| Next changeset 1:ddb1ae2cf028 (2019-08-30) |
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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27 |
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added:
macros_packmol.xml packmol.xml template.j2 test-data/packmol_outfile1.pdb test-data/packmol_outfile2.pdb test-data/packmol_parameteroutfile_1.txt test-data/packmol_parameteroutfile_2.txt test-data/urea.pdb test-data/water.pdb |
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| diff -r 000000000000 -r 0b8a0ce446f5 macros_packmol.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_packmol.xml Mon Oct 08 05:31:29 2018 -0400 |
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| @@ -0,0 +1,106 @@ +<macros> + <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format."> + <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> + <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/> + <section name="structureparams" title="Structure Parameters (Make Changes!)" expanded="false"> + <param name="number" type="integer" multiple="True" value="100" /> + <param name="radius" type="float" multiple="True" value="1.0" /> + <param name="resnumbers" type="integer" multiple="True" value="0" help="Default is to number 1 to n for type 1 and 1 to n for type 2"/> + <repeat name="constraints_repeat" min="1" max="3" title="Select constraint(s) to apply:"> + <conditional name="constraints"> + <param name="constraint" type="select" label="Shape Constraint selection" help="Choose the constraint for the molecules"> + <option value="fixed">fixed - hold 1 molecule in fixed position (hardcoded number=1) Exclusive other constraints not possible</option> + <option selected="True" value="cube">cube</option> + <option value="box">box</option> + <option value="sphere">sphere</option> + <option value="ellipsoid">ellipsoid </option> + <option value="plane">plane</option> + <option value="cylinder">cylinder</option> + </param> + <when value="fixed"> + <param name="center" type="select" label="Center" help="center"> + <option value="Yes">yes</option> + <option value="No">no</option> + </param> + <param name="x" type="float" value="0.0" label="x" /> + <param name="y" type="float" value="0.0" label="y" /> + <param name="z" type="float" value="0.0" label="z" /> + <param name="a" type="float" value="0.0" label="a" /> + <param name="b" type="float" value="0.0" label="b" /> + <param name="g" type="float" value="0.0" label="g" /> + </when> + <when value="cube"> + <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules"> + <option value="inside">inside</option> + <option value="outside">outside</option> + </param> + <param name="xmin" type="float" value="0.0" label="xmin" /> + <param name="ymin" type="float" value="0.0" label="ymin" /> + <param name="zmin" type="float" value="0.0" label="zmin" /> + <param name="d" type="float" value="40.0" label="d" /> + </when> + <when value="box"> + <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules"> + <option value="inside">inside</option> + <option value="outside">outside</option> + </param> + <param name="xmin" type="float" value="0.0" label="xmin" /> + <param name="ymin" type="float" value="0.0" label="ymin" /> + <param name="zmin" type="float" value="0.0" label="zmin" /> + <param