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1 <tool id="chemfp_simsearch" name="Similarity Search" version="0.1">
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2 <description>of fingerprint data sets</description>
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3 <!--<parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="10000" shared_inputs="targets,fastsearch" merge_outputs="outfile"></parallelism>-->
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4 <requirements>
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5 <requirement type="package" version="1.1p1">chemfp</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 simsearch -k $method_opts.k --threshold $method_opts.threshold --in fps --target-format fps -q "${method_opts.query}" "${method_opts.targets}" -o "${outfile}"
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11 #else:
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12 ## 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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13 ## 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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14 ## A workaround is to create a symlink with a proper file-extension.
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15 #import tempfile
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16 #set $temp_file = tempfile.NamedTemporaryFile()
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17 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
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18 $temp_file.close()
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19 ln -s $method_opts.query $temp_link;
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20 obabel -i fs "${os.path.join($method_opts.fastsearch.extra_files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&1;
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21 rm $temp_link
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22 #end if
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23 </command>
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24 <inputs>
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25
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26 <conditional name="method_opts">
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27 <param name="method_opts_selector" type="select" label="Subject database/sequences">
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28 <option value="chemfp">Chemfp fingerprint file</option>
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29 <option value="obabel">OpenBabel Fastsearch Index</option>
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30 </param>
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31 <when value="chemfp">
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32 <param name="query" type='data' format="fps" label="query"/>
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33 <param name="targets" type='data' format="fps" label="Target database"/>
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34 <param name="k" type='text' label="k nearest neighbor" value='all'/>
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35 <param name="threshold" type='float' label="threshold" value='0.7'/>
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36 </when>
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37 <when value="obabel">
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38 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
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39 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
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40 <param name="threshold" type='float' label="threshold" value='0.7'/>
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41 </when>
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42 </conditional>
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43
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44 </inputs>
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45 <outputs>
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46 <data name="outfile" format="tabular" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="targets" ftype="fps" value="targets.fps"/>
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51 <param name="query" ftype="fps" value="q.fps"/>
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52 <param name="k" value='4'/>
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53 <param name="th" value='0.7'/>
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54 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
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55 </test>
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56 </tests>
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57 <help>
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58
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59
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60 **What it does**
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61
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62 similarity search of fingerprint data sets
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63
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64 -----
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65
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66 **Example**
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67
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68 * input::
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69
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70 - Target Database in FPS format
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71
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72 #FPS1
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73 #num_bits=881
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74 #type=CACTVS-E_SCREEN/1.0 extended=2
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75 #software=CACTVS/unknown
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76 #source=Desktop/3579363516810334491.sdf
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77 #date=2012-02-03T13:07:47
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78 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960
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79 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
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80 00200000040080000010000002000000000000 55169009
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81 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960
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82 cc0bed3248000580644626004101b4844805901b041c2e19111e45039b8b2926105609401313e408000000000001
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83 00200000040080000010000002000000000000 55079807
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84 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960
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85 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
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86 00200000040080000010000002000000000000 3153534
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87 07ce0c000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960
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88 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
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89 00200000040080000010000002000000000000 55168823
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90 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960
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91 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
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92 00200000040080000010000002000000000000 55102353
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93 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
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94 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800003000
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95 000100200000040080000010000002000000000000 55091849
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96 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e9
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97 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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98 000100200000040080000010000002000000000000 55091752
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99 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
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100 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
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101 000100200000040080000010000002000000000000 55091467
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102 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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103 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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104 000100200000040080000010000002000000000000 55091466
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105 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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106 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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107 000100200000040080000010000002000000000000 55091416
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108 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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109 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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110 000100200000040080000010000002000000000000 6499094
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111 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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112 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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113 000100200000040080000010000002000000000000 6485578
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114 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e9
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115 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
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116 000100200000040080000010000002000000000000 6485577
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117
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118 - query :
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119 #FPS1
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120 #num_bits=881
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121 #type=CACTVS-E_SCREEN/1.0 extended=2
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122 #software=CACTVS/unknown
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123 #source=CID_28434379.sdf
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124 #date=2012-02-03T13:08:39
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125 07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9
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126 608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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127 000100200000040080000010000002000000000000 28434379
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128 - k : 4
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129 - threshold : 0.7
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130
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131 * output::
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132
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133 #Simsearch/1
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134 #num_bits=881
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135 #type=Tanimoto k=4 threshold=0.7
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136 #software=chemfp/1.0
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137 #queries=q.fps
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138 #targets=target.fps
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139 #query_sources=CID_28434379.sdf
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140 #target_sources=Desktop/3579363516810334491.sdf
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141 4 28434379 55091752 0.9684 55091466 0.9682 55091416 0.9682 55102353 0.9682
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142
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143
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144 </help>
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145 </tool>
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