#
#    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/>.
#
### fragment the molecule and check the number of configs

AT_SETUP([Fragmentation - Fragmentation])
AT_KEYWORDS([fragmentation fragment-molecule])

file=test.conf
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/pre/test.conf $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder -i $file -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
#AT_CHECK([diff BondFragment0.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment0.conf], 0, [ignore], [ignore])
#AT_CHECK([diff BondFragment1.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment1.conf], 0, [ignore], [ignore])
#AT_CHECK([diff BondFragment2.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment2.conf], 0, [ignore], [ignore])
#AT_CHECK([diff BondFragment3.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment3.conf], 0, [ignore], [ignore])
#AT_CHECK([diff BondFragment4.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment4.conf], 0, [ignore], [ignore])
AT_CHECK([ls -l BondFragment*.conf | wc -l], 0, [5
], [ignore])

AT_CLEANUP

AT_SETUP([Fragmentation - Fragmentation with cycles])
AT_KEYWORDS([fragmentation fragment-molecule cycle])

file=benzene.pdb
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/pre/$file $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder -i $file --update-molecules --select-all-atoms --fragment-molecule ./BondFragment --DoCyclesFull 1 --distance 2 --order 2 --output-types "xyz"], 0, [ignore], [ignore])
AT_CHECK([ls -l BondFragment??.xyz | wc -l], 0, [13
], [ignore])
AT_CHECK([cat <BondFragment12.xyz | wc -l], 0, [14
], [ignore])
AT_CHECK([cat <BondFragmentCycles.dat | wc -w], 0, [6
], [ignore])

AT_CLEANUP