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