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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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7
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6 <requirement type="package" version="2.3.2">openbabel</requirement>
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0
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7 </requirements>
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8 <command>
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9 #if $method_opts.method_opts_selector == "chemfp":
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10 ## 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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3
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11 simsearch -k $method_opts.k --threshold $method_opts.threshold --query-format fps --target-format fps -q "${method_opts.query}" "${method_opts.targets}" -o "${outfile}"
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12 #else:
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13 ## 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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14 ## 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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15 ## A workaround is to create a symlink with a proper file-extension.
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16 #import tempfile
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17 #set $temp_file = tempfile.NamedTemporaryFile()
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18 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
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19 $temp_file.close()
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20 ln -s $method_opts.query $temp_link;
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21 obabel -i fs "${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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22 rm $temp_link
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23 #end if
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24 </command>
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25 <inputs>
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26
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27 <conditional name="method_opts">
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28 <param name="method_opts_selector" type="select" label="Subject database/sequences">
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29 <option value="chemfp">Chemfp fingerprint file</option>
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30 <option value="obabel">OpenBabel Fastsearch Index</option>
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31 </param>
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32 <when value="chemfp">
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33 <param name="query" type='data' format="fps" label="query"/>
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34 <param name="targets" type='data' format="fps" label="Target database"/>
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35 <param name="k" type='text' label="k nearest neighbor" value='all'/>
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36 <param name="threshold" type='float' label="threshold" value='0.7'/>
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37 </when>
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38 <when value="obabel">
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39 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
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40 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
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41 <param name="threshold" type='float' label="threshold" value='0.7'/>
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42 </when>
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43 </conditional>
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44
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45 </inputs>
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46 <outputs>
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47 <data name="outfile" format="tabular" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="targets" ftype="fps" value="targets.fps"/>
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52 <param name="query" ftype="fps" value="q.fps"/>
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53 <param name="k" value='4'/>
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54 <param name="th" value='0.7'/>
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55 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
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56 </test>
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57 </tests>
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58 <help>
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59
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60
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61 **What it does**
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62
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63 similarity search of fingerprint data sets
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64
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65 -----
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66
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67 **Example**
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68
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69 * input::
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70
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71 - Target Database in FPS format
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72
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73 #FPS1
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74 #num_bits=881
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75 #type=CACTVS-E_SCREEN/1.0 extended=2
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76 #software=CACTVS/unknown
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77 #source=Desktop/3579363516810334491.sdf
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78 #date=2012-02-03T13:07:47
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79 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960
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80 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
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81 00200000040080000010000002000000000000 55169009
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82 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960
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83 cc0bed3248000580644626004101b4844805901b041c2e19111e45039b8b2926105609401313e408000000000001
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84 00200000040080000010000002000000000000 55079807
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85 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960
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86 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
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87 00200000040080000010000002000000000000 3153534
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88 07ce0c000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960
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89 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
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90 00200000040080000010000002000000000000 55168823
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91 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960
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92 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
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93 00200000040080000010000002000000000000 55102353
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94 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
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95 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800003000
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96 000100200000040080000010000002000000000000 55091849
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97 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e9
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98 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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99 000100200000040080000010000002000000000000 55091752
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100 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
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101 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
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102 000100200000040080000010000002000000000000 55091467
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103 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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104 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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105 000100200000040080000010000002000000000000 55091466
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106 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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107 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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108 000100200000040080000010000002000000000000 55091416
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109 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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110 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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111 000100200000040080000010000002000000000000 6499094
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112 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
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113 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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114 000100200000040080000010000002000000000000 6485578
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115 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e9
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116 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
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117 000100200000040080000010000002000000000000 6485577
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118
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119 - query :
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120 #FPS1
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121 #num_bits=881
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122 #type=CACTVS-E_SCREEN/1.0 extended=2
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123 #software=CACTVS/unknown
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124 #source=CID_28434379.sdf
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125 #date=2012-02-03T13:08:39
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126 07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9
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127 608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
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128 000100200000040080000010000002000000000000 28434379
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129 - k : 4
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130 - threshold : 0.7
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131
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132 * output::
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133
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134 #Simsearch/1
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135 #num_bits=881
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136 #type=Tanimoto k=4 threshold=0.7
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137 #software=chemfp/1.0
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138 #queries=q.fps
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139 #targets=target.fps
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140 #query_sources=CID_28434379.sdf
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141 #target_sources=Desktop/3579363516810334491.sdf
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142 4 28434379 55091752 0.9684 55091466 0.9682 55091416 0.9682 55102353 0.9682
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143
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144
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145 </help>
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146 </tool>
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