Mercurial > repos > marpiech > norwich_tools_dock

annotate smina.xml @ 1:dc6fb5c5d4c8 draft

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planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e
author marpiech
date Mon, 12 Sep 2016 06:00:34 -0400
parents 75f2b4087722
children 958fa7ba4715
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1
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1 <tool id="smina" name="smina" version="1.0">
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2 <description>Scoring and Minimization with AutoDock Vina</description>
0
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command>
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7 <![CDATA[
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8 cat $receptor > receptor.pdbqt;
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9 cat $ligand > ligand.pdbqt;
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10 $__tool_directory__/tools/smina/smina.static
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11 --receptor receptor.pdbqt
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12 --ligand ligand.pdbqt
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13
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14 #if $flex
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15 --flex $flex
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16 #end if
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17 #if $flexres
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18 --flexres $flexres
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19 #end if
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20 #if $flexdist_ligand
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21 --flexdist_ligand $flexdist_ligand
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22 #end if
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23 #if $flexdist
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24 --flexdist $flexdist
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25 #end if
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26
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27 --center_x $center_x
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28 --center_y $center_y
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29 --center_z $center_z
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30 --size_x $size_x
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31 --size_y $size_y
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32 --size_z $size_z
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33
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34 #if $autobox_ligand
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35 --autobox_ligand $autobox_ligand
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36 #end if
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37 #if $autobox_add
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38 --autobox_add $autobox_add
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39 #end if
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40 #if $no_lig=="true"
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41 --no_lig
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42 #end if
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43
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44 --scoring $scoring
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45 #if $custom_scoring
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46 --custom_scoring $custom_scoring
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47 #end if
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48 #if $custom_atoms
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49 --custom_atoms $custom_atoms
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50 #end if
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51 #if $score_only=="true"
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52 --score_only
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53 #end if
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54 #if $local_only=="true"
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55 --local_only
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56 #end if
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57 #if $minimize=="true"
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58 --minimize
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59 #end if
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60 #if $randomize_only=="true"
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61 --randomize_only
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62 #end if
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63 #if $minimize_iters
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64 --minimize_iters $minimize_iters
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65 #end if
1
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66 #if $accurate_line=="true"
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67 --accurate_line
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68 #end if
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69 #if $minimize_early_term=="true"
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70 --minimize_early_term
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71 #end if
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72 #if $approximation
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73 --approximation $approximation
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74 #end if
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75 #if $factor
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76 --factor $factor
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77 #end if
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78 #if $force_cap
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79 --force_cap $force_cap
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80 #end if
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81 #if $user_grid
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82 --user_grid $user_grid
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83 #end if
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84 #if $user_grid_lambda
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85 --user_grid_lambda $user_grid_lambda
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86 #end if
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87 #if $print_terms=="true"
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88 --print_terms
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89 #end if
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90 #if $print_atom_types=="true"
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91 --print_atom_types
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92 #end if
0
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93
1
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94 #if $out
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95 --out $out
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96 #end if
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97 #if $out_flex
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98 --out_flex $out_flex
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99 #end if
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100 #if $atom_terms
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101 --atom_terms $atom_terms
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102 #end if
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103 #if $atom_term_data=="true"
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104 --atom_term_data
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105 #end if
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106
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107 #if $seed
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108 --seed $seed
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109 #end if
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110 #if $exhaustiveness
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111 --exhaustiveness $exhaustiveness
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112 #end if
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113 #if $num_modes
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114 --num_modes $num_modes
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115 #end if
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116 #if $energy_range
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117 --energy_range $energy_range
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118 #end if
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119 #if $min_rmsd_filter
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120 --min_rmsd_filter $min_rmsd_filter
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121 #end if
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122 #if $addH=="false"
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123 --addH false
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124 #end if
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125
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126 > $stand_output;
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127 #if $out # cat $out > $out_output; #end if #
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128 #if $out_flex # cat $out_flex > $out_flex_output; #end if #
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129 #if $atom_terms # cat $atom_terms > $atom_terms_output; #end if #
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130
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131 cat $stand_output > /tmp/ouput
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132 ]]>
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133 </command>
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134 <inputs>
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135 <param name="receptor" type="data" format="pdbqt" label="rigid part of the receptore" help="(--receptor)"/>
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136 <param name="ligand" type="data" format="data" label="ligand(s)" help="(--ligand)"/>
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137
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138 <param name="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex"/>
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139 <param name="flexres" type="text" label="flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/>
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140 <param name="flexdist_ligand" type="data" format="data" label="Ligand to use for flexdist" optional="true" help="(--flexdist_ligand)"/>
