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1 <tool id="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 </requirements>
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7 <command>
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8 sdf2fps --pubchem "${infile}" > "${outfile}"
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9 </command>
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10 <inputs>
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11 <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
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12 </inputs>
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13 <outputs>
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14 <data name="outfile" format="fps"/>
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15 </outputs>
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16 <tests>
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17 </tests>
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18 <help>
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19
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20
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21 **What it does**
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22
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23 Read a SDF file and extract the fingerprints, to stores them in a fps-file.
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24 TODO: currently it only works for PubChem
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25
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26 -----
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27
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28 **Example**
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29 * input::
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30
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31 SDF File
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32
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33 28434379
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34 -OEChem-02031205132D
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35
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36 37 39 0 0 0 0 0 0 0999 V2000
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37 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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38 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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39 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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40 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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41 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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42 7.3704 0.9433 0.0000 C 0 0 0 0
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43 ......
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44 1 15 1 0 0 0 0
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45 1 35 1 0 0 0 0
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46 2 5 1 0 0 0 0
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47 2 11 1 0 0 0 0
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48 2 12 1 0 0 0 0
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49 3 12 2 0 0 0 0
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50 3 13 1 0 0 0 0
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51 4 18 1 0 0 0 0
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52 ......
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53
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54 >PUBCHEM_COMPOUND_CID<
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55 28434379
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56
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57 > <PUBCHEM_COMPOUND_CANONICALIZED>
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58 1
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59
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60 > <PUBCHEM_CACTVS_COMPLEXITY>
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61 280
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62
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63 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
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64 2
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65
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66 > <PUBCHEM_CACTVS_HBOND_DONOR>
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67 2
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68
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69 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
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70 2
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71
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72 > <PUBCHEM_CACTVS_SUBSKEYS>
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73 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
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74
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75 >
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76
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77 * output::
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78
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79 #FPS1
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80 #num_bits=881
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81 #type=CACTVS-E_SCREEN/1.0 extended=2
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82 #software=CACTVS/unknown
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83 #source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
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84 #date=2012-02-03T10:44:12
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85 07ce04000000000000000000000000000080060000000c0600
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86 00000000001a800f0000780008100000101487e9608c0bed32
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87 48000580644626204101b4844805901b041c2e19511e45039b
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88 8b2924101609401b13e4080000000000010020000004008000
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89 0010000002000000000000 28434379
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90
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91
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92 </help>
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93 </tool>
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