name="xmax" type="float" value="40.0" label="xmax" /> + <param name="ymax" type="float" value="40.0" label="ymax" /> + <param name="zmax" type="float" value="40.0" label="zmax" /> + </when> + <when value="sphere"> + <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules"> + <option value="inside">inside</option> + <option value="outside">outside</option> + </param> + <param name="a" type="float" value="0.0" label="a" /> + <param name="b" type="float" value="0.0" label="b" /> + <param name="c" type="float" value="0.0" label="c" /> + <param name="d" type="float" value="40.0" label="d" /> + </when> + <when value="ellipsoid"> + <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules"> + <option value="inside">inside</option> + <option value="outside">outside</option> + </param> + <param name="a1" type="float" value="0.0" label="a1" /> + <param name="b1" type="float" value="0.0" label="b1" /> + <param name="c1" type="float" value="0.0" label="c1" /> + <param name="a2" type="float" value="20.0" label="a2" /> + <param name="b2" type="float" value="20.0" label="b2" /> + <param name="c2" type="float" value="20.0" label="c2" /> + <param name="d" type="float" value="40.0" label="d" /> + </when> + <when value="plane"> + <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules"> + <option value="over">over</option> + <option value="below">below</option> + </param> + <param name="a" type="float" value="0.0" label="a" /> + <param name="b" type="float" value="0.0" label="b" /> + <param name="c" type="float" value="0.0" label="c" /> + <param name="d" type="float" value="10.0" label="d" /> + </when> + <when value="cylinder"> + <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules"> + <option value="inside">inside</option> + <option value="outside">outside</option> + </param> + <param name="a1" type="float" value="0.0" label="a1" /> + <param name="b1" type="float" value="0.0" label="b1" /> + <param name="c1" type="float" value="0.0" label="c1" /> + <param name="a2" type="float" value="40.0" label="a2" /> + <param name="b2" type="float" value="40.0" label="b2" /> + <param name="c2" type="float" value="40.0" label="c2" /> + <param name="d" type="float" value="10.0" label="d" /> + <param name="l" type="float" value="10.0" label="l" /> + </when> + </conditional> + </repeat> + </section> + </repeat> + </xml> +</macros> |
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| diff -r 000000000000 -r 0b8a0ce446f5 packmol.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/packmol.xml Mon Oct 08 05:31:29 2018 -0400 |
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| b'@@ -0,0 +1,176 @@\n+<tool id="packmol" name="PACKMOL" version="18.169">\n+ <description>Initial configurations for Molecular Dynamics Simulations by packing optimization</description>\n+ <macros>\n+ <import>macros_packmol.