Index: tests/GuiChecks/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at
===================================================================
--- tests/GuiChecks/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at	(revision dd6c07d2c5d563c8e46c0a4b01a0de11563eb584)
+++ tests/GuiChecks/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at	(revision dd6c07d2c5d563c8e46c0a4b01a0de11563eb584)
@@ -0,0 +1,105 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2013 University of Bonn
+#    Copyright (C) 2013 Frederik Heber
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+### fragment the molecule and check the number of configs
+#
+# BondFragmentShortRangeResults.dat is created like this:
+# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 0 --server-address 127.0.0.1 --server-port 1026 --fragment-resultfile BondFragmentShortRangeResults.dat
+
+AT_SETUP([Fragmentation - Analyse short-range fragmentation results])
+AT_KEYWORDS([fragmentation analyse-fragment-results])
+
+file=BondFragmentShortRangeResults.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --dry-run --analyse-fragment-results --fragment-resultfile $file --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [ignore])
+AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Fragmentation - Analyse short-range fragmentation results with forces])
+AT_KEYWORDS([fragmentation analyse-fragment-results forces])
+
+file=BondFragmentShortRangeResults.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --dry-run -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --analyse-fragment-results --fragment-resultfile $file --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [ignore])
+AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
+AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+#
+# BondFragmentLongRangeResults.dat is created like this:
+# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 1 --DoValenceOnly 0 --grid-level 4 --near-field-cells 3 --server-address 127.0.0.1 --server-port 1026 --fragment-resultfile BondFragmentLongRangeResults.dat
+
+AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC])
+AT_KEYWORDS([fragmentation analyse-fragment-results])
+
+file=BondFragmentLongRangeResults_OBC.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --dry-run -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --analyse-fragment-results --fragment-resultfile $file --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [stderr])
+AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [stderr])
+#AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
+AT_CHECK([grep "File contains long-range information" stderr], 0, [ignore], [ignore], [
+	AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
+	])
+
+AT_CLEANUP
+
+#
+# BondFragmentLongRangeResults.dat is created like this:
+# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Wrap Wrap Wrap --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 1 --DoValenceOnly 0 --grid-level 4 --near-field-cells 3 --server-address 127.0.0.1 --server-port 1026 --fragment-resultfile BondFragmentLongRangeResults.dat
+
+AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC])
+AT_KEYWORDS([fragmentation analyse-fragment-results])
+
+file=BondFragmentLongRangeResults_PBC.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --dry-run -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --analyse-fragment-results --fragment-resultfile $file --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [stderr])
+AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [stderr])
+#AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
+AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
+AT_CHECK([grep "File contains long-range information" stderr], 0, [ignore], [ignore], [
+	AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
+	])
+
+AT_CLEANUP
