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annotate ob_filter.xml @ 16:988085c7a0ea draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:06:01 +0000
parents ff2dd4b7d918
children
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ff2dd4b7d918 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="openbabel_filter" name="Filter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description> a set of molecules from a file</description>
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
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4 <macros>
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5 <import>macros.xml</import>
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6 <token name="@GALAXY_VERSION@">0</token>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 python '$__tool_directory__/ob_filter.py'
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12 -i '${infile}'
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13 -o '${outfile}'
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14 -iformat "${infile.ext}"
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15 -oformat "${infile.ext}"
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16 #if $filter_methods.filter_methods_opts == "__filter_by_name__":
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17 --list_of_names '$name_file'
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18 --filters '__filter_by_name__'
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19 #else
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20 --filters '{
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21 #if $filter_methods.filter_methods_opts == "ruleof5":
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22 "hbd" : [0, 5],
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23 "hba" : [0, 10],
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24 "molwt" : [0, 500],
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25 "logp" : [-5, 5],
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26 #elif $filter_methods.filter_methods_opts == "LeadLike":
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27 "rotbonds" : [0, 7],
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28 "molwt" : [0, 350],
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29 "logp" : [-5, 3.5],
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30 #elif $filter_methods.filter_methods_opts == "DrugLike":
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31 "hba" : [0, 10],
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32 "rotbonds" : [0, 8],
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33 "molwt" : [150, 500],
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34 "logp" : [-5, 5],
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35 "psa" : [0, 150],
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36 #elif $filter_methods.filter_methods_opts == "FragmentLike":
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37 "rotbonds" : [0, 5],
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38 "molwt" : [0, 250],
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39 "logp" : [-5, 2.5],
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40 #else:
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41 #for $filter in $filter_methods.filter_set:
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42 #if $filter.filter_sel.filter_sel_opts == "field":
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43 #set $filter_selected = $filter.filter_sel['field_name']
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44 "$filter_selected": [$filter.filter_sel['field_min'], $filter.filter_sel['field_max'] ],
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45 #else:
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46 #set $filter_selected = $filter.filter_sel.filter_sel_opts
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47 #set $filter_min = $filter_selected + "_min"
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48 #set $filter_max = $filter_selected + "_max"
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49 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
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50 #end if
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51 #end for
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52 #end if
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53 }'
0
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54 #end if
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55 ]]>
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56 </command>
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57 <inputs>
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58 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
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59 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
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60 <conditional name="filter_methods">
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61 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
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62 <option value="user">User-defined properties</option>
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63 <option value="ruleof5">Lipinski's Rule-of-Five</option>
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64 <option value="LeadLike">Lead-like properties</option>
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65 <option value="DrugLike">Drug-like properties</option>
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66 <option value="FragmentLike">Fragment-like properties</option>
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67 <option value="__filter_by_name__">Filter by molecule name</option>
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68 </param>
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69 <when value="__filter_by_name__">
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70 <param name="name_file" type="data" format="txt,tabular"
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71 label="File with molecule names that match the names in the SDF file" help="Every name one line."/>
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72 </when>
0
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73 <when value="ruleof5" />
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74 <when value="LeadLike" />
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75 <when value="DrugLike" />
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76 <when value="FragmentLike" />
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77 <when value="user">
7
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78 <repeat name="filter_set" title="Select custom filters">
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79 <conditional name="filter_sel">
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80 <param name="filter_sel_opts" type="select" label="Select properties to filter">
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81 <option value="hbd">Number of hydrogen-bond donor groups</option>
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82 <option value="hba">Number of hydrogen-bond acceptor groups</option>
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83 <option value="psa">Total polar surface area</option>
0
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84 <option value="rotbonds">Number of rotatable bonds</option>
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85 <option value="molwt">Molecular weight</option>
7
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86 <option value="logp">Predicted value of logP</option>
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87 <option value="mr">Predicted value for the molecular refractivity</option>
0
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88 <option value="atoms">Number of atoms</option>
12
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89 <option value="field">Filter by a user-defined SDF property</option>
0
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90 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
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91 <option value="hatoms">Number of heavy atoms</option>-->
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92 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html -->
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93 <!--<option value="rings">Number of rings</option>-->
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94 </param>
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95 <when value="hbd">
7
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96 <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/>
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97 <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/>
0
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98 </when>
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99 <when value="hba">
7
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100 <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/>
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101 <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/>
0
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102 </when>
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103 <when value="psa">
7
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104 <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/>
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105 <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/>
0
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106 </when>
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107 <when value="rotbonds">
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108 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/>
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109 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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110 </when>
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111 <when value="molwt">
7
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112 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/>
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113 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/>
0
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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114 </when>
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115 <when value="logp">
7
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116 <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/>
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117 <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/>
0
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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118 </when>
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119 <when value="mr">
7
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120 <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/>
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121 <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/>
0
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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122 </when>
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123 <when value="atoms">
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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124 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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125 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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126 </when>
12
340f8d63c1f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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127 <when value="field">
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128 <param name="field_name" type="text" value="" label="Name of the SDF property to filter by">
340f8d63c1f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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129 <sanitizer invalid_char="">
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130 <valid initial="string.ascii_letters,string.digits">
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131 <add value="_" />
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132 <add value="." />
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133 <add value=" " />
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134 </valid>
340f8d63c1f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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135 </sanitizer>
340f8d63c1f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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136 </param>
340f8d63c1f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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137 <param name="field_min" type="integer" value="" label="Minimum value"/>