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="18.169">packmol</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ python \'$packmol_script\' \'$inputs\' &&\n+ packmol < \'$parameteroutfile\'\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <inputs name="inputs" />\n+ <configfile name="packmol_script"><![CDATA[\n+\n+import os\n+import sys\n+import json\n+\n+from jinja2 import Environment, FileSystemLoader\n+\n+input_json_path = sys.argv[1]\n+params = json.load(open(input_json_path, "r"))\n+\n+# get the inputs\n+input_iter = []\n+#for $i, $s in enumerate( $packmol_format.packmol_inputs )\n+pmfile_index = $i\n+pmfile_path = "${s.input.file_name}"\n+input_iter.append(pmfile_path)\n+params["packmol_format"]["packmol_inputs"][pmfile_index]["file"] = pmfile_path\n+params["packmol_format"]["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}"\n+#end for\n+\n+params["outfile"] = "$outfile"\n+\n+currentpath = "$__tool_directory__" # should work generally\n+template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)\n+template = template_environment.get_template(\'template.j2\')\n+print(params)\n+\n+with open("$parameteroutfile",\'w+\') as f:\n+ f.write(template.render(params))\n+\n+]]>\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="packmol_format">\n+ <param name="selected_format" type="select" label="Select a file format:">\n+ <option value="pdb" selected="true">pdb</option>\n+ <!--option value="xyz">xyz</option>\n+ <option value="tinker">tinker</option>\n+ <option value="moldy">moldy</option-->\n+ </param>\n+ <when value="pdb">\n+ <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="pdb input with molecule type" help_text="Select a pdb file in .pdb format"/>\n+ </when>\n+ <!--when value="xyz">\n+ <expand macro="multiple_input" name="packmol_inputs" format="xyz" label="xyz input with molecule type" help_text="Select a xyz file in .xyz format"/>\n+ </when>\n+ <when value="tinker">\n+ <expand macro="multiple_input" name="packmol_inputs" format="tinker" label="tinker input with molecule type" help_text="Select a tinker file in .tinker format"/>\n+ </when>\n+ <when value="moldy">\n+ <expand macro="multiple_input" name="packmol_inputs" format="moldy" label="moldy input with molecule type" help_text="Select a moldy file in .moldy format"/>\n+ </when-->\n+ </conditional>\n+ <section name="allparams" title="General Parameters" expanded="false">\n+ <param name="tolerance" type="float" value="2.0" label="distance tolerance" min="0.0" max="100.0"/>\n+ <param name="nloop" type="integer" value="20" label="maximum number of optimisation loops" min="1" max="10000"/>\n+ <param name="maxit" type="integer" value="20" label="maximum number of gencan iterations per loop" min="1" max="10000"/>\n+ <param name="seed" type="integer" value="-1" label="random number generator seed, default of -1 used the computer time to set the seed" />\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data format="pdb" name="outfile" label="${tool.name}: structure output">\n+ <change_format>\n+ <when input="selected_format" value="pdb" format="pdb"/>\n+ <!-- <when input="selected_format" value="xyz" format="xyz"/>\n+ <when input="selected_format" value="tinker" format="tinker"/>\n+ <when input="selected_format" value="moldy" format="m'..b'<param name="selected_format" value="pdb"/>\n+ <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/>\n+ <param name="allparams.seed" value="101"/>\n+ <output name="outfile" file="packmol_outfile1.pdb" compare="sim_size" delta="100000">\n+ <assert_contents>\n+ <has_text text="HETATM 300 O HOH"/>\n+ </assert_contents>\n+ </output>\n+ <output