| 1 | #
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| 2 | # MoleCuilder - creates and alters molecular systems
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| 3 | # Copyright (C) 2016 Frederik Heber
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| 4 | #
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| 5 | # This program is free software: you can redistribute it and/or modify
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| 6 | # it under the terms of the GNU General Public License as published by
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| 7 | # the Free Software Foundation, either version 3 of the License, or
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| 8 | # (at your option) any later version.
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| 9 | #
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| 10 | # This program is distributed in the hope that it will be useful,
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| 11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 13 | # GNU General Public License for more details.
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| 14 | #
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| 15 | # You should have received a copy of the GNU General Public License
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| 16 | # along with this program. If not, see <http://www.gnu.org/licenses/>.
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| 17 | #
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| 18 | ### saturate atoms with (partial) bonding
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| 19 |
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| 20 | AT_SETUP([Atoms - saturating water molecule])
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| 21 | AT_KEYWORDS([atoms saturate-atoms])
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| 22 | # this should not do anything as water is fully saturated
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| 23 |
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| 24 | file=saturated_water.pdb
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| 25 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/water.pdb .], 0)
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| 26 | AT_CHECK([chmod u+w water.pdb], 0)
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| 27 | 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])
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| 28 | AT_CHECK([grep -v "Command.*DryRun" session-atoms-saturate-atoms-bonded_atoms.py >session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
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| 29 | AT_CHECK([../../molecuilderguitest session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
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| 30 | AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_water.pdb], 0, [ignore], [ignore])
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| 31 |
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| 32 | AT_CLEANUP
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| 33 |
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| 34 | AT_SETUP([Atoms - saturating partial water molecule])
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| 35 | AT_KEYWORDS([atoms saturate-atoms])
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| 36 |
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| 37 | file=saturated_water_H1.pdb
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| 38 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/water.pdb .], 0)
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| 39 | AT_CHECK([chmod u+w water.pdb], 0)
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| 40 | 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])
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| 41 | AT_CHECK([grep -v "Command.*DryRun" session-atoms-saturate-atoms-bonded_atoms.py >session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
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| 42 | AT_CHECK([../../molecuilderguitest session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
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| 43 | AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_water_H1.pdb], 0, [ignore], [ignore])
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| 44 |
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| 45 | AT_CLEANUP
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| 46 |
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| 47 | AT_SETUP([Atoms - saturating partial cholesterol molecule])
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| 48 | AT_KEYWORDS([atoms saturate-atoms])
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| 49 |
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| 50 | file=saturated_cholesterol.pdb
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| 51 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/cholesterol.pdb .], 0)
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| 52 | AT_CHECK([chmod u+w cholesterol.pdb], 0)
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| 53 | 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])
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| 54 | AT_CHECK([grep -v "Command.*DryRun" session-atoms-saturate-atoms-bonded_atoms.py >session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
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| 55 | AT_CHECK([../../molecuilderguitest session-atoms-saturate-atoms-bonded_atoms_new.py], 0, [ignore], [ignore])
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| 56 | 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])
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| 57 |
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| 58 | AT_CLEANUP
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