Index: tests/regression/Simple_configuration/2/post/test.conf
===================================================================
--- tests/regression/Simple_configuration/2/post/test.conf	(revision e4afb4b989433224538ab4ba0f471e4573bbeaf2)
+++ tests/regression/Simple_configuration/2/post/test.conf	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -28,5 +28,5 @@
 OutSrcStep	5	# Output "restart" data every ..th step
 TargetTemp	0.000950045	# Target temperature
-MaxPsiStep	0	# number of Minimisation steps per state (0 - default)
+MaxPsiStep	3	# number of Minimisation steps per state (0 - default)
 EpsWannier	1e-07	# tolerance value for spread minimisation of orbitals
 
@@ -36,5 +36,5 @@
 RelEpsKineticE	1e-05	# relative change in kinetic energy
 MaxMinStopStep	1	# check every ..th steps
-MaxMinGapStopStep	0	# check every ..th steps
+MaxMinGapStopStep	1	# check every ..th steps
 
 # Values specifying when to stop for INIT, otherwise same as above
@@ -43,5 +43,5 @@
 InitRelEpsKineticE	0.0001	# relative change in kinetic energy
 InitMaxMinStopStep	1	# check every ..th steps
-InitMaxMinGapStopStep	0	# check every ..th steps
+InitMaxMinGapStopStep	1	# check every ..th steps
 
 BoxLength			# (Length of a unit cell)
Index: tests/regression/Simple_configuration/2/post/test.pdb
===================================================================
--- tests/regression/Simple_configuration/2/post/test.pdb	(revision e4afb4b989433224538ab4ba0f471e4573bbeaf2)
+++ tests/regression/Simple_configuration/2/post/test.pdb	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -1,3 +1,3 @@
 REMARK created by molecuilder on Fri Aug 27 12:18:33 2010
-ATOM      1  H01 non b   0        10.0    10.0    10.0   1.0   1.0         0 H 0
+ATOM      1  H01 tes b   0        10.0    10.0    10.0   1.0   1.0         0 H 0
 END
Index: tests/regression/Simple_configuration/2/pre/test.conf
===================================================================
--- tests/regression/Simple_configuration/2/pre/test.conf	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
+++ tests/regression/Simple_configuration/2/pre/test.conf	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -0,0 +1,72 @@
+# ParallelCarParinello - main configuration file - created with molecuilder
+
+mainname	pcp	# programm name (for runtime files)
+defaultpath	not specified	# where to put files during runtime
+pseudopotpath	not specified	# where to find pseudopotentials
+
+ProcPEGamma	8	# for parallel computing: share constants
+ProcPEPsi	1	# for parallel computing: share wave functions
+DoOutVis	0	# Output data for OpenDX
+DoOutMes	1	# Output data for measurements
+DoOutOrbitals	0	# Output all Orbitals
+DoOutCurr	0	# Ouput current density for OpenDx
+DoOutNICS	0	# Output Nucleus independent current shieldings
+DoPerturbation	0	# Do perturbation calculate and determine susceptibility and shielding
+DoFullCurrent	0	# Do full perturbation
+DoConstrainedMD	0	# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD
+Thermostat	Berendsen	2.5	# Which Thermostat and its parameters to use in MD case.
+CommonWannier	0	# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center
+SawtoothStart	0.01	# Absolute value for smooth transition at cell border 
+VectorPlane	0	# Cut plane axis (x, y or z: 0,1,2) for two-dim current vector plot
+VectorCut	0	# Cut plane axis value
+AddGramSch	1	# Additional GramSchmidtOrtogonalization to be safe
+Seed		1	# initial value for random seed for Psi coefficients
+
+MaxOuterStep	0	# number of MolecularDynamics/Structure optimization steps
+Deltat	0.01	# time per MD step
+OutVisStep	10	# Output visual data every ...th step
+OutSrcStep	5	# Output "restart" data every ..th step
+TargetTemp	0.000950045	# Target temperature
+MaxPsiStep	0	# number of Minimisation steps per state (0 - default)
+EpsWannier	1e-07	# tolerance value for spread minimisation of orbitals
+
+# Values specifying when to stop
+MaxMinStep	100	# Maximum number of steps
+RelEpsTotalE	1e-07	# relative change in total energy
+RelEpsKineticE	1e-05	# relative change in kinetic energy
+MaxMinStopStep	1	# check every ..th steps
+MaxMinGapStopStep	0	# check every ..th steps
+
+# Values specifying when to stop for INIT, otherwise same as above
+MaxInitMinStep	100	# Maximum number of steps
+InitRelEpsTotalE	1e-05	# relative change in total energy
+InitRelEpsKineticE	0.0001	# relative change in kinetic energy
+InitMaxMinStopStep	1	# check every ..th steps
+InitMaxMinGapStopStep	0	# check every ..th steps
+
+BoxLength			# (Length of a unit cell)
+20	
+0	20	
+0	0	20	
+
+ECut		128	# energy cutoff for discretization in Hartrees
+MaxLevel	5	# number of different levels in the code, >=2
+Level0Factor	2	# factor by which node number increases from S to 0 level
+RiemannTensor	0	# (Use metric)
+PsiType		1	# 0 - doubly occupied, 1 - SpinUp,SpinDown
+MaxPsiDouble	0	# here: specifying both maximum number of SpinUp- and -Down-states
+PsiMaxNoUp	0	# here: specifying maximum number of SpinUp-states
+PsiMaxNoDown	1	# here: specifying maximum number of SpinDown-states
+AddPsis		0	# Additional unoccupied Psis for bandgap determination
+
+RCut		20	# R-cut for the ewald summation
+StructOpt	0	# Do structure optimization beforehand
+IsAngstroem	1	# 0 - Bohr, 1 - Angstroem
+RelativeCoord	0	# whether ion coordinates are relative (1) or absolute (0)
+MaxTypes	1	# maximum number of different ion types
