Index: tests/regression/Selection/Atoms/ClearAtoms/post/id0_missing.xyz
===================================================================
--- tests/regression/Selection/Atoms/ClearAtoms/post/id0_missing.xyz	(revision b9bfa63421aae8bda04dea61800ff9fe25d337b5)
+++ tests/regression/Selection/Atoms/ClearAtoms/post/id0_missing.xyz	(revision b9bfa63421aae8bda04dea61800ff9fe25d337b5)
@@ -0,0 +1,1030 @@
+1028
+	Created by molecuilder for unselect-all-atoms test
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+O	17.1429	11.4286	17.6471
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+H	17.9015	17.1429	2.85714
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+H	17.9015	17.1429	11.4286
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+H	17.9015	17.1429	15.2943
+H	17.9015	17.1429	14.2857
+O	17.1429	17.1429	17.6471
+H	17.9015	17.1429	18.1514
+H	17.9015	17.1429	17.1429
Index: tests/regression/Selection/Atoms/ClearAtoms/pre/box.xyz
===================================================================
--- tests/regression/Selection/Atoms/ClearAtoms/pre/box.xyz	(revision b9bfa63421aae8bda04dea61800ff9fe25d337b5)
+++ tests/regression/Selection/Atoms/ClearAtoms/pre/box.xyz	(revision b9bfa63421aae8bda04dea61800ff9fe25d337b5)
@@ -0,0 +1,1031 @@
+1029
+	Created by molecuilder on Wed Dec  8 00:25:14 2010
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+H	15.0443	0	8.57143
+O	14.2857	0	11.9329
+H	15.0443	0	12.4371
+H	15.0443	0	11.4286
+O	14.2857	0	14.79
+H	15.0443	0	15.2943
+H	15.0443	0	14.2857
+O	14.2857	0	17.6471
+H	15.0443	0	18.1514
+H	15.0443	0	17.1429
+O	14.2857	2.85714	0.504284
+H	15.0443	2.85714	1.00857
+H	15.0443	2.85714	0
+O	14.2857	2.85714	3.36143
+H	15.0443	2.85714	3.86571
+H	15.0443	2.85714	2.85714
+O	14.2857	2.85714	6.21857
+H	15.0443	2.85714	6.72285
+H	15.0443	2.85714	5.71429
+O	14.2857	2.85714	9.07571
+H	15.0443	2.85714	9.58
+H	15.0443	2.85714	8.57143
+O	14.2857	2.85714	11.9329
+H	15.0443	2.85714	12.4371
+H	15.0443	2.85714	11.4286
+O	14.2857	2.85714	14.79
+H	15.0443	2.85714	15.2943
+H	15.0443	2.85714	14.2857
+O	14.2857	2.85714	17.6471
+H	15.0443	2.85714	18.1514
+H	15.0443	2.85714	17.1429
+O	14.2857	5.71429	0.504284
+H	15.0443	5.71429	1.00857
+H	15.0443	5.71429	0
+O	14.2857	5.71429	3.36143
+H	15.0443	5.71429	3.86571
+H	15.0443	5.71429	2.85714
+O	14.2857	5.71429	6.21857
+H	15.0443	5.71429	6.72285
+H	15.0443	5.71429	5.71429
+O	14.2857	5.71429	9.07571
+H	15.0443	5.71429	9.58
+H	15.0443	5.71429	8.57143
+O	14.2857	5.71429	11.9329
+H	15.0443	5.71429	12.4371
+H	15.0443	5.71429	11.4286
+O	14.2857	5.71429	14.79
+H	15.0443	5.71429	15.2943
+H	15.0443	5.71429	14.2857
+O	14.2857	5.71429	17.6471
+H	15.0443	5.71429	18.1514
+H	15.0443	5.71429	17.1429
+O	14.2857	8.57143	0.504284
+H	15.0443	8.57143	1.00857
+H	15.0443	8.57143	0
+O	14.2857	8.57143	3.36143
+H	15.0443	8.57143	3.86571
+H	15.0443	8.57143	2.85714
+O	14.2857	8.57143	6.21857
+H	15.0443	8.57143	6.72285
+H	15.0443	8.57143	5.71429
+O	14.2857	8.57143	9.07571
+H	15.0443	8.57143	9.58
+H	15.0443	8.57143	8.57143
+O	14.2857	8.57143	11.9329
+H	15.0443	8.57143	12.4371
