Changeset 23b0c2 for tests

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

Files:

• Analysis/AngularDipoleCorrelation-DiscreteAngles/testsuite-analysis-angular-dipole-correlation-discrete-angles.at (modified) (2 diffs)
• Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at (modified) (1 diff)
• Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) (2 diffs)
• Analysis/PointCorrelation/testsuite-analysis-point-correlation.at (modified) (2 diffs)
• Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at (modified) (2 diffs)
• Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) (2 diffs)
• Atoms/ChangeElement/testsuite-atoms-change-element.at (modified) (1 diff)
• Atoms/Remove/testsuite-atoms-remove.at (modified) (1 diff)
• Atoms/RemoveInsideCuboid/testsuite-atoms-remove-inside-cuboid.at (modified) (1 diff)
• Atoms/RemoveInsideSphere/testsuite-atoms-remove-inside-sphere.at (modified) (1 diff)
• Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (modified) (1 diff)
• Atoms/Translation/testsuite-atoms-translation.at (modified) (1 diff)
• Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) (1 diff)
• Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) (1 diff)
• Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) (1 diff)
• Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) (1 diff)
• Domain/ScaleBox/testsuite-domain-scale-box.at (modified) (1 diff)
• Filling/FillVoidWithMolecule/post/empty.xyz (deleted)
• Filling/FillVoidWithMolecule/post/propane.xyz (added)
• Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified) (3 diffs)
• Filling/FillWithMolecule/post/empty.xyz (deleted)
• Filling/FillWithMolecule/post/propane.xyz (added)
• Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified) (3 diffs)
• Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) (1 diff)
• Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) (1 diff)
• Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) (2 diffs)
• Fragmentation/testsuite-fragmentation-2nd-order.at (deleted)
• Fragmentation/testsuite-fragmentation-config-check.at (deleted)
• Fragmentation/testsuite-fragmentation-maxorder.at (deleted)
• Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) (1 diff)
• Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) (1 diff)
• Molecules/BondFile/testsuite-molecules-bond-file.at (modified) (1 diff)
• Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) (1 diff)
• Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified) (1 diff)
• Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified) (1 diff)
• Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified) (1 diff)
• Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) (1 diff)
• Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) (1 diff)
• Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified) (1 diff)
• Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified) (1 diff)
• Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified) (1 diff)
• Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) (1 diff)
• Molecules/Translation/testsuite-molecules-translation.at (modified) (1 diff)
• Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) (1 diff)
• Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) (1 diff)
• Parser/Mpqc/testsuite-parser-mpqc.at (modified) (1 diff)
• Parser/Pcp/testsuite-parser-pcp.at (modified) (1 diff)
• Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at (modified) (1 diff)
• Parser/Tremolo/testsuite-parser-tremolo.at (modified) (1 diff)
• Parser/Xyz/testsuite-parser-xyz.at (modified) (1 diff)
• Selection/Atoms/AllAtoms/post/box.xyz (added)
• Selection/Atoms/AllAtoms/testsuite-selection-all-atoms.at (modified) (1 diff)
• Selection/Atoms/AllAtomsOfMolecule/post/test.xyz (added)
• Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at (modified) (1 diff)
• Selection/Atoms/AtomByElement/testsuite-selection-atoms-by-element.at (modified) (1 diff)
• Selection/Atoms/AtomById/testsuite-selection-atom-by-id.at (modified) (2 diffs)
• Selection/Atoms/AtomsInsideCuboid/testsuite-selection-atoms-inside-cuboid.at (modified) (4 diffs)
• Selection/Atoms/AtomsInsideSphere/testsuite-selection-atoms-inside-sphere.at (modified) (3 diffs)
• Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified) (1 diff)
• Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) (1 diff)
• Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) (1 diff)
• Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) (1 diff)
• Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) (1 diff)

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

@@ -3 +3 @@
 AT_SETUP([Analysis - Angular dipole correlation - same aligned])
 AT_KEYWORDS([analysis,correlation])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/AngularDipoleCorrelation-DiscreteAngles/pre/water.xyz .], 0)
 AT_CHECK([../../molecuilder -i waterbox.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.xyz -o xyz -I --select-all-molecules --dipole-correlation --bin-start -0.5 --bin-width 1. --bin-end 359.5 --output-file waterbox_values.dat --bin-output-file waterbox_histogram.dat], 0, [stdout], [stderr])
 AT_CHECK([file=waterbox_histogram.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/AngularDipoleCorrelation-DiscreteAngles/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Analysis - Angular dipole correlation - same aligned but one])
 AT_KEYWORDS([analysis,correlation])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/AngularDipoleCorrelation-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])
@@ -16 +20 @@
 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 ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/AngularDipoleCorrelation-DiscreteAngles/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at

@@ -3 +3 @@
 AT_SETUP([Analysis - pair correlation range test])
 AT_KEYWORDS([analysis,correlation])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder -i test.conf  -v 3 --select-all-molecules --pair-correlation --elements 1 8 --output-file output-5.csv --bin-output-file bin_output-5.csv --bin-start 0 --bin-end 5], 0, [stdout], [stderr])
 #AT_CHECK([file=output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/post/$file], 0, [ignore], [ignore])
+
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder -i test.conf  -v 3 --select-all-molecules --pair-correlation --elements 1 8 --output-file output-10.csv --bin-output-file bin_output-10.csv --bin-start 5 --bin-end 10], 0, [stdout], [stderr])
 #AT_CHECK([file=output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/post/$file], 0, [ignore], [ignore])
+
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder -i test.conf  -v 3 --select-all-molecules --pair-correlation --elements 1 8 --output-file output-20.csv --bin-output-file bin_output-20.csv --bin-start 10 --bin-end 20], 0, [stdout], [stderr])
 #AT_CHECK([file=output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation-RangeTest/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at

@@ -3 +3 @@
 AT_SETUP([Analysis - pair correlation])
 AT_KEYWORDS([analysis,correlation])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder -i test.conf  -v 3 --select-all-molecules --pair-correlation --elements 1 8 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-end 20], 0, [stdout], [stderr])
@@ -8 +9 @@
 #AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PairCorrelation/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP
 

tests/regression/Analysis/PointCorrelation/testsuite-analysis-point-correlation.at

@@ -3 +3 @@
 AT_SETUP([Analysis - point correlation])
 AT_KEYWORDS([analysis,correlation])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PointCorrelation/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder -i test.conf  -v 7 --select-all-molecules --point-correlation --elements 1 --position "10., 10., 10." --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-end 20], 0, [stdout], [stderr])
@@ -8 +9 @@
 #AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PointCorrelation/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PointCorrelation/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at

@@ -3 +3 @@
 AT_SETUP([Analysis - Principal Axis System])
 AT_KEYWORDS([analysis,correlation])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/PrincipalAxisSystem/pre/water.xyz .], 0)
 AT_CHECK([../../molecuilder -i water.xyz -v 3 --select-all-molecules --principal-axis-system], 0, [stdout], [stderr])
@@ -8 +9 @@
 AT_CHECK([egrep " with eigenvalues.*1.03033" stdout], 0, [ignore], [ignore])
 AT_CHECK([egrep " with eigenvalues.*1.54301" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at

@@ -3 +3 @@
 AT_SETUP([Analysis - surface correlation])
 AT_KEYWORDS([analysis,correlation])
+
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/SurfaceCorrelation/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder -i test.conf  -v 3 -I --select-all-molecules --unselect-molecules-by-formula C3H8 --surface-correlation --elements 1 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-width 1. --bin-end 20 --molecule-by-id 0], 0, [stdout], [stderr])
@@ -8 +9 @@
 #AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/SurfaceCorrelation/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/SurfaceCorrelation/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

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

tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at

@@ -3 +3 @@
 AT_SETUP([Domain - centering with defined boundary])
 AT_KEYWORDS([domain])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/AddEmptyBoundary/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -c "5, 10, 15"], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/AddEmptyBoundary/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  -c "5, 10, 15"], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
-AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/AddEmptyBoundary/post/test.conf], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/AddEmptyBoundary/post/test.conf], 0, [stdout], [stderr])
+
 AT_CLEANUP

tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at

@@ -3 +3 @@
 AT_SETUP([Domain - setting and centering in domain])
 AT_KEYWORDS([domain])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterInBox/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -b "15, 0, 15, 0, 0, 15"], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterInBox/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  -b "15, 0, 15, 0, 0, 15"], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
-AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterInBox/post/test.conf], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterInBox/post/test.conf], 0, [stdout], [stderr])
+
 AT_CLEANUP

tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at

@@ -3 +3 @@
 AT_SETUP([Domain - centering and setting domain])
 AT_KEYWORDS([domain])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterOnEdge/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -O], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterOnEdge/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  -O], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
-AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterOnEdge/post/test.conf], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/CenterOnEdge/post/test.conf], 0, [stdout], [stderr])
+
 AT_CLEANUP

tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at

@@ -3 +3 @@
 AT_SETUP([Domain - duplicating box])
 AT_KEYWORDS([domain])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -o xyz -d "1, 1, 1"], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -o xyz -d "1, 1, 1"], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf test-x.conf], 0)
-AT_CHECK([../../molecuilder -i test-x.conf  -o xyz -d "2, 1, 1"], 0, [stdout], [stderr])
+
+file=test-x.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file -o xyz -d "2, 1, 1"], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
 AT_CHECK([file=test-x.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-x.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test-x.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf test-y.conf], 0)
-AT_CHECK([../../molecuilder -i test-y.conf  -o xyz -d "1, 2, 1"], 0, [stdout], [stderr])
+
+file=test-y.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -o xyz -d "1, 2, 1"], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
 AT_CHECK([file=test-y.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-y.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test-y.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf test-z.conf], 0)
-AT_CHECK([../../molecuilder -i test-z.conf  -o xyz -d "1, 1, 2"], 0, [stdout], [stderr])
+
+file=test-z.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -o xyz -d "1, 1, 2"], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
 AT_CHECK([file=test-z.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-z.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/RepeatBox/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test-z.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
-#AT_CHECK([/bin/false], 12, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at

@@ -3 +3 @@
 AT_SETUP([Domain - scaling box])
 AT_KEYWORDS([domain])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/ScaleBox/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --scale-box "0.5, 1., 0.9"], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/ScaleBox/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --scale-box "0.5, 1., 0.9"], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
-AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/ScaleBox/post/test.conf], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/ScaleBox/post/test.conf], 0, [stdout], [stderr])
+
 AT_CLEANUP

tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at

@@ -3 +3 @@
 AT_SETUP([Filling - filling void space in box])
 AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/test.conf .], 0)
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/test.conf $file], 0)
 AT_DATA([water.xyz], [[3
  # test configuration, created by molecuilder test suite
@@ -10 +12 @@
 H       0.758602 0.     -0.504284 
 ]])
-AT_CHECK([../../molecuilder -i test.conf  -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --distance-to-molecule "1.5" --DoRotate 0], 0, [stdout], [stderr])
-AT_CHECK([file=test.xyz; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --distance-to-molecule "1.5" --DoRotate 0], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*reated by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/post/test.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Filling - filling void space in box with Undo])
 AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/test.conf .], 0)
+
+file=empty.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/test.conf $file], 0)
 AT_DATA([water.xyz], [[3
  # test configuration, created by molecuilder test suite
@@ -23 +29 @@
 H       0.758602 0.     -0.504284 
 ]])
-AT_CHECK([../../molecuilder -i empty.conf  -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --distance-to-molecule "1.5" --DoRotate 0 --undo], 0, [stdout], [stderr])
-AT_CHECK([file=empty.xyz; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --distance-to-molecule "1.5" --DoRotate 0 --undo], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*reated by molecuilder.*' empty.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/post/propane.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
+
+AT_SETUP([Filling - filling void space in box with Redo])
+AT_KEYWORDS([filling])
+AT_XFAIL_IF([/bin/true])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/test.conf $file], 0)
+AT_DATA([water.xyz], [[3
+ # test configuration, created by molecuilder test suite
+O       0.      0.      0.
+H       0.758602 0.     0.504284 
+H       0.758602 0.     -0.504284 
+]])
+AT_CHECK([../../molecuilder -i $file -o xyz --fill-void water.xyz --distances "3.1, 3.1, 3.1"  --distance-to-molecule "1.5" --DoRotate 0 --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*reated by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/post/test.xyz], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
 
