Changeset 23b0c2 for tests/regression/Atoms

Timestamp:

Apr 27, 2011, 8:59:00 AM (14 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:

caeeb8

Parents:

61749d1

Message:

Restructured test*.at files: 3-step-rule.

• three-step rule: setup, test, cleanup is now each separated by empty line.
• test file name is (most of the time) placed into variable $file.

Location:

tests/regression/Atoms

Files:

• ChangeElement/testsuite-atoms-change-element.at (modified) (1 diff)
• Remove/testsuite-atoms-remove.at (modified) (1 diff)
• RemoveInsideCuboid/testsuite-atoms-remove-inside-cuboid.at (modified) (1 diff)
• RemoveInsideSphere/testsuite-atoms-remove-inside-sphere.at (modified) (1 diff)
• SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (modified) (1 diff)
• Translation/testsuite-atoms-translation.at (modified) (1 diff)

tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at

@@ -3 +3 @@
 AT_SETUP([Atoms - Changing element with Undo/Redo])
 AT_KEYWORDS([atoms])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/test.xyz test.xyz], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-atom-by-id 0 -E 6 ], 0, [ignore], [ignore])
-AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/test.xyz test.xyz], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-atom-by-id 0 -E 6 --undo], 0, [ignore], [ignore])
-AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/test.xyz test.xyz], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-atom-by-id 0 -E 6 --undo --redo], 0, [ignore], [ignore])
-AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/post/$file], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-atom-by-id 0 -E 6 ], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/post/$file], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-atom-by-id 0 -E 6 --undo], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/$file], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-atom-by-id 0 -E 6 --undo --redo], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/ChangeElement/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Atoms/Remove/testsuite-atoms-remove.at

@@ -3 +3 @@
 AT_SETUP([Atoms - Atom removal with Undo/Redo])
 AT_KEYWORDS([atoms])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -o mpqc pcp xyz --select-atom-by-id 0 -r], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  -o mpqc pcp xyz --select-atom-by-id 0 -r], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf --select-atom-by-id 0 -r --undo], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf --select-atom-by-id 0 -r --undo --redo], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-atom-by-id 0 -r --undo], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-atom-by-id 0 -r --undo --redo], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Remove/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Atoms/RemoveInsideCuboid/testsuite-atoms-remove-inside-cuboid.at

@@ -3 +3 @@
 AT_SETUP([Atoms - Removing cuboid of atoms with Undo/Redo])
 AT_KEYWORDS([atoms])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/test.xyz test-withoutcuboid.xyz], 0)
-AT_CHECK([../../molecuilder -i test-withoutcuboid.xyz --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([sort -n test-withoutcuboid.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
+
+file=test-withoutcuboid.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/test.xyz test-cuboid.xyz], 0)
-AT_CHECK([../../molecuilder -i test-cuboid.xyz --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([sort -n test-cuboid.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-cuboid.xyz-sorted], 0, [ignore], [ignore])
+
+file=test-cuboid.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/post/$file], 0, [ignore], [ignore])
 AT_CHECK([cat test-cuboid.xyz-sorted test-withoutcuboid.xyz-sorted | sort -n >test.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz --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([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/test.xyz test-withoutcuboid.xyz], 0)
-AT_CHECK([../../molecuilder -i test-withoutcuboid.xyz --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([sort -n test-withoutcuboid.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutcuboid.xyz-sorted], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/$file], 0, [ignore], [ignore])
+
+file=test-withoutcuboid.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz --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([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/test.xyz test-cuboid.xyz], 0)
-AT_CHECK([../../molecuilder -i test-cuboid.xyz --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([sort -n test-cuboid.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-cuboid.xyz-sorted], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/pre/$file], 0, [ignore], [ignore])
+
+file=test-cuboid.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/post/$file], 0, [ignore], [ignore])
 AT_CHECK([cat test-cuboid.xyz-sorted test-withoutcuboid.xyz-sorted | sort -n >test.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideCuboid/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Atoms/RemoveInsideSphere/testsuite-atoms-remove-inside-sphere.at

@@ -3 +3 @@
 AT_SETUP([Atoms - Removing sphere of atoms with Undo/Redo])
 AT_KEYWORDS([atoms])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/test.xyz test-withoutsphere.xyz], 0)
-AT_CHECK([../../molecuilder -i test-withoutsphere.xyz --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([sort -n test-withoutsphere.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
+
+file=test-withoutsphere.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/test.xyz test-sphere.xyz], 0)
-AT_CHECK([../../molecuilder -i test-sphere.xyz --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([sort -n test-sphere.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-sphere.xyz-sorted], 0, [ignore], [ignore])
+
+file=test-sphere.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/post/$file], 0, [ignore], [ignore])
 AT_CHECK([cat test-sphere.xyz-sorted test-withoutsphere.xyz-sorted | sort -n >test.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz --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([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/test.xyz test-withoutsphere.xyz], 0)
-AT_CHECK([../../molecuilder -i test-withoutsphere.xyz --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([sort -n test-withoutsphere.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-withoutsphere.xyz-sorted], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/$file], 0, [ignore], [ignore])
+
+file=test-withoutsphere.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz --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([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/test.xyz test-sphere.xyz], 0)
-AT_CHECK([../../molecuilder -i test-sphere.xyz --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([sort -n test-sphere.xyz | grep -v -E "^[[[:digit:]]]+" | grep -v "Created by" >test-sphere.xyz-sorted], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/pre/$file], 0, [ignore], [ignore])
+
+file=test-sphere.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/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([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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/post/$file], 0, [ignore], [ignore])
 AT_CHECK([cat test-sphere.xyz-sorted test-withoutsphere.xyz-sorted | sort -n >test.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/RemoveInsideSphere/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at

@@ -3 +3 @@
 AT_SETUP([Atoms - Save selected atoms])
 AT_KEYWORDS([atoms,save,selection])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/SaveSelectedAtoms/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz --select-atom-by-id 0 --save-selected-atoms testsave.xyz], 0, [stdout], [stderr])
 AT_CHECK([file=testsave.xyz; diff -I '.*Created by.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/SaveSelectedAtoms/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Atoms/Translation/testsuite-atoms-translation.at

@@ -3 +3 @@
 AT_SETUP([Atoms - Translation with Undo/Redo])
 AT_KEYWORDS([atoms])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz --select-all-atoms -t "1,0,0"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/post/test-shifted.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz --select-all-atoms -t "1,0,0" --undo], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz --select-all-atoms -t "1,0,0" --undo --redo], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/post/test-shifted.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-all-atoms -t "1,0,0"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/post/test-shifted.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-all-atoms -t "1,0,0" --undo], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-all-atoms -t "1,0,0" --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Atoms/Translation/post/test-shifted.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP