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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
author chemteam
date Wed, 13 Apr 2022 16:21:56 +0000
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24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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1 <tool id="pdbfixer" name="PDBFixer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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2 <description>to automatically fix a PDB file before performing molecular dynamics simulation</description>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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3 <macros>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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4 <token name="@TOOL_VERSION@">1.8.1</token>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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5 <token name="@GALAXY_VERSION@">0</token>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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6 </macros>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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7 <requirements>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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8 <requirement type="package" version="@TOOL_VERSION@">pdbfixer</requirement>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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9 </requirements>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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10 <command detect_errors="exit_code"><![CDATA[
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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11 pdbfixer
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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12 '$pdb_input'
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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13 ## --pdbid and --url not implemented here, users can use the get_pdb tool
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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14 --output '$output'
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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15 --add-atoms='$add_atoms' ## which missing atoms to add: all, heavy, hydrogen, or none [default: all]
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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16 --keep-heterogens='$keep_heterogens' ## which heterogens to keep: all, water, or none [default: all]
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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17 $replace_nonstandard ## replace nonstandard residues with standard equivalents
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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18 $add_residues ## add missing residues
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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19 --ph='$ph' ## the pH to use for adding missing hydrogens [default: 7.0]
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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20
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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21 #if $solvent.box.water_box == "true":
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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22 --water-box=$solvent.box.x $solvent.box.y $solvent.box.z ## add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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23 --positive-ion='$solvent.positive_ion' ## positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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24 --negative-ion='$solvent.negative_ion' ## negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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25 --ionic-strength='$solvent.ionic_strength' ## molar concentration of ions to add to the water box [default: 0.0]
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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26 #end if
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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27 --verbose
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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28
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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29 ]]></command>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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30 <inputs>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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31 <param format="pdb" name="pdb_input" type="data" label="PDB input file"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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32 <param name="add_atoms" type="select" label="Missing atoms to be added">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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33 <option value="all" selected="true">All</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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34 <option value="heavy">Heavy atoms only</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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35 <option value="hydrogen">Hydrogen atoms only</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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36 <option value="none">None</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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37 </param>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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38 <param name="keep_heterogens" type="select" label="Which heterogens to keep">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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39 <option value="all" selected="true">All</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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40 <option value="water">Only water</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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41 <option value="none">None</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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42 </param>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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43 <param name="replace_nonstandard" type="boolean" label="Replace nonstandard residues with standard equivalents?" truevalue="--replace-nonstandard" falsevalue="" value=""/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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44 <param name="add_residues" type="boolean" label="Add missing residues?" truevalue="--add-residues" falsevalue="" value=""/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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45 <param name="ph" type="float" min="0" max="14" value="7" label="pH" help="Ignored if not adding hydrogen atoms"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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46 <section name="solvent" title="Solvent parameters" help="Note that you may prefer to modify solvent parameters using other tools.">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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47 <conditional name="box">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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48 <param name="water_box" type="select" label="Add a water box?" help="Dimensions in nanometers">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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49 <option value="true">Yes</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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50 <option value="false" selected="true">No</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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51 </param>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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52 <when value="true">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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53 <param name="x" type="float" min="0" value="0" label="Size in X dimension"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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54 <param name="y" type="float" min="0" value="0" label="Size in Y dimension"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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55 <param name="z" type="float" min="0" value="0" label="Size in Z dimension"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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56 </when>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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57 <when value="false" />
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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58 </conditional>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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59 <param name="positive_ion" type="select" label="Type of positive ion to add">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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60 <option value="Li+">Lithium (Li+)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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61 <option value="Na+" selected="true">Sodium (Na+)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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62 <option value="K+">Potassium (K+)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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63 <option value="Rb+">Rubidium (Rb+)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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64 <option value="Cs+">Cesium (Cs+)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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65 </param>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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66 <param name="negative_ion" type="select" label="Type of negative ion to add">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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67 <option value="Cl-" selected="true">Chloride (Cl-)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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68 <option value="Br-">Bromide (Br-)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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69 <option value="F-">Fluoride (F-)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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70 <option value="I-">Iodide (I-)</option>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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71 </param>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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72 <param name="ionic_strength" type="float" min="0" max="10" value="0" label="Ionic strength" help="Molar concentration of ions to add to the water box"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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73 </section>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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74 </inputs>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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75 <outputs>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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76 <data name="output" format="pdb"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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77 </outputs>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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78 <tests>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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79 <!-- pdbfixer test-data/broken.pdb -add-atoms=all -keep-heterogens=all -replace-nonstandard -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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80 <test>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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81 <param name="pdb_input" value="broken.pdb"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