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141 <param name="flexdist" type="float" label="set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(flexdist)"/>
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142
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143 <param name="center_x" type="float" value="0" label="X coordinate of the center" help="(--center_x)"/>
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144 <param name="center_y" type="float" value="0" label="Y coordinate of the center" help="(--center_y)"/>
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145 <param name="center_z" type="float" value="0" label="Z coordinate of the center" help="(--center_z)"/>
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146 <param name="size_x" type="integer" value="1" label="size in the X dimension" help="(--size_x)"/>
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147 <param name="size_y" type="integer" value="1" label="size in the Y dimension" help="(--size_y)"/>
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148 <param name="size_z" type="integer" value="1" label="size in the Z dimension" help="(--size_z)"/>
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149
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150 <param name="autobox_ligand" type="data" format="data" label="Ligand to use for autobox" optional="true" help="(--autobox_ligand)"/>
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151 <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" help="(autobox_add)"/>
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152 <param name="no_lig" type="select" label="no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" help="(no_lig)">
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153 <option value="false" selected="true">Don't use this option</option>
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154 <option value="true">Use this option</option>
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155 </param>
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156
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157 <param name="scoring" type="select" label="specify alternative builtin scoring function" help="(--scoring)">
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158 <option value="default" selected="true">default</option>
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159 <option value="ad4_scoring">ad4_scoring</option>
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160 <option value="dkoes_fast">dkoes_fast</option>
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161 <option value="dkoes_scoring">dkoes_scoring</option>
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162 <option value="dkoes_scoring_old">dkoes_scoring_old</option>
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163 <option value="vina">vina</option>
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164 <option value="vinardo">vinardo</option>
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165 </param>
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166 <param name="custom_scoring" type="data" format="data" label="custom scoring function file" optional="true" help="(--custom_scoring)"/>
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167 <param name="custom_atoms" type="data" format="data" label="custom atom type parameters file" optional="true" help="(--custom_atoms)"/>
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168 <param name="score_only" type="select" label="score provided ligand pose" help="(--score_only)">
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169 <option value="false" selected="true">Don't use this option</option>
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170 <option value="true">Use this option</option>
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171 </param>
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172 <param name="local_only" type="select" label="local search only using autobox (you probably want to use --minimize)" help="(--local_only)">
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173 <option value="false" selected="true">Don't use this option</option>
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174 <option value="true">Use this option</option>
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175 </param>
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176 <param name="minimize" type="select" label="energy minimization" help="(--minimize)">
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177 <option value="false" selected="true">Don't use this option</option>
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178 <option value="true">Use this option</option>
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179 </param>
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180 <param name="randomize_only" type="select" label="generate random poses, attempting to avoid clashes" help="(--randomize_only)">
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181 <option value="false" selected="true">Don't use this option</option>
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182 <option value="true">Use this option</option>
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183 </param>
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184 <param name="minimize_iters" type="integer" label="number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" help="(--minimize_iters)"/>
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185 <param name="accurate_line" type="select" label="use accurate line search" help="(--accurate_line)">
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186 <option value="false" selected="true">Don't use this option</option>
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187 <option value="true">Use this option</option>
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188 </param>
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189 <param name="minimize_early_term" type="select" label="Stop minimization before convergence conditions are fully met" help="(--minimize_early_term)">
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190 <option value="false" selected="true">Don't use this option</option>
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191 <option value="true">Use this option</option>
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192 </param>
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193 <param name="approximation" type="select" label="approximation (linear, spline, or exact) to use" optional="true" help="(--approximation)">
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194 <option value="linear">linear</option>
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195 <option value="spline">spline</option>
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196 <option value="exact">exact</option>
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197 </param>
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198 <param name="factor" type="float" label="approximation factor: higher results in a finer-grained approximation" optional="true" help="(--factor)">
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199 <validator type="in_range" min="0"/>
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200 </param>
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201 <param name="force_cap" type="float" label="max allowed force; lower values more gently minimize clashing structures" optional="true" help="(--force_cap)"/>
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202 <param name="user_grid" type="float" label="Autodock map file for user grid data based calculations" optional="true" help="(--user_grid)"/>
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203 <param name="user_grid_lambda" type="float" label="Scales user_grid and functional scoring" optional="true" help="(--user_grid)"/>
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204 <param name="print_terms" type="select" label="Print all available terms with default parameterizations" help="(--print_terms)">
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205 <option value="false" selected="true">Don't use this option</option>
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206 <option value="true">Use this option</option>
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207 </param>
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208 <param name="print_atom_types" type="select" label="Print all available atom types" help="(--print_atom_types)">
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209 <option value="false" selected="true">Don't use this option</option>
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210 <option value="true">Use this option</option>
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211 </param>
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212
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213 <param name="out" type="text" label="output file name, format taken from file extension" optional="true" help="(--out)"/>
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214 <param name="out_flex" type="text" label="output file for flexible receptor residues" optional="true" help="(--out_flex)"/>
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215 <param name="atom_terms" type="text" label="output file for flexible receptor residues" optional="true" help="(--atom_terms)"/>
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216 <param name="atom_term_data" type="select" label="embedded per-atom interaction terms in output sd data" help="(--atom_term_data)">
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217 <option value="false" selected="true">Don't use this option</option>
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218 <option value="true">Use this option</option>
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219 </param>
1
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220
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221 <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/>
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222 <param name="exhaustiveness" type="integer" label="exhaustiveness of the global search (roughly proportional to time)" optional="true" help="(--exhaustiveness)"/>
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223 <param name="num_modes" type="integer" label="exhaustiveness of the global search (roughly proportional to time)" optional="true" help="(--num_modes)">
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224 <validator type="in_range" min="1"/>
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225 </param>