 AT_SETUP([Filling - filling void space besides tenside micelle in box])
 AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/*.data .], 0)
-AT_CHECK([../../molecuilder -i tensid.data  -B "30,0,30,0,0,30" --fill-void water.data --distances "3.1, 3.1, 3.1" --distance-to-molecule "2.1" --DoRotate 0], 0, [stdout], [stderr])
-AT_CHECK([file=tensid.data; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/post/$file], 0, [ignore], [ignore])
+
+file=tensid.data
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/tensid.data $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/pre/water.data .], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -B "30,0,30,0,0,30" --fill-void water.data --distances "3.1, 3.1, 3.1" --distance-to-molecule "2.1" --DoRotate 0], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillVoidWithMolecule/post/tensid.data], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at

@@ -3 +3 @@
 AT_SETUP([Filling - filling box around molecule's surface])
 AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/pre/test.conf .], 0)
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_DATA([water.xyz], [[3
  # test configuration, created by molecuilder test suite
@@ -10 +13 @@
 H       0.758602 0.     -0.504284 
 ]])
-AT_CHECK([../../molecuilder -i test.conf  -v 3 -F water.xyz --MaxDistance -1 --distances "3.1, 3.1, 3.1"  --distance-to-molecule "2.1" --DoRotate 0], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file  -v 3 -F water.xyz --MaxDistance -1 --distances "3.1, 3.1, 3.1"  --distance-to-molecule "2.1" --DoRotate 0], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/post/test.conf], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Filling - filling box around molecule's surface with Undo])
 AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/pre/test.conf .], 0)
+
+file=empty.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/pre/test.conf $file], 0)
 AT_DATA([water.xyz], [[3
  # test configuration, created by molecuilder test suite
@@ -23 +30 @@
 H       0.758602 0.     -0.504284 
 ]])
-AT_CHECK([../../molecuilder -i empty.conf  -o xyz -F water.xyz --MaxDistance -1 --distances "3.1, 3.1, 3.1"  --distance-to-molecule "2.1" --DoRotate 0 --undo], 0, [stdout], [stderr])
-AT_CHECK([file=empty.xyz; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file -o xyz -F water.xyz --MaxDistance -1 --distances "3.1, 3.1, 3.1"  --distance-to-molecule "2.1" --DoRotate 0 --undo], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*reated by molecuilder.*' empty.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/FillWithMolecule/post/propane.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at

@@ -2 +2 @@
 
 AT_SETUP([Filling - suspend in water])
+AT_KEYWORDS([filling])
 AT_XFAIL_IF([/bin/true])
-AT_KEYWORDS([filling])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/SuspendInWater/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 3 --select-molecule-by-id 0 -u 1.3], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/SuspendInWater/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/SuspendInWater/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 3 --select-molecule-by-id 0 -u 1.3], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/SuspendInWater/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at

@@ -4 +4 @@
 AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
 AT_XFAIL_IF([/bin/true])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/FragmentMolecule-MaxOrder/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 1 --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i test.conf  -v 1 --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2], 2, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/FragmentMolecule-MaxOrder/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 1 --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file  -v 1 --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2], 2, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at

@@ -3 +3 @@
 AT_SETUP([Fragmentation - Fragmentation])
 AT_KEYWORDS([fragmentation])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/FragmentMolecule/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 1 -I --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/FragmentMolecule/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 1 -I --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2], 0, [ignore], [ignore])
 #AT_CHECK([diff BondFragment0.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/FragmentMolecule/post/BondFragment0.conf], 0, [ignore], [ignore])
 #AT_CHECK([diff BondFragment1.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/FragmentMolecule/post/BondFragment1.conf], 0, [ignore], [ignore])
@@ -12 +14 @@
 AT_CHECK([ls -l BondFragment*.conf | wc -l], 0, [5
 ], [ignore])
+
 AT_CLEANUP

tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at

@@ -3 +3 @@
 AT_SETUP([Graph - DFS analysis])
 AT_KEYWORDS([graph])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/DepthFirstSearch/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf -v 3 --select-all-atoms --create-adjacency -D 2.], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/DepthFirstSearch/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --create-adjacency -D 2.], 0, [stdout], [stderr])
 AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
 ], [ignore])
+
 AT_CLEANUP

tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at

@@ -3 +3 @@
 AT_SETUP([Graph - subgraph dissection with Undo/Redo])
 AT_KEYWORDS([graph])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/SubgraphDissection/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 3 -I], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/SubgraphDissection/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 3 -I], 0, [stdout], [stderr])
 AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/SubgraphDissection/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 3 -I], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/SubgraphDissection/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 3 -I --undo], 0, [stdout], [stderr])
 AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/SubgraphDissection/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 3 -I --undo], 0, [stdout], [stderr])
-AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/SubgraphDissection/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 3 -I --undo --redo], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/SubgraphDissection/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 3 -I --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([grep -c "I scanned 31 molecules." stdout], 0, [2
 ], [ignore])
+
 AT_CLEANUP
 

tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Fragmentation bonds file])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/test.conf $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/test.dbond .], 0)
+AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0], 0, [stdout], [stderr])
 AT_CHECK([file=test.pdb; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Molecules - TREMOLO dbond file])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/silica.* .], 0)
-AT_CHECK([../../molecuilder -i silica.pov1.0000.pdb -v 4 --select-molecule-by-id 0 -A silica.dbond.0000 --skiplines 2 --offset 1], 0, [stdout], [stderr])
-AT_CHECK([fgrep -c "CONECT 7153 6098 5949 5922" silica.pov1.0000.pdb], 0, [1
+
+file=silica.pov1.0000.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/silica.pov1.0000.pdb $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/silica.dbond.0000 .], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 4 --select-molecule-by-id 0 -A silica.dbond.0000 --skiplines 2 --offset 1], 0, [stdout], [stderr])
+AT_CHECK([fgrep -c "CONECT 7153 6098 5949 5922" $file], 0, [1
 ], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Copy molecule with Undo/Redo])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz test-copy.xyz], 0)
-AT_CHECK([../../molecuilder -i test-copy.xyz  --copy-molecule 0 --position "0,0,10"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/test-copy.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz test-copy.xyz], 0)
-AT_CHECK([../../molecuilder -i test-copy.xyz  --copy-molecule 0 --position "0,0,10" --undo], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz test-copy.xyz], 0)
-AT_CHECK([../../molecuilder -i test-copy.xyz  --copy-molecule 0 --position "0,0,10" --undo --redo], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/test-copy.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/tensid.* .], 0)
-AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i tensid.data  --copy-molecule 0 --position "0,0,10"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' tensid.data ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/tensid.data], 0, [ignore], [ignore])
+
+file=test-copy.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --copy-molecule 0 --position "0,0,10"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/test-copy.xyz], 0, [ignore], [ignore])
+
+file=test-copy.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --copy-molecule 0 --position "0,0,10" --undo], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz], 0, [ignore], [ignore])
+
+file=test-copy.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --copy-molecule 0 --position "0,0,10" --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/test-copy.xyz], 0, [ignore], [ignore])
+
+file=tensid.data
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/tensid.data $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/tensid.potentials .], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i $file --copy-molecule 0 --position "0,0,10"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/tensid.data], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Linear interpolation])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/LinearInterpolationofTrajectories/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-all-atoms --linear-interpolation-of-trajectories --start-step 0 --interpolation-steps 9 --end-step 1 --id-mapping 1 -S teststep.conf], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/LinearInterpolationofTrajectories/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-atoms --linear-interpolation-of-trajectories --start-step 0 --interpolation-steps 9 --end-step 1 --id-mapping 1 -S teststep.conf], 0, [stdout], [stderr])
 AT_CHECK([fgrep -c 'Ion_Type1_1' teststep.conf], 0, [10
 ], [ignore])
 AT_CHECK([diff teststep.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/LinearInterpolationofTrajectories/post/teststep.conf], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Rotate around origin])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-atoms --rotate-around-origin 90. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-atoms --rotate-around-origin 180. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-atoms --rotate-around-origin 360. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-atoms --rotate-around-origin 20. --position "1,2,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-atoms --rotate-around-origin 90. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-atoms --rotate-around-origin 180. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-atoms --rotate-around-origin 360. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-atoms --rotate-around-origin 20. --position "1,2,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundOrigin/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Rotate around self])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-molecules --rotate-around-self 90. --axis "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-molecules --rotate-around-self 180. --axis "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-molecules --rotate-around-self 360. --axis "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz  --select-all-molecules --rotate-around-self 20. --axis "1,2,1"], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-molecules --rotate-around-self 90. --axis "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-molecules --rotate-around-self 180. --axis "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-molecules --rotate-around-self 360. --axis "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-molecules --rotate-around-self 20. --axis "1,2,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateAroundSelf/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Rotate to PAS])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/pre/test-*.xyz .], 0)
-AT_CHECK([../../molecuilder -i test-rotated-z90.xyz  --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-z90.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i test-rotated-z180.xyz  --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-z180.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i test-rotated-z360.xyz  --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-z360.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i test-rotated-xYz20.xyz  --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-xYz20.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/$file], 0, [ignore], [ignore])
+
+file=test-rotated-z90.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-z90.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
+
+file=test-rotated-z180.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-z180.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
+
+file=test-rotated-z360.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-z360.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
+
+file=test-rotated-xYz20.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/pre/test-rotated-xYz20.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/RotateToPrincipalAxisSystem/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Storing adjacency info])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveAdjacency/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 1 --select-all-atoms --create-adjacency --select-molecule-by-id 0 -J test.adj], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveAdjacency/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 1 --select-all-atoms --create-adjacency --select-molecule-by-id 0 -J test.adj], 0, [stdout], [stderr])
 AT_CHECK([file=test.adj; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveAdjacency/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Storing bond info])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveBonds/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 1 --select-all-atoms --create-adjacency --select-molecule-by-id 0 -j test.dbond], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveBonds/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  -v 1 --select-all-atoms --create-adjacency --select-molecule-by-id 0 -j test.dbond], 0, [stdout], [stderr])
 AT_CHECK([file=test.dbond; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveBonds/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Save selected molecules])
 AT_KEYWORDS([Molecules,save,selection])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveSelectedMolecules/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder -i test.xyz -I --select-molecule-by-order 1 -s testsave.xyz], 0, [stdout], [stderr])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveSelectedMolecules/pre/test.xyz $file], 0)
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-order 1 -s testsave.xyz], 0, [stdout], [stderr])
 AT_CHECK([file=testsave.xyz; diff -I '.*Created by.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveSelectedMolecules/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Storing temperature])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveTemperature/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-all-atoms --save-temperature test.ekin], 0, [stdout], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveTemperature/pre/test.conf $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-atoms --save-temperature test.ekin], 0, [stdout], [stderr])
 AT_CHECK([file=test.ekin; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/SaveTemperature/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Translation with periodic boundaries])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation-Periodic/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 --select-molecules-atoms -t "-8., -8., -8." --periodic 1], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation-Periodic/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation-Periodic/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --select-molecules-atoms -t "-8., -8., -8." --periodic 1], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation-Periodic/post/test.conf], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/Translation/testsuite-molecules-translation.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Translation])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 --select-molecules-atoms -t "1., 1., 1." --periodic 0], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/pre/test2.* .], 0)
-AT_CHECK([../../molecuilder -i test2.conf  --select-molecule-by-id 0 --select-molecules-atoms -t "-1., -1., -1." --periodic 0], 0, [stdout], [stderr])
-AT_CHECK([file=test2.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "1., 1., 1." --periodic 0], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/post/test.conf], 0, [ignore], [ignore])
+
+file=test2.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/pre/test2.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "-1., -1., -1." --periodic 0], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Translation/post/test2.conf], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at

