| 1 | #
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| 2 | # MoleCuilder - creates and alters molecular systems
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| 3 | # Copyright (C) 2013 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 | ### fit fragment partial particle charges
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| 19 |
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| 20 | AT_SETUP([Potential - Fit fragment partial charges - atomfragment check])
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| 21 | AT_KEYWORDS([potential parse-fragment-results fit-fragment-partial-charges save-particle-parameters])
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| 22 | AT_SKIP_IF([../../molecuilder --help fit-fragment-partial-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 23 |
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| 24 | input=water.pdb
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| 25 | resultsfile=results_grid.dat
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| 26 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitFragmentPartialCharges/pre/$input $input], 0)
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| 27 | AT_CHECK([chmod u+w $input], 0, [ignore], [ignore])
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| 28 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitFragmentPartialCharges/pre/$resultsfile $resultsfile], 0)
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| 29 | AT_CHECK([chmod u+w $resultsfile], 0, [ignore], [ignore])
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| 30 | # fails because atomFragments has not been parsed
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| 31 | AT_CHECK([../../molecuilder -l $input --select-all-atoms --parse-fragment-results $resultsfile --fit-fragment-partial-charges --radius 1.5 --save-particle-parameters water.particles], 5, [stdout], [ignore])
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| 32 |
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| 33 | AT_CLEANUP
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| 34 |
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| 35 | AT_SETUP([Potential - Fit partial charges to water])
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| 36 | AT_KEYWORDS([potential parse-fragment-results fit-partial-charges save-particle-parameters])
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| 37 | AT_SKIP_IF([../../molecuilder --help fit-partial-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 38 |
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| 39 | # homology file created with water.pdb and as follows:
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| 40 | # molecuilder -i water.pdb --select-all-atoms --fragment-molecule --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 5 --store-grids 1 --save-fragment-results results_grid.dat --save-atom-fragments atomfragments.dat
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| 41 | input=water.pdb
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| 42 | resultsfile=results_grid.dat
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| 43 | atomfragmentsfile=atomfragments.dat
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| 44 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitFragmentPartialCharges/pre/$input $input], 0)
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| 45 | AT_CHECK([chmod u+w $input], 0, [ignore], [ignore])
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| 46 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitFragmentPartialCharges/pre/$resultsfile $resultsfile], 0)
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| 47 | AT_CHECK([chmod u+w $resultsfile], 0, [ignore], [ignore])
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| 48 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitFragmentPartialCharges/pre/$atomfragmentsfile $atomfragmentsfile], 0)
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| 49 | AT_CHECK([chmod u+w $atomfragmentsfile], 0, [ignore], [ignore])
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| 50 | AT_CHECK([../../molecuilder -l $input --select-all-atoms --parse-fragment-results $resultsfile --parse-atom-fragments $atomfragmentsfile --fit-fragment-partial-charges --radius 1.5 --save-particle-parameters water.particles], 0, [stdout], [ignore])
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| 51 | # check that L_2 error is below 1e-6
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| 52 | AT_CHECK([grep "L2-Norm" stdout | awk '{if ($6 > 1e1) exit 1}'], 0, [ignore], [ignore])
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| 53 | AT_CHECK([grep "L1-Norm" stdout | awk '{if ($6 > 1e0) exit 1}'], 0, [ignore], [ignore])
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| 54 | AT_CHECK([grep "Adding particle O1.*-0.73" stdout], 0, [ignore], [ignore])
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| 55 | AT_CHECK([grep "Adding particle H1.*0.36" stdout], 0, [ignore], [ignore])
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| 56 | AT_CHECK([grep "atom O1.*received .*O1" stdout], 0, [ignore], [ignore])
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| 57 | AT_CHECK([grep "atom H2.*received .*H1" stdout], 0, [ignore], [ignore])
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| 58 | AT_CHECK([grep "atom H3.*received .*H1" stdout], 0, [ignore], [ignore])
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| 59 | AT_CHECK([diff water.particles ${abs_top_srcdir}/tests/regression/Potential/FitFragmentPartialCharges/post/water.particles], 0)
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| 60 |
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| 61 | AT_CLEANUP
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