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annotate simsearch.xml @ 13:dbe9c82028d1

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Sat, 01 Jun 2013 20:03:57 +0200
parents 526f6e88fbe7
children 47d2bf691908
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13
dbe9c82028d1 ChemicalToolBoX update.
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1 <tool id="ctb_simsearch" name="Similarity Search" version="0.1.1">
0
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2 <description>of fingerprint data sets</description>
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3 <requirements>
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4 <requirement type="package" version="1.1p1">chemfp</requirement>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command>
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8 #if $method_opts.method_opts_selector == "chemfp":
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9 ## TODO: remove all comment lines, in muti mode many comment lines will be appear, also in the middle of the result file, remove them
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10 #if int($method_opts.knn) == 0:
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11 #set $k = 'all'
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12 #else:
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13 #set $k = int($method_opts.knn)
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14 #end if
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15 simsearch
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16 -k $k
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17 --threshold $method_opts.threshold
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18 --query-format fps
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19 $method_opts.counts
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20 --target-format fps
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21 -o "${outfile}"
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22
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23 ## build and search an in-memory data structure (faster for multiple queries)
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24 --memory
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25
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26 #if $method_opts.query_opts.query_opts_selector == "normal":
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27 -q "${method_opts.query_opts.query}"
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28 #else:
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29 --NxN
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30 #end if
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31
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32 "${method_opts.query_opts.targets}"
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33 #else:
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34 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
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35 ## Furthermore OpenBabel is really picky with fileextensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
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36 ## A workaround is to create a symlink with a proper file-extension.
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37 #import tempfile
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38 #set $temp_file = tempfile.NamedTemporaryFile()
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39 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
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40 $temp_file.close()
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41 ln -s $method_opts.query $temp_link;
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42 obabel -i fs "${os.path.join($method_opts.fastsearch.extra_files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&#38;1;
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43 rm $temp_link
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44 #end if
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45 </command>
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46 <inputs>
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47
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48 <conditional name="method_opts">
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49 <param name="method_opts_selector" type="select" label="Subject database/sequences">
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50 <option value="chemfp">Chemfp fingerprint file</option>
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51 <option value="obabel">OpenBabel Fastsearch Index</option>
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52 </param>
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53 <when value="chemfp">
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54 <conditional name="query_opts">
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55 <param name="query_opts_selector" type="select" label="Query Mode">
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56 <option value="normal">Query molecules are stores in a separate file</option>
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57 <option value="nxn">Target molecules are also queries (NxN)</option>
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58 </param>
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59 <when value="normal">
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60 <param name='query' type='data' format="fps" label='Query molecules'/>
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61 <param name='targets' type='data' format="fps" label='Target molecules'/>
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62 </when>
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63 <when value="nxn">
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64 <param name='targets' type='data' format="fps" label='Target moleculs'/>
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65 </when>
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66 </conditional>
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67 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'>
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68 <validator type="in_range" min="0" />
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69 </param>
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70 <param name='threshold' type='float' label='threshold' value='0.7'/>
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71 <param name="counts" type="boolean" label="report counts (-c)" truevalue="-c" falsevalue="" checked="false" />
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72 </when>
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73 <when value="obabel">
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74 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
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75 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
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76 <param name="threshold" type='float' label="threshold" value='0.7'/>
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77 </when>
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78 </conditional>
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79
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80 </inputs>
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81 <outputs>
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82 <data name="outfile" format="tabular" />
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="targets" ftype="fps" value="targets.fps"/>
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87 <param name="query" ftype="fps" value="q.fps"/>
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88 <param name="k" value='4'/>
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89 <param name="th" value='0.7'/>
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90 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
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91 </test>
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92 </tests>
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93 <help>
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94
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95
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96 **What it does**
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97
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98 similarity search of fingerprint data sets
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99
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100 -----
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101
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102 **Example**
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103
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104 * input::
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105
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106 - Target Database in FPS format
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107
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108 #FPS1
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109 #num_bits=881
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110 #type=CACTVS-E_SCREEN/1.0 extended=2
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111 #software=CACTVS/unknown
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112 #source=Desktop/3579363516810334491.sdf
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113 #date=2012-02-03T13:07:47
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114 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960
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115 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
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116 00200000040080000010000002000000000000 55169009
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117 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960
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118 cc0bed3248000580644626004101b4844805901b041c2e19111e45039b8b2926105609401313e408000000000001
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119 00200000040080000010000002000000000000 55079807
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120 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960
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121 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
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122 00200000040080000010000002000000000000 3153534
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123 07ce0c000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960
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124 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
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125 00200000040080000010000002000000000000 55168823
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126 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960
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127 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
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128 00200000040080000010000002000000000000 55102353
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129 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
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130 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800003000
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131 000100200000040080000010000002000000000000 55091849
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132 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e9
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133 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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134 000100200000040080000010000002000000000000 55091752
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135 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
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136 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
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137 000100200000040080000010000002000000000000 55091467
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138 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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139 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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140 000100200000040080000010000002000000000000 55091466
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141 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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142 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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143 000100200000040080000010000002000000000000 55091416
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144 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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145 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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146 000100200000040080000010000002000000000000 6499094
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147 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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148 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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149 000100200000040080000010000002000000000000 6485578
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150 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e9
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151 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
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152 000100200000040080000010000002000000000000 6485577
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153
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154 - query :
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155 #FPS1
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156 #num_bits=881
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157 #type=CACTVS-E_SCREEN/1.0 extended=2
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158 #software=CACTVS/unknown
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159 #source=CID_28434379.sdf
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160 #date=2012-02-03T13:08:39
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161 07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9
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162 608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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163 000100200000040080000010000002000000000000 28434379
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164 - k : 4
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165 - threshold : 0.7
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166
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parents:
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167 * output::
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parents:
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168
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parents:
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169 #Simsearch/1
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parents:
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170 #num_bits=881
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parents:
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171 #type=Tanimoto k=4 threshold=0.7
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parents:
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172 #software=chemfp/1.0
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parents:
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173 #queries=q.fps
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parents:
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174 #targets=target.fps
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parents:
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175 #query_sources=CID_28434379.sdf
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parents:
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176 #target_sources=Desktop/3579363516810334491.sdf
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parents:
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177 4 28434379 55091752 0.9684 55091466 0.9682 55091416 0.9682 55102353 0.9682
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parents:
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178
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parents:
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179
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parents:
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180 </help>
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parents:
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181 </tool>