Changeset eff536 for tests

Timestamp:

Nov 15, 2012, 5:31:07 PM (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:

d0cd6d

Parents:

09eaac

git-author:

Michael Ankele <ankele@…> (09/07/12 13:55:53)

git-committer:

Frederik Heber <heber@…> (11/15/12 17:31:07)

Message:

AllAtomsInsideCuboid/SphereAction > AllAtomsInsideVolumeAction (using ShapeFactory)

Location:

tests/regression

Files:

• Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) (1 diff)
• Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) (6 diffs)
• Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) (6 diffs)
• Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) (3 diffs)
• Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) (3 diffs)
• Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) (3 diffs)
• Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) (3 diffs)
• Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) (3 diffs)
• Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) (3 diffs)
• Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) (3 diffs)

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

@@ -51 +51 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/pre/water.xyz .], 0)
 AT_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])
-AT_CHECK([../../molecuilder -i waterbox-mirrored.xyz -I -v 3 --select-atoms-inside-sphere 0.2 --position "5.63,5.71,5.71" --select-atoms-molecules --rotate-around-self 180 --axis "0,1,0"], 0, [stdout], [stderr])
+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" --select-atoms-inside-volume --select-atoms-molecules --rotate-around-self 180 --axis "0,1,0"], 0, [stdout], [stderr])
 AT_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])
 AT_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

@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atoms-inside-cuboid "2,2,2" --position "9.78,2.64,2.64" --angle-x 0. --angle-y 0. --angle-z 0. -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-withoutcuboid.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/post/test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
@@ -48 +48 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-all-atoms --unselect-atoms-inside-cuboid "2,2,2" --position "9.78,2.64,2.64" --angle-x 0. --angle-y 0. --angle-z 0. -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-cuboid.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-cuboid.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/post/test-cuboid.xyz-sorted], 0, [ignore], [ignore])
@@ -63 +63 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-all-atoms --unselect-atoms-inside-cuboid "2,2,2" --position "9.78,2.64,2.64" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/$file], 0, [ignore], [ignore])
 
@@ -69 +69 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atoms-inside-cuboid "2,2,2" --position "9.78,2.64,2.64" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/$file], 0, [ignore], [ignore])
 
@@ -81 +81 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atoms-inside-cuboid "2,2,2" --position "9.78,2.64,2.64" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo --redo], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-withoutcuboid.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/post/test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
@@ -88 +88 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveCuboid/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-all-atoms --unselect-atoms-inside-cuboid "2,2,2" --position "9.78,2.64,2.64" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo --redo], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-cuboid.xyz-sorted], 0, [ignore], [ignore])
 AT_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

@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atoms-inside-sphere 7. --position "7.283585982, 3.275186040, 3.535886037" --angle-x 0. --angle-y 0. --angle-z 0. -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-withoutsphere.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/post/test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
@@ -48 +48 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-all-atoms --unselect-atoms-inside-sphere 7. --position "7.283585982, 3.275186040, 3.535886037" --angle-x 0. --angle-y 0. --angle-z 0. -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-sphere.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-sphere.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/post/test-sphere.xyz-sorted], 0, [ignore], [ignore])
@@ -63 +63 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atoms-inside-sphere 7. --position "7.283585982, 3.275186040, 3.535886037" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/$file], 0, [ignore], [ignore])
 
@@ -69 +69 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-all-atoms --unselect-atoms-inside-sphere 7. --position "7.283585982, 3.275186040, 3.535886037" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume -r --undo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/$file], 0, [ignore], [ignore])
 
@@ -81 +81 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atoms-inside-sphere 7. --position "7.283585982, 3.275186040, 3.535886037" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo --redo], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-withoutsphere.xyz-sorted; diff $file ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/post/test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
@@ -88 +88 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/RemoveSphere/pre/test.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-all-atoms --unselect-atoms-inside-sphere 7. --position "7.283585982, 3.275186040, 3.535886037" --angle-x 0. --angle-y 0. --angle-z 0. -r --undo --redo], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume -r --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([sort -n $file | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-sphere.xyz-sorted], 0, [ignore], [ignore])
 AT_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/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at

@@ -42 +42 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-cuboid "10,10,10" --position "0,0,0" -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 
@@ -63 +63 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-cuboid "10,10,10" --position "0,0,0" --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -75 +75 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-cuboid "10,10,10" --position "0,0,0" --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 

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

@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-cuboid "10,10,10" --position "0,0,0" --angle-x 0 --angle-y 0 --angle-z 0 -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 
@@ -62 +62 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-cuboid "10,10,10" --position "0,0,0" --angle-x 0 --angle-y 0 --angle-z 0  --undo -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -74 +74 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-cuboid "10,10,10" --position "0,0,0" --angle-x 0 --angle-y 0 --angle-z 0  --undo --redo -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 

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

@@ -42 +42 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-cuboid "10,10,10" --position "0,0,0" --angle-x 0 --angle-y 0 --angle-z 0 -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume 0 -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
 
@@ -63 +63 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-cuboid "10,10,10" --position "0,0,0" --angle-x 0 --angle-y 0 --angle-z 0  --undo -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/empty.xyz], 0, [ignore], [ignore])
 
@@ -75 +75 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-cuboid "10,10,10" --position "0,0,0" --angle-x 0 --angle-y 0 --angle-z 0  --undo --redo -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
 

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

@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-sphere 10 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
 
@@ -62 +62 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-sphere 10 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -74 +74 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-sphere 10 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
 

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

@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-sphere 1.65 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
 
@@ -62 +62 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-sphere 1.65 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -74 +74 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-atoms-inside-sphere 1.65 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
 

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

@@ -42 +42 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-sphere 10 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume  -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
 
@@ -63 +63 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-sphere 10 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
 
@@ -75 +75 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-sphere 10 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
 

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

@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-sphere 1.65 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])
 
@@ -62 +62 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-sphere 1.65 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
 
@@ -74 +74 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --unselect-atoms-inside-sphere 1.65 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])