#
#    MoleCuilder - creates and alters molecular systems
#    Copyright (C) 2016 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/>.
#
### saturate atoms with (partial) bonding

AT_SETUP([Atoms - saturating water molecule])
AT_KEYWORDS([atoms saturate-atoms])
# this should not do anything as water is fully saturated

file=saturated_water.pdb
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/water.pdb .], 0)
AT_CHECK([chmod u+w water.pdb], 0)
AT_CHECK([../../molecuilder --dry-run -i water.pdb --select-atom-by-element 8 --saturate-atoms --output-as $file --no-dry-run --store-session session-atoms-saturate-atoms-bonded_atoms.py --session-type python], 0, [ignore], [ignore])
AT_CHECK([grep -v "Command.*DryRun" session-atoms-saturate-atoms-bonded_atoms.py >session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
AT_CHECK([../../molecuilderguitest session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_water.pdb], 0, [ignore], [ignore])

AT_CLEANUP

AT_SETUP([Atoms - saturating partial water molecule])
AT_KEYWORDS([atoms saturate-atoms])

file=saturated_water_H1.pdb
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/water.pdb .], 0)
AT_CHECK([chmod u+w water.pdb], 0)
AT_CHECK([../../molecuilder --dry-run -i water.pdb --select-atom-by-id 2 --remove-atom --select-atom-by-element 8 --saturate-atoms --output-as $file --no-dry-run --store-session session-atoms-saturate-atoms-bonded_atoms.py --session-type python], 0, [ignore], [ignore])
AT_CHECK([grep -v "Command.*DryRun" session-atoms-saturate-atoms-bonded_atoms.py >session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
AT_CHECK([../../molecuilderguitest session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_water_H1.pdb], 0, [ignore], [ignore])

AT_CLEANUP

AT_SETUP([Atoms - saturating partial cholesterol molecule])
AT_KEYWORDS([atoms saturate-atoms])

file=saturated_cholesterol.pdb
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/cholesterol.pdb .], 0)
AT_CHECK([chmod u+w cholesterol.pdb], 0)
AT_CHECK([../../molecuilder --dry-run -i cholesterol.pdb --select-atom-by-id 48 50 53 67 73 --remove-atom --select-all-atoms --correct-bonddegree --unselect-atom-by-element 1 --saturate-atoms --output-as $file --no-dry-run --store-session session-atoms-saturate-atoms-bonded_atoms.py --session-type python], 0, [ignore], [ignore])
AT_CHECK([grep -v "Command.*DryRun" session-atoms-saturate-atoms-bonded_atoms.py >session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
AT_CHECK([../../molecuilderguitest session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_cholesterol_H48_50_53_67_73.pdb], 0, [ignore], [ignore])

AT_CLEANUP