+
+# Ion type data (PP = PseudoPotential, Z = atomic number)
+#Ion_TypeNr.	Amount	Z	RGauss	L_Max(PP)L_Loc(PP)IonMass	# chemical name, symbol
+Ion_Type1	1	1	1.0	3	3	1.00800000000	Hydrogen	H
+#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
+Ion_Type1_1	10.000000000	10.000000000	10.000000000	0 # molecule nr 0
Index: tests/regression/Simple_configuration/2/pre/test.pdb
===================================================================
--- tests/regression/Simple_configuration/2/pre/test.pdb	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
+++ tests/regression/Simple_configuration/2/pre/test.pdb	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -0,0 +1,3 @@
+REMARK created by molecuilder on Fri Aug 27 12:18:33 2010
+ATOM      1  H01 pre b   0        10.0    10.0    10.0   1.0   1.0         0 H 0
+END
Index: tests/regression/Simple_configuration/2/pre/test.xyz
===================================================================
--- tests/regression/Simple_configuration/2/pre/test.xyz	(revision e4afb4b989433224538ab4ba0f471e4573bbeaf2)
+++ tests/regression/Simple_configuration/2/pre/test.xyz	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -1,3 +1,3 @@
 1
- # test configuration, created by molecuilder test suite
-H	10.	10.	10.
+	Created by molecuilder on Tue Oct  6 18:34:23 2009
+H	10	10	10
Index: tests/regression/testsuite-domain.at
===================================================================
--- tests/regression/testsuite-domain.at	(revision e4afb4b989433224538ab4ba0f471e4573bbeaf2)
+++ tests/regression/testsuite-domain.at	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -36,5 +36,5 @@
 AT_KEYWORDS([domain])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/5/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -s "0.5, 1., 0.9"], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ --scale-box "0.5, 1., 0.9"], 0, [stdout], [stderr])
 AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/5/post/test.conf], 0, [stdout], [stderr])
 AT_CLEANUP
Index: tests/regression/testsuite-molecules.at
===================================================================
--- tests/regression/testsuite-molecules.at	(revision e4afb4b989433224538ab4ba0f471e4573bbeaf2)
+++ tests/regression/testsuite-molecules.at	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -57,11 +57,11 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/pre/test-*.xyz .], 0)
 AT_CHECK([../../molecuilder -i test-rotated-z90.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-z90.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file="test-rotated-z90.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder -i test-rotated-z180.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-z180.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file="test-rotated-z180.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder -i test-rotated-z360.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-z360.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file="test-rotated-z360.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder -i test-rotated-xYz20.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([file="test-rotated-xYz20.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file="test-rotated-xYz20.xyz"; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -71,15 +71,15 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --rotate-origin 90. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --rotate-origin 180. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --rotate-origin 360. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --rotate-origin 20. --position "1,2,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -89,15 +89,15 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 90. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 180. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 360. --position "0,0,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 20. --position "1,2,1"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -107,5 +107,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/pre/test.xyz test-copy.xyz], 0)
 AT_CHECK([../../molecuilder -i test-copy.xyz -e ${abs_top_srcdir}/src/ --copy-molecule 0 --position "0,0,10"], 0, [stdout], [stderr])
-AT_CHECK([diff test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/post/test-copy.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/post/test-copy.xyz], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -114,7 +114,7 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/pre/test.xyz test-copy.xyz], 0)
 AT_CHECK([../../molecuilder -i test-copy.xyz -e ${abs_top_srcdir}/src/ --copy-molecule 0 --position "0,0,10" --undo], 0, [stdout], [stderr])
-AT_CHECK([diff test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/pre/test.xyz test-copy.xyz], 0)
 AT_CHECK([../../molecuilder -i test-copy.xyz -e ${abs_top_srcdir}/src/ --copy-molecule 0 --position "0,0,10" --undo --redo], 0, [stdout], [stderr])
-AT_CHECK([diff test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/post/test-copy.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/11/post/test-copy.xyz], 0, [ignore], [ignore])
 AT_CLEANUP
Index: tests/regression/testsuite-simple_configuration.at
===================================================================
--- tests/regression/testsuite-simple_configuration.at	(revision e4afb4b989433224538ab4ba0f471e4573bbeaf2)
