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1 <tool id="ctb_filter" name="Filter" 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 <requirements>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 <requirement type="package" version="0.1">cheminfolib</requirement>
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7 </requirements>
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8 <command interpreter="python">
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9 ob_filter.py
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10 -i "${infile}"
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11 -o "${outfile}"
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12 -iformat "${infile.ext}"
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13 -oformat "${infile.ext}"
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14 --filters '{
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15 #if $filter_methods.filter_methods_opts == "ruleof5":
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16 "hbd" : [0, 5],
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17 "hba" : [0, 10],
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18 "molwt" : [0, 500],
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19 "logp" : [-5, 5],
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20 #elif $filter_methods.filter_methods_opts == "LeadLike":
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21 "rotbonds" : [0, 7],
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22 "molwt" : [0, 350],
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23 "logp" : [-5, 3.5],
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24 #elif $filter_methods.filter_methods_opts == "DrugLike":
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25 "hba" : [0, 10],
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26 "rotbonds" : [0, 8],
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27 "molwt" : [150, 500],
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28 "logp" : [-5, 5],
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29 "psa" : [0, 150],
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30 #elif $filter_methods.filter_methods_opts == "FragmentLike":
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31 "rotbonds" : [0, 5],
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32 "molwt" : [0, 250],
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33 "logp" : [-5, 2.5],
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34 #else:
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35 #for $filter in $filter_methods.filter_set:
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36 #set $filter_selected = $filter.filter_sel.filter_sel_opts
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37 #set $filter_min = $filter_selected + "_min"
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38 #set $filter_max = $filter_selected + "_max"
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39 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
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40 #end for
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41 #end if
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42 }'
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43 </command>
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44 <inputs>
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45 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/>
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46 <conditional name="filter_methods">
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47 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
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48 <option value="user">User-defined properties</option>
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49 <option value="ruleof5">Lipinski's Rule-of-Five</option>
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50 <option value="LeadLike">Lead-like properties</option>
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51 <option value="DrugLike">Drug-like properties</option>
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52 <option value="FragmentLike">Fragment-like properties</option>
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53 </param>
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54 <when value="ruleof5" />
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55 <when value="LeadLike" />
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56 <when value="DrugLike" />
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57 <when value="FragmentLike" />
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58 <when value="user">
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59 <repeat name="filter_set" title="Filters selection">
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60 <conditional name="filter_sel">
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61 <param name="filter_sel_opts" type="select" label="Select properties to filter">
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62 <option value="hbd">Number of Hydrogen-bond donor groups</option>
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63 <option value="hba">Number of Hydrogen-bond acceptor groups</option>
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64 <option value="psa">Total polar Surface Area</option>
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65 <option value="rotbonds">Number of rotatable bonds</option>
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66 <option value="molwt">Molecular weight</option>
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67 <option value="logp">Predicted value of LogP</option>
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68 <option value="mr">Predicted value for the Molecular Refractivity</option>
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69 <option value="atoms">Number of atoms</option>
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7
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70 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
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71 <option value="hatoms">Number of heavy atoms</option>-->
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72 <!-- 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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73 <!--<option value="rings">Number of rings</option>-->
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74 </param>
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75 <when value="hbd">
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76 <param name="hbd_min" size="3" type="integer" value="" label="Minimum number of HB donors"/>
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77 <param name="hbd_max" size="3" type="integer" value="" label="Maximum number of HB donors"/>
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78 </when>
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79 <when value="hba">
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80 <param name="hba_min" size="3" type="integer" value="" label="Minimum number of HB acceptors"/>
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81 <param name="hba_max" size="3" type="integer" value="" label="Maximum number of HB acceptors"/>
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82 </when>
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83 <when value="psa">
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84 <param name="psa_min" size="5" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/>
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85 <param name="psa_max" size="5" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/>
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86 </when>
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87 <when value="rotbonds">
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88 <param name="rotbonds_min" size="3" type="integer" value="" label="Minimum number of rotatable bonds"/>
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89 <param name="rotbonds_max" size="3" type="integer" value="" label="Maximum number of rotatable bonds"/>
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90 </when>
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91 <when value="molwt">
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92 <param name="molwt_min" size="5" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/>
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93 <param name="molwt_max" size="5" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/>
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94 </when>
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95 <when value="logp">
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96 <param name="logp_min" size="4" type="float" value="" label="Minimum threshold value for the log-P"/>
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97 <param name="logp_max" size="4" type="float" value="" label="Maximum threshold value for the log-P"/>
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98 </when>
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99 <when value="mr">
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100 <param name="mr_min" size="4" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/>
