Mercurial > repos > bgruening > openbabel_filter

annotate ob_filter.xml @ 10:da03b00048b1 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
author bgruening
date Sat, 21 Mar 2020 10:26:39 -0400
parents 0e382252d23d
children 340f8d63c1f4
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10
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1 <tool id="openbabel_filter" name="Filter" version="@VERSION@.1">
0
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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 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 python '$__tool_directory__/ob_filter.py'
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11 -i '${infile}'
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12 -o '${outfile}'
10
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13 -iformat '${infile.ext}'
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14 -oformat '${infile.ext}'
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15 #if $filter_methods.filter_methods_opts == "__filter_by_name__":
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16 --list_of_names '$name_file'
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17 --filters '__filter_by_name__'
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18 #else
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19 --filters '{
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20 #if $filter_methods.filter_methods_opts == "ruleof5":
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21 "hbd" : [0, 5],
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22 "hba" : [0, 10],
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23 "molwt" : [0, 500],
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24 "logp" : [-5, 5],
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25 #elif $filter_methods.filter_methods_opts == "LeadLike":
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26 "rotbonds" : [0, 7],
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27 "molwt" : [0, 350],
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28 "logp" : [-5, 3.5],
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29 #elif $filter_methods.filter_methods_opts == "DrugLike":
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30 "hba" : [0, 10],
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31 "rotbonds" : [0, 8],
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32 "molwt" : [150, 500],
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33 "logp" : [-5, 5],
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34 "psa" : [0, 150],
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35 #elif $filter_methods.filter_methods_opts == "FragmentLike":
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36 "rotbonds" : [0, 5],
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37 "molwt" : [0, 250],
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38 "logp" : [-5, 2.5],
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39 #else:
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40 #for $filter in $filter_methods.filter_set:
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41 #set $filter_selected = $filter.filter_sel.filter_sel_opts
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42 #set $filter_min = $filter_selected + "_min"
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43 #set $filter_max = $filter_selected + "_max"
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44 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
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45 #end for
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46 #end if
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47 }'
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48 #end if
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49 ]]>
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50 </command>
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51 <inputs>
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52 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
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53 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
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54 <conditional name="filter_methods">
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55 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
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56 <option value="user">User-defined properties</option>
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57 <option value="ruleof5">Lipinski's Rule-of-Five</option>
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58 <option value="LeadLike">Lead-like properties</option>
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59 <option value="DrugLike">Drug-like properties</option>
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60 <option value="FragmentLike">Fragment-like properties</option>
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61 <option value="__filter_by_name__">Filter by molecule name</option>
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62 </param>
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63 <when value="__filter_by_name__">
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64 <param name="name_file" type="data" format="txt,tabular"
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65 label="File with molecule names that match the names in the SDF file" help="Every name one line."/>
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66 </when>
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67 <when value="ruleof5" />
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68 <when value="LeadLike" />
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69 <when value="DrugLike" />
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70 <when value="FragmentLike" />
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71 <when value="user">
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72 <repeat name="filter_set" title="Select custom filters">
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73 <conditional name="filter_sel">
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74 <param name="filter_sel_opts" type="select" label="Select properties to filter">
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75 <option value="hbd">Number of hydrogen-bond donor groups</option>
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76 <option value="hba">Number of hydrogen-bond acceptor groups</option>
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77 <option value="psa">Total polar surface area</option>
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78 <option value="rotbonds">Number of rotatable bonds</option>
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79 <option value="molwt">Molecular weight</option>
7
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80 <option value="logp">Predicted value of logP</option>
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81 <option value="mr">Predicted value for the molecular refractivity</option>
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82 <option value="atoms">Number of atoms</option>
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83 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
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84 <option value="hatoms">Number of heavy atoms</option>-->
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85 <!-- 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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86 <!--<option value="rings">Number of rings</option>-->
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87 </param>
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88 <when value="hbd">
7
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89 <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/>
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90 <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/>
0
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91 </when>
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92 <when value="hba">
7
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93 <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/>
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94 <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/>
0
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95 </when>
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96 <when value="psa">
7
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97 <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/>
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98 <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/>
0
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99 </when>
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100 <when value="rotbonds">
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101 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/>
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102 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/>
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103 </when>
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104 <when value="molwt">
7
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105 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/>
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106 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/>
0
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107 </when>
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108 <when value="logp">
7
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109 <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/>
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110 <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/>
0
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111 </when>
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112 <when value="mr">
7
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113 <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/>
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114 <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/>
0
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115 </when>
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116 <when value="atoms">