@@ -3 +3 @@
 AT_SETUP([Molecules - Verlet force integration])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/VerletIntegration/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-all-atoms -P test.forces --MDSteps 1 --deltat 0.01 --keep-fixed-CenterOfMass 0], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/VerletIntegration/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/VerletIntegration/pre/test.conf $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/VerletIntegration/pre/test.forces .], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  --select-all-atoms -P test.forces --MDSteps 1 --deltat 0.01 --keep-fixed-CenterOfMass 0], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/VerletIntegration/post/test.conf], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at

@@ -3 +3 @@
 AT_SETUP([Standard Options - invalid commands on present configs])
 AT_KEYWORDS([options])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Options/InvalidCommands/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -t], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -s -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -E -c -b -a -U -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -c -b -a -U -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -b -a -U -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -a -U -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -U -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -T -u], 134, [ignore], [stderr])
-AT_CHECK([../../molecuilder -i test.conf  -u], 134, [ignore], [stderr])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Options/InvalidCommands/pre/test.conf $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file  -t], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -s -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -E -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder -i $file  -u], 134, [ignore], [stderr])
+
 AT_CLEANUP

tests/regression/Parser/Mpqc/testsuite-parser-mpqc.at

@@ -3 +3 @@
 AT_SETUP([Parser - loading empty mpqc file])
 AT_KEYWORDS([parser,mpqc,emptyfile])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/empty.in .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i empty.in -o mpqc], 0, [ignore], [ignore])
+
+file=empty.in
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/empty.in $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -o mpqc], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - loading mpqc file])
 AT_KEYWORDS([parser,mpqc])
-AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testCLHF.in] -o mpqc, 0, [ignore], [ignore])
-AT_CHECK([file=testCLHF.in; diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testCLKS.in] -o mpqc, 0, [ignore], [ignore])
-AT_CHECK([file=testCLKS.in; diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testMBPT2.in] -o mpqc, 0, [ignore], [ignore])
-AT_CHECK([file=testMBPT2.in; diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testMBPT2_R12.in] -o mpqc, 0, [ignore], [ignore])
-AT_CHECK([file=testMBPT2_R12.in; diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/$file], 0, [ignore], [ignore])
+
+file=testCLHF.in
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testCLHF.in $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file] -o mpqc, 0, [ignore], [ignore])
+AT_CHECK([diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/testCLHF.in], 0, [ignore], [ignore])
+
+file=testCLKS.in
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testCLKS.in $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file] -o mpqc, 0, [ignore], [ignore])
+AT_CHECK([diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/testCLKS.in], 0, [ignore], [ignore])
+
+file=testMBPT2.in
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testMBPT2.in $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file] -o mpqc, 0, [ignore], [ignore])
+AT_CHECK([diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/testMBPT2.in], 0, [ignore], [ignore])
+
+file=testMBPT2_R12.in
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/testMBPT2_R12.in $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file] -o mpqc, 0, [ignore], [ignore])
+AT_CHECK([diff -I '%.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/testMBPT2_R12.in], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - storing mpqc from loaded xyz file])
 AT_KEYWORDS([parser,mpqc,xyz])
+
 AT_CHECK([../../molecuilder -i test.xyz  -o mpqc -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/test.xyz], 0, [ignore], [ignore])
-AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/test.in], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - saving mpqc (from parsed xyz) file])
 AT_KEYWORDS([parser,mpqc,xyz])
+
 AT_CHECK([../../molecuilder -i test.xyz  -o mpqc -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/pre/test.xyz --output store.in], 0, [ignore], [ignore])
 AT_CHECK([diff store.in ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Mpqc/post/test.in], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Parser/Pcp/testsuite-parser-pcp.at

@@ -3 +3 @@
 AT_SETUP([Parser - loading empty conf file])
 AT_KEYWORDS([parser,pcp,emptyfile])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/pre/empty.conf .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i empty.conf -o pcp], 0, [ignore], [ignore])
+
+file=empty.conf
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/pre/empty.conf $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -o pcp], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - loading conf file])
 AT_KEYWORDS([parser,pcp])
+
 AT_CHECK([../../molecuilder -i test.conf -o pcp -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/pre/test.conf], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - saving conf file])
 AT_KEYWORDS([parser,pcp])
+
 AT_CHECK([../../molecuilder -i test.conf -o pcp -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/pre/test.conf --output store.conf], 0, [ignore], [ignore])
 AT_CHECK([diff store.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/post/test.conf], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - loading with multiple time steps])
 AT_KEYWORDS([parser,pcp])
+
 AT_CHECK([../../molecuilder -i testmulti.conf -o pcp -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/pre/testmulti.conf], 0, [ignore], [ignore])
 AT_CHECK([file=testmulti.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Pcp/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at

@@ -3 +3 @@
 AT_SETUP([Parser - parse potentials file])
 AT_KEYWORDS([parser,tremolo,potentials])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/pre/argon.potentials .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -v 2 --parse-tremolo-potentials argon.potentials], 0, [stdout], [ignore])
+
+file=argon.potentials
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/pre/argon.potentials $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -v 2 --parse-tremolo-potentials $file], 0, [stdout], [ignore])
 AT_CHECK([grep "Added Type Argon as reference to element Ar" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - load tremolo file with potentials])
 AT_KEYWORDS([parser,tremolo,load,potentials])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/pre/argon.* .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -v 2 --parse-tremolo-potentials argon.potentials -i argon.data], 0, [stdout], [ignore])
+
+file=argon.data
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/pre/argon.data $file], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/pre/argon.potentials .], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -v 2 --parse-tremolo-potentials argon.potentials -i $file], 0, [stdout], [ignore])
 AT_CHECK([grep "Chemical formula is Ar2" stdout], 0, [ignore], [ignore])
-AT_CHECK([file=argon.data; diff -w -I '#.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -w -I '#.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/post/argon.data], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - saving tremolo file from loaded xyz file with potentials])
 AT_KEYWORDS([parser,tremolo,save,potentials])
+
 AT_CHECK([../../molecuilder -v 2 --parse-tremolo-potentials argon.potentials -i test.data -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([file=test.data; diff -w -I '#.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo-Potentials/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Parser/Tremolo/testsuite-parser-tremolo.at