+H	15.0443	8.57143	11.4286
+O	14.2857	8.57143	14.79
+H	15.0443	8.57143	15.2943
+H	15.0443	8.57143	14.2857
+O	14.2857	8.57143	17.6471
+H	15.0443	8.57143	18.1514
+H	15.0443	8.57143	17.1429
+O	14.2857	11.4286	0.504284
+H	15.0443	11.4286	1.00857
+H	15.0443	11.4286	0
+O	14.2857	11.4286	3.36143
+H	15.0443	11.4286	3.86571
+H	15.0443	11.4286	2.85714
+O	14.2857	11.4286	6.21857
+H	15.0443	11.4286	6.72285
+H	15.0443	11.4286	5.71429
+O	14.2857	11.4286	9.07571
+H	15.0443	11.4286	9.58
+H	15.0443	11.4286	8.57143
+O	14.2857	11.4286	11.9329
+H	15.0443	11.4286	12.4371
+H	15.0443	11.4286	11.4286
+O	14.2857	11.4286	14.79
+H	15.0443	11.4286	15.2943
+H	15.0443	11.4286	14.2857
+O	14.2857	11.4286	17.6471
+H	15.0443	11.4286	18.1514
+H	15.0443	11.4286	17.1429
+O	14.2857	14.2857	0.504284
+H	15.0443	14.2857	1.00857
+H	15.0443	14.2857	0
+O	14.2857	14.2857	3.36143
+H	15.0443	14.2857	3.86571
+H	15.0443	14.2857	2.85714
+O	14.2857	14.2857	6.21857
+H	15.0443	14.2857	6.72285
+H	15.0443	14.2857	5.71429
+O	14.2857	14.2857	9.07571
+H	15.0443	14.2857	9.58
+H	15.0443	14.2857	8.57143
+O	14.2857	14.2857	11.9329
+H	15.0443	14.2857	12.4371
+H	15.0443	14.2857	11.4286
+O	14.2857	14.2857	14.79
+H	15.0443	14.2857	15.2943
+H	15.0443	14.2857	14.2857
+O	14.2857	14.2857	17.6471
+H	15.0443	14.2857	18.1514
+H	15.0443	14.2857	17.1429
+O	14.2857	17.1429	0.504284
+H	15.0443	17.1429	1.00857
+H	15.0443	17.1429	0
+O	14.2857	17.1429	3.36143
+H	15.0443	17.1429	3.86571
+H	15.0443	17.1429	2.85714
+O	14.2857	17.1429	6.21857
+H	15.0443	17.1429	6.72285
+H	15.0443	17.1429	5.71429
+O	14.2857	17.1429	9.07571
+H	15.0443	17.1429	9.58
+H	15.0443	17.1429	8.57143
+O	14.2857	17.1429	11.9329
+H	15.0443	17.1429	12.4371
+H	15.0443	17.1429	11.4286
+O	14.2857	17.1429	14.79
+H	15.0443	17.1429	15.2943
+H	15.0443	17.1429	14.2857
+O	14.2857	17.1429	17.6471
+H	15.0443	17.1429	18.1514
+H	15.0443	17.1429	17.1429
+O	17.1429	0	0.504284
+H	17.9015	0	1.00857
+H	17.9015	0	0
+O	17.1429	0	3.36143
+H	17.9015	0	3.86571
+H	17.9015	0	2.85714
+O	17.1429	0	6.21857
+H	17.9015	0	6.72285
+H	17.9015	0	5.71429
+O	17.1429	0	9.07571
+H	17.9015	0	9.58
+H	17.9015	0	8.57143
+O	17.1429	0	11.9329
+H	17.9015	0	12.4371
+H	17.9015	0	11.4286
+O	17.1429	0	14.79
+H	17.9015	0	15.2943
+H	17.9015	0	14.2857
+O	17.1429	0	17.6471
+H	17.9015	0	18.1514
+H	17.9015	0	17.1429
+O	17.1429	2.85714	0.504284
+H	17.9015	2.85714	1.00857
+H	17.9015	2.85714	0
+O	17.1429	2.85714	3.36143
+H	17.9015	2.85714	3.86571
+H	17.9015	2.85714	2.85714
+O	17.1429	2.85714	6.21857
+H	17.9015	2.85714	6.72285
+H	17.9015	2.85714	5.71429
+O	17.1429	2.85714	9.07571
+H	17.9015	2.85714	9.58
+H	17.9015	2.85714	8.57143
+O	17.1429	2.85714	11.9329
+H	17.9015	2.85714	12.4371
+H	17.9015	2.85714	11.4286
+O	17.1429	2.85714	14.79
+H	17.9015	2.85714	15.2943
+H	17.9015	2.85714	14.2857
+O	17.1429	2.85714	17.6471
+H	17.9015	2.85714	18.1514
+H	17.9015	2.85714	17.1429
+O	17.1429	5.71429	0.504284
+H	17.9015	5.71429	1.00857
+H	17.9015	5.71429	0
+O	17.1429	5.71429	3.36143
+H	17.9015	5.71429	3.86571
+H	17.9015	5.71429	2.85714
+O	17.1429	5.71429	6.21857
+H	17.9015	5.71429	6.72285