82 <param name="add_atoms" value="all"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
83 <param name="keep_heterogens" value="all"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
84 <param name="replace_nonstandard" value="true"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
85 <param name="add_residues" value="false"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
86 <param name="ph" value="7"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
87 <output name="output">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
88 <assert_contents>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
89 <has_n_lines n="162"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
90 <!-- check LYS8 is fixed -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
91 <has_text text="CD LYS A 8"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
92 <has_text text="CE LYS A 8"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
93 <!-- check hydration -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
94 <has_text_matching expression="H \n" n="81"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
95 </assert_contents>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
96 </output>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
97 </test>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
98 <!-- pdbfixer test-data/broken.pdb -add-atoms=heavy -keep-heterogens=all -replace-nonstandard -add-residues -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
99 <test>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
100 <param name="pdb_input" value="broken.pdb"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
101 <param name="add_atoms" value="heavy"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
102 <param name="keep_heterogens" value="all"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
103 <param name="replace_nonstandard" value="true"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
104 <param name="add_residues" value="false"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
105 <output name="output">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
106 <assert_contents>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
107 <has_n_lines n="81"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
108 <!-- check LYS8 is fixed -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
109 <has_text text="CD LYS A 8"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
110 <has_text text="CE LYS A 8"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
111 <!-- check no hydration -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
112 <has_text_matching expression="H \n" negate="true"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
113 </assert_contents>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
114 </output>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
115 </test>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
116 <test>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
117 <param name="pdb_input" value="broken.pdb"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
118 <param name="add_atoms" value="all"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
119 <param name="keep_heterogens" value="all"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
120 <param name="replace_nonstandard" value="true"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
121 <param name="add_residues" value="false"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
122 <param name="ph" value="14"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
123 <param name="water_box" value="true"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
124 <param name="x" value="5"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
125 <param name="y" value="5"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
126 <param name="z" value="5"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
127 <param name="positive_ion" value="Li+"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
128 <param name="negative_ion" value="I-"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
129 <param name="ionic_strength" value="2"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
130 <output name="output">
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
131 <assert_contents>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
132 <!-- seems insertion of water is random and not fully reproducible -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
133 <has_n_lines n="11482" delta="100"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
134 <!-- check LYS8 is fixed -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
135 <has_text text="CD LYS A 8"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
136 <has_text text="CE LYS A 8"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
137 <!-- check hydration one less due to raised pH -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
138 <has_text_matching expression="ATOM.* H \n" n="80"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
139 <!-- check water and ions -->
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
140 <has_text_matching expression="HOH" n="11041" delta="100"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
141 <has_text_matching expression=" I .*\n" n="144"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
142 <has_text_matching expression=" Li .*\n" n="144"/>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
143 </assert_contents>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
144 </output>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
145 </test>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
146 </tests>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
147 <help><![CDATA[
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
148 .. class:: infomark
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
149
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
150 **What it does**
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
151
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
152 Fixes any issues in a PDB file (for example, adding missing residues, or missing atoms) prior to performing molecular dynamics simulations.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
153
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
154 PDBFixer can do any or all of the following:
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
155
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
156 - Add missing heavy atoms.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
157 - Add missing hydrogen atoms.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
158 - Build missing loops.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
159 - Convert non-standard residues to their standard equivalents.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
160 - Select a single position for atoms with multiple alternate positions listed.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
161 - Delete unwanted chains from the model.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
162 - Delete unwanted heterogens.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
163 - Build a water box for explicit solvent simulations.
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
164
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
165 _____
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
166
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
167
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
diff changeset
168 .. class:: infomark
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
chemteam
parents:
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169
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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170 **Input**
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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171
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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172 - PDB file
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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173
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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174 _____
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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175
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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176
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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177 .. class:: infomark
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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178
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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179 **Output**
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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180
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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181 - PDB file
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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182
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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183 ]]></help>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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184 <citations>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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185 <citation type="doi">10.1371/journal.pcbi.1005659</citation>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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186 <citation type="bibtex">@misc{pdbfixer, author = {{Peter Eastman et al.}}, title = {PDBFixer}, url={https://github.com/openmm/PDBFixer}, abstract = {PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them.}, urldate = {2022-03-25}, publisher = {GitHub}, year = {2022}, month = mar, }</citation>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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187 </citations>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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188 </tool>
24bf162ef74b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
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189