| Previous changeset 0:d97433b7d482 (2018-10-04) Next changeset 2:2e28934c1d8c (2019-08-30) |
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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb |
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modified:
md.xml |
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added:
merge_top.py test-data/top_output.top |
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| diff -r d97433b7d482 -r 609d93596b61 md.xml --- a/md.xml Thu Oct 04 18:23:17 2018 -0400 +++ b/md.xml Thu Mar 28 10:20:54 2019 -0400 |
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| @@ -147,7 +147,7 @@ </tests> <help><![CDATA[ -Upload GRO and TOP files for the production simulation, as well as the checkpoint (CPT) file from the NPT equilibration. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/online/mdp_opt.html for more information on the options. +Upload GRO and TOP files for the production simulation, as well as the checkpoint (CPT) file from the NPT equilibration. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options. ]]></help> <expand macro="citations" /> |
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| diff -r d97433b7d482 -r 609d93596b61 merge_top.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge_top.py Thu Mar 28 10:20:54 2019 -0400 |
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| @@ -0,0 +1,38 @@ +import re +import sys + + +def combine_tops(top_text, itp_texts): + """ + Search through parent topology top_text and replace + #include lines with the relevant child topologies + from the dictionary itp_texts + """ + for itp in itp_texts: + # split on include string, then rejoin around itp file + spl = re.split('#include ".*{}"\n'.format(itp), top_text) + top_text = itp_texts[itp].join(spl) + return top_text + + +top = sys.argv[1] # parent topology file +itps_file = sys.argv[2] # file with list of child topologies (.itp files) + +with open(itps_file) as f: + itps = f.read().split() + +with open(top, 'r') as f: + top_text = f.read() + +itp_texts = {} # create dictionary of child topologies +for itp in itps: + with open(itp, 'r') as f: + itp_texts[itp] = f.read() + +for itp in itp_texts: + # child tops may also refer to each other; we need to check this + itp_texts[itp] = combine_tops(itp_texts[itp], itp_texts) + +with open('top_output.top', 'w') as f: + # now combine all children into the parent + f.write(combine_tops(top_text, itp_texts)) |
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| diff -r d97433b7d482 -r 609d93596b61 test-data/top_output.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/top_output.top Thu Mar 28 10:20:54 2019 -0400 |
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| b'@@ -0,0 +1,19416 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-laptop\n+;\tAt date: Thu Aug 16 20:54:28 2018\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2018.2 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gromacs2/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gromacs2\n+;\tWorking dir: /home/simon/moldyn-galaxy/protein/test-data\n+;\tCommand line:\n+;\t gmx pdb2gmx -f 1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein_chain_A 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027 ; qtot -0.3\n+ 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03\n+ 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36\n+ 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94\n+ 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1\n+ 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2\n+ 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067 ; qtot 1.5\n+ 26 opls_241 2 VAL H 8 0.3 