name="parameteroutfile" file="packmol_parameteroutfile_1.txt" compare="diff" lines_diff="6"/>\n+ </test>\n+ <test>\n+ <param name="selected_format" value="pdb"/>\n+ <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/>\n+ <param name="packmol_inputs_1|input" value="urea.pdb" ftype="pdb"/>\n+ <param name="packmol_inputs_0|structureparams|number" value="1000"/>\n+ <param name="packmol_inputs_1|structureparams|number" value="400"/>\n+ <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|constraint" value="box"/>\n+ <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/>\n+ <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/>\n+ <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/>\n+ <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|constraint" value="box"/>\n+ <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/>\n+ <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/>\n+ <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/>\n+ <param name="allparams.seed" value="-1"/>\n+ <output name="outfile" file="packmol_outfile2.pdb" compare="sim_size" delta="100000">\n+ <assert_contents>\n+ <has_text text="HETATM 3000 O HOH"/>\n+ <has_text text="HETATM 6200 H 2 B"/>\n+ </assert_contents>\n+ </output>\n+ <output name="parameteroutfile" file="packmol_parameteroutfile_2.txt" compare="diff" lines_diff="6"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+Packmol creates initial MD configurations from input molecules. For example, create a water and urea mixture.\n+\n+.. class:: infomark\n+\n+**How it works**\n+\n+- Select a molecule file type e.g. pdb,xyz\n+- Select single molecule from your history (can select multiple)\n+- For each molecule:\n+ - choose how many molecules to create (number variable)\n+ - optionally choose:\n+ - molecular radius\n+ - how to number the molecules (resnumber variable)\n+ - choose one or more placement constraint(s). Each constraint has different parameters:\n+ - for example, specify placement inside a cube of size 40 Angstroms placed at the origin\n+ - all units are in Angstroms for distances and degrees for angles\n+\n+.. class:: infomark\n+\n+**Outputs created**\n+\n+- A pdb file, view this in Galaxy by clicking on visualise and choosing a viewer. The NGLViewer works well for small molecules.\n+- A packmol input script (for debugging and repeatability)\n+\n+.. class:: infomark\n+\n+**User guide and documentation**\n+\n+- Packmol `userguide`_\n+- Calculating the number of molecules using the `volume guesser`_\n+\n+.. class:: infomark\n+\n+**Known issues**\n+\n+- fixed constraint only allows 1 atom but this is not set for the user. user has to set this. Job may fail.\n+\n+.. _`userguide`: http://m3g.iqm.unicamp.br/packmol/userguide.shtml#more\n+.. _`volume guesser`: http://m3g.iqm.unicamp.br/packmol/utilities.shtml\n+\n+]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1002/jcc.21224</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 0b8a0ce446f5 template.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template.j2 Mon Oct 08 05:31:29 2018 -0400 |
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| @@ -0,0 +1,42 @@ +# Template for packmol in Galaxy +# + +tolerance {{ allparams.tolerance }} +nloop {{ allparams.nloop }} +maxit {{ allparams.maxit }} +seed {{ allparams.seed }} +filetype {{packmol_format.selected_format}} +output {{outfile}} + +{% for struct in packmol_format.packmol_inputs %} +structure {{struct.file}} +# Galaxy datasetname - {{struct.datasetname}} + number {{struct.structureparams.number}} + radius {{struct.structureparams.radius}} + resnumbers {{struct.structureparams.resnumbers}} +{% for c in struct.structureparams.constraints_repeat %} + {% if c.constraints.constraint == 'fixed' %} + {% if c.constraints.center == 'Yes' %} + center + {% endif %} + {{c.constraints.constraint}} {{c.constraints.x}} {{c.constraints.y}} {{c.constraints.z}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.g}} + {% elif c.constraints.constraint == 'cube' %} + {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.d}} + {% elif c.constraints.constraint == 'box' %} + {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.xmax}} {{c.constraints.ymax}} {{c.constraints.zmax}} + {% elif c.constraints.constraint == 'sphere' %} + {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}} + {% elif c.constraints.constraint == 'ellipsoid' %} + {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}} + {% elif c.constraints.constraint == 'plane' %} + {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}} + {% elif c.constraints.constraint == 'cylinder' %} + {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}} {{c.constraints.l}} + {% else %} + unknowntype specified {{c.constraints}} +{% endif %} +{% endfor %} +end structure + +{% endfor %} + |
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| diff -r 000000000000 -r 0b8a0ce446f5 test-data/packmol_outfile1.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/packmol_outfile1.pdb Mon Oct 08 05:31:29 2018 -0400 |
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| b'@@ -0,0 +1,306 @@\n+HEADER \n+TITLE Built with Packmol \n+REMARK Packmol generated pdb file \n+REMARK Home-Page: http://www.ime.unicamp.br/~martinez/packmol\n+REMARK\n+HETATM 1 H HOH A 1 9.274 18.459 24.988 \n+HETATM 2 H HOH A 1 7.739 18.902 24.651 \n+HETATM 3 O HOH A 1 8.666 18.832 24.286 \n+HETATM 4 H HOH A 2 38.440 20.929 14.513 \n+HETATM 5 H HOH A 2 39.987 21.222 14.946 \n+HETATM 6 O HOH A 2 39.331 20.512 14.694 \n+HETATM 7 H HOH A 3 3.756 39.733 36.425 \n+HETATM 8 H HOH A 3 5.149 39.108 37.002 \n+HETATM 9 O HOH A 3 4.744 39.672 36.284 \n+HETATM 10 H HOH A 4 36.428 26.732 19.466 \n+HETATM 11 H HOH A 4 36.144 28.169 20.189 \n+HETATM 12 O HOH A 4 36.799 27.643 19.648 \n+HETATM 13 H HOH A 5 25.380 10.824 25.072 \n+HETATM 14 H HOH A 5 24.509 11.242 26.389 \n+HETATM 15 O HOH A 5 24.596 11.352 25.399 \n+HETATM 16 H HOH A 6 22.963 27.548 3.198 \n+HETATM 17 H HOH A 6 21.510 28.033 3.764 \n+HETATM 18 O HOH A 6 22.367 28.337 3.349 \n+HETATM 19 H HOH A 7 5.703 4.916 6.848 \n+HETATM 20 H HOH A 7 6.380 3.446 7.074 \n+HETATM 21 O HOH A 7 6.564 4.424 6.983 \n+HETATM 22 H HOH A 8 22.545 21.992 36.433 \n+HETATM 23 H HOH A 8 21.587 22.436 37.678 \n+HETATM 24 O HOH A 8 22.287 22.747 37.036 \n+HETATM 25 H HOH A 9 25.853 36.397 30.817 \n+HETATM 26 H HOH A 9 26.030 37.979 30.455 \n+HETATM 27 O HOH A 9 26.405 37.216 30.979 \n+HETATM 28 H HOH A 10 29.624 32.655 32.811 \n+HETATM 29 H HOH A 10 29.363 31.221 32.074 \n+HETATM 30 O HOH A 10 29.962 32.019 