Index: tests/regression/testsuite-analysis.at
===================================================================
--- tests/regression/testsuite-analysis.at	(revision 8d4aa17e45d4c4924afa38b6058dad577c3d5117)
+++ tests/regression/testsuite-analysis.at	(revision ff6a100b82687d82d4c2fef31bdf265072bad599)
@@ -4,5 +4,5 @@
 AT_KEYWORDS([analysis])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E --elements 1 8 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-end 20], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -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])
 AT_CHECK([fgrep "Begin of PairCorrelation" stdout], 0, [ignore], [ignore])
 #AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/post/$file], 0, [ignore], [ignore])
@@ -14,11 +14,11 @@
 AT_KEYWORDS([analysis])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E --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([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -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/2/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E --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([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -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/2/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E --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([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -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/2/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=bin_output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
@@ -29,5 +29,5 @@
 AT_KEYWORDS([analysis])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 7 -C P --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])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -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])
 AT_CHECK([fgrep "Begin of CorrelationToPoint" stdout], 0, [ignore], [ignore])
 #AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/post/$file], 0, [ignore], [ignore])
@@ -39,5 +39,5 @@
 AT_KEYWORDS([analysis])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -I -C S --elements 1 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-width 1. --bin-end 20 --molecule-by-id 207], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -v 3 -I --select-all-molecules --unselect-molecule-by-id 207 --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 207], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Begin of CorrelationToSurface" stdout], 0, [ignore], [ignore])
 #AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])