340f8d63c1f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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138 <param name="field_max" type="integer" value="" label="Maximum value"/>
340f8d63c1f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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139 </when>
0
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140 <!--<when value="rings">
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141 <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
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142 <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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143 </when>-->
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144 </conditional>
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145 </repeat>
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146 </when>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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147 </conditional>
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148 </inputs>
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149 <outputs>
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150 <expand macro="output_like_input"/>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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151 </outputs>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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152 <tests>
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153 <test>
10
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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154 <param name="infile" value="ligands_with_title.sdf" ftype="sdf" />
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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155 <param name="filter_methods_opts" value="__filter_by_name__" />
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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156 <param name="name_file" value="name_file.txt" />
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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157 <output name="outfile" file="filterd_by_name.sdf" ftype="sdf" lines_diff="4" />
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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158 </test>
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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159 <test>
0
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160 <param name="infile" ftype="smi" value="CID_2244.smi"/>
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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161 <param name="filter_methods_opts" value="ruleof5" />
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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162 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
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163 </test>
12
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164 <test>
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165 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
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166 <param name="filter_methods_opts" value="user" />
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167 <param name="filter_sel_opts" value="field" />
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168 <param name="field_name" value="PUBCHEM_EXACT_MASS"/>
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169 <param name="field_min" value="100"/>
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170 <param name="field_max" value="200"/>
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171 <output name="outfile" ftype="sdf" file="ob_filter_on_CID2244.sdf" lines_diff="2"/>
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172 </test>
0
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173 <!--
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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174 Limitation of the test framework:
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175 https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820
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176 <test>
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177 <param name="infile" ftype="smi" value="CID_2244.smi"/>
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178 <param name="filter_methods_opts" value="user" />
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179 <param name="filter_sel_opts" value="hba" />
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180 <param name="hbd_min" value="0" />
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181 <param name="hbd_max" value="5" />
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182 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" />
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183 </test>
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184 -->
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185 </tests>
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186 <help>
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187 <![CDATA[
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188
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189
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190 .. class:: infomark
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191
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192 **What this tool does**
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193
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194 Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries.
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195
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196 -----
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197
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198 .. class:: warningmark
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199
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200 **Hint**
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201
7
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202 | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. This should be faster and the file can be reused, although it is larger than a SMILES file.
0
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203 |
7
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204 | For exact matches use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
0
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205 |
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206 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).
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207
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208 -----
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209
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210 .. class:: infomark
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211
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212 **Definition of the pre-defined filtering rules**
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213
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214 **# Lipinski's Rule of Five:**
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215 =< 5 Hydrogen-bond donor groups
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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216
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217 =< 10 Hydrogen-bond acceptor groups
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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218
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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219 =< 500 Molecular weight
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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220
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221 =< 5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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222
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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223 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
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224 =< 7 rotatable bonds
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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225
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226 =< 350 Molecular weight
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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227
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228 =< 3.5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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229
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230 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
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231 =< 10 Hydrogen-bond acceptor groups
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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232
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233 =< 8 rotatable bonds
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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234
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235 150 =< Molecular weight =< 500
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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236
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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237 =< 150 Polar Surface Area
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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238
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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239 =< 5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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240
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241 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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242 =< 5 rotatable bonds
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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243
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244 =< 250 Molecular weight
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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245
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246 =< 2.5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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247
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248 -----
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0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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250 .. class:: infomark
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251
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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252 **Input**
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253
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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254 | - `SD-Format`_
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255 | - `SMILES Format`_
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256
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257 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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258 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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259
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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260 -----
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0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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262 .. class:: infomark
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0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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264 **Output**
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265
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266 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
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267 |
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268 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
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272 ]]>
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273 </help>
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274 <expand macro="citations">
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275 <citation type="doi">10.1186/1752-153X-2-5</citation>
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276 </expand>
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277 </tool>