32.116 \n+HETATM 31 H HOH A 11 22.570 6.775 9.646 \n+HETATM 32 H HOH A 11 24.062 6.675 10.304 \n+HETATM 33 O HOH A 11 23.272 7.271 10.158 \n+HETATM 34 H HOH A 12 1.908 0.785 8.972 \n+HETATM 35 H HOH A 12 1.194 1.700 7.823 \n+HETATM 36 O HOH A 12 1.072 1.271 8.717 \n+HETATM 37 H HOH A 13 25.533 20.545 24.058 \n+HETATM 38 H HOH A 13 24.666 19.262 24.578 \n+HETATM 39 O HOH A 13 25.461 19.548 24.043 \n+HETATM 40 H HOH A 14 2.975 24.413 16.764 \n+HETATM 41 H HOH A 14 1.842 23.518 17.526 \n+HETATM 42 O HOH A 14 2.706 23.486 17.025 \n+HETATM 43 H HOH A 15 8.204 13.660 15.248 \n+HETATM 44 H HOH A 15 8.924 12.494 14.360 \n+HETATM 45 O HOH A 15 8.998 13.055 15.184 \n+HETATM 46 H HOH A 16 5.023 33.627 9.840 \n+HETATM 47 '..b' 84 3.301 21.302 13.918 \n+HETATM 253 H HOH A 85 36.314 14.381 30.404 \n+HETATM 254 H HOH A 85 37.185 14.841 31.707 \n+HETATM 255 O HOH A 85 37.063 14.128 31.017 \n+HETATM 256 H HOH A 86 21.365 14.264 11.548 \n+HETATM 257 H HOH A 86 22.773 14.009 10.762 \n+HETATM 258 O HOH A 86 22.132 14.706 11.082 \n+HETATM 259 H HOH A 87 34.896 11.110 8.540 \n+HETATM 260 H HOH A 87 36.056 11.074 9.689 \n+HETATM 261 O HOH A 87 35.880 11.172 8.710 \n+HETATM 262 H HOH A 88 11.617 31.553 14.100 \n+HETATM 263 H HOH A 88 10.061 31.062 14.041 \n+HETATM 264 O HOH A 88 10.890 31.079 14.598 \n+HETATM 265 H HOH A 89 9.644 23.483 39.343 \n+HETATM 266 H HOH A 89 8.318 24.428 39.220 \n+HETATM 267 O HOH A 89 9.108 24.063 38.729 \n+HETATM 268 H HOH A 90 31.221 14.405 25.689 \n+HETATM 269 H HOH A 90 29.903 13.620 25.129 \n+HETATM 270 O HOH A 90 30.233 14.290 25.793 \n+HETATM 271 H HOH A 91 0.698 39.943 24.679 \n+HETATM 272 H HOH A 91 0.098 38.450 24.401 \n+HETATM 273 O HOH A 91 0.927 38.973 24.595 \n+HETATM 274 H HOH A 92 13.710 2.270 37.555 \n+HETATM 275 H HOH A 92 14.712 1.320 38.428 \n+HETATM 276 O HOH A 92 14.530 2.256 38.128 \n+HETATM 277 H HOH A 93 30.810 22.813 33.200 \n+HETATM 278 H HOH A 93 30.849 21.181 33.212 \n+HETATM 279 O HOH A 93 30.253 21.983 33.223 \n+HETATM 280 H HOH A 94 13.006 18.513 1.360 \n+HETATM 281 H HOH A 94 12.193 17.841 2.607 \n+HETATM 282 O HOH A 94 12.105 18.232 1.691 \n+HETATM 283 H HOH A 95 34.249 6.193 20.751 \n+HETATM 284 H HOH A 95 34.196 7.803 21.017 \n+HETATM 285 O HOH A 95 33.803 6.921 21.273 \n+HETATM 286 H HOH A 96 39.513 38.648 1.366 \n+HETATM 287 H HOH A 96 39.946 37.719 2.638 \n+HETATM 288 O HOH A 96 39.313 37.807 1.870 \n+HETATM 289 H HOH A 97 39.580 22.335 30.984 \n+HETATM 290 H HOH A 97 38.435 21.174 30.899 \n+HETATM 291 O HOH A 97 39.351 21.440 30.601 \n+HETATM 292 H HOH A 98 15.157 27.942 5.491 \n+HETATM 293 H HOH A 98 14.011 26.781 5.409 \n+HETATM 294 O HOH A 98 14.176 27.767 5.400 \n+HETATM 295 H HOH A 99 12.832 12.991 17.051 \n+HETATM 296 H HOH A 99 13.338 13.396 18.550 \n+HETATM 297 O HOH A 99 12.771 12.763 18.023 \n+HETATM 298 H HOH A 100 12.618 22.846 20.145 \n+HETATM 299 H HOH A 100 12.208 21.772 21.305 \n+HETATM 300 O HOH A 100 12.469 22.720 21.126 \n+END\n' |
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| diff -r 000000000000 -r 0b8a0ce446f5 test-data/packmol_outfile2.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/packmol_outfile2.pdb Mon Oct 08 05:31:29 2018 -0400 |
| b |