+++ tests/regression/testsuite-simple_configuration.at	(revision 001f8a9151f2367cc32119fef0f83b2bfdaf9222)
@@ -10,15 +10,54 @@
 AT_CLEANUP
 
-# 2. parsing an xyz
-AT_SETUP([Simple configuration - parsing xyz file])
-AT_KEYWORDS([configuration])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz parsertest.xyz], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp pdb xyz -p parsertest.xyz], 0, [ignore], [ignore])
-AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1	10.000000000	10.000000000	10.000000000	0 # molecule nr 0
-], [ignore])
+# 2. parsing and storing an xyz
+AT_SETUP([Simple configuration - loading conf file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o pcp -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.conf], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP
+AT_SETUP([Simple configuration - not implemented: loading mpqc file])
+AT_KEYWORDS([configuration])
+#AT_CHECK([../../molecuilder -i test.in -e ${abs_top_srcdir}/src/ -o mpqc -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.in], 139, [ignore], [ignore])
+# not working with NDEBUG it's 139, without its 132
+AT_CLEANUP
+AT_SETUP([Simple configuration - storing mpqc from loaded xyz file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ -o mpqc -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP
+AT_SETUP([Simple configuration - loading mpqc file])
+AT_KEYWORDS([configuration])
+#AT_CHECK([../../molecuilder -i test.in -e ${abs_top_srcdir}/src/ -o mpqc -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.in], 139, [ignore], [ignore])
+# not working with NDEBUG it's 139, without its 132
+AT_CLEANUP
+AT_SETUP([Simple configuration - loading pdb file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.pdb -e ${abs_top_srcdir}/src/ -o pdb -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.pdb], 0, [ignore], [ignore])
+AT_CHECK([file=test.pdb; diff -I '.*created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP
+AT_SETUP([Simple configuration - loading xyz file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ -o xyz -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test.pdb; diff -I '.*created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP
+AT_SETUP([Simple configuration - saving conf file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o pcp -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.conf -s store.conf], 0, [ignore], [ignore])
+AT_CHECK([diff store.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/test.conf], 0, [ignore], [ignore])
+AT_CLEANUP
+AT_SETUP([Simple configuration - saving mpqc (from parsed xyz) file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ -o mpqc -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz -s store.in], 0, [ignore], [ignore])
+AT_CHECK([diff store.in ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/test.in], 0, [ignore], [ignore])
+AT_CLEANUP
+AT_SETUP([Simple configuration - saving pdb file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.pdb -e ${abs_top_srcdir}/src/ -o pdb -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.pdb -s store.pdb], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*created by molecuilder.*' store.pdb ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/test.pdb], 0, [ignore], [ignore])
+AT_CLEANUP
+AT_SETUP([Simple configuration - saving xyz file])
+AT_KEYWORDS([configuration])
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ -o xyz -l ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz -s store.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' store.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/test.xyz], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -47,5 +86,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.xyz test.xyz], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-atom-by-id 0 -E 6 ], 0, [ignore], [ignore])
-AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 AT_SETUP([Simple configuration - Changing element with Undo/Redo])
@@ -53,8 +92,8 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.xyz test.xyz], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-atom-by-id 0 -E 6 --undo], 0, [ignore], [ignore])
-AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.xyz test.xyz], 0)
 AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-atom-by-id 0 -E 6 --undo --redo], 0, [ignore], [ignore])
-AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -172,5 +211,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz --select-all-atoms -t "1,0,0"], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/post/test-shifted.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/post/test-shifted.xyz], 0, [ignore], [ignore])
 AT_CLEANUP
 AT_SETUP([Simple configuration - Translation with Undo/Redo])
@@ -178,7 +217,7 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/pre/test.xyz .], 0)
 AT_CHECK([../../molecuilder -i test.xyz --select-all-atoms -t "1,0,0" --undo], 0, [stdout], [stderr])
-AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/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 test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/post/test-shifted.xyz], 0, [ignore], [ignore])
-AT_CLEANUP
+AT_CHECK([diff -I '.*Created by molecuilder.*' test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/9/post/test-shifted.xyz], 0, [ignore], [ignore])
+AT_CLEANUP
