| [55e1bc] | 1 | #
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| 2 | # MoleCuilder - creates and alters molecular systems
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| 3 | # Copyright (C) 2013 University of Bonn
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| [5aaa43] | 4 | # Copyright (C) 2013 Frederik Heber
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| [55e1bc] | 5 | #
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| 6 | # This program is free software: you can redistribute it and/or modify
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| 7 | # it under the terms of the GNU General Public License as published by
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| 8 | # the Free Software Foundation, either version 3 of the License, or
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| 9 | # (at your option) any later version.
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| 10 | #
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| 11 | # This program is distributed in the hope that it will be useful,
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| 12 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 13 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 14 | # GNU General Public License for more details.
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| 15 | #
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| 16 | # You should have received a copy of the GNU General Public License
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| 17 | # along with this program. If not, see <http://www.gnu.org/licenses/>.
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| 18 | #
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| 19 | ### fragment the molecule and check the number of configs
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| [6ff62c] | 20 | #
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| [e2925fd] | 21 | # BondFragmentShortRangeResults.dat is created like this:
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| [ea63cb] | 22 | # ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 0 --server-address 127.0.0.1 --server-port 1026 --save-fragment-results BondFragmentShortRangeResults.dat
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| [55e1bc] | 23 |
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| [e2925fd] | 24 | AT_SETUP([Fragmentation - Analyse short-range fragmentation results])
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| [d20335] | 25 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
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| [55e1bc] | 26 |
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| [e2925fd] | 27 | file=BondFragmentShortRangeResults.dat
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| [55e1bc] | 28 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 29 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d20335] | 30 | AT_CHECK([../../molecuilder --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [ignore])
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| [e2925fd] | 31 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 32 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 33 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 34 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 35 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| [47cee7] | 36 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| [e2925fd] | 37 |
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| 38 | AT_CLEANUP
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| 39 |
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| [e5ebaf] | 40 | AT_SETUP([Fragmentation - Analyse short-range fragmentation results with forces])
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| [d20335] | 41 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces])
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| [e5ebaf] | 42 |
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| 43 | file=BondFragmentShortRangeResults.dat
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| 44 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 45 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d20335] | 46 | AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [ignore])
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| [e5ebaf] | 47 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
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| 48 |
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| 49 | AT_CLEANUP
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| 50 |
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| [e2925fd] | 51 | #
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| 52 | # BondFragmentLongRangeResults.dat is created like this:
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| [ea63cb] | 53 | # ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 1 --DoValenceOnly 0 --grid-level 4 --near-field-cells 3 --server-address 127.0.0.1 --server-port 1026 --save-fragment-results BondFragmentLongRangeResults_OBC.dat
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| [e2925fd] | 54 |
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| [6531a7] | 55 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC])
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| [d20335] | 56 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
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| [e2925fd] | 57 |
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| [6531a7] | 58 | file=BondFragmentLongRangeResults_OBC.dat
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| [e2925fd] | 59 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 60 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d20335] | 61 | AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
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| [6531a7] | 62 | #AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
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| 63 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 64 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 65 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 66 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 67 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 68 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| [72b467] | 69 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [6531a7] | 70 | AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 71 | ])
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| 72 |
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| 73 | AT_CLEANUP
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| 74 |
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| [d93d2c] | 75 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC and forces])
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| [d20335] | 76 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
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| [d93d2c] | 77 |
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| 78 | file=BondFragmentLongRangeResults_OBC.dat
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| 79 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 80 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d20335] | 81 | AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
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| [72b467] | 82 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [835b53] | 83 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data], 0, [ignore], [ignore])
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| 84 | ])
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| [d93d2c] | 85 |
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| 86 | AT_CLEANUP
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| 87 |
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| [6531a7] | 88 | #
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| 89 | # BondFragmentLongRangeResults.dat is created like this:
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| [ea63cb] | 90 | # ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Wrap Wrap Wrap --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 1 --DoValenceOnly 0 --grid-level 4 --near-field-cells 3 --server-address 127.0.0.1 --server-port 1026 --save-fragment-results BondFragmentLongRangeResults_PBC.dat
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| [6531a7] | 91 |
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| 92 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC])
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| [d20335] | 93 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
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| [6531a7] | 94 |
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| 95 | file=BondFragmentLongRangeResults_PBC.dat
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| 96 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 97 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d20335] | 98 | AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
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| [6531a7] | 99 | #AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
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| 100 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 101 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 102 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 103 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 104 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 105 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| [72b467] | 106 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [6531a7] | 107 | AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| [e2925fd] | 108 | ])
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| [55e1bc] | 109 |
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| 110 | AT_CLEANUP
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| [d93d2c] | 111 |
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| 112 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC and forces])
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| [d20335] | 113 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
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| [d93d2c] | 114 |
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| 115 | file=BondFragmentLongRangeResults_PBC.dat
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| 116 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 117 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d20335] | 118 | AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
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| [72b467] | 119 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [835b53] | 120 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data], 0, [ignore], [ignore])
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| 121 | ])
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| [d93d2c] | 122 |
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| 123 | AT_CLEANUP
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