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101 <param name="mr_max" size="4" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/>
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102 </when>
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103 <when value="atoms">
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104 <param name="atoms_min" size="3" type="integer" value="" label="Minimum number of atoms"/>
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105 <param name="atoms_max" size="3" type="integer" value="" label="Maximum number of atoms"/>
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106 </when>
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107 <!--<when value="rings">
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108 <param name="rings_min" size="3" type="integer" value="" label="Minimum number of rings"/>
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109 <param name="rings_max" size="3" type="integer" value="" label="Maximum number of rings"/>
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110 </when>-->
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111 </conditional>
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112 </repeat>
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113 </when>
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114 </conditional>
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115 </inputs>
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116 <outputs>
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117 <data format_source="infile" name="outfile" />
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118 </outputs>
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119 <tests>
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120 <test>
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121 <param name="infile" ftype="smi" value="CID_2244.smi"/>
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122 <param name="filter_methods_opts" value="ruleof5" />
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123 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
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124 </test>
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125 <!--
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126 Limitation of the test framework:
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127 https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820
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128 <test>
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129 <param name="infile" ftype="smi" value="CID_2244.smi"/>
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130 <param name="filter_methods_opts" value="user" />
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131 <param name="filter_sel_opts" value="hba" />
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132 <param name="hbd_min" value="0" />
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133 <param name="hbd_max" value="5" />
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134 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" />
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135 </test>
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136 -->
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137 </tests>
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138 <help>
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139
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140
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141 **What does this tool do?**
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142
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143 This tool filters a library of compounds provided by the user, based on a set of physico-chemical user-defined parameters. Multiple parameters can be selected for more specific queries.
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144
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145 -----
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146
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147 .. class:: infomark
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148
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149 **Tip:** 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. It should be faster and can be reused but its bigger than a SMILES file.
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150
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151 **Tip:** for exact matchings please use the target value for both the minimum and maximum parameters (e.g. a selection of EXACTLY 4 rotatable bonds can be performed by selecting 4 minimum and 4 maximum as values for the property).
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152
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153 **Tip:** selecting multiple times the same property 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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154
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155 -----
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156
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157 .. class:: infomark
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158
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159 **Definition of the pre-defined filtering rules:**
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160 **# Lipinski's Rule of Five:**
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161 =< 5 Hydrogen-bond donor groups
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162
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163 =< 10 Hydrogen-bond acceptor groups
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164
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165 =< 500 Molecular weight
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166
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167 =< 5 octanol/water partition coefficient (log P)
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168
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169 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
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170 =< 7 rotatable bonds
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171
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172 =< 350 Molecular weight
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173
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174 =< 3.5 octanol/water partition coefficient (log P)
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175
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176 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
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177 =< 10 Hydrogen-bond acceptor groups
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178
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179 =< 8 rotatable bonds
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180
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181 150 =< Molecular weight =< 500
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182
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183 =< 150 Polar Surface Area
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184
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185 =< 5 octanol/water partition coefficient (log P)
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186
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187 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
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188 =< 5 rotatable bonds
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189
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190 =< 250 Molecular weight
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191
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192 =< 2.5 octanol/water partition coefficient (log P)
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193
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194 -----
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195
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196 .. class:: infomark
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197
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198 **Output:** the output formats included in this implementation are:
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199
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200 # sdf formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
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201
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202 # SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
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203
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204 -----
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205
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206 **This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5.
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207
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208 </help>
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209 </tool>
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