| b'@@ -0,0 +1,6206 @@\n+HEADER \n+TITLE Built with Packmol \n+REMARK Packmol generated pdb file \n+REMARK Home-Page: http://www.ime.unicamp.br/~martinez/packmol\n+REMARK\n+HETATM 1 H HOH A 1 2.385 24.122 0.119 \n+HETATM 2 H HOH A 1 2.006 22.544 0.305 \n+HETATM 3 O HOH A 1 1.643 23.475 0.303 \n+HETATM 4 H HOH A 2 16.854 10.994 20.320 \n+HETATM 5 H HOH A 2 17.163 12.347 21.180 \n+HETATM 6 O HOH A 2 16.505 11.895 20.578 \n+HETATM 7 H HOH A 3 22.852 27.560 16.919 \n+HETATM 8 H HOH A 3 22.253 26.042 16.972 \n+HETATM 9 O HOH A 3 22.022 27.007 16.850 \n+HETATM 10 H HOH A 4 24.450 30.140 20.847 \n+HETATM 11 H HOH A 4 23.406 28.929 21.181 \n+HETATM 12 O HOH A 4 23.523 29.921 21.153 \n+HETATM 13 H HOH A 5 36.734 35.594 34.812 \n+HETATM 14 H HOH A 5 37.604 34.580 35.751 \n+HETATM 15 O HOH A 5 37.143 34.684 34.870 \n+HETATM 16 H HOH A 6 19.713 34.571 34.235 \n+HETATM 17 H HOH A 6 20.498 35.905 34.756 \n+HETATM 18 O HOH A 6 19.645 35.388 34.808 \n+HETATM 19 H HOH A 7 36.984 36.850 39.773 \n+HETATM 20 H HOH A 7 36.605 38.140 38.846 \n+HETATM 21 O HOH A 7 36.372 37.636 39.677 \n+HETATM 22 H HOH A 8 8.163 37.579 5.945 \n+HETATM 23 H HOH A 8 7.472 38.749 5.039 \n+HETATM 24 O HOH A 8 7.314 37.882 5.512 \n+HETATM 25 H HOH A 9 11.757 7.586 5.085 \n+HETATM 26 H HOH A 9 10.533 6.537 5.347 \n+HETATM 27 O HOH A 9 10.768 7.498 5.206 \n+HETATM 28 H HOH A 10 9.516 35.171 5.485 \n+HETATM 29 H HOH A 10 8.815 33.845 4.841 \n+HETATM 30 O HOH A 10 8.646 34.709 5.313 \n+HETATM 31 H HOH A 11 6.372 27.789 38.494 \n+HETATM 32 H HOH A 11 7.099 27.347 39.887 \n+HETATM 33 O HOH A 11 6.853 28.121 39.305 \n+HETATM 34 H HOH A 12 29.153 23.000 32.754 \n+HETATM 35 H HOH A 12 28.068 21.818 32.452 \n+HETATM 36 O HOH A 12 28.380 22.728 32.182 \n+HETATM 37 H HOH A 13 20.195 -0.004 27.989 \n+HETATM 38 H HOH A 13 21.139 1.295 28.287 \n+HETATM 39 O HOH A 13 20.865 0.392 28.617 \n+HETATM 40 H HOH A 14 10.418 21.031 2.909 \n+HETATM 41 H HOH A 14 9.761 22.518 3.062 \n+HETATM 42 O HOH A 14 10.616 22.010 2.964 \n+HETATM 43 H HOH A 15 31.210 17.895 21.940 \n+HETATM 44 H HOH A 15 31.973 18.845 23.027 \n+HETATM 45 O HOH A 15 32.096 18.258 22.228 \n+HETATM 46 H HOH A 16 11.086 23.831 30.350 \n+HETATM 47 '..b'394 33.321 32.593 15.068 \n+HETATM 6153 C 2 B 395 25.861 23.755 33.063 \n+HETATM 6154 N 2 B 395 26.907 24.328 33.886 \n+HETATM 6155 O 2 B 395 26.190 22.879 32.021 \n+HETATM 6156 N 2 B 395 24.472 24.088 33.318 \n+HETATM 6157 H 2 B 395 24.417 24.725 34.097 \n+HETATM 6158 H 2 B 395 23.544 23.894 32.976 \n+HETATM 6159 H 2 B 395 26.496 24.930 34.582 \n+HETATM 6160 H 2 B 395 27.910 24.326 33.995 \n+HETATM 6161 C 2 B 396 36.346 8.134 34.241 \n+HETATM 6162 N 2 B 396 37.452 7.281 33.853 \n+HETATM 6163 O 2 B 396 35.662 7.892 35.439 \n+HETATM 6164 N 2 B 396 35.947 9.237 33.388 \n+HETATM 6165 H 2 B 396 36.541 9.265 32.574 \n+HETATM 6166 H 2 B 396 35.273 9.986 33.338 \n+HETATM 6167 H 2 B 396 37.826 7.595 32.971 \n+HETATM 6168 H 2 B 396 37.973 6.478 34.172 \n+HETATM 6169 C 2 B 397 7.470 15.615 25.594 \n+HETATM 6170 N 2 B 397 6.331 15.326 24.744 \n+HETATM 6171 O 2 B 397 7.280 15.869 26.957 \n+HETATM 6172 N 2 B 397 8.807 15.641 25.031 \n+HETATM 6173 H 2 B 397 8.760 15.439 24.045 \n+HETATM 6174 H 2 B 397 9.767 15.795 25.298 \n+HETATM 6175 H 2 B 397 6.647 15.169 23.800 \n+HETATM 6176 H 2 B 397 5.328 15.229 24.783 \n+HETATM 6177 C 2 B 