Index: tests/Fragmentations/Fragmenting/anthracene/pre/anthracene.pdb
===================================================================
--- tests/Fragmentations/Fragmenting/anthracene/pre/anthracene.pdb	(revision ec7511a359cc1cad57d684179dda96580726d26d)
+++ tests/Fragmentations/Fragmenting/anthracene/pre/anthracene.pdb	(revision ec7511a359cc1cad57d684179dda96580726d26d)
@@ -0,0 +1,52 @@
+COMPND    UNNAMED
+AUTHOR    GENERATED BY OPEN BABEL 2.3.0
+HETATM    1  C   LIG     1      25.220 -16.237   0.000  1.00  0.00           C  
+HETATM    2  C   LIG     1      25.220 -17.639   0.000  1.00  0.00           C  
+HETATM    3  C   LIG     1      26.437 -18.339   0.000  1.00  0.00           C  
+HETATM    4  C   LIG     1      26.437 -15.536   0.000  1.00  0.00           C  
+HETATM    5  C   LIG     1      27.647 -16.237   0.000  1.00  0.00           C  
+HETATM    6  C   LIG     1      27.641 -17.639   0.000  1.00  0.00           C  
+HETATM    7  C   LIG     1      28.852 -18.345   0.000  1.00  0.00           C  
+HETATM    8  C   LIG     1      28.864 -15.541   0.000  1.00  0.00           C  
+HETATM    9  C   LIG     1      30.076 -16.247   0.000  1.00  0.00           C  
+HETATM   10  C   LIG     1      30.133 -17.645   0.000  1.00  0.00           C  
+HETATM   11  C   LIG     1      31.267 -18.355   0.000  1.00  0.00           C  
+HETATM   12  C   LIG     1      32.485 -17.667   0.000  1.00  0.00           C  
+HETATM   13  C   LIG     1      32.497 -16.269   0.000  1.00  0.00           C  
+HETATM   14  C   LIG     1      31.293 -15.559   0.000  1.00  0.00           C  
+HETATM   15  H   LIG     1      24.327 -15.720   0.000  1.00  0.00           H  
+HETATM   16  H   LIG     1      24.327 -18.155   0.000  1.00  0.00           H  
+HETATM   17  H   LIG     1      26.440 -19.371   0.000  1.00  0.00           H  
+HETATM   18  H   LIG     1      26.439 -14.504   0.000  1.00  0.00           H  
+HETATM   19  H   LIG     1      28.838 -19.376   0.000  1.00  0.00           H  
+HETATM   20  H   LIG     1      28.869 -14.509   0.000  1.00  0.00           H  
+HETATM   21  H   LIG     1      31.244 -19.387   0.000  1.00  0.00           H  
+HETATM   22  H   LIG     1      33.374 -18.191   0.000  1.00  0.00           H  
+HETATM   23  H   LIG     1      33.396 -15.761   0.000  1.00  0.00           H  
+HETATM   24  H   LIG     1      31.302 -14.527   0.000  1.00  0.00           H  
+CONECT    1    4    2   15                                            
+CONECT    2    1    3   16                                            
+CONECT    3    2    6   17                                            
+CONECT    4    5    1   18                                            
+CONECT    5    8    4    6                                            
+CONECT    6    3    5    7                                            
+CONECT    7    6   10   19                                            
+CONECT    8    9    5   20                                            
+CONECT    9    8   10   14                                            
+CONECT   10    9   11    7                                            
+CONECT   11   10   12   21                                            
+CONECT   12   11   13   22                                            
+CONECT   13   12   14   23                                            
+CONECT   14   13    9   24                                            
+CONECT   15    1                                                      
+CONECT   16    2                                                      
+CONECT   17    3                                                      
+CONECT   18    4                                                      
+CONECT   19    7                                                      
+CONECT   20    8                                                      
+CONECT   21   11                                                      
+CONECT   22   12                                                      
+CONECT   23   13                                                      
+CONECT   24   14                                                      
+MASTER        0    0    0    0    0    0    0    0   24    0   24    0
+END
Index: tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at
===================================================================
--- tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
+++ tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
@@ -0,0 +1,69 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2008-2012 University of Bonn
+#
+#    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/>.
+#
+#
+#    MoleCuilder - creates and alters molecular systems
+#    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/>.
+#
+### anthracene - order 1 w cycles
+
+AT_SETUP([Fragmentations - anthracene order 1 w cycles])
+AT_KEYWORDS([fragmentation non-convex-envelope])
+
+MOL=anthracene
+DISTANCE="2."
