#
#    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/>.
#
### phenanthrene - order 1 w cycles

AT_SETUP([Fragmentations - phenanthrene order 1 w cycles])
AT_KEYWORDS([fragmentation non-convex-envelope])

MOL=phenanthrene
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 --correct-bonddegree --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