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226 <param name="energy_range" type="float" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" optional="true" help="(--energy_range)"/>
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227 <param name="min_rmsd_filter" type="float" label="rmsd value used to filter final poses to remove redundancy" optional="true" help="(--min_rmsd_filter)"/>
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228 <param name="addH" type="select" label="automatically add hydrogens in ligands (on by default)" help="(--addH)">
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229 <option value="false" >Don't use this option</option>
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230 <option value="true" selected="true">Use this option</option>
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231 </param>
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232
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233 </inputs>
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234 <outputs>
1
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235 <data name="stand_output" format="data" />
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236 <data name="out_output" format="data" />
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237 <data name="out_flex_output" format="data" />
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238 <data name="atom_terms_output" format="data" />
0
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239 </outputs>
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240 <tests>
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241 <test>
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242 <param name="receptor" value="smina/protein.pdbqt" />
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243 <param name="ligand" value="smina/ligand.pdbqt" />
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244 <param name="center_x" value="11" />
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245 <param name="center_y" value="90.5" />
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246 <param name="center_z" value="57.5" />
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247 <param name="size_x" value="22" />
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248 <param name="size_y" value="24" />
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249 <param name="size_z" value="28" />
1
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250 <output name="stand_output" >
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251 <assert_contents>
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252 <has_text_matching expression="Using random seed" />
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253 </assert_contents>
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254 </output>
0
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255 </test>
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256 </tests>
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257 <help>
1
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258 <![CDATA[
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259 ************
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260 Description
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261 ************
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262
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263 A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
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264
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265 ******
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266 Help
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267 ******
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268
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269 **Input**
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270
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271 --receptor arg rigid part of the receptor (PDBQT)
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272 --flex arg flexible side chains, if any (PDBQT)
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273 --ligand arg ligand(s)
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274 --flexres arg flexible side chains specified by comma separated list of chain:resid
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275 --flexdist_ligand arg Ligand to use for flexdist
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276 --flexdist arg set all side chains within
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277 specified distance to flexdist_ligand to flexible
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278
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279 **Search space**
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280
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281 --center_x arg X coordinate of the center
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282 --center_y arg Y coordinate of the center
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283 --center_z arg Z coordinate of the center
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284 --size_x arg size in the X dimension (Angstroms)
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285 --size_y arg size in the Y dimension (Angstroms)
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286 --size_z arg size in the Z dimension (Angstroms)
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287 --autobox_ligand arg Ligand to use for autobox
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288 --autobox_add arg Amount of buffer space to add
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289 to auto-generated box (default +4 on all six sides)
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290 --no_lig no ligand; for
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291 sampling/minimizing flexible residues
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292
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293 **Scoring and minimization options**
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294
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295 --scoring arg specify alternative
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296 builtin scoring function
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297 --custom_scoring arg custom scoring function file
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298 --custom_atoms arg custom atom type parameters file
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299 --score_only score provided ligand pose
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300 --local_only local search only using autobox (you probably want to use --minimize)
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301 --minimize energy minimization
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302 --randomize_only generate random poses, attempting to avoid clashes
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303 --minimize_iters arg number iterations of steepest descent;
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304 default scales with rotors and usually isn't
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305 sufficient for convergence
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306 --accurate_line use accurate line search
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307 --minimize_early_term Stop minimization before convergence conditions are fully met.
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308 --approximation arg approximation (linear, spline, or exact) to use
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309 --factor arg approximation factor: higher results in a finer-grained approximation
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310 --force_cap arg max allowed force; lower values more gently minimize clashing structures
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311 --user_grid arg Autodock map file for user grid data based calculations
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312 --user_grid_lambda arg Scales user_grid and functional scoring
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313 --print_terms Print all available terms with default parameterizations
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314 --print_atom_types Print all available atom types
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315
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316 **Output**
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317
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318 --out arg output file name, format taken from file extension
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319 --out_flex arg output file for flexible receptor residues
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320 --atom_terms arg optionally write per-atom interaction term values
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321 --atom_term_data embedded per-atom
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322 interaction terms in output sd data
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323
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324 **Misc**
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325
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326 --seed arg explicit random seed
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327 --exhaustiveness arg exhaustiveness of the global search (roughly proportional to time)
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328 --num_modes arg maximum number of binding modes to generate
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329 --energy_range arg maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)
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330 --min_rmsd_filter arg rmsd value used to filter final poses to remove redundancy
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331 --addH arg automatically add hydrogens
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332 in ligands (on by default)
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333
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334 ]]>
0
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335 </help>
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336 <citations>
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337 <citation type="bibtex">
1
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338 @misc{url = {https://sourceforge.net/projects/smina/}, }
0
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339 </citation>
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340 </citations>
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341 </tool>