2
+ − 1 <tool id="smina" name="smina" version="0.1.0">
+ − 2 <requirements>
+ − 3 </requirements>
+ − 4 <stdio>
+ − 5 <exit_code range="1:" />
+ − 6 </stdio>
+ − 7 <command>
+ − 8 <![CDATA[
+ − 9 cat $receptor > receptor.pdbqt;
+ − 10 cat $ligand > ligand.pdbqt;
+ − 11 $__tool_directory__/tools/smina/smina.static
+ − 12 --receptor receptor.pdbqt
+ − 13 --ligand ligand.pdbqt
+ − 14
+ − 15 #if $flex
+ − 16 --flex $flex
+ − 17 #end if
+ − 18 #if $flexres
+ − 19 --flexres $flexres
+ − 20 #end if
+ − 21 #if $flexdist_ligand
+ − 22 --flexdist_ligand $flexdist_ligand
+ − 23 #end if
+ − 24 #if $flexdist
+ − 25 --flexdist $flexdist
+ − 26 #end if
+ − 27
+ − 28 --center_x $center_x
+ − 29 --center_y $center_y
+ − 30 --center_z $center_z
+ − 31 --size_x $size_x
+ − 32 --size_y $size_y
+ − 33 --size_z $size_z
+ − 34
+ − 35 #if $autobox_ligand
+ − 36 --autobox_ligand $autobox_ligand
+ − 37 #end if
+ − 38 #if $autobox_add
+ − 39 --autobox_add $autobox_add
+ − 40 #end if
+ − 41 #if $no_lig=="true"
+ − 42 --no_lig
+ − 43 #end if
+ − 44
+ − 45 --scoring $scoring
+ − 46 #if $custom_scoring
+ − 47 --custom_scoring $custom_scoring
+ − 48 #end if
+ − 49 #if $custom_atoms
+ − 50 --custom_atoms $custom_atoms
+ − 51 #end if
+ − 52 #if $score_only=="true"
+ − 53 --score_only
+ − 54 #end if
+ − 55 #if $local_only=="true"
+ − 56 --local_only
+ − 57 #end if
+ − 58 #if $minimize=="true"
+ − 59 --minimize
+ − 60 #end if
+ − 61 #if $randomize_only=="true"
+ − 62 --randomize_only
+ − 63 #end if
+ − 64 #if $minimize_iters
+ − 65 --minimize_iters $minimize_iters
+ − 66 #end if
+ − 67
+ − 68 --seed 1000 > $output;
+ − 69 cat $output > /tmp/ouput
+ − 70 ]]>
+ − 71 </command>
+ − 72 <inputs>
+ − 73 <param name="receptor" type="data" format="pdbqt" label="receptor: rigid part of the receptore" />
+ − 74 <param name="ligand" type="data" format="data" label="ligand: ligand(s)" />
+ − 75
+ − 76 <param name="flex" type="data" format="pdbqt" label="flex: flexible side chains, if any" optional="true" />
+ − 77 <param name="flexres" type="text" label="flexres: flexible side chains specified by comma separated list of chain:resid" optional="true" />
+ − 78 <param name="flexdist_ligand" type="data" format="data" label="flexdist_ligand: Ligand to use for flexdist" optional="true" />
+ − 79 <param name="flexdist" type="float" label="flexdist: set all side chains within specified distance to flexdist_ligand to flexible" optional="true" />
+ − 80
+ − 81 <param name="center_x" type="float" value="0" label="center_x: X coordinate of the center" />
+ − 82 <param name="center_y" type="float" value="0" label="center_y: Y coordinate of the center" />
+ − 83 <param name="center_z" type="float" value="0" label="center_z: Z coordinate of the center" />
+ − 84 <param name="size_x" type="integer" value="1" label="size_x: size in the X dimension" />
+ − 85 <param name="size_y" type="integer" value="1" label="size_y: size in the Y dimension" />
+ − 86 <param name="size_z" type="integer" value="1" label="size_z: size in the Z dimension" />
+ − 87
+ − 88 <param name="autobox_ligand" type="data" format="data" label="autobox_ligand: Ligand to use for autobox" optional="true" />
+ − 89 <param name="autobox_add" type="float" value="4" label="autobox_add: Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" />
+ − 90 <param name="no_lig" type="select" label="no_lig: no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" optional="true">
+ − 91 <option value="false" selected="true">Don't use this option</option>
+ − 92 <option value="true">Use this option</option>
+ − 93 </param>
+ − 94
+ − 95 <param name="scoring" type="select" label="scoring: specify alternative builtin scoring function" optional="true">
+ − 96 <option value="default" selected="true">default</option>
+ − 97 <option value="ad4_scoring">ad4_scoring</option>
+ − 98 <option value="dkoes_fast">dkoes_fast</option>
+ − 99 <option value="dkoes_scoring">dkoes_scoring</option>
+ − 100 <option value="dkoes_scoring_old">dkoes_scoring_old</option>
+ − 101 <option value="vina">vina</option>
+ − 102 <option value="vinardo">vinardo</option>
+ − 103 </param>
+ − 104 <param name="custom_scoring" type="data" format="data" label="custom_scoring: custom scoring function file" optional="true" />
+ − 105 <param name="custom_atoms" type="data" format="data" label="custom_atoms: custom atom type parameters file" optional="true" />
+ − 106 <param name="score_only" type="select" label="score_only: score provided ligand pose" optional="true">
+ − 107 <option value="false" selected="true">Don't use this option</option>
+ − 108 <option value="true">Use this option</option>
+ − 109 </param>
+ − 110 <param name="local_only" type="select" label="local_only: local search only using autobox (you probably want to use --minimize)" optional="true">
+ − 111 <option value="false" selected="true">Don't use this option</option>
+ − 112 <option value="true">Use this option</option>
+ − 113 </param>
+ − 114 <param name="minimize" type="select" label="minimize: energy minimization" optional="true">
+ − 115 <option value="false" selected="true">Don't use this option</option>
+ − 116 <option value="true">Use this option</option>
+ − 117 </param>
+ − 118 <param name="randomize_only" type="select" label="randomize_only: generate random poses, attempting to avoid clashes" optional="true">
+ − 119 <option value="false" selected="true">Don't use this option</option>
+ − 120 <option value="true">Use this option</option>
+ − 121 </param>
+ − 122 <param name="minimize_iters" type="integer" label="minimize_iters: number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" />
+ − 123 </inputs>
+ − 124 <outputs>
+ − 125 <data name="output" format="data" />
+ − 126 </outputs>
+ − 127 <tests>
+ − 128 <test>
+ − 129 <param name="receptor" value="smina/protein.pdbqt" />
+ − 130 <param name="ligand" value="smina/ligand.pdbqt" />
+ − 131 <param name="center_x" value="11" />
+ − 132 <param name="center_y" value="90.5" />
+ − 133 <param name="center_z" value="57.5" />
+ − 134 <param name="size_x" value="22" />
+ − 135 <param name="size_y" value="24" />
+ − 136 <param name="size_z" value="28" />
+ − 137 <output name="output" file="smina/output_smina" />
+ − 138 </test>
+ − 139 </tests>
+ − 140 <help>
+ − 141 "Smina help"
+ − 142 </help>
+ − 143 <citations>
+ − 144 <citation type="bibtex">
+ − 145 @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, }
+ − 146 </citation>
+ − 147 </citations>
+ − 148 </tool>
