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1 <tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.1.1">
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2 <description>extract fingerprints from sdf files metadata</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="1.1p1">chemfp</requirement>
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6 <requirement type="package" version="2.3.2">openbabel</requirement>
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7 </requirements>
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8 <command>
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9 sdf2fps --pubchem "${infile}" > "${outfile}"
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10 </command>
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11 <inputs>
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12 <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
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13 </inputs>
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14 <outputs>
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15 <data name="outfile" format="fps"/>
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16 </outputs>
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17 <tests>
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18 </tests>
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19 <help>
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20
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21 .. class:: infomark
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22
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23 **What this tool does**
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24
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25 Read an input SD file, extract the fingerprints and store them in a FPS-file.
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26
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27 -----
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28
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29 .. class:: infomark
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30
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31 **Input**
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32
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33 `SD-Format`_
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34
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35 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
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36
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37 * Example::
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38
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39 28434379
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40 -OEChem-02031205132D
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41
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42 37 39 0 0 0 0 0 0 0999 V2000
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43 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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44 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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45 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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46 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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47 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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48 7.3704 0.9433 0.0000 C 0 0 0 0
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49 ......
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50 1 15 1 0 0 0 0
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51 1 35 1 0 0 0 0
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52 2 5 1 0 0 0 0
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53 2 11 1 0 0 0 0
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54 2 12 1 0 0 0 0
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55 3 12 2 0 0 0 0
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56 3 13 1 0 0 0 0
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57 4 18 1 0 0 0 0
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58 ......
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59
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60 >PUBCHEM_COMPOUND_CID<
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61 28434379
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62
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63 > <PUBCHEM_COMPOUND_CANONICALIZED>
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64 1
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65
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66 > <PUBCHEM_CACTVS_COMPLEXITY>
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67 280
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68
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69 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
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70 2
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71
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72 > <PUBCHEM_CACTVS_HBOND_DONOR>
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73 2
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74
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75 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
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76 2
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77
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78 > <PUBCHEM_CACTVS_SUBSKEYS>
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79 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
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80
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81 >
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82
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83 -----
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84
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85 .. class:: infomark
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86
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87 **Output**
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88
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89 * Example::
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90
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91 #FPS1
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92 #num_bits=881
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93 #type=CACTVS-E_SCREEN/1.0 extended=2
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94 #software=CACTVS/unknown
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95 #source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
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96 #date=2012-02-03T10:44:12
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97 07ce04000000000000000000000000000080060000000c0600
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98 00000000001a800f0000780008100000101487e9608c0bed32
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99 48000580644626204101b4844805901b041c2e19511e45039b
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100 8b2924101609401b13e4080000000000010020000004008000
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101 0010000002000000000000 28434379
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102
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103 -----
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104
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105 .. class:: infomark
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106
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107 **Cite**
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108
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109 chemfp_ project
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110
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111 .. _chemfp: http://chemfp.com/
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112
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113
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114 </help>
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115 </tool>
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