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117 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
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118 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
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119 </when>
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120 <!--<when value="rings">
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121 <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
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122 <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
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123 </when>-->
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124 </conditional>
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125 </repeat>
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126 </when>
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127 </conditional>
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128 </inputs>
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129 <outputs>
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130 <expand macro="output_like_input"/>
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131 </outputs>
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132 <tests>
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133 <test>
10
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134 <param name="infile" value="ligands_with_title.sdf" ftype="sdf" />
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135 <param name="filter_methods_opts" value="__filter_by_name__" />
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136 <param name="name_file" value="name_file.txt" />
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137 <output name="outfile" file="filterd_by_name.sdf" ftype="sdf" lines_diff="4" />
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138 </test>
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139 <test>
0
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140 <param name="infile" ftype="smi" value="CID_2244.smi"/>
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141 <param name="filter_methods_opts" value="ruleof5" />
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142 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
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143 </test>
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144 <!--
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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145 Limitation of the test framework:
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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146 https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820
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147 <test>
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148 <param name="infile" ftype="smi" value="CID_2244.smi"/>
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149 <param name="filter_methods_opts" value="user" />
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150 <param name="filter_sel_opts" value="hba" />
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151 <param name="hbd_min" value="0" />
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152 <param name="hbd_max" value="5" />
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153 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" />
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154 </test>
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155 -->
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156 </tests>
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157 <help>
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158 <![CDATA[
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159
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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160
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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161 .. class:: infomark
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162
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163 **What this tool does**
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164
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165 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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166
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167 -----
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168
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169 .. class:: warningmark
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170
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171 **Hint**
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172
7
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173 | 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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174 |
7
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175 | 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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176 |
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177 | 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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178
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179 -----
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180
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181 .. class:: infomark
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182
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183 **Definition of the pre-defined filtering rules**
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184
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185 **# Lipinski's Rule of Five:**
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186 =< 5 Hydrogen-bond donor groups
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187
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188 =< 10 Hydrogen-bond acceptor groups
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189
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190 =< 500 Molecular weight
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191
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192 =< 5 octanol/water partition coefficient (log P)
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193
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194 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
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195 =< 7 rotatable bonds
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196
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197 =< 350 Molecular weight
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198
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199 =< 3.5 octanol/water partition coefficient (log P)
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200
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201 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
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202 =< 10 Hydrogen-bond acceptor groups
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203
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204 =< 8 rotatable bonds
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205
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206 150 =< Molecular weight =< 500
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207
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208 =< 150 Polar Surface Area
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209
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210 =< 5 octanol/water partition coefficient (log P)
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211
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212 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
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213 =< 5 rotatable bonds
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214
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215 =< 250 Molecular weight
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216
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217 =< 2.5 octanol/water partition coefficient (log P)
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218
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219 -----
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220
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221 .. class:: infomark
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222
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223 **Input**
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224
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225 | - `SD-Format`_
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226 | - `SMILES Format`_
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227
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228 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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229 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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230
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231 -----
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232
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233 .. class:: infomark
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234
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235 **Output**
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236
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237 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
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238 |
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239 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
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240
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241
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242
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243 ]]>
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244 </help>
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245 <expand macro="citations">
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246 <citation type="doi">10.1186/1752-153X-2-5</citation>
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247 </expand>
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248 </tool>