Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate prepare_box.xml @ 4:ad35eaa204ea draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:16:17 -0400
parents 908880455b2d
children 668c60aa4799
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4
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="prepare_box" name="Calculate the box parameters using RDKit" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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2 <macros>
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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3 <token name="@TOOL_VERSION@">2020.03.4</token>
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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4 <token name="@GALAXY_VERSION@">0</token>
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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5 </macros>
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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6 <description>for an AutoDock Vina job from a ligand input file (confounding box)</description>
0
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7 <requirements>
4
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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8 <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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9 <requirement type="package" version="1.19.1">numpy</requirement>
0
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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12 python '$__tool_directory__/calc_vina_box_params.py'
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73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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13 --ligand '$ligand'
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14 --ftype '${ligand.ext}'
2
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15 --config '$output'
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16 --bufx '$bufx'
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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17 --bufy '$bufy'
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18 --bufz '$bufz'
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73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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19 #if $exh:
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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20 --exh '$exh'
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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21 #end if
1
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22 #if $seed_value:
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23 --seed '$seed_value'
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24 #end if
0
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25 ]]></command>
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26 <inputs>
3
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27 <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand"
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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28 help="The input ligand with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/>
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29 <param name="bufx" type="float" value="0" label="x-axis buffer"
1
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30 help="Buffer in the x direction (in angs.)"/>
0
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31 <param name="bufy" type="float" value="0" label="y-axis buffer"
1
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32 help="Buffer in the y direction (in angs.)"/>
0
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33 <param name="bufz" type="float" value="0" label="z-axis buffer"
1
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34 help="Buffer in the z direction (in angs.)"/>
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35 <param name="exh" type="integer" optional="true" label="Exhaustiveness (optional)"
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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36 help="Exhaustiveness of global search (optional, default = 8)"/>
1
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37 <param type="integer" name="seed_value" optional="true" label="Random seed (optional)"
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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38 help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
0
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39 </inputs>
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40 <outputs>
2
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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41 <data name="output" format="txt" />
0
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42 </outputs>
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43 <tests>
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44 <test>
3
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45 <param name="ligand" value="NUDT5A-x0114_2.mol" ftype="mol"/>
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46 <param name="bufx" value="1" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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47 <param name="bufy" value="2" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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48 <param name="bufz" value="3" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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49 <output name="output" file="box_params_1.txt" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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50 </test>
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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51 <test>
3
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52 <param name="ligand" value="NUDT5A-x0114_2.sdf" ftype="sdf"/>
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53 <param name="bufx" value="1" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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54 <param name="bufy" value="2" />
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55 <param name="bufz" value="3" />
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56 <param name="exh" value="10" />
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57 <param name="seed_value" value="1" />
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58 <output name="output" file="box_params_2.txt" />
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59 </test>
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60 <test>
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61 <param name="ligand" value="NUDT5A-x0114_2.mol2"/>
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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62 <param name="bufx" value="1" />
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63 <param name="bufy" value="2" />
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64 <param name="bufz" value="3" />
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65 <output name="output" file="box_params_1.txt" />
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66 </test>
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67 <test>
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68 <param name="ligand" value="NUDT5A-x0114_2.pdb" ftype="pdb"/>
0
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69 <param name="bufx" value="1" />
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70 <param name="bufy" value="2" />
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71 <param name="bufz" value="3" />
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72 <param name="exh" value="10" />
1
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73 <param name="seed_value" value="1" />
2
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74 <output name="output" file="box_params_2.txt" />
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75 </test>
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76 </tests>
1
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77 <help>
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78 <![CDATA[
0
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79
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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80 .. class:: infomark
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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81
1
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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82 **Description**
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83
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84 This tool calculates a confounding box around an input ligand and
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85 uses it to generate the input parameters for an autodock vina job.
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86
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87 The output file can be fed into the AutoDock Vina tool as an alternative to creating the
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88 parameter file manually.
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89
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90 -----
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91
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92 .. class:: infomark
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93
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94 **Inputs:**
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95
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96 This tool requires:
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97
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98 * An input ligand - This should be a file (MOL, SDF, PDB or MOL2 format) representing the ligand you wish to dock.
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99
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100 * (OPTIONAL) Buffers for each direction (x,y,z), which defaults to 0 Å. This value will be added to the confounding box that the tool generates in each respective direction. We recommend that you visualise the calculated box from an initial run of this tool, and calculate the expansion needed in each direction to cover the area of the binding site you wish to explore.
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101
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102
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103 -----
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104
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105 .. class:: infomark
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106
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107 **Output:**
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108
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109 The output for this tool is a txt file containing the parameters needed to run an autodock
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110 vina docking calculation with the docking tool. For example: ::
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111
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112 size_x = 12.443000000000001
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113 size_y = 11.888
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114 size_z = 9.290999999999997
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115 center_x = -29.8395
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116 center_y = 4.364
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117 center_z = -64.5925
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118 num_modes = 9999
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119 energy_range = 9999
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120 exhaustiveness = 10
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121 cpu = 4
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122 seed = 1
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123
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124 The values for num_modes, energy range, cpu and seed are set to default values here.
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125
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126 This file can be used as the box parameter for the docking tool.
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127
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128 ]]>
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129 </help>
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130 <citations>
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131 <citation type="bibtex">
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132 @article{rdkit,
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133 author = {Greg Landrum},
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134 title = {RDKit: Open-source cheminformatics},
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135 url ={http://www.rdkit.org}
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136 }</citation>
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137 </citations>
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138 </tool>