+FILENAME="BondFragment"
+
+CycleNo=3
+FragNo=14
+let FragNo=$FragNo+$CycleNo
+
+file=${MOL}.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/Fragmentations/Fragmenting/${MOL}/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.pdb | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.in | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+
+# check cycles just have six non-hydrogen
+let i=$FragNo-$CycleNo
+while test $i -lt $FragNo; do
+	AT_CHECK([grep -c "^HETATM.*C 0" ${FILENAME}`printf %02d $i`.pdb], 0, [stdout], [ignore])
+	AT_CHECK([test 6 == `cat stdout`], 0, [ignore], [ignore])
+	let i=$i+1
+done
+
+AT_CLEANUP
+
Index: tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at
===================================================================
--- tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
+++ tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
@@ -0,0 +1,61 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2008-2012 University of Bonn
+#
+#    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/>.
+#
+#
+#    MoleCuilder - creates and alters molecular systems
+#    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/>.
+#
+### anthracene - order 2 w cycles
+
+AT_SETUP([Fragmentations - anthracene order 2 w cycles])
+AT_KEYWORDS([fragmentation non-convex-envelope])
+
+MOL=anthracene
+DISTANCE="2."
+FILENAME="BondFragment"
+
+CycleNo=3
+FragNo=30
+let FragNo=$FragNo+$CycleNo
+
+file=${MOL}.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/Fragmentations/Fragmenting/${MOL}/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.pdb | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.in | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
Index: tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at
===================================================================
--- tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
+++ tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
@@ -0,0 +1,61 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2008-2012 University of Bonn
+#
+#    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/>.
+#
+#
+#    MoleCuilder - creates and alters molecular systems
+#    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/>.
+#
+### anthracene - order 3 w cycles
+
+AT_SETUP([Fragmentations - anthracene order 3 w cycles])
+AT_KEYWORDS([fragmentation non-convex-envelope])
+
+MOL=anthracene
+DISTANCE="2."
+FILENAME="BondFragment"
+
+CycleNo=3
+FragNo=52
+let FragNo=$FragNo+$CycleNo
+
+file=${MOL}.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/Fragmentations/Fragmenting/${MOL}/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.pdb | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.in | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
Index: tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at
===================================================================
--- tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
+++ tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
@@ -0,0 +1,61 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2008-2012 University of Bonn
+#
+#    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/>.
+#
+#
+#    MoleCuilder - creates and alters molecular systems
+#    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/>.
+#
+### anthracene - order 4 w cycles
+
+AT_SETUP([Fragmentations - anthracene order 4 w cycles])
+AT_KEYWORDS([fragmentation non-convex-envelope])
+
+MOL=anthracene
+DISTANCE="2."
+FILENAME="BondFragment"
+
+CycleNo=3
+FragNo=86
+let FragNo=$FragNo+$CycleNo
+
+file=${MOL}.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/Fragmentations/Fragmenting/${MOL}/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.pdb | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.in | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
Index: tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at
===================================================================
--- tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
+++ tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
@@ -0,0 +1,61 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2008-2012 University of Bonn
+#
+#    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/>.
+#
+#
+#    MoleCuilder - creates and alters molecular systems
+#    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/>.
+#
+### anthracene - order 5 w cycles
+
+AT_SETUP([Fragmentations - anthracene order 5 w cycles])
+AT_KEYWORDS([fragmentation non-convex-envelope])
+
+MOL=anthracene
+DISTANCE="2."
+FILENAME="BondFragment"
+
+CycleNo=3
+FragNo=142
+let FragNo=$FragNo+$CycleNo
+
+file=${MOL}.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/Fragmentations/Fragmenting/${MOL}/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.pdb | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.in | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
Index: tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at
===================================================================
--- tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
+++ tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at	(revision ec7511a359cc1cad57d684179dda96580726d26d)
@@ -0,0 +1,61 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2008-2012 University of Bonn
+#
+#    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/>.
+#
+#
+#    MoleCuilder - creates and alters molecular systems
+#    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/>.
+#
+### anthracene - order 6 w cycles
+
+AT_SETUP([Fragmentations - anthracene order 6 w cycles])
+AT_KEYWORDS([fragmentation non-convex-envelope])
+
+MOL=anthracene
+DISTANCE="2."
+FILENAME="BondFragment"
+
+CycleNo=3
+FragNo=223
+#let FragNo=$FragNo+$CycleNo
+
+file=${MOL}.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/Fragmentations/Fragmenting/${MOL}/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.pdb | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+AT_CHECK([ls ${FILENAME}*.in | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
+AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
