Index: tests/regression/Selection/Atoms/testsuite-selection-atoms-of-molecule.at
===================================================================
--- tests/regression/Selection/Atoms/testsuite-selection-atoms-of-molecule.at	(revision fc5c3aecf61bf757b27c7c4f9060569db2b116c7)
+++ tests/regression/Selection/Atoms/testsuite-selection-atoms-of-molecule.at	(revision 1a0987486025bfa5a57b606108e288ec7f8fe19f)
@@ -5,21 +5,21 @@
 file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecules-atoms 1 -r], 0, [stdout], [stderr])
+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/4/post/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecules-atoms 1 --undo -r], 0, [stdout], [stderr])
+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/4/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecules-atoms 1 --undo --redo -r], 0, [stdout], [stderr])
+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/4/post/$file], 0, [ignore], [ignore])
 file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecules-atoms 2 -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 2 --select-molecules-atoms -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/post/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecules-atoms 2 --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 2 --select-molecules-atoms --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecules-atoms 2 --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 2 --select-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
@@ -29,21 +29,21 @@
 file=molecule0.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --unselect-molecules-atoms 1 -r], 0, [stdout], [stderr])
+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/4/post/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --unselect-molecules-atoms 1 --undo -r], 0, [stdout], [stderr])
+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/4/post/empty.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --unselect-molecules-atoms 1 --undo --redo -r], 0, [stdout], [stderr])
+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/4/post/$file], 0, [ignore], [ignore])
 file=molecule1.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --unselect-molecules-atoms 2 -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 2 --unselect-molecules-atoms -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/post/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --unselect-molecules-atoms 2 --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 2 --unselect-molecules-atoms --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/post/empty.xyz], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --unselect-molecules-atoms 2 --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 2 --unselect-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/4/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
Index: tests/regression/testsuite-molecules.at
===================================================================
--- tests/regression/testsuite-molecules.at	(revision fc5c3aecf61bf757b27c7c4f9060569db2b116c7)
+++ tests/regression/testsuite-molecules.at	(revision 1a0987486025bfa5a57b606108e288ec7f8fe19f)
@@ -45,8 +45,8 @@
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ --select-molecules-atoms 0 -t "1., 1., 1." --periodic 0], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ --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/6/post/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/pre/test2.* .], 0)
-AT_CHECK([../../molecuilder -i test2.conf -e ${abs_top_srcdir}/src/ --select-molecules-atoms 0 -t "-1., -1., -1." --periodic 0], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test2.conf -e ${abs_top_srcdir}/src/ --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/6/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