@@ -3 +3 @@
 AT_SETUP([Parser - loading empty tremolo file])
 AT_KEYWORDS([parser,tremolo,emptyfile])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/pre/empty.data .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i empty.data -o tremolo], 0, [ignore], [ignore])
+
+file=empty.data
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/pre/empty.data $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -o tremolo], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - loading tremolo file])
 AT_KEYWORDS([parser,tremolo])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/pre/argon.data .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i argon.data -o tremolo], 0, [ignore], [ignore])
-AT_CHECK([file=argon.data; diff -w -I '#.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/post/$file], 0, [ignore], [ignore])
+
+file=argon.data
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/pre/argon.data $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -o tremolo], 0, [ignore], [ignore])
+AT_CHECK([diff -w -I '#.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/post/argon.data], 0, [ignore], [ignore])
 AT_CLEANUP
+
 
 AT_SETUP([Parser - saving tremolo file])
 AT_KEYWORDS([parser,tremolo])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/pre/test.data .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i test.data -o tremolo --output store.data], 0, [ignore], [ignore])
+
+file=test.data
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/pre/test.data $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file -o tremolo --output store.data], 0, [ignore], [ignore])
 AT_CHECK([diff -w -I '#.*' store.data ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/post/test.data], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Parser - storing tremolo from loaded xyz file])
 AT_KEYWORDS([parser,tremolo,xyz])
+
 AT_CHECK([../../molecuilder -i test.xyz  -o tremolo -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([file=test.data; diff -w -I '#.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Tremolo/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Parser/Xyz/testsuite-parser-xyz.at

@@ -3 +3 @@
 AT_SETUP([Parser - loading empty xyz file])
 AT_KEYWORDS([parser,xyz,emptyfile])
-AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/pre/empty.xyz .], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i empty.xyz -o xyz], 0, [ignore], [ignore])
+
+file=empty.xyz
+AT_CHECK([/bin/cp ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/pre/empty.xyz $file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -o xyz], 0, [ignore], [ignore])
 AT_CLEANUP
 
 AT_SETUP([Parser - loading xyz file])
 AT_KEYWORDS([parser,xyz])
-AT_CHECK([../../molecuilder -i test.xyz -o xyz -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/pre/test.xyz], 0, [ignore], [ignore])
-AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i testmulti.xyz -o xyz -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/pre/testmulti.xyz], 0, [ignore], [ignore])
-AT_CHECK([file=testmulti.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/post/$file], 0, [ignore], [ignore])
+
+file=test.xyz
+AT_CHECK([../../molecuilder -i $file -o xyz -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/post/test.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
+
+AT_SETUP([Parser - loading xyz file with multiple time steps])
+AT_KEYWORDS([parser,xyz])
+
+file=testmulti.xyz
+AT_CHECK([../../molecuilder -i $file -o xyz -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/pre/testmulti.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/post/testmulti.xyz], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
 
 AT_SETUP([Parser - saving xyz file])
 AT_KEYWORDS([parser,xyz])
+
 AT_CHECK([../../molecuilder -i test.xyz  -o xyz -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/pre/test.xyz --output store.xyz], 0, [ignore], [ignore])
 AT_CHECK([diff -I '.*Created by molecuilder.*' store.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Parser/Xyz/post/test.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-all-atoms.at

@@ -3 +3 @@
 AT_SETUP([Selection - All Atoms])
 AT_KEYWORDS([selection])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz allatoms.xyz], 0)
-AT_CHECK([../../molecuilder -i allatoms.xyz -v 3 --select-all-atoms -r], 0, [stdout], [stderr])
-AT_CHECK([file=allatoms.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz allatoms.xyz], 0)
-AT_CHECK([../../molecuilder -i allatoms.xyz -v 3 --select-all-atoms --undo -r], 0, [stdout], [stderr])
-AT_CHECK([file=allatoms.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz allatoms.xyz], 0)
-AT_CHECK([../../molecuilder -i allatoms.xyz -v 3 --select-all-atoms --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([file=allatoms.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/$file], 0, [ignore], [ignore])
+
+file=allatoms.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/allatoms.xyz], 0, [ignore], [ignore])
+
+file=allatoms.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --undo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/box.xyz], 0, [ignore], [ignore])
+
+file=allatoms.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/allatoms.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Unselection - All Atoms])
 AT_KEYWORDS([selection])
+
+file=box.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id 0 --unselect-all-atoms -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/box.xyz], 0, [ignore], [ignore])
+
+file=id0_missing.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/id0_missing.xyz], 0, [ignore], [ignore])
+
+file=box.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz .], 0)
-AT_CHECK([../../molecuilder -i box.xyz -v 3 --select-atom-by-id 0 --unselect-all-atoms -r], 0, [stdout], [stderr])
-AT_CHECK([file=box.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz id0_missing.xyz], 0)
-AT_CHECK([../../molecuilder -i id0_missing.xyz -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo -r], 0, [stdout], [stderr])
-AT_CHECK([file=id0_missing.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/box.xyz .], 0)
-AT_CHECK([../../molecuilder -i box.xyz -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([file=box.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/pre/$file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtoms/post/box.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at