398 32.020 29.539 39.141 \n+HETATM 6178 N 2 B 398 33.278 30.166 39.501 \n+HETATM 6179 O 2 B 398 32.018 28.337 38.423 \n+HETATM 6180 N 2 B 398 30.766 30.157 39.525 \n+HETATM 6181 H 2 B 398 30.951 31.008 40.031 \n+HETATM 6182 H 2 B 398 29.769 30.018 39.453 \n+HETATM 6183 H 2 B 398 33.095 31.016 40.011 \n+HETATM 6184 H 2 B 398 34.273 30.035 39.411 \n+HETATM 6185 C 2 B 399 37.130 39.320 13.459 \n+HETATM 6186 N 2 B 399 36.687 39.197 12.084 \n+HETATM 6187 O 2 B 399 38.317 40.000 13.754 \n+HETATM 6188 N 2 B 399 36.342 38.738 14.529 \n+HETATM 6189 H 2 B 399 35.527 38.290 14.141 \n+HETATM 6190 H 2 B 399 36.339 38.632 15.532 \n+HETATM 6191 H 2 B 399 35.821 38.682 12.054 \n+HETATM 6192 H 2 B 399 36.957 39.455 11.147 \n+HETATM 6193 C 2 B 400 21.143 23.134 28.380 \n+HETATM 6194 N 2 B 400 22.079 22.882 27.301 \n+HETATM 6195 O 2 B 400 20.406 24.324 28.403 \n+HETATM 6196 N 2 B 400 20.972 22.154 29.435 \n+HETATM 6197 H 2 B 400 21.575 21.365 29.262 \n+HETATM 6198 H 2 B 400 20.450 21.999 30.283 \n+HETATM 6199 H 2 B 400 22.520 21.987 27.441 \n+HETATM 6200 H 2 B 400 22.435 23.304 26.457 \n+END\n' |
| b |
| diff -r 000000000000 -r 0b8a0ce446f5 test-data/packmol_parameteroutfile_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/packmol_parameteroutfile_1.txt Mon Oct 08 05:31:29 2018 -0400 |
| b |
| @@ -0,0 +1,18 @@ +# Template for packmol in Galaxy +# + +tolerance 2.0 +nloop 20 +maxit 20 +seed 101 +filetype pdb +output /tmp/tmprvsgniri/files/000/dataset_2.dat + +structure /tmp/tmprvsgniri/files/000/dataset_1.dat +# Galaxy datasetname - water.pdb + number 100 + radius 1.0 + resnumbers 0 + inside cube 0.0 0.0 0.0 40.0 +end structure + |
| b |
| diff -r 000000000000 -r 0b8a0ce446f5 test-data/packmol_parameteroutfile_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/packmol_parameteroutfile_2.txt Mon Oct 08 05:31:29 2018 -0400 |
| b |
| @@ -0,0 +1,26 @@ +# Template for packmol in Galaxy +# + +tolerance 2.0 +nloop 20 +maxit 20 +seed -1 +filetype pdb +output /tmp/tmpgg9o1466/files/000/dataset_5.dat + +structure /tmp/tmpgg9o1466/files/000/dataset_1.dat +# Galaxy datasetname - water.pdb + number 1000 + radius 1.0 + resnumbers 0 + inside box 0.0 0.0 0.0 40.0 40.0 40.0 +end structure + +structure /tmp/tmpgg9o1466/files/000/dataset_4.dat +# Galaxy datasetname - urea.pdb + number 400 + radius 1.0 + resnumbers 0 + inside box 0.0 0.0 0.0 40.0 40.0 40.0 +end structure + |
| b |
| diff -r 000000000000 -r 0b8a0ce446f5 test-data/urea.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/urea.pdb Mon Oct 08 05:31:29 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ +HEADER +HETATM 1 C 2 2 0.000 0.000 1.400 +HETATM 2 N 2 2 -1.256 0.000 2.125 +HETATM 3 O 2 2 0.000 0.000 0.000 +HETATM 4 N 2 2 1.256 0.000 2.125 +HETATM 5 H 2 2 1.072 0.000 3.116 +HETATM 6 H 2 2 2.252 0.000 1.968 +HETATM 7 H 2 2 -1.072 0.000 3.116 +HETATM 8 H 2 2 -2.252 0.000 1.968 |
| b |
| diff -r 000000000000 -r 0b8a0ce446f5 test-data/water.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/water.pdb Mon Oct 08 05:31:29 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +HEADER water +COMPND +SOURCE +HETATM 1 H HOH 1 9.626 6.787 12.673 +HETATM 2 H HOH 1 9.626 8.420 12.673 +HETATM 3 O HOH 1 10.203 7.604 12.673 +CONECT 1 3 +CONECT 2 3 +CONECT 3 1 2 +END |