1.008 ; qtot 1.8\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011 ; qtot 1.94\n+ 28 opls_140 2 VAL HA 8 0.06 1.008 ; qtot 2\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011 ; qtot 1.94\n+ 30 opls_140 2 VAL HB 9 0.06 1.008 ; qtot 2\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011 ; qtot 1.82\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008 ; qtot 1.88\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008 ; qtot 1.94\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008 ; qtot 2\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011 ; qtot 1.82\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008 ; qtot 1.88\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008 ; qtot 1.9'..b'000 1000\n+ 1737 1 1000 1000 1000\n+ 1739 1 1000 1000 1000\n+ 1742 1 1000 1000 1000\n+ 1745 1 1000 1000 1000\n+ 1748 1 1000 1000 1000\n+ 1751 1 1000 1000 1000\n+ 1755 1 1000 1000 1000\n+ 1756 1 1000 1000 1000\n+ 1757 1 1000 1000 1000\n+ 1759 1 1000 1000 1000\n+ 1762 1 1000 1000 1000\n+ 1763 1 1000 1000 1000\n+ 1764 1 1000 1000 1000\n+ 1766 1 1000 1000 1000\n+ 1768 1 1000 1000 1000\n+ 1770 1 1000 1000 1000\n+ 1772 1 1000 1000 1000\n+ 1776 1 1000 1000 1000\n+ 1777 1 1000 1000 1000\n+ 1778 1 1000 1000 1000\n+ 1780 1 1000 1000 1000\n+ 1782 1 1000 1000 1000\n+ 1785 1 1000 1000 1000\n+ 1786 1 1000 1000 1000\n+ 1787 1 1000 1000 1000\n+ 1788 1 1000 1000 1000\n+ 1789 1 1000 1000 1000\n+ 1790 1 1000 1000 1000\n+ 1792 1 1000 1000 1000\n+ 1794 1 1000 1000 1000\n+ 1796 1 1000 1000 1000\n+ 1800 1 1000 1000 1000\n+ 1804 1 1000 1000 1000\n+ 1805 1 1000 1000 1000\n+ 1806 1 1000 1000 1000\n+ 1808 1 1000 1000 1000\n+ 1810 1 1000 1000 1000\n+ 1813 1 1000 1000 1000\n+ 1816 1 1000 1000 1000\n+ 1817 1 1000 1000 1000\n+ 1818 1 1000 1000 1000\n+ 1821 1 1000 1000 1000\n+ 1822 1 1000 1000 1000\n+ 1823 1 1000 1000 1000\n+ 1825 1 1000 1000 1000\n+ 1827 1 1000 1000 1000\n+ 1831 1 1000 1000 1000\n+ 1832 1 1000 1000 1000\n+ 1833 1 1000 1000 1000\n+ 1835 1 1000 1000 1000\n+ 1837 1 1000 1000 1000\n+ 1840 1 1000 1000 1000\n+ 1841 1 1000 1000 1000\n+ 1843 1 1000 1000 1000\n+ 1844 1 1000 1000 1000\n+ 1846 1 1000 1000 1000\n+ 1847 1 1000 1000 1000\n+ 1849 1 1000 1000 1000\n+ 1851 1 1000 1000 1000\n+ 1853 1 1000 1000 1000\n+ 1855 1 1000 1000 1000\n+ 1856 1 1000 1000 1000\n+ 1857 1 1000 1000 1000\n+ 1859 1 1000 1000 1000\n+ 1861 1 1000 1000 1000\n+ 1863 1 1000 1000 1000\n+ 1866 1 1000 1000 1000\n+ 1870 1 1000 1000 1000\n+ 1874 1 1000 1000 1000\n+ 1875 1 1000 1000 1000\n+ 1876 1 1000 1000 1000\n+ 1878 1 1000 1000 1000\n+ 1880 1 1000 1000 1000\n+ 1883 1 1000 1000 1000\n+ 1886 1 1000 1000 1000\n+ 1889 1 1000 1000 1000\n+ 1891 1 1000 1000 1000\n+ 1892 1 1000 1000 1000\n+ 1895 1 1000 1000 1000\n+ 1898 1 1000 1000 1000\n+ 1899 1 1000 1000 1000\n+ 1900 1 1000 1000 1000\n+ 1902 1 1000 1000 1000\n+ 1905 1 1000 1000 1000\n+ 1906 1 1000 1000 1000\n+ 1907 1 1000 1000 1000\n+ 1909 1 1000 1000 1000\n+ 1911 1 1000 1000 1000\n+ 1914 1 1000 1000 1000\n+ 1915 1 1000 1000 1000\n+ 1916 1 1000 1000 1000\n+ 1917 1 1000 1000 1000\n+ 1919 1 1000 1000 1000\n+ 1921 1 1000 1000 1000\n+ 1924 1 1000 1000 1000\n+ 1927 1 1000 1000 1000\n+ 1930 1 1000 1000 1000\n+ 1932 1 1000 1000 1000\n+ 1933 1 1000 1000 1000\n+ 1936 1 1000 1000 1000\n+ 1939 1 1000 1000 1000\n+ 1940 1 1000 1000 1000\n+ 1941 1 1000 1000 1000\n+ 1943 1 1000 1000 1000\n+ 1945 1 1000 1000 1000\n+ 1948 1 1000 1000 1000\n+ 1950 1 1000 1000 1000\n+ 1954 1 1000 1000 1000\n+ 1958 1 1000 1000 1000\n+ 1959 1 1000 1000 1000\n+ 1960 1 1000 1000 1000\n+#endif\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+LYSOZYME\n+\n+[ molecules ]\n+; Compound #mols\n+Protein_chain_A 1\n+SOL 78\n' |