@@ -3 +3 @@
 AT_SETUP([Selection - All atoms of selected molecules])
 AT_KEYWORDS([selection])
+
 file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 0 --select-molecules-atoms -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule1.xyz], 0, [ignore], [ignore])
+
+file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 0 --select-molecules-atoms --undo -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/test.xyz], 0, [ignore], [ignore])
+
+file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 0 --select-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule1.xyz], 0, [ignore], [ignore])
+
 file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 1 --select-molecules-atoms -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule0.xyz], 0, [ignore], [ignore])
+
+file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 1 --select-molecules-atoms --undo -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/test.xyz], 0, [ignore], [ignore])
+
+file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 1 --select-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule0.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Unselection - All atoms of selected molecules])
 AT_KEYWORDS([selection])
+
 file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 0 --unselect-molecules-atoms -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule0.xyz], 0, [ignore], [ignore])
+
+file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 0 --unselect-molecules-atoms --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/empty.xyz], 0, [ignore], [ignore])
+
+file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 0 --unselect-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule0.xyz], 0, [ignore], [ignore])
+
 file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 1 --unselect-molecules-atoms -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule1.xyz], 0, [ignore], [ignore])
+
+file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 1 --unselect-molecules-atoms --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/empty.xyz], 0, [ignore], [ignore])
+
+file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
 AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 1 --unselect-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/molecule1.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-atoms-by-element.at

@@ -4 +4 @@
 AT_SETUP([Selection - All atoms with specific element by atomic number])
 AT_KEYWORDS([selection,atom,element,atomic number])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz test-H_missing.xyz], 0)
-AT_CHECK([../../molecuilder -i test-H_missing.xyz -v 3 --select-atom-by-element 1 -r], 0, [stdout], [stderr])
-AT_CHECK([file=test-H_missing.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz test-Be_missing.xyz], 0)
-AT_CHECK([../../molecuilder -i test-Be_missing.xyz -v 3 --select-atom-by-element 4 -r], 0, [stdout], [stderr])
-AT_CHECK([file=test-Be_missing.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/$file], 0, [ignore], [ignore])
+
+file=test-H_missing.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-element 1 -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/test-H_missing.xyz], 0, [ignore], [ignore])
+
+file=test-Be_missing.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-element 4 -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/test-Be_missing.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Selection - All atoms with specific element by symbol with Undo/Redo])
 AT_KEYWORDS([element,symbol])
+
+file=test.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-element 1 --undo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/test.xyz], 0, [ignore], [ignore])
+
+file=test.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz test.xyz], 0)
-AT_CHECK([../../molecuilder -i test.xyz -v 3 --select-atom-by-element 1 --undo -r], 0, [stdout], [stderr])
-AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz test.xyz], 0)
-AT_CHECK([../../molecuilder -i test.xyz -v 3 --select-atom-by-element 4 --undo -r], 0, [stdout], [stderr])
-AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/$file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-element 4 --undo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/test.xyz], 0, [ignore], [ignore])
+
+file=test-H_missing.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz test-H_missing.xyz], 0)
-AT_CHECK([../../molecuilder -i test-H_missing.xyz -v 3 --select-atom-by-element 1 --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([file=test-H_missing.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/$file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-element 1 --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/test-H_missing.xyz], 0, [ignore], [ignore])
+
+file=test-Be_missing.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/pre/test.xyz test-Be_missing.xyz], 0)
-AT_CHECK([../../molecuilder -i test-Be_missing.xyz -v 3 --select-atom-by-element 4 --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([file=test-Be_missing.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/$file], 0, [ignore], [ignore])
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-element 4 --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomByElement/post/test-Be_missing.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Selection/Atoms/AtomById/testsuite-selection-atom-by-id.at

@@ -9 +9 @@
   # normal
   AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/pre/test.xyz $file])
+  AT_CHECK([chmod u+w $file], 0)
   AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id ${i} -r], [], [ignore], [ignore])
   AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/post/$file])
   # normal
   AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/pre/test.xyz $file])
+  AT_CHECK([chmod u+w $file], 0)
   AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id ${i} --undo -r], [], [ignore], [ignore])
   AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/pre/test.xyz])
   # redo
   AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/pre/test.xyz $file])
+  AT_CHECK([chmod u+w $file], 0)
   AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id ${i} --undo --redo -r], [], [ignore], [ignore])
   AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/post/$file])
@@ -31 +34 @@
   # normal
   AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/pre/test.xyz $file])
+  AT_CHECK([chmod u+w $file], 0)
   AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --unselect-atom-by-id ${i} -r], [], [ignore], [ignore])
   AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/post/$file])
   # normal
   AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/pre/test.xyz $file])
+  AT_CHECK([chmod u+w $file], 0)
   AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --unselect-atom-by-id ${i} --undo -r], [], [ignore], [ignore])
   AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/post/empty.xyz])
   # redo
   AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/pre/test.xyz $file])
+  AT_CHECK([chmod u+w $file], 0)
   AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --unselect-atom-by-id ${i} --undo --redo -r], [], [ignore], [ignore])
   AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomById/post/$file])

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

@@ -3 +3 @@
 AT_SETUP([Selection - All atoms inside cuboid])
 AT_KEYWORDS([selection,cuboid])
+
 file=allatomsoutsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
+
+file=allatomsoutsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
+
+file=allatomsoutsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
+
 # check size of cuboid
 AT_SKIP_IF([! awk '' < /dev/null])  # check whether awk is there
@@ -21 +30 @@
 AT_CHECK([cat < $file | awk -F" " '{ if (($2 < 10) && ($3 < 10) && ($4 < 10)) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
 AT_CHECK([fgrep "1" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Selection - All atoms inside cuboid with defaults])
 AT_KEYWORDS([selection,cuboid])
+
 file=allatomsoutsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
+
+file=allatomsoutsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
+
+file=allatomsoutsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
+
 # check size of cuboid
 AT_SKIP_IF([! awk '' < /dev/null])  # check whether awk is there
@@ -43 +63 @@
 AT_CHECK([cat < $file | awk -F" " '{ if (($2 < 10) && ($3 < 10) && ($4 < 10)) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
 AT_CHECK([fgrep "1" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
 
 AT_SETUP([Unselection - All atoms inside cuboid])
 AT_KEYWORDS([selection,cuboid])
+
 file=allatomsinsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
+
+file=allatomsinsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/empty.xyz], 0, [ignore], [ignore])
+
+file=allatomsinsidecuboid.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
+
 # check size of cuboid
 AT_SKIP_IF([! awk '' < /dev/null])  # check whether awk is there
@@ -65 +96 @@
 AT_CHECK([cat < $file | awk -F" " '{ if (($2 > 10) && ($3 > 10) && ($4 > 10)) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
 AT_CHECK([fgrep "1" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP

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

@@ -3 +3 @@
 AT_SETUP([Selection - All atoms inside sphere])
 AT_KEYWORDS([selection,sphere])
+
 file=allatomsoutsidesphere.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
+
+file=allatomsoutsidesphere.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
+
+file=allatomsoutsidesphere.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
+
 # check size of sphere
 AT_SKIP_IF([! awk '' < /dev/null])  # check whether awk is there
@@ -21 +30 @@
 AT_CHECK([cat < $file | awk -F" " '{ if (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) < 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
 AT_CHECK([fgrep "0" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP
+
+
 
 AT_SETUP([Unselection - All atoms inside sphere])
 AT_KEYWORDS([selection,sphere])
+
 file=allatomsinsidesphere.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
+
+file=allatomsinsidesphere.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
+
+file=allatomsinsidesphere.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/$file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
+
 # check size of sphere
 AT_SKIP_IF([! awk '' < /dev/null])  # check whether cat is there
@@ -43 +64 @@
 AT_CHECK([cat < $file | awk -F" " '{ if (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) < 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
 AT_CHECK([fgrep "524" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP
 

tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at

@@ -3 +3 @@
 AT_SETUP([Unselection - clear atom selection])
 AT_KEYWORDS([selection,clear])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz .], 0)
-AT_CHECK([../../molecuilder -i box.xyz -v 3 --select-atom-by-id 0 --unselect-all-atoms -r], 0, [stdout], [stderr])
-AT_CHECK([file=box.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz id0_missing.xyz], 0)
-AT_CHECK([../../molecuilder -i id0_missing.xyz -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo -r], 0, [stdout], [stderr])
-AT_CHECK([file=id0_missing.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/post/$file], 0, [ignore], [ignore])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz .], 0)
-AT_CHECK([../../molecuilder -i box.xyz -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo --redo -r], 0, [stdout], [stderr])
-AT_CHECK([file=box.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/$file], 0, [ignore], [ignore])
+
+file=box.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id 0 --unselect-all-atoms -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz], 0, [ignore], [ignore])
+
+file=id0_missing.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/post/id0_missing.xyz], 0, [ignore], [ignore])
+
+file=box.xyz
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file -v 3 --select-atom-by-id 0 --unselect-all-atoms --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/ClearAtoms/pre/box.xyz], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at

@@ -4 +4 @@
 AT_KEYWORDS([Tesselation,convex])
 AT_XFAIL_IF([/bin/true])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigConvex/pre/* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 --convex-envelope --convex-file ConvexEnvelope --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
-AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigConvex/post/$file], 0, [ignore], [ignore])
-#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigConvex/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigConvex/pre/test./conf $file], 0)
+convexfile=ConvexEnvelope
+AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --convex-envelope --convex-file $convexfile --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
+AT_CHECK([diff ${convexfile}.dat ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigConvex/post/ConvexEnvelope.dat], 0, [ignore], [ignore])
+#AT_CHECK([diff ${convexfile}.r3d ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigConvex/post/ConvexEnvelope.r3d], 0, [ignore], [ignore])
 AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at

@@ -3 +3 @@
 AT_SETUP([Tesselation - Big non-Convex Envelope])
 AT_KEYWORDS([Tesselation,nonconvex])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigNonConvex/pre/* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 -N 4. --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
-AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigNonConvex/post/$file], 0, [ignore], [ignore])
-#AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigNonConvex/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigNonConvex/pre/test.conf $file], 0)
+nonconvexfile=NonConvexEnvelope
+AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 -N 4. --nonconvex-file $nonconvexfile], 0, [stdout], [stderr])
+AT_CHECK([diff ${nonconvexfile}.dat ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigNonConvex/post/NonConvexEnvelope.dat], 0, [ignore], [ignore])
+#AT_CHECK([diff ${nonconvexfile}.r3d ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/BigNonConvex/post/NonConvexEnvelope.r3d], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at

@@ -3 +3 @@
 AT_SETUP([Tesselation - Convex Envelope])
 AT_KEYWORDS([Tesselation,convex])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/Convex/pre/* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 --convex-envelope --convex-file ConvexEnvelope --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
-AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/Convex/post/$file], 0, [ignore], [ignore])
-#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/Convex/post/$file], 0, [ignore], [ignore])
+
+file=test.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/Convex/pre/test.conf $file], 0)
+convexfile=ConvexEnvelope
+AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --convex-envelope --convex-file $convexfile --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
+AT_CHECK([diff ${convexfile}.dat ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/Convex/post/ConvexEnvelope.dat], 0, [ignore], [ignore])
+#AT_CHECK([diff ${convexfile}.r3d ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/Convex/post/ConvexEnvelope.r3d], 0, [ignore], [ignore])
 AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
 AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
+
 AT_CLEANUP

tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at

@@ -3 +3 @@
 AT_SETUP([Tesselation - Non-Convex Envelope])
 AT_KEYWORDS([Tesselation,nonconvex])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/NonConvex/pre/* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 -N 4. --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
-AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/NonConvex/post/$file], 0, [ignore], [ignore])
-#AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/NonConvex/post/$file], 0, [ignore], [ignore])
+
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/NonConvex/pre/test.conf .], 0)
+nonconvexfile=NonConvexEnvelope
+AT_CHECK([../../molecuilder -i test.conf  --select-molecule-by-id 0 -N 4. --nonconvex-file $nonconvexfile], 0, [stdout], [stderr])
+AT_CHECK([diff ${nonconvexfile}.dat ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/NonConvex/post/NonConvexEnvelope.dat], 0, [ignore], [ignore])
+#AT_CHECK([diff ${nonconvexfile}.r3d ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/NonConvex/post/NonConvexEnvelope.r3d], 0, [ignore], [ignore])
+
 AT_CLEANUP