+H	17.9015	5.71429	5.71429
+O	17.1429	5.71429	9.07571
+H	17.9015	5.71429	9.58
+H	17.9015	5.71429	8.57143
+O	17.1429	5.71429	11.9329
+H	17.9015	5.71429	12.4371
+H	17.9015	5.71429	11.4286
+O	17.1429	5.71429	14.79
+H	17.9015	5.71429	15.2943
+H	17.9015	5.71429	14.2857
+O	17.1429	5.71429	17.6471
+H	17.9015	5.71429	18.1514
+H	17.9015	5.71429	17.1429
+O	17.1429	8.57143	0.504284
+H	17.9015	8.57143	1.00857
+H	17.9015	8.57143	0
+O	17.1429	8.57143	3.36143
+H	17.9015	8.57143	3.86571
+H	17.9015	8.57143	2.85714
+O	17.1429	8.57143	6.21857
+H	17.9015	8.57143	6.72285
+H	17.9015	8.57143	5.71429
+O	17.1429	8.57143	9.07571
+H	17.9015	8.57143	9.58
+H	17.9015	8.57143	8.57143
+O	17.1429	8.57143	11.9329
+H	17.9015	8.57143	12.4371
+H	17.9015	8.57143	11.4286
+O	17.1429	8.57143	14.79
+H	17.9015	8.57143	15.2943
+H	17.9015	8.57143	14.2857
+O	17.1429	8.57143	17.6471
+H	17.9015	8.57143	18.1514
+H	17.9015	8.57143	17.1429
+O	17.1429	11.4286	0.504284
+H	17.9015	11.4286	1.00857
+H	17.9015	11.4286	0
+O	17.1429	11.4286	3.36143
+H	17.9015	11.4286	3.86571
+H	17.9015	11.4286	2.85714
+O	17.1429	11.4286	6.21857
+H	17.9015	11.4286	6.72285
+H	17.9015	11.4286	5.71429
+O	17.1429	11.4286	9.07571
+H	17.9015	11.4286	9.58
+H	17.9015	11.4286	8.57143
+O	17.1429	11.4286	11.9329
+H	17.9015	11.4286	12.4371
+H	17.9015	11.4286	11.4286
+O	17.1429	11.4286	14.79
+H	17.9015	11.4286	15.2943
+H	17.9015	11.4286	14.2857
+O	17.1429	11.4286	17.6471
+H	17.9015	11.4286	18.1514
+H	17.9015	11.4286	17.1429
+O	17.1429	14.2857	0.504284
+H	17.9015	14.2857	1.00857
+H	17.9015	14.2857	0
+O	17.1429	14.2857	3.36143
+H	17.9015	14.2857	3.86571
+H	17.9015	14.2857	2.85714
+O	17.1429	14.2857	6.21857
+H	17.9015	14.2857	6.72285
+H	17.9015	14.2857	5.71429
+O	17.1429	14.2857	9.07571
+H	17.9015	14.2857	9.58
+H	17.9015	14.2857	8.57143
+O	17.1429	14.2857	11.9329
+H	17.9015	14.2857	12.4371
+H	17.9015	14.2857	11.4286
+O	17.1429	14.2857	14.79
+H	17.9015	14.2857	15.2943
+H	17.9015	14.2857	14.2857
+O	17.1429	14.2857	17.6471
+H	17.9015	14.2857	18.1514
+H	17.9015	14.2857	17.1429
+O	17.1429	17.1429	0.504284
+H	17.9015	17.1429	1.00857
+H	17.9015	17.1429	0
+O	17.1429	17.1429	3.36143
+H	17.9015	17.1429	3.86571
+H	17.9015	17.1429	2.85714
+O	17.1429	17.1429	6.21857
+H	17.9015	17.1429	6.72285
+H	17.9015	17.1429	5.71429
+O	17.1429	17.1429	9.07571
+H	17.9015	17.1429	9.58
+H	17.9015	17.1429	8.57143
+O	17.1429	17.1429	11.9329
+H	17.9015	17.1429	12.4371
+H	17.9015	17.1429	11.4286
+O	17.1429	17.1429	14.79
+H	17.9015	17.1429	15.2943
+H	17.9015	17.1429	14.2857
+O	17.1429	17.1429	17.6471
+H	17.9015	17.1429	18.1514
+H	17.9015	17.1429	17.1429
Index: tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at
===================================================================
--- tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at	(revision b9bfa63421aae8bda04dea61800ff9fe25d337b5)
+++ tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at	(revision b9bfa63421aae8bda04dea61800ff9fe25d337b5)
@@ -0,0 +1,14 @@
+### clear atom selection
+
+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])
+AT_CLEANUP
