242AT_CHECK([chmod u+w $file], 0)
    43 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
    4444AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])
    4545
    … …  
    6262AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    6363AT_CHECK([chmod u+w $file], 0)
    64 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
     64AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
    6565AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
    6666
    … …  
    7474AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
    7575AT_CHECK([chmod u+w $file], 0)
    76 AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
     76AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
    7777AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])
    7878
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